From 5291a622e45c32712dd271499c7b24ecce5113a9 Mon Sep 17 00:00:00 2001
From: jiajic <72078254+jiajic@users.noreply.github.com>
Date: Mon, 28 Oct 2024 18:24:29 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20drieslab?=
 =?UTF-8?q?/GiottoClass@ec5acccebd20e22aa86edd98f7f18d4ba0e81028=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 404.html                                      |   2 +-
 LICENSE-text.html                             |   2 +-
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 articles/image_tools.html                     |   4 +-
 articles/index.html                           |   2 +-
 articles/overview.html                        |   4 +-
 articles/spatial_geometries.html              |   4 +-
 authors.html                                  |   6 +-
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 news/index.html                               |  13 ++-
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 reference/as.character.html                   |   2 +-
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 reference/as.matrix.html                      |   2 +-
 reference/as.points.html                      |   2 +-
 reference/as.polygons.html                    |   2 +-
 reference/buffer,giottoPoints-method.html     |   8 ++
 reference/buffer,giottoPolygon-method.html    |   8 ++
 reference/buffer,spatLocsObj-method.html      |   8 ++
 reference/buffer-1.png                        | Bin 0 -> 160520 bytes
 reference/buffer.html                         | 108 ++++++++++++++++++
 reference/calculateMetaTable.html             |   2 +-
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 reference/centroids-generic.html              |   2 +-
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 reference/decomp_affine.html                  |   2 +-
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 reference/dot-find_grid_z.html                |   2 +-
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 reference/dot-install_giotto_environment.html |   2 +-
 reference/dot-install_github_link_pip.html    |   2 +-
 reference/dot-install_py_pkg_reticulate.html  |   2 +-
 reference/dot-merge_spatial_enrich_info.html  |   2 +-
 reference/dot-overlap_points_per_polygon.html |   2 +-
 ...ot-overlap_points_per_polygon_wrapped.html |   2 +-
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 reference/dot-plot_giottoimage_mg.html        |   2 +-
 reference/dot-plot_giottolargeimage.html      |   2 +-
 reference/dot-print_leaf.html                 |   2 +-
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 reference/getFeatureInfo.html                 |   2 +-
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 reference/getGiottoImage.html                 |   2 +-
 reference/getMultiomics.html                  |  42 +++----
 reference/getNearestNetwork.html              |   2 +-
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 reference/get_distance.html                   |   2 +-
 reference/get_img_minmax.html                 |   2 +-
 reference/get_multiomics.html                 |  42 +++----
 reference/giotto-class.html                   |   2 +-
 reference/giottoAffineImage-class.html        |   2 +-
 reference/giottoImage-class.html              |   2 +-
 reference/giottoLargeImage-class.html         |   2 +-
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 reference/hexVertices.html                    |   2 +-
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 reference/pDataDT.html                        |   2 +-
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 reference/polyStamp-1.png                     | Bin 15772 -> 15709 bytes
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 reference/r_spatial_conversions.html          |   2 +-
 reference/rbind-generic.html                  |   2 +-
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 reference/readSpatLocsData.html               |   2 +-
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 reference/read_data_params.html               |   2 +-
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 reference/reconnectGiottoImage.html           |   2 +-
 reference/reconnect_giottoImage_MG.html       |   2 +-
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 reference/setMultiomics.html                  |   2 +-
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 reference/setSpatialLocations.html            |   2 +-
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 reference/set_default_feat_type.html          |   2 +-
 reference/set_default_spat_unit.html          |   2 +-
 reference/set_multiomics.html                 |   2 +-
 reference/settleGeom,SpatVector-method.html   |   8 ++
 .../settleGeom,giottoPolygon-method.html      |   8 ++
 reference/settleGeom-1.png                    | Bin 0 -> 209312 bytes
 reference/settleGeom-2.png                    | Bin 0 -> 169252 bytes
 reference/settleGeom.html                     | 103 +++++++++++++++++
 reference/seuratToGiotto.html                 |   2 +-
 reference/seuratToGiottoV4.html               |   2 +-
 reference/seuratToGiottoV5.html               |   2 +-
 reference/shear.html                          |   2 +-
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 reference/showGiottoDimRed.html               |   2 +-
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 reference/showGiottoSpatNetworks.html         |   2 +-
 reference/showGiottoSpatialInfo.html          |   2 +-
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 reference/sliceGiotto.html                    |   2 +-
 reference/smoothGiottoPolygons.html           |   2 +-
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 reference/spatQueryGiottoPolygons.html        |   2 +-
 reference/spatShift.html                      |   2 +-
 reference/spatUnit-generic.html               |   2 +-
 reference/spatValues.html                     |   2 +-
 reference/spat_net_to_igraph.html             |   2 +-
 reference/spatialExperimentToGiotto.html      |   2 +-
 reference/spatialGridObj-class.html           |   2 +-
 reference/spatialNetworkObj-class.html        |   2 +-
 reference/spatial_binary_ops.html             |   2 +-
 reference/spatialdataToGiotto.html            |   2 +-
 reference/spin.html                           |   2 +-
 reference/splitGiotto.html                    |   2 +-
 reference/standardise_flex.html               |   2 +-
 reference/stitchFieldCoordinates.html         |   2 +-
 reference/stitchGiottoLargeImage.html         |   2 +-
 reference/stitchTileCoordinates.html          |  26 ++---
 reference/subsetGiotto.html                   |   2 +-
 reference/subsetGiottoLocs.html               |   2 +-
 reference/subsetGiottoLocsMulti.html          |   2 +-
 reference/subsetGiottoLocsSubcellular.html    |   2 +-
 reference/subset_bracket.html                 |   2 +-
 reference/subset_dollar.html                  |   2 +-
 reference/subset_giotto.html                  |   2 +-
 reference/subset_giotto_subobjects.html       |   2 +-
 reference/t_flex.html                         |  46 ++++----
 reference/terraVectData-class.html            |   2 +-
 reference/tessellate.html                     |   2 +-
 reference/transpose.html                      |   2 +-
 reference/updateGiottoImage.html              |   2 +-
 reference/updateGiottoImageMG.html            |   2 +-
 reference/updateGiottoLargeImage.html         |   2 +-
 reference/updateGiottoObject.html             |   2 +-
 reference/updateGiottoPointsObject.html       |   2 +-
 reference/updateGiottoPolygonObject.html      |   2 +-
 reference/update_giotto_params.html           |   2 +-
 reference/wrap.html                           |   2 +-
 reference/writeGiottoLargeImage.html          |   2 +-
 reference/zoom.html                           |   2 +-
 search.json                                   |   2 +-
 sitemap.xml                                   |   2 +
 422 files changed, 800 insertions(+), 524 deletions(-)
 create mode 100644 reference/buffer,giottoPoints-method.html
 create mode 100644 reference/buffer,giottoPolygon-method.html
 create mode 100644 reference/buffer,spatLocsObj-method.html
 create mode 100644 reference/buffer-1.png
 create mode 100644 reference/buffer.html
 create mode 100644 reference/settleGeom,SpatVector-method.html
 create mode 100644 reference/settleGeom,giottoPolygon-method.html
 create mode 100644 reference/settleGeom-1.png
 create mode 100644 reference/settleGeom-2.png
 create mode 100644 reference/settleGeom.html

diff --git a/404.html b/404.html
index fc190788..e5bf9b22 100644
--- a/404.html
+++ b/404.html
@@ -22,7 +22,7 @@
 
     <a class="navbar-brand me-2" href="https://drieslab.github.io/GiottoClass/index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index a7d34b39..fb05346a 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/LICENSE.html b/LICENSE.html
index 427aa985..12157913 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/image_tools.html b/articles/image_tools.html
index 45f3e206..def026a1 100644
--- a/articles/image_tools.html
+++ b/articles/image_tools.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -188,7 +188,7 @@ <h4 id="todos">TODOs:<a class="anchor" aria-label="anchor" href="#todos"></a>
 <span><span class="co">## [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## other attached packages:</span></span>
-<span><span class="co">## [1] GiottoClass_0.4.0</span></span>
+<span><span class="co">## [1] GiottoClass_0.4.1</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## loaded via a namespace (and not attached):</span></span>
 <span><span class="co">##  [1] sass_0.4.9                  SparseArray_1.4.8          </span></span>
diff --git a/articles/index.html b/articles/index.html
index bfe1950a..5613da4c 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/overview.html b/articles/overview.html
index d2ae0264..2c68b5c2 100644
--- a/articles/overview.html
+++ b/articles/overview.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -544,7 +544,7 @@ <h3 id="setting-information">Setting information<a class="anchor" aria-label="an
 <span><span class="co">## [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## other attached packages:</span></span>
-<span><span class="co">## [1] GiottoClass_0.4.0</span></span>
+<span><span class="co">## [1] GiottoClass_0.4.1</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## loaded via a namespace (and not attached):</span></span>
 <span><span class="co">##  [1] rappdirs_0.3.3              sass_0.4.9                 </span></span>
diff --git a/articles/spatial_geometries.html b/articles/spatial_geometries.html
index 1ffbaf98..a90de12a 100644
--- a/articles/spatial_geometries.html
+++ b/articles/spatial_geometries.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -473,7 +473,7 @@ <h2 id="overlaps-to-matrix">6.2 Overlaps to matrix<a class="anchor" aria-label="
 <span><span class="co">## [1] stats     graphics  grDevices utils     datasets  methods   base     </span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## other attached packages:</span></span>
-<span><span class="co">## [1] GiottoClass_0.4.0</span></span>
+<span><span class="co">## [1] GiottoClass_0.4.1</span></span>
 <span><span class="co">## </span></span>
 <span><span class="co">## loaded via a namespace (and not attached):</span></span>
 <span><span class="co">##  [1] tidyselect_1.2.1            dplyr_1.1.4                </span></span>
diff --git a/authors.html b/authors.html
index 013a7875..ae1b176f 100644
--- a/authors.html
+++ b/authors.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -69,13 +69,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Dries R, George Chen J, Yuan G, O'Brien M, Chávez-Fuentes J, Ruiz E (2024).
 <em>GiottoClass: Giotto Suite object definitions and framework</em>.
-R package version 0.4.0, <a href="https://drieslab.github.io/GiottoClass/">https://drieslab.github.io/GiottoClass/</a>.
+R package version 0.4.1, <a href="https://drieslab.github.io/GiottoClass/">https://drieslab.github.io/GiottoClass/</a>.
 </p>
       <pre>@Manual{,
   title = {GiottoClass: Giotto Suite object definitions and framework},
   author = {Ruben Dries and Jiaji {George Chen} and Guo-Cheng Yuan and Matthew O'Brien and Joselyn C. Chávez-Fuentes and Edward Ruiz},
   year = {2024},
-  note = {R package version 0.4.0},
+  note = {R package version 0.4.1},
   url = {https://drieslab.github.io/GiottoClass/},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index 6ca2790e..a48b9721 100644
--- a/index.html
+++ b/index.html
@@ -24,7 +24,7 @@
 
     <a class="navbar-brand me-2" href="index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index 0440a088..3e948025 100644
--- a/news/index.html
+++ b/news/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -35,6 +35,17 @@
       <small>Source: <a href="https://github.com/drieslab/Giotto/blob/website/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="0.4.1" id="giottoclass-041-20241028">GiottoClass 0.4.1 (2024/10/28)<a class="anchor" aria-label="anchor" href="#giottoclass-041-20241028"></a></h2>
+<div class="section level3">
+<h3 id="new-0-4-1">new<a class="anchor" aria-label="anchor" href="#new-0-4-1"></a></h3>
+<ul><li>
+<code><a href="../reference/buffer.html">buffer()</a></code> for <code>giottoPolygon</code>, <code>giottoPoints</code>, <code>spatLocsObj</code>. Default is to crop by voronoi borders with <code><a href="../reference/settleGeom.html">settleGeom()</a></code>
+</li>
+<li>
+<code><a href="../reference/settleGeom.html">settleGeom()</a></code> for <code>giottoPolygon</code> and <code>SpatVector</code> for finding non overlapping borders determined by voronoi</li>
+</ul></div>
+</div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.4.0" id="giottoclass-040-20241027">GiottoClass 0.4.0 (2024/10/27)<a class="anchor" aria-label="anchor" href="#giottoclass-040-20241027"></a></h2>
 <div class="section level3">
diff --git a/pkgdown.yml b/pkgdown.yml
index d957c9ae..dbfada23 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -5,7 +5,7 @@ articles:
   image_tools: image_tools.html
   overview: overview.html
   spatial_geometries: spatial_geometries.html
-last_built: 2024-10-28T04:45Z
+last_built: 2024-10-28T18:14Z
 urls:
   reference: https://drieslab.github.io/GiottoClass/reference
   article: https://drieslab.github.io/GiottoClass/articles
diff --git a/reference/S3toS4dimObj.html b/reference/S3toS4dimObj.html
index 14ce040b..d245d373 100644
--- a/reference/S3toS4dimObj.html
+++ b/reference/S3toS4dimObj.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/S3toS4spatGridObj.html b/reference/S3toS4spatGridObj.html
index 87d24047..a2d1ff47 100644
--- a/reference/S3toS4spatGridObj.html
+++ b/reference/S3toS4spatGridObj.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/XY.html b/reference/XY.html
index d7a850e2..444a4db2 100644
--- a/reference/XY.html
+++ b/reference/XY.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/activeFeatType-generic.html b/reference/activeFeatType-generic.html
index d083e450..5be1ad36 100644
--- a/reference/activeFeatType-generic.html
+++ b/reference/activeFeatType-generic.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/activeSpatUnit-generic.html b/reference/activeSpatUnit-generic.html
index b9236e85..7495933d 100644
--- a/reference/activeSpatUnit-generic.html
+++ b/reference/activeSpatUnit-generic.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addCellMetadata.html b/reference/addCellMetadata.html
index 69874cd8..bc5c0f8c 100644
--- a/reference/addCellMetadata.html
+++ b/reference/addCellMetadata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addFeatMetadata.html b/reference/addFeatMetadata.html
index b1cb902b..81fca280 100644
--- a/reference/addFeatMetadata.html
+++ b/reference/addFeatMetadata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addGiottoImage.html b/reference/addGiottoImage.html
index c71aa4fd..ea4d9490 100644
--- a/reference/addGiottoImage.html
+++ b/reference/addGiottoImage.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addGiottoImageMG.html b/reference/addGiottoImageMG.html
index 1eed2991..27037b4d 100644
--- a/reference/addGiottoImageMG.html
+++ b/reference/addGiottoImageMG.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addGiottoLargeImage.html b/reference/addGiottoLargeImage.html
index e24d619b..266b81e3 100644
--- a/reference/addGiottoLargeImage.html
+++ b/reference/addGiottoLargeImage.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addGiottoPoints.html b/reference/addGiottoPoints.html
index ca104121..765d4957 100644
--- a/reference/addGiottoPoints.html
+++ b/reference/addGiottoPoints.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addGiottoPolygons.html b/reference/addGiottoPolygons.html
index d628ece0..bdd7585d 100644
--- a/reference/addGiottoPolygons.html
+++ b/reference/addGiottoPolygons.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addNetworkLayout.html b/reference/addNetworkLayout.html
index a31abe87..b51b41d1 100644
--- a/reference/addNetworkLayout.html
+++ b/reference/addNetworkLayout.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addSpatialCentroidLocations.html b/reference/addSpatialCentroidLocations.html
index 17fe5a88..5bf1a400 100644
--- a/reference/addSpatialCentroidLocations.html
+++ b/reference/addSpatialCentroidLocations.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/addSpatialCentroidLocationsLayer.html b/reference/addSpatialCentroidLocationsLayer.html
index 15694866..de8e8f3e 100644
--- a/reference/addSpatialCentroidLocationsLayer.html
+++ b/reference/addSpatialCentroidLocationsLayer.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/add_img_array_alpha.html b/reference/add_img_array_alpha.html
index 0c97f654..157e7815 100644
--- a/reference/add_img_array_alpha.html
+++ b/reference/add_img_array_alpha.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
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index ea7bdf0f..5e2cbdd5 100644
--- a/reference/affine.html
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index fc499f4f..99c2819e 100644
--- a/reference/aggregateStacks.html
+++ b/reference/aggregateStacks.html
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index eeef23ba..b4bd4dda 100644
--- a/reference/aggregateStacksExpression.html
+++ b/reference/aggregateStacksExpression.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index b7ef2664..cf50caeb 100644
--- a/reference/aggregateStacksLocations.html
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 3751a2e2..abc03c29 100644
--- a/reference/aggregateStacksPolygonOverlaps.html
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@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 7bc4b012..5139f1db 100644
--- a/reference/aggregateStacksPolygons.html
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 37f2cdfe..4befbb2e 100644
--- a/reference/anndataToGiotto.html
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/annotateGiotto.html b/reference/annotateGiotto.html
index d6c8b9a3..d750b416 100644
--- a/reference/annotateGiotto.html
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index a26ece6b..042aab3b 100644
--- a/reference/annotateSpatialGrid.html
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@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index d91f4049..87730572 100644
--- a/reference/annotateSpatialNetwork.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 19aea550..0d2ac075 100644
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 3bfa86b9..9bffe699 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index cd108632..49d47e0a 100644
--- a/reference/area.html
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@@ -7,7 +7,7 @@
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index a5574626..c9f356b4 100644
--- a/reference/as.character.html
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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new file mode 100644
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diff --git a/reference/buffer.html b/reference/buffer.html
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--- /dev/null
+++ b/reference/buffer.html
@@ -0,0 +1,108 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Create a buffer around vector geometries — buffer • GiottoClass</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/JetBrains_Mono-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Create a buffer around vector geometries — buffer"><meta name="description" content="Calculate a buffer around all geometries of a SpatVector"><meta property="og:description" content="Calculate a buffer around all geometries of a SpatVector"><meta property="og:image" content="https://drieslab.github.io/GiottoClass/logo.png"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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+</nav><div class="container template-reference-topic">
+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="../logo.png" class="logo" alt=""><h1>Create a buffer around vector geometries</h1>
+      <small class="dont-index">Source: <a href="https://github.com/drieslab/Giotto/blob/website/R/buffer.R" class="external-link"><code>R/buffer.R</code></a></small>
+      <div class="d-none name"><code>buffer.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Calculate a buffer around all geometries of a <code>SpatVector</code></p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'spatLocsObj'</span></span>
+<span><span class="fu">buffer</span><span class="op">(</span><span class="va">x</span>, <span class="va">width</span>, <span class="va">...</span>, settle <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S4 method for class 'giottoPoints'</span></span>
+<span><span class="fu">buffer</span><span class="op">(</span><span class="va">x</span>, <span class="va">width</span>, <span class="va">...</span>, settle <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S4 method for class 'giottoPolygon'</span></span>
+<span><span class="fu">buffer</span><span class="op">(</span><span class="va">x</span>, <span class="va">width</span>, <span class="va">...</span>, settle <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dd><p>SpatRaster or SpatVector</p></dd>
+
+
+<dt id="arg-width">width<a class="anchor" aria-label="anchor" href="#arg-width"></a></dt>
+<dd><p>numeric. Unit is meter if <code>x</code> has a longitude/latitude CRS, or in the units of the coordinate reference system in other cases (typically also meter). The value should be &gt; 0 if <code>x</code> is a SpatRaster. If <code>x</code> is a SpatVector, this argument is vectorized, meaning that you can provide a different value for each geometry in <code>x</code>; and you can also use the name of a variable in <code>x</code> that has the widths</p></dd>
+
+
+<dt id="arg--">...<a class="anchor" aria-label="anchor" href="#arg--"></a></dt>
+<dd><p>additional params to pass</p></dd>
+
+
+<dt id="arg-settle">settle<a class="anchor" aria-label="anchor" href="#arg-settle"></a></dt>
+<dd><p>logical. Settle the borders between polygons by cutting them
+where they touch based on voronoi boundaries.</p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <p><code>giottoPolygon</code> of buffer polygons</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">sl</span> <span class="op">&lt;-</span> <span class="fu">GiottoData</span><span class="fu">::</span><span class="fu"><a href="https://drieslab.github.io/GiottoData/reference/loadSubObjectMini.html" class="external-link">loadSubObjectMini</a></span><span class="op">(</span><span class="st">"spatLocsObj"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">slb</span> <span class="op">&lt;-</span> <span class="fu">buffer</span><span class="op">(</span><span class="va">sl</span>, <span class="fl">30</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="plot-generic.html">plot</a></span><span class="op">(</span><span class="va">slb</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="buffer-1.png" alt="" width="700" height="433"></span>
+</code></pre></div>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
+
+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, <a href="https://github.com/jiajic" class="external-link">Jiaji George Chen</a>, <a href="https://labs.icahn.mssm.edu/yuanlab/" class="external-link">Guo-Cheng Yuan</a>, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn C. Chávez-Fuentes</a>, Edward Ruiz.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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+  </body></html>
+
diff --git a/reference/calculateMetaTable.html b/reference/calculateMetaTable.html
index 95010376..3174b4aa 100644
--- a/reference/calculateMetaTable.html
+++ b/reference/calculateMetaTable.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculateMetaTableCells.html b/reference/calculateMetaTableCells.html
index d0c8b5b9..7ef6f5c6 100644
--- a/reference/calculateMetaTableCells.html
+++ b/reference/calculateMetaTableCells.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculateOverlap.html b/reference/calculateOverlap.html
index 21d1a4a1..3d0a3a25 100644
--- a/reference/calculateOverlap.html
+++ b/reference/calculateOverlap.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculateOverlapParallel.html b/reference/calculateOverlapParallel.html
index e9f3950b..2f20210f 100644
--- a/reference/calculateOverlapParallel.html
+++ b/reference/calculateOverlapParallel.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculateOverlapPolygonImages.html b/reference/calculateOverlapPolygonImages.html
index 4acce6fd..c4975c77 100644
--- a/reference/calculateOverlapPolygonImages.html
+++ b/reference/calculateOverlapPolygonImages.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculateOverlapRaster.html b/reference/calculateOverlapRaster.html
index ed8384fc..08e8017d 100644
--- a/reference/calculateOverlapRaster.html
+++ b/reference/calculateOverlapRaster.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculateOverlapSerial.html b/reference/calculateOverlapSerial.html
index cc9777ca..49ed50ea 100644
--- a/reference/calculateOverlapSerial.html
+++ b/reference/calculateOverlapSerial.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/calculateSpatCellMetadataProportions.html b/reference/calculateSpatCellMetadataProportions.html
index cc334ef0..0a2f92e4 100644
--- a/reference/calculateSpatCellMetadataProportions.html
+++ b/reference/calculateSpatCellMetadataProportions.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cellMetaObj-class.html b/reference/cellMetaObj-class.html
index 57a0ee88..41cd6ba7 100644
--- a/reference/cellMetaObj-class.html
+++ b/reference/cellMetaObj-class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/centroids-generic.html b/reference/centroids-generic.html
index fb9812a0..0ecabe2d 100644
--- a/reference/centroids-generic.html
+++ b/reference/centroids-generic.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/changeGiottoInstructions.html b/reference/changeGiottoInstructions.html
index 783850c5..eb47236b 100644
--- a/reference/changeGiottoInstructions.html
+++ b/reference/changeGiottoInstructions.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/changeImageBg.html b/reference/changeImageBg.html
index c29aaf3d..86f291cd 100644
--- a/reference/changeImageBg.html
+++ b/reference/changeImageBg.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/checkPythonPackage.html b/reference/checkPythonPackage.html
index c452914c..00290979 100644
--- a/reference/checkPythonPackage.html
+++ b/reference/checkPythonPackage.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/check_py_for_scanpy.html b/reference/check_py_for_scanpy.html
index bc275014..4a37be7e 100644
--- a/reference/check_py_for_scanpy.html
+++ b/reference/check_py_for_scanpy.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/circleVertices.html b/reference/circleVertices.html
index 21ea9876..9cedea28 100644
--- a/reference/circleVertices.html
+++ b/reference/circleVertices.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/colMeans_flex.html b/reference/colMeans_flex.html
index 29121137..15882990 100644
--- a/reference/colMeans_flex.html
+++ b/reference/colMeans_flex.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,8 +63,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">colMeans_flex</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.33020071 -0.14415435  0.13720593  0.38627780 -0.15823532 -0.21262668</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.04357001  0.35755432 -0.45103539  0.06068702</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.1115180 -0.2079954  0.2838068  0.3373178 -0.1238467 -0.2577087</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.2453714  0.5362443 -0.4952991  0.2693857</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/colSums_flex.html b/reference/colSums_flex.html
index b410a72f..a12230ef 100644
--- a/reference/colSums_flex.html
+++ b/reference/colSums_flex.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,8 +63,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">colSums_flex</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]   1.3396257   4.9253110 -11.5121833  -1.9314278   3.6286812  -0.6779535</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  -4.7705262  -1.3051013   5.4512605  -0.7708679</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]   0.5626158   2.5194923 -10.1333315  -2.4267322   3.8784106  -1.9650656</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  -2.8342559  -1.9619765   6.9062217  -2.2261136</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/combineCellData.html b/reference/combineCellData.html
index 92fabb7b..d00571cc 100644
--- a/reference/combineCellData.html
+++ b/reference/combineCellData.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/combineFeatureData.html b/reference/combineFeatureData.html
index 217f763c..b41b492a 100644
--- a/reference/combineFeatureData.html
+++ b/reference/combineFeatureData.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/combineFeatureOverlapData.html b/reference/combineFeatureOverlapData.html
index 2d3f429c..616912f1 100644
--- a/reference/combineFeatureOverlapData.html
+++ b/reference/combineFeatureOverlapData.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/combineMetadata.html b/reference/combineMetadata.html
index f42cfd44..755ad309 100644
--- a/reference/combineMetadata.html
+++ b/reference/combineMetadata.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/combineSpatialCellMetadataInfo.html b/reference/combineSpatialCellMetadataInfo.html
index 9c556819..426288a8 100644
--- a/reference/combineSpatialCellMetadataInfo.html
+++ b/reference/combineSpatialCellMetadataInfo.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/combineToMultiPolygon.html b/reference/combineToMultiPolygon.html
index 00cbaf9a..fed908e0 100644
--- a/reference/combineToMultiPolygon.html
+++ b/reference/combineToMultiPolygon.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/compatible_spatial_network.html b/reference/compatible_spatial_network.html
index 13ff217c..127ca91f 100644
--- a/reference/compatible_spatial_network.html
+++ b/reference/compatible_spatial_network.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/convHull.html b/reference/convHull.html
index 932173f4..2244d231 100644
--- a/reference/convHull.html
+++ b/reference/convHull.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/convertGiottoLargeImageToMG.html b/reference/convertGiottoLargeImageToMG.html
index 78a00309..adeb8e37 100644
--- a/reference/convertGiottoLargeImageToMG.html
+++ b/reference/convertGiottoLargeImageToMG.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/convert_mgImage_to_array_DT.html b/reference/convert_mgImage_to_array_DT.html
index 384bcccb..f1730af7 100644
--- a/reference/convert_mgImage_to_array_DT.html
+++ b/reference/convert_mgImage_to_array_DT.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/convert_to_full_spatial_network.html b/reference/convert_to_full_spatial_network.html
index 35625dc5..b8c3a4fc 100644
--- a/reference/convert_to_full_spatial_network.html
+++ b/reference/convert_to_full_spatial_network.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/convert_to_reduced_spatial_network.html b/reference/convert_to_reduced_spatial_network.html
index 3a86d3d5..a357df75 100644
--- a/reference/convert_to_reduced_spatial_network.html
+++ b/reference/convert_to_reduced_spatial_network.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/copy.html b/reference/copy.html
index 065d9711..9e288272 100644
--- a/reference/copy.html
+++ b/reference/copy.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/cor_flex.html b/reference/cor_flex.html
index 732a1756..4f90e2fc 100644
--- a/reference/cor_flex.html
+++ b/reference/cor_flex.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -68,27 +68,27 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">cor_flex</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>              [,1]        [,2]       [,3]        [,4]        [,5]        [,6]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  1.00000000  0.16620711 -0.8131547  0.61575948 -0.33493205 -0.11683719</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.16620711  1.00000000 -0.1017779 -0.28227526 -0.12280489 -0.69807239</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.81315474 -0.10177789  1.0000000 -0.37518400  0.16724480  0.24837238</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.61575948 -0.28227526 -0.3751840  1.00000000 -0.30441692 -0.08505474</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.33493205 -0.12280489  0.1672448 -0.30441692  1.00000000  0.31606004</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.11683719 -0.69807239  0.2483724 -0.08505474  0.31606004  1.00000000</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -0.25438824  0.06612684  0.1753142 -0.36953253 -0.29526718  0.10431025</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.06386097  0.22412738  0.4751030  0.16334164 -0.02844134  0.06738725</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.36653910 -0.50689849 -0.1461906  0.65778248 -0.27050220  0.32750529</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.11525415 -0.32583704 -0.1610563 -0.13885239 -0.48178336  0.43514813</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  1.00000000  0.28099280 -0.6867656  0.42283126 -0.38987371 -0.07468685</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.28099280  1.00000000 -0.1659979 -0.51534964 -0.04087937 -0.59687113</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.68676564 -0.16599789  1.0000000 -0.48483005  0.23503091  0.37132983</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.42283126 -0.51534964 -0.4848301  1.00000000 -0.15473094  0.04134032</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.38987371 -0.04087937  0.2350309 -0.15473094  1.00000000  0.19145228</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.07468685 -0.59687113  0.3713298  0.04134032  0.19145228  1.00000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  0.17213620  0.19751817  0.1650136 -0.50007590 -0.30859664  0.18060348</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.11188918  0.05397874  0.4688130 -0.20095484  0.20343973  0.51007047</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.15068347 -0.65991342 -0.2022737  0.67766661 -0.15672350  0.39082372</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.07803746 -0.34887195 -0.1485405  0.02694660 -0.47862493  0.34358459</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>              [,7]        [,8]        [,9]       [,10]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.25438824 -0.06386097  0.36653910  0.11525415</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.06612684  0.22412738 -0.50689849 -0.32583704</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.17531418  0.47510298 -0.14619059 -0.16105627</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.36953253  0.16334164  0.65778248 -0.13885239</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.29526718 -0.02844134 -0.27050220 -0.48178336</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  0.10431025  0.06738725  0.32750529  0.43514813</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  1.00000000 -0.09626645 -0.45177865  0.69848177</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.09626645  1.00000000  0.27557036 -0.31735424</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.45177865  0.27557036  1.00000000  0.07936429</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.69848177 -0.31735424  0.07936429  1.00000000</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  0.17213620  0.11188918  0.15068347 -0.07803746</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.19751817  0.05397874 -0.65991342 -0.34887195</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.16501365  0.46881300 -0.20227374 -0.14854052</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.50007590 -0.20095484  0.67766661  0.02694660</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.30859664  0.20343973 -0.15672350 -0.47862493</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  0.18060348  0.51007047  0.39082372  0.34358459</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  1.00000000  0.08919887 -0.55902381  0.24693050</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.08919887  1.00000000  0.06649927 -0.36539126</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.55902381  0.06649927  1.00000000  0.22054868</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.24693050 -0.36539126  0.22054868  1.00000000</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/createBentoAdata.html b/reference/createBentoAdata.html
index 3568332c..816e519d 100644
--- a/reference/createBentoAdata.html
+++ b/reference/createBentoAdata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createCellMetaObj.html b/reference/createCellMetaObj.html
index b9e3b5d0..a23d3720 100644
--- a/reference/createCellMetaObj.html
+++ b/reference/createCellMetaObj.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createDimObj.html b/reference/createDimObj.html
index ae809078..473ac36f 100644
--- a/reference/createDimObj.html
+++ b/reference/createDimObj.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createExprObj.html b/reference/createExprObj.html
index 6b8ee185..b48e050b 100644
--- a/reference/createExprObj.html
+++ b/reference/createExprObj.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createFeatMetaObj.html b/reference/createFeatMetaObj.html
index b2887b02..5187e9f5 100644
--- a/reference/createFeatMetaObj.html
+++ b/reference/createFeatMetaObj.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createGiottoImage.html b/reference/createGiottoImage.html
index c164b69c..5aeb08eb 100644
--- a/reference/createGiottoImage.html
+++ b/reference/createGiottoImage.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createGiottoLargeImage.html b/reference/createGiottoLargeImage.html
index 8144303f..797b3354 100644
--- a/reference/createGiottoLargeImage.html
+++ b/reference/createGiottoLargeImage.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createGiottoLargeImageList.html b/reference/createGiottoLargeImageList.html
index 87721c82..0594c20c 100644
--- a/reference/createGiottoLargeImageList.html
+++ b/reference/createGiottoLargeImageList.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createGiottoObject.html b/reference/createGiottoObject.html
index cf8c28e0..125fad81 100644
--- a/reference/createGiottoObject.html
+++ b/reference/createGiottoObject.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createGiottoObjectSubcellular.html b/reference/createGiottoObjectSubcellular.html
index 0745614e..ebb1387b 100644
--- a/reference/createGiottoObjectSubcellular.html
+++ b/reference/createGiottoObjectSubcellular.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createGiottoPoints.html b/reference/createGiottoPoints.html
index 6cba1a63..123ae4f5 100644
--- a/reference/createGiottoPoints.html
+++ b/reference/createGiottoPoints.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createGiottoPolygon.html b/reference/createGiottoPolygon.html
index 5dc92b07..2ed0dd2c 100644
--- a/reference/createGiottoPolygon.html
+++ b/reference/createGiottoPolygon.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createMetafeats.html b/reference/createMetafeats.html
index 46ddcf9d..6cebf539 100644
--- a/reference/createMetafeats.html
+++ b/reference/createMetafeats.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createNearestNetObj.html b/reference/createNearestNetObj.html
index 70584908..9f984c77 100644
--- a/reference/createNearestNetObj.html
+++ b/reference/createNearestNetObj.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createNearestNetwork.html b/reference/createNearestNetwork.html
index ce5cd6b6..538ddfa2 100644
--- a/reference/createNearestNetwork.html
+++ b/reference/createNearestNetwork.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createNetwork.html b/reference/createNetwork.html
index ed1db2ff..311a0394 100644
--- a/reference/createNetwork.html
+++ b/reference/createNetwork.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/createSpatEnrObj.html b/reference/createSpatEnrObj.html
index ea180132..39bc02d1 100644
--- a/reference/createSpatEnrObj.html
+++ b/reference/createSpatEnrObj.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
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index 831d57e6..c22d1397 100644
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index f3affea8..ad87d98f 100644
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index c3d65630..73259fa7 100644
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index 1bb72959..193bb154 100644
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index 77a875cd..8054f78d 100644
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index 3248401e..3c88348d 100644
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index 222ce05a..270bcb2e 100644
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index 9f7a6912..73eaf709 100644
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index ee31b986..a35cf5f0 100644
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index 07fe3927..4ea535e9 100644
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index ee7f2535..25e72e0f 100644
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index 5656fbfe..c974552a 100644
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index 94ea41da..9314522c 100644
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index 9a64327c..9921f05d 100644
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index c9cf790d..801aeff6 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/dot-scale_spatial_locations.html b/reference/dot-scale_spatial_locations.html
index 962c52fb..145513c5 100644
--- a/reference/dot-scale_spatial_locations.html
+++ b/reference/dot-scale_spatial_locations.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/dot-shift_spatial_locations.html b/reference/dot-shift_spatial_locations.html
index 4fcd5665..89cb1107 100644
--- a/reference/dot-shift_spatial_locations.html
+++ b/reference/dot-shift_spatial_locations.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/dot-shift_spatial_network.html b/reference/dot-shift_spatial_network.html
index 1245a489..4234e7df 100644
--- a/reference/dot-shift_spatial_network.html
+++ b/reference/dot-shift_spatial_network.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/dot-spatraster_sample_values.html b/reference/dot-spatraster_sample_values.html
index b5531b8a..7f96048f 100644
--- a/reference/dot-spatraster_sample_values.html
+++ b/reference/dot-spatraster_sample_values.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/dot-spatvector_to_dt.html b/reference/dot-spatvector_to_dt.html
index 93c8a3ae..e64ebbbf 100644
--- a/reference/dot-spatvector_to_dt.html
+++ b/reference/dot-spatvector_to_dt.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/dot-spline_poly.html b/reference/dot-spline_poly.html
index 4990d422..69d8943d 100644
--- a/reference/dot-spline_poly.html
+++ b/reference/dot-spline_poly.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/dot-subset_giotto.html b/reference/dot-subset_giotto.html
index c28ae304..2508d5b8 100644
--- a/reference/dot-subset_giotto.html
+++ b/reference/dot-subset_giotto.html
@@ -31,7 +31,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/dot-terra_writeraster_datatype.html b/reference/dot-terra_writeraster_datatype.html
index 731c922f..2fb8d327 100644
--- a/reference/dot-terra_writeraster_datatype.html
+++ b/reference/dot-terra_writeraster_datatype.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/edge_distances.html b/reference/edge_distances.html
index b2fe8a3b..cc9fd8b4 100644
--- a/reference/edge_distances.html
+++ b/reference/edge_distances.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/estimateImageBg.html b/reference/estimateImageBg.html
index 50c89134..e9d1265d 100644
--- a/reference/estimateImageBg.html
+++ b/reference/estimateImageBg.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/evaluate_input.html b/reference/evaluate_input.html
index 2fbba0f5..b4396ee4 100644
--- a/reference/evaluate_input.html
+++ b/reference/evaluate_input.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/exprObj-class.html b/reference/exprObj-class.html
index 26318c81..c2b0c565 100644
--- a/reference/exprObj-class.html
+++ b/reference/exprObj-class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/ext.html b/reference/ext.html
index 1838f33e..be9ac0bc 100644
--- a/reference/ext.html
+++ b/reference/ext.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/fDataDT.html b/reference/fDataDT.html
index d1022e43..29d7bef5 100644
--- a/reference/fDataDT.html
+++ b/reference/fDataDT.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/featMetaObj-class.html b/reference/featMetaObj-class.html
index 864caf0d..5986b829 100644
--- a/reference/featMetaObj-class.html
+++ b/reference/featMetaObj-class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/featType-generic.html b/reference/featType-generic.html
index 4e7b0b15..78a2da2d 100644
--- a/reference/featType-generic.html
+++ b/reference/featType-generic.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/featureNetwork-class.html b/reference/featureNetwork-class.html
index 8d53abaa..b6a28fd1 100644
--- a/reference/featureNetwork-class.html
+++ b/reference/featureNetwork-class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/flip.html b/reference/flip.html
index a8c58e80..196c2e7e 100644
--- a/reference/flip.html
+++ b/reference/flip.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/gefToGiotto.html b/reference/gefToGiotto.html
index 2ec430f1..64d87325 100644
--- a/reference/gefToGiotto.html
+++ b/reference/gefToGiotto.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/generate_grid.html b/reference/generate_grid.html
index b1d7d24b..58082c04 100644
--- a/reference/generate_grid.html
+++ b/reference/generate_grid.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getCellMetadata.html b/reference/getCellMetadata.html
index 886f6eca..330ff903 100644
--- a/reference/getCellMetadata.html
+++ b/reference/getCellMetadata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getDimReduction.html b/reference/getDimReduction.html
index d43bca8b..ec0823a7 100644
--- a/reference/getDimReduction.html
+++ b/reference/getDimReduction.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getExpression.html b/reference/getExpression.html
index df0e7756..5ab48a6a 100644
--- a/reference/getExpression.html
+++ b/reference/getExpression.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getFeatureInfo.html b/reference/getFeatureInfo.html
index ab928b37..8ca919aa 100644
--- a/reference/getFeatureInfo.html
+++ b/reference/getFeatureInfo.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getFeatureMetadata.html b/reference/getFeatureMetadata.html
index 51506daf..72797b50 100644
--- a/reference/getFeatureMetadata.html
+++ b/reference/getFeatureMetadata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getGiottoImage.html b/reference/getGiottoImage.html
index 3d6188ab..f9060d53 100644
--- a/reference/getGiottoImage.html
+++ b/reference/getGiottoImage.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getMultiomics.html b/reference/getMultiomics.html
index 1408c74f..12cc0504 100644
--- a/reference/getMultiomics.html
+++ b/reference/getMultiomics.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -125,27 +125,27 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">getMultiomics</span><span class="op">(</span>gobject <span class="op">=</span> <span class="va">g</span>, spat_unit <span class="op">=</span> <span class="st">"cell"</span>, feat_type <span class="op">=</span> <span class="st">"rna_protein"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>               [,1]        [,2]       [,3]        [,4]        [,5]       [,6]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.701836993  0.90639045  1.6667728 -1.25745550  0.37969672 -0.2013585</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.573351259 -0.77007572  1.0805134 -0.27499746  0.81051411 -1.7947501</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.653506513 -0.10392922  1.0956876  1.18512009  0.16798153 -1.5936760</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  1.102562583 -0.59883015 -0.8235445  0.03108054 -0.82634150 -0.5880921</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.331979510  0.86307592 -0.7896969 -0.20427061  0.48015487 -2.4436502</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.006015914  1.53498056 -2.2300375 -1.34758305 -0.22734637  0.8733072</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  0.542548136 -0.07677495  1.2682960  0.32840023 -0.38144334 -1.5700947</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  1.073179083  0.36398407  0.7477098  1.50785612 -0.51130892  1.2064433</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.431113801  0.80003990  0.2902944  0.51282324  1.61615062 -0.6020315</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.899647924 -1.51114608 -0.2336790  0.27261523  0.05862038  0.6160790</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  0.573351259 -0.77007572  1.0805134 -0.27499746  0.81051411 -1.7947501</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.653506513 -0.10392922  1.0956876  1.18512009  0.16798153 -1.5936760</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  1.102562583 -0.59883015 -0.8235445  0.03108054 -0.82634150 -0.5880921</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.331979510  0.86307592 -0.7896969 -0.20427061  0.48015487 -2.4436502</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.006015914  1.53498056 -2.2300375 -1.34758305 -0.22734637  0.8733072</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  0.542548136 -0.07677495  1.2682960  0.32840023 -0.38144334 -1.5700947</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  1.073179083  0.36398407  0.7477098  1.50785612 -0.51130892  1.2064433</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.431113801  0.80003990  0.2902944  0.51282324  1.61615062 -0.6020315</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.899647924 -1.51114608 -0.2336790  0.27261523  0.05862038  0.6160790</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.906390447  1.66677279 -1.2574555  0.37969672 -0.20135846 -0.2994089</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>              [,7]        [,8]        [,9]       [,10]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.29940886  0.61040765  0.21277709 -0.43014614</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -0.54314989  0.86164700 -0.36930863 -0.23013339</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.11165896  0.88285986 -0.10648446  1.82750672</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.59879136  0.25782948 -0.52105633  1.63416402</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.64283303 -2.41919619 -0.31239384 -0.30347819</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -2.18494492  0.98255604 -1.73132386  0.05761964</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  0.11409361  0.73347719  1.46947149 -0.50750744</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.01148282  0.76860157  0.01044213 -1.61633811</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.35329552 -0.01777067  0.40827683  0.89181656</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  2.29670311 -1.10088452  1.70418504 -0.03268551</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.54314989  0.86164700 -0.36930863 -0.23013339</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -0.11165896  0.88285986 -0.10648446  1.82750672</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.59879136  0.25782948 -0.52105633  1.63416402</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.64283303 -2.41919619 -0.31239384 -0.30347819</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -2.18494492  0.98255604 -1.73132386  0.05761964</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  0.11409361  0.73347719  1.46947149 -0.50750744</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  0.01148282  0.76860157  0.01044213 -1.61633811</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.35329552 -0.01777067  0.40827683  0.89181656</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  2.29670311 -1.10088452  1.70418504 -0.03268551</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.61040765  0.21277709 -0.43014614 -0.16986547</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/getNearestNetwork.html b/reference/getNearestNetwork.html
index c6efd9fb..f0bd8513 100644
--- a/reference/getNearestNetwork.html
+++ b/reference/getNearestNetwork.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getPolygonInfo.html b/reference/getPolygonInfo.html
index 66408a53..ac9bc7fc 100644
--- a/reference/getPolygonInfo.html
+++ b/reference/getPolygonInfo.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getSpatialEnrichment.html b/reference/getSpatialEnrichment.html
index 90e04778..9f6f8519 100644
--- a/reference/getSpatialEnrichment.html
+++ b/reference/getSpatialEnrichment.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getSpatialGrid.html b/reference/getSpatialGrid.html
index 4dde62f9..fdb7d874 100644
--- a/reference/getSpatialGrid.html
+++ b/reference/getSpatialGrid.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getSpatialLocations.html b/reference/getSpatialLocations.html
index a0964520..482c42e9 100644
--- a/reference/getSpatialLocations.html
+++ b/reference/getSpatialLocations.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/getSpatialNetwork.html b/reference/getSpatialNetwork.html
index e72267a7..981c157e 100644
--- a/reference/getSpatialNetwork.html
+++ b/reference/getSpatialNetwork.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_adj_rescale_img.html b/reference/get_adj_rescale_img.html
index a7d8e6fb..1ce12f39 100644
--- a/reference/get_adj_rescale_img.html
+++ b/reference/get_adj_rescale_img.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_distance.html b/reference/get_distance.html
index 88b55c9d..91219bec 100644
--- a/reference/get_distance.html
+++ b/reference/get_distance.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_img_minmax.html b/reference/get_img_minmax.html
index caac7b05..460cfcb4 100644
--- a/reference/get_img_minmax.html
+++ b/reference/get_img_minmax.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/get_multiomics.html b/reference/get_multiomics.html
index 14963d14..bc9ca006 100644
--- a/reference/get_multiomics.html
+++ b/reference/get_multiomics.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -125,27 +125,27 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">get_multiomics</span><span class="op">(</span>gobject <span class="op">=</span> <span class="va">g</span>, spat_unit <span class="op">=</span> <span class="st">"cell"</span>, feat_type <span class="op">=</span> <span class="st">"rna_protein"</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>             [,1]        [,2]       [,3]       [,4]       [,5]        [,6]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.1698655 -1.24095435 -2.7800737 -1.5206390 -2.5197112  0.47131362</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  1.1884979  1.47605219 -1.9719497  1.7008620 -1.1675388 -0.05642605</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.6211862 -0.07589098 -0.4848200 -0.4662269 -0.7923482  1.19142146</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.4248148  0.62842700 -1.3848879 -0.3168777 -0.3003550 -0.02745457</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -1.2693983  0.19674511 -0.1762610 -1.2131392  0.1794639  0.88144485</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.2533625  0.08158049  0.2596137  0.2466786 -0.9374372 -3.09168198</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -0.1116180 -0.89830298 -0.2510197  0.1118254  1.4479660  1.12917805</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.1315426 -0.61990929 -1.0445444 -1.0078516  1.3361280  1.96047642</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.8725992 -1.06214909 -2.0920704  1.2416995  0.4995538  0.24592419</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.1657629  0.78311754 -0.5391583  1.3815616 -2.7557557 -0.43052706</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  1.1884979  1.47605219 -1.9719497  1.7008620 -1.1675388 -0.05642605</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -0.6211862 -0.07589098 -0.4848200 -0.4662269 -0.7923482  1.19142146</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.4248148  0.62842700 -1.3848879 -0.3168777 -0.3003550 -0.02745457</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -1.2693983  0.19674511 -0.1762610 -1.2131392  0.1794639  0.88144485</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.2533625  0.08158049  0.2596137  0.2466786 -0.9374372 -3.09168198</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.1116180 -0.89830298 -0.2510197  0.1118254  1.4479660  1.12917805</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -0.1315426 -0.61990929 -1.0445444 -1.0078516  1.3361280  1.96047642</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.8725992 -1.06214909 -2.0920704  1.2416995  0.4995538  0.24592419</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.1657629  0.78311754 -0.5391583  1.3815616 -2.7557557 -0.43052706</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -1.2409544 -2.78007372 -1.5206390 -2.5197112  0.4713136 -0.28259708</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>              [,7]       [,8]        [,9]       [,10]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.28259708 -0.9525677 -0.61461492  0.01302273</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -0.37221254 -0.4087357 -0.87151065  1.04067074</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.18263134 -2.2371918 -0.50174591  0.48370651</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.06055847  1.6845247  0.61345388 -1.38514216</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.28844587  0.8478142 -2.27293071 -0.98822934</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  1.40416927 -1.4393261 -0.02903636 -0.81254630</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  1.96437541  0.7074581 -1.31878087 -0.03695966</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -1.76916228  2.4144420 -1.59245568  0.12226510</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.11502054 -0.9043406 -0.15879473 -0.74855108</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.47298787  0.4745312  0.39397965  0.09353390</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.37221254 -0.4087357 -0.87151065  1.04067074</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  0.18263134 -2.2371918 -0.50174591  0.48370651</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.06055847  1.6845247  0.61345388 -1.38514216</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -0.28844587  0.8478142 -2.27293071 -0.98822934</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  1.40416927 -1.4393261 -0.02903636 -0.81254630</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  1.96437541  0.7074581 -1.31878087 -0.03695966</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -1.76916228  2.4144420 -1.59245568  0.12226510</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,]  0.11502054 -0.9043406 -0.15879473 -0.74855108</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.47298787  0.4745312  0.39397965  0.09353390</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.95256772 -0.6146149  0.01302273  1.73000527</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/giotto-class.html b/reference/giotto-class.html
index 4ed8c7af..4ad43c78 100644
--- a/reference/giotto-class.html
+++ b/reference/giotto-class.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoAffineImage-class.html b/reference/giottoAffineImage-class.html
index ba7fa3ad..992db3c5 100644
--- a/reference/giottoAffineImage-class.html
+++ b/reference/giottoAffineImage-class.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoImage-class.html b/reference/giottoImage-class.html
index 6ab3b05b..b8c6e927 100644
--- a/reference/giottoImage-class.html
+++ b/reference/giottoImage-class.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoLargeImage-class.html b/reference/giottoLargeImage-class.html
index dd150996..db03cb3a 100644
--- a/reference/giottoLargeImage-class.html
+++ b/reference/giottoLargeImage-class.html
@@ -17,7 +17,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoMasterToSuite.html b/reference/giottoMasterToSuite.html
index c6868008..8c2c3925 100644
--- a/reference/giottoMasterToSuite.html
+++ b/reference/giottoMasterToSuite.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoPoints-class.html b/reference/giottoPoints-class.html
index e903307a..819bde28 100644
--- a/reference/giottoPoints-class.html
+++ b/reference/giottoPoints-class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoPolygon-class.html b/reference/giottoPolygon-class.html
index c3b9b0c0..1e2964c6 100644
--- a/reference/giottoPolygon-class.html
+++ b/reference/giottoPolygon-class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoToAnnData.html b/reference/giottoToAnnData.html
index ed141480..09c5a09e 100644
--- a/reference/giottoToAnnData.html
+++ b/reference/giottoToAnnData.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoToSeurat.html b/reference/giottoToSeurat.html
index 4cb70196..bbb6ec32 100644
--- a/reference/giottoToSeurat.html
+++ b/reference/giottoToSeurat.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoToSeuratV4.html b/reference/giottoToSeuratV4.html
index a293833f..6b114786 100644
--- a/reference/giottoToSeuratV4.html
+++ b/reference/giottoToSeuratV4.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoToSeuratV5.html b/reference/giottoToSeuratV5.html
index 59f9ab9a..b8c7ec6b 100644
--- a/reference/giottoToSeuratV5.html
+++ b/reference/giottoToSeuratV5.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoToSpatialData.html b/reference/giottoToSpatialData.html
index 13e84bf8..e5bff88e 100644
--- a/reference/giottoToSpatialData.html
+++ b/reference/giottoToSpatialData.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giottoToSpatialExperiment.html b/reference/giottoToSpatialExperiment.html
index af0e5076..20529fcc 100644
--- a/reference/giottoToSpatialExperiment.html
+++ b/reference/giottoToSpatialExperiment.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giotto_instructions.html b/reference/giotto_instructions.html
index 548c1b37..1d26f0cb 100644
--- a/reference/giotto_instructions.html
+++ b/reference/giotto_instructions.html
@@ -27,7 +27,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/giotto_python.html b/reference/giotto_python.html
index cc8edb34..026d5b01 100644
--- a/reference/giotto_python.html
+++ b/reference/giotto_python.html
@@ -79,7 +79,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hexVertices.html b/reference/hexVertices.html
index 9514f6d5..ae9700aa 100644
--- a/reference/hexVertices.html
+++ b/reference/hexVertices.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/hist.html b/reference/hist.html
index cf3c7258..5737aca4 100644
--- a/reference/hist.html
+++ b/reference/hist.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 7bb4bbf0..ebaa175e 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -1563,6 +1563,18 @@ <h3 id="manipulation">Manipulation<a class="anchor" aria-label="anchor" href="#m
         <dd>Convex hull, minimal bounding rotated rectangle, and minimal bounding circle</dd>
       </dl><dl><dt>
 
+          <code><a href="buffer.html">buffer(<i>&lt;spatLocsObj&gt;</i>)</a></code> <code><a href="buffer.html">buffer(<i>&lt;giottoPoints&gt;</i>)</a></code> <code><a href="buffer.html">buffer(<i>&lt;giottoPolygon&gt;</i>)</a></code>
+
+        </dt>
+        <dd>Create a buffer around vector geometries</dd>
+      </dl><dl><dt>
+
+          <code><a href="settleGeom.html">settleGeom(<i>&lt;giottoPolygon&gt;</i>)</a></code> <code><a href="settleGeom.html">settleGeom(<i>&lt;SpatVector&gt;</i>)</a></code>
+
+        </dt>
+        <dd>Settle polygon bounds</dd>
+      </dl><dl><dt>
+
           <code><a href="relate.html">relate(<i>&lt;giottoSpatial&gt;</i>,<i>&lt;giottoSpatial&gt;</i>)</a></code> <code><a href="relate.html">relate(<i>&lt;giotto&gt;</i>,<i>&lt;giottoSpatial&gt;</i>)</a></code>
 
         </dt>
diff --git a/reference/init_cell_metadata.html b/reference/init_cell_metadata.html
index a1225d9f..b6501117 100644
--- a/reference/init_cell_metadata.html
+++ b/reference/init_cell_metadata.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/init_feat_metadata.html b/reference/init_feat_metadata.html
index b7fd778f..d5abfe5e 100644
--- a/reference/init_feat_metadata.html
+++ b/reference/init_feat_metadata.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/joinGiottoObjects.html b/reference/joinGiottoObjects.html
index e0f91d8a..b0bdaaec 100644
--- a/reference/joinGiottoObjects.html
+++ b/reference/joinGiottoObjects.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_cell_id_names.html b/reference/list_cell_id_names.html
index 8b87de71..1261d294 100644
--- a/reference/list_cell_id_names.html
+++ b/reference/list_cell_id_names.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_cell_metadata.html b/reference/list_cell_metadata.html
index 0ddd7496..f73d8e80 100644
--- a/reference/list_cell_metadata.html
+++ b/reference/list_cell_metadata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_dim_reductions.html b/reference/list_dim_reductions.html
index 3d530949..6f78ccda 100644
--- a/reference/list_dim_reductions.html
+++ b/reference/list_dim_reductions.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_dim_reductions_names.html b/reference/list_dim_reductions_names.html
index 365c3a59..7b6a0525 100644
--- a/reference/list_dim_reductions_names.html
+++ b/reference/list_dim_reductions_names.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_expression.html b/reference/list_expression.html
index 8e2463ca..d36c0751 100644
--- a/reference/list_expression.html
+++ b/reference/list_expression.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_expression_names.html b/reference/list_expression_names.html
index 485efcb4..a3e1727e 100644
--- a/reference/list_expression_names.html
+++ b/reference/list_expression_names.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_feat_id_names.html b/reference/list_feat_id_names.html
index 99c04a3b..f7bea74b 100644
--- a/reference/list_feat_id_names.html
+++ b/reference/list_feat_id_names.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_feat_metadata.html b/reference/list_feat_metadata.html
index ebcbd1e2..0169be62 100644
--- a/reference/list_feat_metadata.html
+++ b/reference/list_feat_metadata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_feature_info.html b/reference/list_feature_info.html
index 0dff2f19..e02483e3 100644
--- a/reference/list_feature_info.html
+++ b/reference/list_feature_info.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_feature_info_names.html b/reference/list_feature_info_names.html
index 295d4568..3b44cd16 100644
--- a/reference/list_feature_info_names.html
+++ b/reference/list_feature_info_names.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_giotto_data.html b/reference/list_giotto_data.html
index 8f365b91..5987400d 100644
--- a/reference/list_giotto_data.html
+++ b/reference/list_giotto_data.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_images.html b/reference/list_images.html
index 10486514..ddf17376 100644
--- a/reference/list_images.html
+++ b/reference/list_images.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_images_names.html b/reference/list_images_names.html
index ec7c4745..10b9d25e 100644
--- a/reference/list_images_names.html
+++ b/reference/list_images_names.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_nearest_networks.html b/reference/list_nearest_networks.html
index 2328c934..b98c2524 100644
--- a/reference/list_nearest_networks.html
+++ b/reference/list_nearest_networks.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_nearest_networks_names.html b/reference/list_nearest_networks_names.html
index 1f4e3c73..d949cfd7 100644
--- a/reference/list_nearest_networks_names.html
+++ b/reference/list_nearest_networks_names.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_enrichments.html b/reference/list_spatial_enrichments.html
index 68a60167..812bb631 100644
--- a/reference/list_spatial_enrichments.html
+++ b/reference/list_spatial_enrichments.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_enrichments_names.html b/reference/list_spatial_enrichments_names.html
index c96f5139..f61d4f6e 100644
--- a/reference/list_spatial_enrichments_names.html
+++ b/reference/list_spatial_enrichments_names.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_grids.html b/reference/list_spatial_grids.html
index 2eb28ee5..4ebf760a 100644
--- a/reference/list_spatial_grids.html
+++ b/reference/list_spatial_grids.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_grids_names.html b/reference/list_spatial_grids_names.html
index fe8bd6a5..6999ab57 100644
--- a/reference/list_spatial_grids_names.html
+++ b/reference/list_spatial_grids_names.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_info.html b/reference/list_spatial_info.html
index f955285e..fa84cb9e 100644
--- a/reference/list_spatial_info.html
+++ b/reference/list_spatial_info.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_info_names.html b/reference/list_spatial_info_names.html
index 1cdfeabc..799ddeeb 100644
--- a/reference/list_spatial_info_names.html
+++ b/reference/list_spatial_info_names.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_locations.html b/reference/list_spatial_locations.html
index 866b4d46..a07b7899 100644
--- a/reference/list_spatial_locations.html
+++ b/reference/list_spatial_locations.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_locations_names.html b/reference/list_spatial_locations_names.html
index 3f94893a..3f070712 100644
--- a/reference/list_spatial_locations_names.html
+++ b/reference/list_spatial_locations_names.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_networks.html b/reference/list_spatial_networks.html
index 054f2ad9..e57bf14b 100644
--- a/reference/list_spatial_networks.html
+++ b/reference/list_spatial_networks.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/list_spatial_networks_names.html b/reference/list_spatial_networks_names.html
index 858ba9d1..cdfe70c2 100644
--- a/reference/list_spatial_networks_names.html
+++ b/reference/list_spatial_networks_names.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/loadGiotto.html b/reference/loadGiotto.html
index 1eec435e..bdf8643d 100644
--- a/reference/loadGiotto.html
+++ b/reference/loadGiotto.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/makePseudoVisium.html b/reference/makePseudoVisium.html
index 676b0c34..c7d42bae 100644
--- a/reference/makePseudoVisium.html
+++ b/reference/makePseudoVisium.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/mean_flex.html b/reference/mean_flex.html
index 35bb831d..c86b5f09 100644
--- a/reference/mean_flex.html
+++ b/reference/mean_flex.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -67,7 +67,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">mean_flex</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.06142303</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.05046857</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/miscData-class.html b/reference/miscData-class.html
index cb27a146..9b14016b 100644
--- a/reference/miscData-class.html
+++ b/reference/miscData-class.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/my_arowMeans.html b/reference/my_arowMeans.html
index b96062ee..8289f1ed 100644
--- a/reference/my_arowMeans.html
+++ b/reference/my_arowMeans.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,8 +63,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">my_arowMeans</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.2884262 -0.5417610 -0.2227548  0.1578376  0.2002051  0.1017837</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.6461654  0.8037910 -0.3705254 -0.4083799</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.5417610 -0.2227548  0.1578376  0.2002051  0.1017837 -0.6461654</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.8037910 -0.3705254 -0.4083799  0.4040291</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/my_growMeans.html b/reference/my_growMeans.html
index 7c5077ad..ffd8176d 100644
--- a/reference/my_growMeans.html
+++ b/reference/my_growMeans.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -67,8 +67,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">my_growMeans</span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/MathFun.html" class="external-link">abs</a></span><span class="op">(</span><span class="va">m</span><span class="op">)</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.6858454 0.4898760 0.5735737 0.6441830 0.5510774 0.7287629 0.7224097</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] 0.4566198 0.8709865 0.6379915</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] 0.4898760 0.5735737 0.6441830 0.5510774 0.7287629 0.7224097 0.4566198</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8] 0.8709865 0.6379915 0.7580299</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/my_rowMeans.html b/reference/my_rowMeans.html
index 9ff1d44f..0f689455 100644
--- a/reference/my_rowMeans.html
+++ b/reference/my_rowMeans.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -71,8 +71,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">my_rowMeans</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.31935467 -0.11429801  0.06630945 -0.38510854 -0.38755999 -0.08956358</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7]  0.84401809 -0.06373938  0.25949145 -0.02899145</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.11429801  0.06630945 -0.38510854 -0.38755999 -0.08956358  0.84401809</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.06373938  0.25949145 -0.02899145  0.44829355</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/nnDT_to_kNN.html b/reference/nnDT_to_kNN.html
index b5a5ac86..3d3114a1 100644
--- a/reference/nnDT_to_kNN.html
+++ b/reference/nnDT_to_kNN.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/nnNetObj-class.html b/reference/nnNetObj-class.html
index 5aa99d84..e58d88fb 100644
--- a/reference/nnNetObj-class.html
+++ b/reference/nnNetObj-class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
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--- a/reference/objHistory.html
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 9dd53f3a..30a5626e 100644
--- a/reference/objName-generic.html
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 0498725c..7b58f9e4 100644
--- a/reference/objectlist_name_utils.html
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index 252099d2..bbd0e954 100644
--- a/reference/ometif_metadata.html
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index d44c3de6..2880414f 100644
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index 10bb78e1..deb3b024 100644
--- a/reference/overlapImagesToMatrix.html
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 5c63192c..ff829664 100644
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index d302b890..3240782f 100644
--- a/reference/polyStamp.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/polygon_to_raster.html b/reference/polygon_to_raster.html
index bb1eb967..1302575f 100644
--- a/reference/polygon_to_raster.html
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@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/prov-generic.html b/reference/prov-generic.html
index 079fb941..e830abc6 100644
--- a/reference/prov-generic.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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diff --git a/reference/r_spatial_conversions.html b/reference/r_spatial_conversions.html
index e4b74f65..36ba2bbe 100644
--- a/reference/r_spatial_conversions.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rbind-generic.html b/reference/rbind-generic.html
index 01d4add9..2d5ca775 100644
--- a/reference/rbind-generic.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rbind2_giotto_polygon_hetero.html b/reference/rbind2_giotto_polygon_hetero.html
index 5ebeaa85..7aad14be 100644
--- a/reference/rbind2_giotto_polygon_hetero.html
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@@ -13,7 +13,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rbind2_giotto_polygon_homo.html b/reference/rbind2_giotto_polygon_homo.html
index 535697a4..0ecdd328 100644
--- a/reference/rbind2_giotto_polygon_homo.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/readCellMetadata.html b/reference/readCellMetadata.html
index 2d2dce18..4652d374 100644
--- a/reference/readCellMetadata.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/readDimReducData.html b/reference/readDimReducData.html
index 5fdbc54e..8f3ace8b 100644
--- a/reference/readDimReducData.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/readExprData.html b/reference/readExprData.html
index 9f513a47..a9ff9569 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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diff --git a/reference/readExprMatrix.html b/reference/readExprMatrix.html
index a8cb9351..8fa07fb3 100644
--- a/reference/readExprMatrix.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/readFeatData.html b/reference/readFeatData.html
index ffd3710c..f2955a9a 100644
--- a/reference/readFeatData.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/readFeatMetadata.html b/reference/readFeatMetadata.html
index e9dfeb54..cc9daec4 100644
--- a/reference/readFeatMetadata.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/readGiottoInstructions.html b/reference/readGiottoInstructions.html
index ec623f34..fd7b7beb 100644
--- a/reference/readGiottoInstructions.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
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index 6ee059cf..e756f5cd 100644
--- a/reference/readNearestNetData.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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index c42f68d1..dc494da3 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 4a3a5a32..7935ac9a 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index d23b7fab..3120efe9 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
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index c082307c..07fd4864 100644
--- a/reference/readSpatNetData.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/read_data_params.html b/reference/read_data_params.html
index e03e10cf..076e8585 100644
--- a/reference/read_data_params.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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index 02b00f6c..c5ddb2fe 100644
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diff --git a/reference/reconnectGiottoImage.html b/reference/reconnectGiottoImage.html
index f8e4545d..73c1559a 100644
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/reconnect_giottoLargeImage.html b/reference/reconnect_giottoLargeImage.html
index f2c685a8..c719f35a 100644
--- a/reference/reconnect_giottoLargeImage.html
+++ b/reference/reconnect_giottoLargeImage.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/reconnect_image_object.html b/reference/reconnect_image_object.html
index 025f13eb..a726b75a 100644
--- a/reference/reconnect_image_object.html
+++ b/reference/reconnect_image_object.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rectVertices.html b/reference/rectVertices.html
index 88cf3dde..ade5ddd6 100644
--- a/reference/rectVertices.html
+++ b/reference/rectVertices.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/reexports.html b/reference/reexports.html
index 4d6a2923..f501cfe9 100644
--- a/reference/reexports.html
+++ b/reference/reexports.html
@@ -21,7 +21,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/relate.html b/reference/relate.html
index fd6646d3..24e7c1e5 100644
--- a/reference/relate.html
+++ b/reference/relate.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/removeCellAnnotation.html b/reference/removeCellAnnotation.html
index a0c908ae..4ee8d3f2 100644
--- a/reference/removeCellAnnotation.html
+++ b/reference/removeCellAnnotation.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/removeFeatAnnotation.html b/reference/removeFeatAnnotation.html
index a5d9e4a5..670c484d 100644
--- a/reference/removeFeatAnnotation.html
+++ b/reference/removeFeatAnnotation.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/replaceGiottoInstructions.html b/reference/replaceGiottoInstructions.html
index 84aa080c..65d77d0b 100644
--- a/reference/replaceGiottoInstructions.html
+++ b/reference/replaceGiottoInstructions.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/replace_bracket.html b/reference/replace_bracket.html
index 64a4a717..e6b89bad 100644
--- a/reference/replace_bracket.html
+++ b/reference/replace_bracket.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/replace_dollar.html b/reference/replace_dollar.html
index 1235c634..fe5c3624 100644
--- a/reference/replace_dollar.html
+++ b/reference/replace_dollar.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rescale.html b/reference/rescale.html
index 5508effb..8ad8ff82 100644
--- a/reference/rescale.html
+++ b/reference/rescale.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rescalePolygons.html b/reference/rescalePolygons.html
index ed788689..9280d66b 100644
--- a/reference/rescalePolygons.html
+++ b/reference/rescalePolygons.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/row-plus-colnames-generic.html b/reference/row-plus-colnames-generic.html
index e6c5a60b..4ac3051f 100644
--- a/reference/row-plus-colnames-generic.html
+++ b/reference/row-plus-colnames-generic.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/rowMeans_flex.html b/reference/rowMeans_flex.html
index 984cf9a5..2c2aa6b5 100644
--- a/reference/rowMeans_flex.html
+++ b/reference/rowMeans_flex.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,8 +63,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">rowMeans_flex</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.03455096  0.08871945 -0.29999737  0.47536178 -0.66005505 -0.03974135</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.45622412 -0.14340232 -0.50460708  0.45589154</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1]  0.08871945 -0.29999737  0.47536178 -0.66005505 -0.03974135 -0.45622412</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -0.14340232 -0.50460708  0.45589154 -0.04022921</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/rowSums_flex.html b/reference/rowSums_flex.html
index 94afc1a6..e8ed9611 100644
--- a/reference/rowSums_flex.html
+++ b/reference/rowSums_flex.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,8 +63,8 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">rowSums_flex</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -0.2852256 -4.7180057  3.5983422 -1.4346828  2.0426869  2.0530418</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -4.1031143 -3.5399338  1.3677829  9.0450398</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1] -4.7180057  3.5983422 -1.4346828  2.0426869  2.0530418 -4.1031143</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7] -3.5399338  1.3677829  9.0450398 -0.2253641</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/saveGiotto.html b/reference/saveGiotto.html
index 43ddcfa3..3c32dfd3 100644
--- a/reference/saveGiotto.html
+++ b/reference/saveGiotto.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setCellMetadata.html b/reference/setCellMetadata.html
index 339bdb14..139602f6 100644
--- a/reference/setCellMetadata.html
+++ b/reference/setCellMetadata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setDimReduction.html b/reference/setDimReduction.html
index 63bb340f..3e5a22fa 100644
--- a/reference/setDimReduction.html
+++ b/reference/setDimReduction.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setExpression.html b/reference/setExpression.html
index a5ad60a7..67fa0131 100644
--- a/reference/setExpression.html
+++ b/reference/setExpression.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setFeatureInfo.html b/reference/setFeatureInfo.html
index e4849747..911bf1e4 100644
--- a/reference/setFeatureInfo.html
+++ b/reference/setFeatureInfo.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setFeatureMetadata.html b/reference/setFeatureMetadata.html
index 7bda0567..ee9981cb 100644
--- a/reference/setFeatureMetadata.html
+++ b/reference/setFeatureMetadata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setGiotto.html b/reference/setGiotto.html
index 4fbf0c1b..7517ae8f 100644
--- a/reference/setGiotto.html
+++ b/reference/setGiotto.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setGiottoImage.html b/reference/setGiottoImage.html
index 57c88c5a..21e1de70 100644
--- a/reference/setGiottoImage.html
+++ b/reference/setGiottoImage.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setMultiomics.html b/reference/setMultiomics.html
index 63c8535f..de76286c 100644
--- a/reference/setMultiomics.html
+++ b/reference/setMultiomics.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setNearestNetwork.html b/reference/setNearestNetwork.html
index 67376ce8..8e61ccb8 100644
--- a/reference/setNearestNetwork.html
+++ b/reference/setNearestNetwork.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setPolygonInfo.html b/reference/setPolygonInfo.html
index e5d1024d..4808e0ac 100644
--- a/reference/setPolygonInfo.html
+++ b/reference/setPolygonInfo.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setSpatialEnrichment.html b/reference/setSpatialEnrichment.html
index 2feda8fb..1555033a 100644
--- a/reference/setSpatialEnrichment.html
+++ b/reference/setSpatialEnrichment.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/setSpatialGrid.html b/reference/setSpatialGrid.html
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diff --git a/reference/settleGeom.html b/reference/settleGeom.html
new file mode 100644
index 00000000..79d25e17
--- /dev/null
+++ b/reference/settleGeom.html
@@ -0,0 +1,103 @@
+<!DOCTYPE html>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Settle polygon bounds — settleGeom • GiottoClass</title><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/JetBrains_Mono-0.4.9/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.4.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><meta property="og:title" content="Settle polygon bounds — settleGeom"><meta name="description" content="Settle the boundaries between polygons when they overlap by
+splitting both at the point where they touch. Works through intersection
+with the voronoi of the centroids."><meta property="og:description" content="Settle the boundaries between polygons when they overlap by
+splitting both at the point where they touch. Works through intersection
+with the voronoi of the centroids."><meta property="og:image" content="https://drieslab.github.io/GiottoClass/logo.png"></head><body>
+    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
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+<div class="row">
+  <main id="main" class="col-md-9"><div class="page-header">
+      <img src="../logo.png" class="logo" alt=""><h1>Settle polygon bounds</h1>
+      <small class="dont-index">Source: <a href="https://github.com/drieslab/Giotto/blob/website/R/buffer.R" class="external-link"><code>R/buffer.R</code></a></small>
+      <div class="d-none name"><code>settleGeom.Rd</code></div>
+    </div>
+
+    <div class="ref-description section level2">
+    <p>Settle the boundaries between polygons when they overlap by
+splitting both at the point where they touch. Works through intersection
+with the voronoi of the centroids.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="co"># S4 method for class 'giottoPolygon'</span></span>
+<span><span class="fu">settleGeom</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
+<span></span>
+<span><span class="co"># S4 method for class 'SpatVector'</span></span>
+<span><span class="fu">settleGeom</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
+    </div>
+
+    <div class="section level2">
+    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
+
+
+<dl><dt id="arg-x">x<a class="anchor" aria-label="anchor" href="#arg-x"></a></dt>
+<dd><p>a <code>SpatVector</code> of type "polygons" or object inheriting from
+<code>giottoPolygon</code></p></dd>
+
+</dl></div>
+    <div class="section level2">
+    <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
+    <p>same class as <code>x</code>, with the contained polygons borders settled
+in relation to each other.</p>
+    </div>
+
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">svp</span> <span class="op">&lt;-</span> <span class="fu">GiottoData</span><span class="fu">::</span><span class="fu"><a href="https://drieslab.github.io/GiottoData/reference/loadSubObjectMini.html" class="external-link">loadSubObjectMini</a></span><span class="op">(</span><span class="st">"giottoPolygon"</span><span class="op">)</span><span class="op">[</span><span class="op">]</span></span></span>
+<span class="r-in"><span><span class="va">svp</span> <span class="op">&lt;-</span> <span class="fu"><a href="buffer.html">buffer</a></span><span class="op">(</span><span class="va">svp</span>, <span class="fl">5</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="plot-generic.html">plot</a></span><span class="op">(</span><span class="va">svp</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="settleGeom-1.png" alt="" width="700" height="433"></span>
+<span class="r-in"><span><span class="va">svp</span> <span class="op">&lt;-</span> <span class="fu">settleGeom</span><span class="op">(</span><span class="va">svp</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="plot-generic.html">plot</a></span><span class="op">(</span><span class="va">svp</span><span class="op">)</span></span></span>
+<span class="r-plt img"><img src="settleGeom-2.png" alt="" width="700" height="433"></span>
+</code></pre></div>
+    </div>
+  </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
+    </nav></aside></div>
+
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+    <footer><div class="pkgdown-footer-left">
+  <p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, <a href="https://github.com/jiajic" class="external-link">Jiaji George Chen</a>, <a href="https://labs.icahn.mssm.edu/yuanlab/" class="external-link">Guo-Cheng Yuan</a>, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn C. Chávez-Fuentes</a>, Edward Ruiz.</p>
+</div>
+
+<div class="pkgdown-footer-right">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.1.1.</p>
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diff --git a/reference/seuratToGiotto.html b/reference/seuratToGiotto.html
index 04e7eb5f..5435e6cb 100644
--- a/reference/seuratToGiotto.html
+++ b/reference/seuratToGiotto.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/seuratToGiottoV4.html b/reference/seuratToGiottoV4.html
index b71a390d..5080639e 100644
--- a/reference/seuratToGiottoV4.html
+++ b/reference/seuratToGiottoV4.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/seuratToGiottoV5.html b/reference/seuratToGiottoV5.html
index 4004b23e..3fc9be15 100644
--- a/reference/seuratToGiottoV5.html
+++ b/reference/seuratToGiottoV5.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/shear.html b/reference/shear.html
index b277f6b2..14b16b11 100644
--- a/reference/shear.html
+++ b/reference/shear.html
@@ -13,7 +13,7 @@
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/show.html b/reference/show.html
index 7138a9c3..beb8f08f 100644
--- a/reference/show.html
+++ b/reference/show.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoCellMetadata.html b/reference/showGiottoCellMetadata.html
index 880f050c..52eeaa17 100644
--- a/reference/showGiottoCellMetadata.html
+++ b/reference/showGiottoCellMetadata.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoDimRed.html b/reference/showGiottoDimRed.html
index eeea2f8b..47fca739 100644
--- a/reference/showGiottoDimRed.html
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoExpression.html b/reference/showGiottoExpression.html
index b9f6d2df..f6cbeef8 100644
--- a/reference/showGiottoExpression.html
+++ b/reference/showGiottoExpression.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoFeatInfo.html b/reference/showGiottoFeatInfo.html
index 880016cc..6d8b922d 100644
--- a/reference/showGiottoFeatInfo.html
+++ b/reference/showGiottoFeatInfo.html
@@ -7,7 +7,7 @@
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
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diff --git a/reference/showGiottoFeatMetadata.html b/reference/showGiottoFeatMetadata.html
index 416ddb75..edcea444 100644
--- a/reference/showGiottoFeatMetadata.html
+++ b/reference/showGiottoFeatMetadata.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoImageNames.html b/reference/showGiottoImageNames.html
index 70e5ee95..e7551be1 100644
--- a/reference/showGiottoImageNames.html
+++ b/reference/showGiottoImageNames.html
@@ -9,7 +9,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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diff --git a/reference/showGiottoInstructions.html b/reference/showGiottoInstructions.html
index 46cc2106..9c6ec3ec 100644
--- a/reference/showGiottoInstructions.html
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@@ -7,7 +7,7 @@
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoNearestNetworks.html b/reference/showGiottoNearestNetworks.html
index 5e9ab4a8..f282e5c9 100644
--- a/reference/showGiottoNearestNetworks.html
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@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoSpatEnrichments.html b/reference/showGiottoSpatEnrichments.html
index bde7a8c2..51cf7924 100644
--- a/reference/showGiottoSpatEnrichments.html
+++ b/reference/showGiottoSpatEnrichments.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoSpatGrids.html b/reference/showGiottoSpatGrids.html
index 144a826f..b802d88f 100644
--- a/reference/showGiottoSpatGrids.html
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoSpatLocs.html b/reference/showGiottoSpatLocs.html
index 6c767d12..94dcf177 100644
--- a/reference/showGiottoSpatLocs.html
+++ b/reference/showGiottoSpatLocs.html
@@ -7,7 +7,7 @@
 
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+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoSpatNetworks.html b/reference/showGiottoSpatNetworks.html
index d7f4a5a0..c45754e7 100644
--- a/reference/showGiottoSpatNetworks.html
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@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGiottoSpatialInfo.html b/reference/showGiottoSpatialInfo.html
index 02395cd0..474f85ae 100644
--- a/reference/showGiottoSpatialInfo.html
+++ b/reference/showGiottoSpatialInfo.html
@@ -7,7 +7,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showGrids.html b/reference/showGrids.html
index 8673cee1..0bbf17e5 100644
--- a/reference/showGrids.html
+++ b/reference/showGrids.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showNetworks.html b/reference/showNetworks.html
index dd8a145d..b6be11b3 100644
--- a/reference/showNetworks.html
+++ b/reference/showNetworks.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/showProcessingSteps.html b/reference/showProcessingSteps.html
index 2cc6033a..2380b62a 100644
--- a/reference/showProcessingSteps.html
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@@ -9,7 +9,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/sliceGiotto.html b/reference/sliceGiotto.html
index d7d4a20f..64fe7ea0 100644
--- a/reference/sliceGiotto.html
+++ b/reference/sliceGiotto.html
@@ -9,7 +9,7 @@
 
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/smoothGiottoPolygons.html b/reference/smoothGiottoPolygons.html
index 8b7fc1fb..a05d9119 100644
--- a/reference/smoothGiottoPolygons.html
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@@ -7,7 +7,7 @@
 
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spatEnrObj-class.html b/reference/spatEnrObj-class.html
index c1476190..cacf0d6b 100644
--- a/reference/spatEnrObj-class.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spatIDs-generic.html b/reference/spatIDs-generic.html
index c4e03d31..1269f7b4 100644
--- a/reference/spatIDs-generic.html
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index aca2f1af..65d5c035 100644
--- a/reference/spatLocsObj-class.html
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spatQueryGiottoPolygons.html b/reference/spatQueryGiottoPolygons.html
index de6053c3..e1ae195f 100644
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@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spatShift.html b/reference/spatShift.html
index ff45751d..de1f177b 100644
--- a/reference/spatShift.html
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@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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index 44a66c27..e1bd0246 100644
--- a/reference/spatUnit-generic.html
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@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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diff --git a/reference/spatValues.html b/reference/spatValues.html
index d4b53b4a..2bc62ea7 100644
--- a/reference/spatValues.html
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-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
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index f0fa81b0..2c96ed68 100644
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+++ b/reference/spat_net_to_igraph.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spatialExperimentToGiotto.html b/reference/spatialExperimentToGiotto.html
index b28f6fb8..1ae00ec1 100644
--- a/reference/spatialExperimentToGiotto.html
+++ b/reference/spatialExperimentToGiotto.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spatialGridObj-class.html b/reference/spatialGridObj-class.html
index eace7702..ec44859b 100644
--- a/reference/spatialGridObj-class.html
+++ b/reference/spatialGridObj-class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spatialNetworkObj-class.html b/reference/spatialNetworkObj-class.html
index 8220b0a9..50c360e3 100644
--- a/reference/spatialNetworkObj-class.html
+++ b/reference/spatialNetworkObj-class.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spatial_binary_ops.html b/reference/spatial_binary_ops.html
index 1156b75d..6154b89a 100644
--- a/reference/spatial_binary_ops.html
+++ b/reference/spatial_binary_ops.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spatialdataToGiotto.html b/reference/spatialdataToGiotto.html
index 049826ef..561da3fd 100644
--- a/reference/spatialdataToGiotto.html
+++ b/reference/spatialdataToGiotto.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/spin.html b/reference/spin.html
index dd4b4122..f1c9eb3a 100644
--- a/reference/spin.html
+++ b/reference/spin.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/splitGiotto.html b/reference/splitGiotto.html
index 5f48b826..8a219e41 100644
--- a/reference/splitGiotto.html
+++ b/reference/splitGiotto.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/standardise_flex.html b/reference/standardise_flex.html
index 47bb470a..7f4449fc 100644
--- a/reference/standardise_flex.html
+++ b/reference/standardise_flex.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/stitchFieldCoordinates.html b/reference/stitchFieldCoordinates.html
index 57f28597..8bf5d617 100644
--- a/reference/stitchFieldCoordinates.html
+++ b/reference/stitchFieldCoordinates.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/stitchGiottoLargeImage.html b/reference/stitchGiottoLargeImage.html
index 2644db90..0c26f241 100644
--- a/reference/stitchGiottoLargeImage.html
+++ b/reference/stitchGiottoLargeImage.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/stitchTileCoordinates.html b/reference/stitchTileCoordinates.html
index 209830e1..e38b97c7 100644
--- a/reference/stitchTileCoordinates.html
+++ b/reference/stitchTileCoordinates.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -78,18 +78,18 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">stitchTileCoordinates</span><span class="op">(</span><span class="va">location_file</span>, Xtilespan <span class="op">=</span> <span class="fl">0.5</span>, Ytilespan <span class="op">=</span> <span class="fl">0.5</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>     field         X.X        Y.Y XtileIndex YtileIndex     Xcoord      Ycoord</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>     &lt;num&gt;       &lt;num&gt;      &lt;num&gt;      &lt;int&gt;      &lt;int&gt;      &lt;num&gt;       &lt;num&gt;</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  1:     1  1.18770051 -0.4300296          1          1  1.1877005 -0.43002963</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  2:     2  0.01308331  0.7811606          2          2  0.5130833  1.28116058</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  3:     1  0.64365001  0.3784188          3          3  1.6436500  1.37841880</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  4:     2 -2.48768926 -1.0124020          4          4 -0.9876893  0.48759798</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  5:     1  0.93101913 -2.0656557          5          5  2.9310191 -0.06565571</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  6:     2 -1.89955741  1.0928168          6          6  0.6004426  3.59281676</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  7:     1  1.21015863 -1.7202851          7          7  4.2101586  1.27971492</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  8:     2 -1.46457418 -0.3058085          8          8  2.0354258  3.19419149</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  9:     1  0.75557357 -0.3731366          9          9  4.7555736  3.62686344</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10:     2  0.42274803  0.4004511         10         10  4.9227480  4.90045106</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     field         X.X        Y.Y XtileIndex YtileIndex      Xcoord      Ycoord</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>     &lt;num&gt;       &lt;num&gt;      &lt;num&gt;      &lt;int&gt;      &lt;int&gt;       &lt;num&gt;       &lt;num&gt;</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  1:     1  0.01308331  0.7811606          1          1  0.01308331  0.78116058</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  2:     2  0.64365001  0.3784188          2          2  1.14365001  0.87841880</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  3:     1 -2.48768926 -1.0124020          3          3 -1.48768926 -0.01240202</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  4:     2  0.93101913 -2.0656557          4          4  2.43101913 -0.56565571</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  5:     1 -1.89955741  1.0928168          5          5  0.10044259  3.09281676</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  6:     2  1.21015863 -1.7202851          6          6  3.71015863  0.77971492</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  7:     1 -1.46457418 -0.3058085          7          7  1.53542582  2.69419149</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  8:     2  0.75557357 -0.3731366          8          8  4.25557357  3.12686344</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  9:     1  0.42274803  0.4004511          9          9  4.42274803  4.40045106</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10:     2 -0.43002963  1.1347597         10         10  4.06997037  5.63475968</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/subsetGiotto.html b/reference/subsetGiotto.html
index 0ceb0b00..1b594fc0 100644
--- a/reference/subsetGiotto.html
+++ b/reference/subsetGiotto.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/subsetGiottoLocs.html b/reference/subsetGiottoLocs.html
index 2e05b56a..7683e806 100644
--- a/reference/subsetGiottoLocs.html
+++ b/reference/subsetGiottoLocs.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/subsetGiottoLocsMulti.html b/reference/subsetGiottoLocsMulti.html
index 67562afd..1abc42e4 100644
--- a/reference/subsetGiottoLocsMulti.html
+++ b/reference/subsetGiottoLocsMulti.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/subsetGiottoLocsSubcellular.html b/reference/subsetGiottoLocsSubcellular.html
index 10c4ad73..91f4dcfd 100644
--- a/reference/subsetGiottoLocsSubcellular.html
+++ b/reference/subsetGiottoLocsSubcellular.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/subset_bracket.html b/reference/subset_bracket.html
index 079e280e..515bc0b2 100644
--- a/reference/subset_bracket.html
+++ b/reference/subset_bracket.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/subset_dollar.html b/reference/subset_dollar.html
index 19969003..ffebcae6 100644
--- a/reference/subset_dollar.html
+++ b/reference/subset_dollar.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/subset_giotto.html b/reference/subset_giotto.html
index 12c33668..2b521009 100644
--- a/reference/subset_giotto.html
+++ b/reference/subset_giotto.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/subset_giotto_subobjects.html b/reference/subset_giotto_subobjects.html
index 6a1ca27c..bb54c03d 100644
--- a/reference/subset_giotto_subobjects.html
+++ b/reference/subset_giotto_subobjects.html
@@ -19,7 +19,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/t_flex.html b/reference/t_flex.html
index f6d8b1f8..2ab0ad28 100644
--- a/reference/t_flex.html
+++ b/reference/t_flex.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -63,28 +63,28 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
     <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">m</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/matrix.html" class="external-link">matrix</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/stats/Normal.html" class="external-link">rnorm</a></span><span class="op">(</span><span class="fl">100</span><span class="op">)</span>, nrow <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">t_flex</span><span class="op">(</span><span class="va">m</span><span class="op">)</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>              [,1]       [,2]       [,3]        [,4]       [,5]        [,6]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  1.13475968 -0.1236010  0.8402388  0.09488557 -0.3051016  2.61356953</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,]  1.23346046 -0.7598318  1.2102308 -0.79255887 -1.0285583  0.53468162</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.07576892  0.5285784  0.6529490  1.65551988  0.8628259  1.48753032</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -2.09101499  0.6828611  1.2112902  0.95150212 -2.6957950 -0.90818349</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  0.47029282 -0.3990772 -0.2482703 -0.07380394 -1.9934812 -1.42041042</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,]  0.50937786 -0.5727822 -1.8640852  0.09639107 -0.5443541  1.48551609</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -2.18684352  0.1086828  0.7365619  0.09315147  0.0132255 -1.04726906</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -1.31266853 -0.7109888  0.2669893  0.53664180  0.2404480  0.01366106</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  1.59534811  0.6553744  0.1503795 -0.59067813  0.6122497  0.37854906</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  2.50702432 -0.2506748 -0.6089946 -0.88808468 -0.6624071  0.73643913</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>             [,7]       [,8]        [,9]       [,10]</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  0.4033562  2.4011713  1.49373183 -0.07131230</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -0.2549574 -1.3450848  0.25582422 -1.24728794</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.7928009 -0.4488620 -1.00887476 -1.68556568</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,] -3.0512252  0.7783738  2.81270232 -0.73703947</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,]  1.2947209 -1.1102363  0.08404357 -0.09540202</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.3448927 -0.2134763  1.15903245 -0.45740931</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -0.7027522 -0.2350337  0.82302884  1.67890702</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.5580017 -0.4879339  0.87933344  0.87836272</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.7803218 -0.9206261  0.67446169 -1.17164534</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> [10,]  0.6153136 -1.5068803 -1.14078881 -0.48878187</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>             [,1]       [,2]        [,3]       [,4]        [,5]       [,6]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,] -0.1236010  0.8402388  0.09488557 -0.3051016  2.61356953  0.4033562</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -0.7598318  1.2102308 -0.79255887 -1.0285583  0.53468162 -0.2549574</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,]  0.5285784  0.6529490  1.65551988  0.8628259  1.48753032 -0.7928009</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.6828611  1.2112902  0.95150212 -2.6957950 -0.90818349 -3.0512252</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -0.3990772 -0.2482703 -0.07380394 -1.9934812 -1.42041042  1.2947209</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.5727822 -1.8640852  0.09639107 -0.5443541  1.48551609 -0.3448927</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,]  0.1086828  0.7365619  0.09315147  0.0132255 -1.04726906 -0.7027522</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.7109888  0.2669893  0.53664180  0.2404480  0.01366106 -0.5580017</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,]  0.6553744  0.1503795 -0.59067813  0.6122497  0.37854906 -0.7803218</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -0.2506748 -0.6089946 -0.88808468 -0.6624071  0.73643913  0.6153136</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>             [,7]        [,8]        [,9]       [,10]</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [1,]  2.4011713  1.49373183 -0.07131230  1.23346046</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [2,] -1.3450848  0.25582422 -1.24728794 -0.07576892</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [3,] -0.4488620 -1.00887476 -1.68556568 -2.09101499</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [4,]  0.7783738  2.81270232 -0.73703947  0.47029282</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [5,] -1.1102363  0.08404357 -0.09540202  0.50937786</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [6,] -0.2134763  1.15903245 -0.45740931 -2.18684352</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [7,] -0.2350337  0.82302884  1.67890702 -1.31266853</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [8,] -0.4879339  0.87933344  0.87836272  1.59534811</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span>  [9,] -0.9206261  0.67446169 -1.17164534  2.50702432</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [10,] -1.5068803 -1.14078881 -0.48878187 -2.01225221</span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
diff --git a/reference/terraVectData-class.html b/reference/terraVectData-class.html
index ca035867..51fef029 100644
--- a/reference/terraVectData-class.html
+++ b/reference/terraVectData-class.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/tessellate.html b/reference/tessellate.html
index 290af9c7..ee02c4dd 100644
--- a/reference/tessellate.html
+++ b/reference/tessellate.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/transpose.html b/reference/transpose.html
index 96fab1ec..aa0406b5 100644
--- a/reference/transpose.html
+++ b/reference/transpose.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/updateGiottoImage.html b/reference/updateGiottoImage.html
index 66acd043..403f0d1a 100644
--- a/reference/updateGiottoImage.html
+++ b/reference/updateGiottoImage.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/updateGiottoImageMG.html b/reference/updateGiottoImageMG.html
index a7431f15..a9b46eb6 100644
--- a/reference/updateGiottoImageMG.html
+++ b/reference/updateGiottoImageMG.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/updateGiottoLargeImage.html b/reference/updateGiottoLargeImage.html
index 25168d30..425372ad 100644
--- a/reference/updateGiottoLargeImage.html
+++ b/reference/updateGiottoLargeImage.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/updateGiottoObject.html b/reference/updateGiottoObject.html
index ec1d49ab..58e5d661 100644
--- a/reference/updateGiottoObject.html
+++ b/reference/updateGiottoObject.html
@@ -9,7 +9,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/updateGiottoPointsObject.html b/reference/updateGiottoPointsObject.html
index 0f7e0905..489aa9c8 100644
--- a/reference/updateGiottoPointsObject.html
+++ b/reference/updateGiottoPointsObject.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/updateGiottoPolygonObject.html b/reference/updateGiottoPolygonObject.html
index d05b8a63..c0b1fdea 100644
--- a/reference/updateGiottoPolygonObject.html
+++ b/reference/updateGiottoPolygonObject.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/update_giotto_params.html b/reference/update_giotto_params.html
index 4c5dcbab..1bd67fcd 100644
--- a/reference/update_giotto_params.html
+++ b/reference/update_giotto_params.html
@@ -7,7 +7,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/wrap.html b/reference/wrap.html
index 1aac36d5..04be1302 100644
--- a/reference/wrap.html
+++ b/reference/wrap.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/writeGiottoLargeImage.html b/reference/writeGiottoLargeImage.html
index af6d3c0f..196904bf 100644
--- a/reference/writeGiottoLargeImage.html
+++ b/reference/writeGiottoLargeImage.html
@@ -11,7 +11,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
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diff --git a/reference/zoom.html b/reference/zoom.html
index 1408e78e..1f15b13a 100644
--- a/reference/zoom.html
+++ b/reference/zoom.html
@@ -13,7 +13,7 @@
 
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.0</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">0.4.1</small>
 
 
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index eac7d0b7..fbcdbcff 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 GiottoClass authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/articles/image_tools.html","id":"overview","dir":"Articles","previous_headings":"Giotto Image Tools","what":"1. Overview","title":"Giotto image tools","text":"Giotto uses giottoLargeImage represent images raster information. S4 class built based terra SpatRaster. older class called giottoImage based magick package also exists, currently phased . Ideally, giottoLargeImages also renamed giottoImage afterwards, simplifying naming scheme. object structure giottoLargeImage","code":"giottoLargeImage \\- name                (object name) \\- raster_object       (terra raster object) \\- extent              (current spatial extent) \\- overall_extent      (spatial extent of original image - experimental) \\- scale_factor        (pixels per coordinate unit - experimental) \\- resolution          (coordinate units covered per pixel) \\- max_intensity       (approximate maximum intensity value) \\- min_intensity       (approximate minimum intensity value) \\- max_window          (value to set as maximum intensity in color scaling) \\- colors              (vector of color mappings provided as hex codes) \\- is_int              (whether values are integers) \\- file_path           (filepath to the image) \\- OS_platform         (operating system)"},{"path":"https://drieslab.github.io/GiottoClass/articles/image_tools.html","id":"sampling","dir":"Articles","previous_headings":"Giotto Image Tools","what":"2. Sampling","title":"Giotto image tools","text":"Spatial images often extremely large files. high detail (resolution), large spatial region captured, precision recorded values (bitdepth) often results files 10s gigabytes. makes full size images difficult work . One way get around perform regular sampling image, touching values original image needed generate downscaled representation. implemented terra spatSample(). plotting, Giotto optimizes speed sampling striking balance terra::crop() terra::spatSample() try prevent sampling unnecessary regions, also avoid large crop operations fullsize image, can costly. done plot_auto_largeImage_resample() giottoLargeImages can also resampled image formats (magick EBImage) addition data.table array using GiottoClass:::.spatraster_sample_values() two functions experimental exported using common function names future.","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/image_tools.html","id":"color-scaling","dir":"Articles","previous_headings":"Giotto Image Tools","what":"3 Color scaling","title":"Giotto image tools","text":"distGiottoImage() can used look values present within giottoLargeImage. often case values recorded within image map full set values allowed bitdepth. Giotto plots images guessing bitdepth based estimated maximum value detected. mapping may always optimal.   Since values beyond 70, try setting max_window 70 color mapping better represents available information.  colormap use image can also edited. default greyscale image monochrome black white. color scales can supplied. monochrome colorscales: getMonochromeColors()","code":"library(GiottoClass) gimg <- GiottoData::loadSubObjectMini(\"giottoLargeImage\", idx = 2) gimg <- GiottoClass:::.update_giotto_image(gimg) # update older images that are missing slots  plot(gimg) distGiottoImage(giottoLargeImage = gimg) gimg@max_window <- 70 plot(gimg) # plot(gimg, max_intensity = 150) # can be used without setting the slot gimg@colors <- getMonochromeColors(\"green\") plot(gimg) viridis_colors <- hcl.colors(256, palette = \"viridis\") plot(gimg, col = viridis_colors) # can be used without setting the slot"},{"path":"https://drieslab.github.io/GiottoClass/articles/image_tools.html","id":"todos","dir":"Articles","previous_headings":"Giotto Image Tools > 3 Color scaling","what":"TODOs:","title":"Giotto image tools","text":"provide accessors slots make ggplot-based plotting also obey settings","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.5 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        ##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    ##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           ## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] GiottoClass_0.4.0 ##  ## loaded via a namespace (and not attached): ##  [1] sass_0.4.9                  SparseArray_1.4.8           ##  [3] gtools_3.9.5                lattice_0.22-6              ##  [5] digest_0.6.37               magrittr_2.0.3              ##  [7] evaluate_1.0.1              grid_4.4.1                  ##  [9] fastmap_1.2.0               jsonlite_1.8.9              ## [11] Matrix_1.7-0                backports_1.5.0             ## [13] GenomeInfoDb_1.40.1         GiottoData_0.2.15           ## [15] httr_1.4.7                  SingleCellExperiment_1.26.0 ## [17] UCSC.utils_1.0.0            codetools_0.2-20            ## [19] textshaping_0.4.0           jquerylib_0.1.4             ## [21] abind_1.4-8                 cli_3.6.3                   ## [23] rlang_1.1.4                 crayon_1.5.3                ## [25] XVector_0.44.0              Biobase_2.64.0              ## [27] cachem_1.1.0                DelayedArray_0.30.1         ## [29] yaml_2.3.10                 S4Arrays_1.4.1              ## [31] tools_4.4.1                 GiottoUtils_0.2.0           ## [33] checkmate_2.3.2             SpatialExperiment_1.14.0    ## [35] GenomeInfoDbData_1.2.12     SummarizedExperiment_1.34.0 ## [37] BiocGenerics_0.50.0         R6_2.5.1                    ## [39] magick_2.8.5                matrixStats_1.4.1           ## [41] stats4_4.4.1                lifecycle_1.0.4             ## [43] zlibbioc_1.50.0             S4Vectors_0.42.1            ## [45] fs_1.6.4                    htmlwidgets_1.6.4           ## [47] IRanges_2.38.1              ragg_1.3.3                  ## [49] desc_1.4.3                  pkgdown_2.1.1               ## [51] terra_1.7-83                bslib_0.8.0                 ## [53] data.table_1.16.2           Rcpp_1.0.13                 ## [55] systemfonts_1.1.0           highr_0.11                  ## [57] xfun_0.48                   GenomicRanges_1.56.2        ## [59] MatrixGenerics_1.16.0       knitr_1.48                  ## [61] rjson_0.2.23                htmltools_0.5.8.1           ## [63] rmarkdown_2.28              compiler_4.4.1"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"spatial-unit-and-feature-type","dir":"Articles","previous_headings":"","what":"Spatial unit and feature type","title":"Overview","text":"","code":"library(GiottoClass)  vizmini <- GiottoData::loadGiottoMini(\"vizgen\") ## 1. read Giotto object ## 2. read Giotto feature information ## 3. read Giotto spatial information ## 3.1 read Giotto spatial shape information ## 3.2 read Giotto spatial centroid information ## 3.3 read Giotto spatial overlap information ## 4. read Giotto image information ## checking default envname 'giotto_env' ## a system default python environment was found ## Using python path: ##  \"/usr/share/miniconda/envs/giotto_env/bin/python\" vizmini ## An object of class giotto  ## >Active spat_unit:  z0  ## >Active feat_type:  rna  ## dimensions    : 337, 498 (features, cells) ## [SUBCELLULAR INFO] ## polygons      : z0 z1 aggregate  ## features      : rna  ## [AGGREGATE INFO] ## expression ----------------------- ##   [z0][rna] raw ##   [z1][rna] raw ##   [aggregate][rna] raw normalized scaled pearson ## spatial locations ---------------- ##   [z0] raw ##   [z1] raw ##   [aggregate] raw ## spatial networks ----------------- ##   [aggregate] Delaunay_network kNN_network ## spatial enrichments -------------- ##   [aggregate][rna] cluster_metagene ## dim reduction -------------------- ##   [aggregate][rna] pca umap tsne ## nearest neighbor networks -------- ##   [aggregate][rna] sNN.pca ## attached images ------------------ ## images      : 4 items... ##  ##  ## Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"show-and-list-functions","dir":"Articles","previous_headings":"","what":"Show and list functions","title":"Overview","text":"Show list functions also provided determining information exists within slots nesting. show functions print preview data within slot, return information","code":"showGiottoSpatLocs(vizmini) ## ├──Spatial unit \"z0\" ## │  └──S4 spatLocsObj \"raw\" coordinates:   (498 rows) ## │        An object of class spatLocsObj  ## │        provenance: z0 ## │            ------------------------ ## │              sdimx     sdimy                                 cell_ID ## │              <num>     <num>                                  <char> ## │        1: 6405.067 -4780.499  40951783403982682273285375368232495429 ## │        2: 6426.020 -4972.519 240649020551054330404932383065726870513 ## │        3: 6428.456 -4799.158 274176126496863898679934791272921588227 ## │        4: 6408.155 -4816.583 323754550002953984063006506310071917306 ## │         ## │        ranges: ## │                sdimx     sdimy ## │        [1,] 6402.438 -5146.726 ## │        [2,] 6899.203 -4700.157 ## │         ## │         ## │      ## ├──Spatial unit \"z1\" ## │  └──S4 spatLocsObj \"raw\" coordinates:   (504 rows) ## │        An object of class spatLocsObj  ## │        provenance: z1 ## │            ------------------------ ## │              sdimx     sdimy                                 cell_ID ## │              <num>     <num>                                  <char> ## │        1: 6404.014 -4779.625  40951783403982682273285375368232495429 ## │        2: 6408.296 -4970.794  17685062374745280598492217386845129350 ## │        3: 6401.148 -4991.061 223553142498364321238189328942498473503 ## │        4: 6430.153 -4971.251 240649020551054330404932383065726870513 ## │         ## │        ranges: ## │                sdimx     sdimy ## │        [1,] 6401.148 -5147.193 ## │        [2,] 6899.323 -4700.410 ## │         ## │         ## │      ## └──Spatial unit \"aggregate\" ##    └──S4 spatLocsObj \"raw\" coordinates:   (462 rows) ##          An object of class spatLocsObj  ##          provenance: z0 z1 ##              ------------------------ ##                sdimx     sdimy                                 cell_ID ##                <num>     <num>                                  <char> ##          1: 6637.881 -5140.465 100210519278873141813371229408401071444 ##          2: 6471.978 -4883.541 101161259912191124732236989250178928032 ##          3: 6801.610 -4968.685 101488859781016188084173008420811094152 ##          4: 6789.055 -5105.338 101523780333017320796881555775415156847 ##           ##          ranges: ##                  sdimx     sdimy ##          [1,] 6401.412 -5146.747 ##          [2,] 6899.108 -4700.326 ##           ##           ## list_expression(vizmini) ##    spat_unit feat_type       name ##       <char>    <char>     <char> ## 1:        z0       rna        raw ## 2:        z1       rna        raw ## 3: aggregate       rna        raw ## 4: aggregate       rna normalized ## 5: aggregate       rna     scaled ## 6: aggregate       rna    pearson # Find specific spat_unit objects # list_expression(vizmini, spat_unit = \"z0\") ##    spat_unit feat_type   name ##       <char>    <char> <char> ## 1:        z0       rna    raw list_expression_names(vizmini, spat_unit = \"z1\", feat_type = \"rna\") ## [1] \"raw\""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"provenance","dir":"Articles","previous_headings":"","what":"Provenance","title":"Overview","text":"Going , sometimes different sources information can used aggregating particular spatial unit. easily shown subcellular datasets Vizgen MERSCOPE platform provide feature polygon information multiple confocal planes within tissue. aggregated information produced drawn different z-planes combinations thereof. Giotto tracks provenance information set aggregated data.","code":"expr_mat <- getExpression(vizmini, spat_unit = \"aggregate\") prov(expr_mat) ## [1] \"z0\" \"z1\""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"giotto-subobjects","dir":"Articles","previous_headings":"","what":"Giotto subobjects","title":"Overview","text":"Giotto 3.0 update introduced S4 subobjects used within giotto object processing. subobjects provide formalized definitions information formatting needed giotto object slots order functional. objects standalone extensible commonly used spatial manipulation plotting methods implemented . addition, subobjects carry several pieces metadata additional slots alongside main information (e.g. also slots spat_unit feat_type alongside exprDT slot exprObj S4). makes nesting information retained taken giotto object nesting information need supplied anymore interacting setter functions. getter functions now output param defaults extracting information giotto object S4 subobject. extracting information modified returned giotto object, preferred information extracted S4 tagged information lost, convenient work S4’s main data slot [ [<- generics.","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"constructors","dir":"Articles","previous_headings":"","what":"Constructors","title":"Overview","text":"directly creating subobject, constructor functions can used. constructors createExprObj() createCellMetaObj() createFeatMetaObj() createDimObj() createNearestNetObj() createSpatLocsObj() createSpatNetObj() createSpatEnrObj() createSpatialGrid() createGiottoPoints() createGiottoPolygonsFromDfr() createGiottoPolygonsFromMask() createGiottoImage() createGiottoLargeImage() non numeric integer columns spatial location input column position(s): 3 first non-numeric column considered cell ID test consistency expression matrix. non numeric columns removed","code":"coords <- data.table::data.table(     sdimx = c(1, 2, 3),     sdimy = c(1, 2, 3),     cell_ID = c(\"A\", \"B\", \"C\") )  st <- createSpatLocsObj(     name = \"test\",     spat_unit = \"cell\",     coordinates = coords,     provenance = \"cell\" ) ## There are non numeric or integer columns for the spatial location ##  input at column position(s): 3 ##  The first non-numeric column will be considered as a cell ID ##  to test for consistency with the expression matrix ##  Other non numeric columns will be removed print(st) ## An object of class spatLocsObj : \"test\" ## spat_unit : \"cell\" ## provenance: cell  ## dimensions: 3 3  ## preview   : ##    sdimx sdimy cell_ID ##    <num> <num>  <char> ## 1:     1     1       A ## 2:     2     2       B ## 3:     3     3       C ##  ## ranges: ##      sdimx sdimy ## [1,]     1     1 ## [2,]     3     3"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"readers","dir":"Articles","previous_headings":"","what":"Readers","title":"Overview","text":"Alternatively, read functions can used take named nested lists raw data input convert lists subobjects directly usable setter functions. readers readPolygonData() readFeatData() readExprData() readCellMetadata() readFeatMetadata() readSpatLocsData() readSpatNetData() readSpatEnrichData() readDimReducData() readNearestNetData() non numeric integer columns spatial location input column position(s): 3. first non-numeric column considered cell ID test consistency expression matrix. non numeric columns removed non numeric integer columns spatial location input column position(s): 3. first non-numeric column considered cell ID test consistency expression matrix. non numeric columns removed","code":"st2 <- readSpatLocsData(list(cell2 = list(     test1 = coords,     test2 = coords ))) ## list depth of 2 ##  ## List item [1]: ##  spat_unit: cell2 ##  name: test1 ## There are non numeric or integer columns for the spatial location ##  input at column position(s): 3 ##  The first non-numeric column will be considered as a cell ID ##  to test for consistency with the expression matrix ##  Other non numeric columns will be removed ##  ## List item [2]: ##  spat_unit: cell2 ##  name: test2 ## There are non numeric or integer columns for the spatial location ##  input at column position(s): 3 ##  The first non-numeric column will be considered as a cell ID ##  to test for consistency with the expression matrix ##  Other non numeric columns will be removed print(st2) ## [[1]] ## An object of class spatLocsObj : \"test1\" ## spat_unit : \"cell2\" ## provenance: cell2  ## dimensions: 3 3  ## preview   : ##    sdimx sdimy cell_ID ##    <num> <num>  <char> ## 1:     1     1       A ## 2:     2     2       B ## 3:     3     3       C ##  ## ranges: ##      sdimx sdimy ## [1,]     1     1 ## [2,]     3     3 ##  ##  ## [[2]] ## An object of class spatLocsObj : \"test2\" ## spat_unit : \"cell2\" ## provenance: cell2  ## dimensions: 3 3  ## preview   : ##    sdimx sdimy cell_ID ##    <num> <num>  <char> ## 1:     1     1       A ## 2:     2     2       B ## 3:     3     3       C ##  ## ranges: ##      sdimx sdimy ## [1,]     1     1 ## [2,]     3     3"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"giotto-accessors","dir":"Articles","previous_headings":"","what":"Giotto Accessors","title":"Overview","text":"Giotto provides getter setter functions manually accessing information contained within giotto object. Note setters require data provided compatible S4 subobjects lists thereof. External data can read appropriate formats using reader functions. getter functions return S4 subobjects default. getters getExpression() getCellMetadata() getFeatMetadata() getSpatialLocations() getDimReduction() getNearestNetwork() getSpatialNetwork() getPolygonInfo() getFeatureInfo() getSpatialEnrichment() getGiottoImage() setters setExpression() setCellMetadata() setFeatureMetadata() setSpatialLocations() setDimReduction() setNearestNetwork() setSpatialNetwork() setPolygonInfo() setFeatureInfo() setSpatialEnrichment() setGiottoImage()","code":"expval <- getExpression(vizmini) print(expval) ## An object of class exprObj : \"raw\" ## spat_unit : \"z0\" ## feat_type : \"rna\" ## provenance: z0  ##  ## contains: ## 337 x 498 sparse Matrix of class \"dgCMatrix\" ##                                          ## Mlc1   . . . . . . . .  . . . . . ...... ## Gprc5b . . 1 . 1 . . .  1 . 2 . . ...... ## Gfap   . . . 1 1 . . . 27 . . . . ...... ##  ##  ........suppressing 485 columns and 331 rows in show(); maybe adjust options(max.print=, width=) ##                                            ## Adgrf4    . . . . . . . . . . . . . ...... ## Epha2     . . . . . . . . . . . . . ...... ## Blank-139 . . . . . . . . . . . . . ...... ##  ##  First four colnames: ##  40951783403982682273285375368232495429 ##  240649020551054330404932383065726870513 ##  274176126496863898679934791272921588227 ##  323754550002953984063006506310071917306"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"get-and-set-s4-spat_unit-feat_type-provenance","dir":"Articles","previous_headings":"","what":"Get and set S4 spat_unit, feat_type, provenance","title":"Overview","text":"spatUnit(), featType(), prov() replacement functions tagged spatial unit, feature type, provenance information respectively.","code":"# spat_unit spatUnit(expval) <- \"new_spat\" spatUnit(expval) ## [1] \"new_spat\" # feat_type featType(expval) <- \"new_feat\" featType(expval) ## [1] \"new_feat\" # provenance prov(expval) <- \"cell\" prov(expval) ## [1] \"cell\""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"setting-an-s4-subobject","dir":"Articles","previous_headings":"","what":"Setting an S4 subobject","title":"Overview","text":"spat_unit, feat_type, name params longer need given setting S4 subobject tagged information giottoObject. However, input given set function parameters prioritized tagged information tagged information updated.","code":"# set exprObj to tagged nesting location vizmini <- setExpression(vizmini, expval) ## Setting expression [new_spat][new_feat] raw list_expression(vizmini) ##    spat_unit feat_type       name ##       <char>    <char>     <char> ## 1:        z0       rna        raw ## 2:        z1       rna        raw ## 3: aggregate       rna        raw ## 4: aggregate       rna normalized ## 5: aggregate       rna     scaled ## 6: aggregate       rna    pearson ## 7:  new_spat  new_feat        raw"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"working-with-s4-subobjects","dir":"Articles","previous_headings":"","what":"Working with S4 subobjects","title":"Overview","text":"Giotto’s S4 subobjects wrap one main data object. empty [] []<- operators defined shorthand directly accessing slot contains data. example, spatLocsObj: class(spatLocsObj[]) equivalent class(spatLocsObj@coordinates) way, S4 subobjects can used contexts wrapped objects .","code":"st <- getSpatialLocations(vizmini) class(st) ## [1] \"spatLocsObj\" ## attr(,\"package\") ## [1] \"GiottoClass\" # With empty brackets class(st[]) ## [1] \"data.table\" \"data.frame\""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"setting-information","dir":"Articles","previous_headings":"Working with S4 subobjects","what":"Setting information","title":"Overview","text":"","code":"print(st) ## An object of class spatLocsObj : \"raw\" ## spat_unit : \"z0\" ## provenance: z0  ## dimensions: 498 3  ## preview   : ##       sdimx     sdimy                                 cell_ID ##       <num>     <num>                                  <char> ## 1: 6405.067 -4780.499  40951783403982682273285375368232495429 ## 2: 6426.020 -4972.519 240649020551054330404932383065726870513 ## 3: 6428.456 -4799.158 274176126496863898679934791272921588227 ##  ## ranges: ##         sdimx     sdimy ## [1,] 6402.438 -5146.726 ## [2,] 6899.203 -4700.157 st[] <- coords print(st) ## An object of class spatLocsObj : \"raw\" ## spat_unit : \"z0\" ## provenance: z0  ## dimensions: 3 3  ## preview   : ##    sdimx sdimy cell_ID ##    <num> <num>  <char> ## 1:     1     1       A ## 2:     2     2       B ## 3:     3     3       C ##  ## ranges: ##      sdimx sdimy ## [1,]     1     1 ## [2,]     3     3 sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.5 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        ##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    ##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           ## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] GiottoClass_0.4.0 ##  ## loaded via a namespace (and not attached): ##  [1] rappdirs_0.3.3              sass_0.4.9                  ##  [3] SparseArray_1.4.8           gtools_3.9.5                ##  [5] lattice_0.22-6              digest_0.6.37               ##  [7] magrittr_2.0.3              evaluate_1.0.1              ##  [9] grid_4.4.1                  fastmap_1.2.0               ## [11] jsonlite_1.8.9              Matrix_1.7-0                ## [13] backports_1.5.0             GenomeInfoDb_1.40.1         ## [15] GiottoData_0.2.15           httr_1.4.7                  ## [17] SingleCellExperiment_1.26.0 UCSC.utils_1.0.0            ## [19] codetools_0.2-20            textshaping_0.4.0           ## [21] jquerylib_0.1.4             abind_1.4-8                 ## [23] cli_3.6.3                   rlang_1.1.4                 ## [25] crayon_1.5.3                XVector_0.44.0              ## [27] Biobase_2.64.0              withr_3.0.1                 ## [29] cachem_1.1.0                DelayedArray_0.30.1         ## [31] yaml_2.3.10                 S4Arrays_1.4.1              ## [33] tools_4.4.1                 GiottoUtils_0.2.0           ## [35] checkmate_2.3.2             SpatialExperiment_1.14.0    ## [37] GenomeInfoDbData_1.2.12     SummarizedExperiment_1.34.0 ## [39] BiocGenerics_0.50.0         reticulate_1.39.0           ## [41] png_0.1-8                   R6_2.5.1                    ## [43] magick_2.8.5                matrixStats_1.4.1           ## [45] stats4_4.4.1                lifecycle_1.0.4             ## [47] zlibbioc_1.50.0             S4Vectors_0.42.1            ## [49] fs_1.6.4                    htmlwidgets_1.6.4           ## [51] IRanges_2.38.1              ragg_1.3.3                  ## [53] pkgconfig_2.0.3             desc_1.4.3                  ## [55] pkgdown_2.1.1               terra_1.7-83                ## [57] bslib_0.8.0                 glue_1.8.0                  ## [59] data.table_1.16.2           Rcpp_1.0.13                 ## [61] systemfonts_1.1.0           xfun_0.48                   ## [63] GenomicRanges_1.56.2        MatrixGenerics_1.16.0       ## [65] knitr_1.48                  rjson_0.2.23                ## [67] igraph_2.1.1                htmltools_0.5.8.1           ## [69] rmarkdown_2.28              compiler_4.4.1"},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"overview","dir":"Articles","previous_headings":"","what":"1. Overview","title":"Giotto spatial geometry classes","text":"GiottoClass represents spatial polygons points respectively S4 classes giottoPolygon giottoPoints. objects built top terra SpatVectors order represent spatial biology. also respond many terra’s generics, enhancements. objects spatVector slot contains main information. common slot inherited VIRTUAL terraVectData class, however naming may subject change data representations added. structures classes : note unique_ID_cache slots used get around memory usage incurred frequently accessing SpatVectors attributes. caches updated modifications object. automatically performed using [] subsetting.","code":"terraVectData \\- spatVector  giottoPolygon \\- spatVector           (spatial polygons SpatVector) \\- spatVectorCentroids  (centroids points SpatVector) \\- overlaps             (list of overlapped features info) \\- name                 (object name/spat_unit) \\- unique_ID_cache      (cache of polygon IDs)  giottoPoints \\- spatVector           (spatial points SpatVector) \\- networks             (feature network) \\- feat_type            (object name/feat_type) \\- unique_ID_cache      (cache of feature IDs)"},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"polygon-object-creation","dir":"Articles","previous_headings":"","what":"2.1 Polygon object creation","title":"Giotto spatial geometry classes","text":"createGiottoPolygon() accepts number inputs, including filepaths spatial files .wkt, .shp, .GeoJSON mask image files common formats .tif .png. reading files, passed respective methods SpatVector SpatRaster (mask image). data.frame-like inputs also allowed long formatted similarly terra’s matrix representation polygon geometries, least following columns. geom: integer identifier polygon part: integer identifier part polygon, case multi polygon x: numeric x coordinate polygon vertex y: numeric y coordinate polygon vertex hole: integer identifier hole within polygon poly_ID: standard Giotto identifier polygon. Akin cell_ID Additional columns can included attributes, set poly_IDs required. de-novo generation simple polygon arrays, see documentation polyStamp() tessellate()","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"points-object-creation","dir":"Articles","previous_headings":"","what":"2.2 Points object creation","title":"Giotto spatial geometry classes","text":"relatively fewer input methods giottoPoints since currently tend provided flat files opposed spatial-specific formats. createGiottoPoints() works data.frame-like inputs least columns x-coordinate, y-coordinate, ID information. first two detected numeric columns expected x y respectively. first character column assumed feat_IDs. terra SpatVector inputs also accepted. helpful parameter split_keyword accepts list regex keywords pull matched features separate giottoPoints objects. useful situations multiple feature modalities /QC targets provided together interfere analyzed together. (see examples createGiottoPoints() documentation)","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"subsetting","dir":"Articles","previous_headings":"","what":"3. Subsetting","title":"Giotto spatial geometry classes","text":"giottoPoints giottoPolygons can subset either logical vectors ID.      $ extraction can used pull attributes objects vectors","code":"library(GiottoClass) gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  # full objects print(gpoly) ## An object of class giottoPolygon ## spat_unit : \"aggregate\" ## Spatial Information: ##  class       : SpatVector  ##  geometry    : polygons  ##  dimensions  : 462, 4  (geometries, attributes) ##  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       :                   poly_ID stack agg_n valid ##  type        :                     <chr> <chr> <int> <int> ##  values      : 100210519278873141813371~    NA     2     1 ##                101161259912191124732236~    NA     2     1 ##                101488859781016188084173~    NA     2     1 ##  centroids   : calculated ##  overlaps    : rna print(gpoints) ## An object of class giottoPoints ## feat_type : \"rna\" ## Feature Information: ##  class       : SpatVector  ##  geometry    : points  ##  dimensions  : 79761, 3  (geometries, attributes) ##  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       : feat_ID global_z feat_ID_uniq ##  type        :   <chr>    <int>        <int> ##  values      :    Mlc1        0            1 ##                 Gprc5b        0            2 ##                   Gfap        0            3 # subsets plot(gpoly) plot(gpoly[c(\"100210519278873141813371229408401071444\", \"101161259912191124732236989250178928032\", \"101488859781016188084173008420811094152\")]) print(gpoly[c(\"100210519278873141813371229408401071444\", \"101161259912191124732236989250178928032\", \"101488859781016188084173008420811094152\")]) ## An object of class giottoPolygon ## spat_unit : \"aggregate\" ## Spatial Information: ##  class       : SpatVector  ##  geometry    : polygons  ##  dimensions  : 3, 4  (geometries, attributes) ##  extent      : 6463.427, 6806.944, -5146.466, -4876.088  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       :                   poly_ID stack agg_n valid ##  type        :                     <chr> <chr> <int> <int> ##  values      : 100210519278873141813371~    NA     2     1 ##                101161259912191124732236~    NA     2     1 ##                101488859781016188084173~    NA     2     1 ##  centroids   : calculated ##  overlaps    : rna plot(gpoly[c(T,F)]) plot(gpoints) plot(gpoints[c(\"Fn1\")]) print(gpoints[c(\"Fn1\")]) ## An object of class giottoPoints ## feat_type : \"rna\" ## Feature Information: ##  class       : SpatVector  ##  geometry    : points  ##  dimensions  : 814, 3  (geometries, attributes) ##  extent      : 6400.663, 6884.093, -5149.767, -4711.758  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       : feat_ID global_z feat_ID_uniq ##  type        :   <chr>    <int>        <int> ##  values      :     Fn1        0          166 ##                    Fn1        0          181 ##                    Fn1        0          195 head(gpoly$poly_ID) ## [1] \"100210519278873141813371229408401071444\" ## [2] \"101161259912191124732236989250178928032\" ## [3] \"101488859781016188084173008420811094152\" ## [4] \"101523780333017320796881555775415156847\" ## [5] \"102184699197574201819246996094734116255\" ## [6] \"102893953956695364131894293580364005295\""},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"conversion-to-data-table","dir":"Articles","previous_headings":"","what":"4. Conversion to data.table","title":"Giotto spatial geometry classes","text":"GiottoClass set functions converting giottoPoints giottoPolygon objects spatial classes using .sf(), .sp(), .stars(), .terra(). terra-based giottoPoints giottoPolygon objects can also converted data.table geometry manipulation. method largely piggybacks terra’s .data.frame() adds support geom = \"XY\" polygon geometry. tables can either re-ingested using createGiottoPolygon() createGiottoPoints() converted SpatVector using .polygons() .points()","code":"gpoly_dt <- data.table::as.data.table(gpoly, geom = \"XY\") gpoints_dt <- data.table::as.data.table(gpoints, geom = \"XY\")  print(gpoly_dt) ## Key: <geom> ##         geom  part        x         y  hole ##        <int> <num>    <num>     <num> <num> ##     1:     1     1 6642.257 -5136.674     0 ##     2:     1     1 6642.711 -5137.020     0 ##     3:     1     1 6643.050 -5137.462     0 ##     4:     1     1 6643.310 -5137.956     0 ##     5:     1     1 6643.484 -5138.518     0 ##    ---                                      ## 35971:   462     1 6788.764 -4942.998     0 ## 35972:   462     1 6788.905 -4942.999     0 ## 35973:   462     1 6789.575 -4942.999     0 ## 35974:   462     1 6789.576 -4943.000     0 ## 35975:   462     1 6789.695 -4943.000     0 ##                                        poly_ID  stack agg_n valid ##                                         <char> <char> <int> <int> ##     1: 100210519278873141813371229408401071444   <NA>     2     1 ##     2: 100210519278873141813371229408401071444   <NA>     2     1 ##     3: 100210519278873141813371229408401071444   <NA>     2     1 ##     4: 100210519278873141813371229408401071444   <NA>     2     1 ##     5: 100210519278873141813371229408401071444   <NA>     2     1 ##    ---                                                            ## 35971:  98561957902191275233320065611022298397   <NA>     2     1 ## 35972:  98561957902191275233320065611022298397   <NA>     2     1 ## 35973:  98561957902191275233320065611022298397   <NA>     2     1 ## 35974:  98561957902191275233320065611022298397   <NA>     2     1 ## 35975:  98561957902191275233320065611022298397   <NA>     2     1 print(gpoints_dt) ##          feat_ID global_z feat_ID_uniq        x         y ##           <char>    <int>        <int>    <num>     <num> ##     1:      Mlc1        0            1 6400.037 -4966.651 ##     2:    Gprc5b        0            2 6400.041 -4965.377 ##     3:      Gfap        0            3 6400.078 -5081.453 ##     4:      Gfap        0            4 6400.084 -5038.288 ##     5:     Ednrb        0            5 6400.172 -4816.516 ##    ---                                                    ## 79757:    Adgra1        1        80339 6900.010 -4773.595 ## 79758:     Cspg5        1        80340 6900.023 -4772.980 ## 79759: Adcyap1r1        1        80341 6900.024 -5007.432 ## 79760:   Slc17a7        1        80342 6900.026 -4924.840 ## 79761:     Cldn5        1        80343 6900.030 -4746.916 print(as.polygons(gpoly_dt)) ##  class       : SpatVector  ##  geometry    : polygons  ##  dimensions  : 462, 4  (geometries, attributes) ##  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       :                   poly_ID stack agg_n valid ##  type        :                     <chr> <chr> <int> <int> ##  values      : 100210519278873141813371~    NA     2     1 ##                101161259912191124732236~    NA     2     1 ##                101488859781016188084173~    NA     2     1 # gpoints currently still requires addition of geom, part, and hole cols gpoints_dt[, geom := 1:.N] gpoints_dt[, part := 1] gpoints_dt[, hole := 0] print(as.points(gpoints_dt)) ##  class       : SpatVector  ##  geometry    : points  ##  dimensions  : 79761, 3  (geometries, attributes) ##  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       : feat_ID global_z feat_ID_uniq ##  type        :   <chr>    <int>        <int> ##  values      :    Mlc1        0            1 ##                 Gprc5b        0            2 ##                   Gfap        0            3"},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"centroids","dir":"Articles","previous_headings":"","what":"5. Centroids","title":"Giotto spatial geometry classes","text":"Centroids information carried giottoPolygon objects spatVectorCentroids slot. centroids() generic terra pulls slot information already exists. Otherwise, calculates returns set centroids polygons SpatVector points. append_gpolygon param makes giottoPolygon centroids info appended returned instead.","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"overlaps","dir":"Articles","previous_headings":"","what":"6.1 Overlaps","title":"Giotto spatial geometry classes","text":"Overlaps sets features overlapped polygons. calculateOverlaps() generic function performs overlapping polygons points polygons raster (intensity) data. Overlaps stored list giottoPolygon overlaps slot, separated modalities. list can retrieved using overlaps(). case overlapped points geometries, list items points SpatVector objects. poly_ID column tracks polygon overlapping point feature designated feat_ID feat_ID_uniq. NA values mean feature overlapped. overlaps intensities, results stored data.tables nested list called intensity main overlaps list.","code":"gpoly@overlaps <- NULL # reset overlaps info gpoly <- calculateOverlap(gpoly, gpoints, verbose = FALSE)  gimg <- GiottoData::loadSubObjectMini(\"giottoLargeImage\") gpoly <- calculateOverlap(gpoly, gimg, verbose = FALSE, progress = FALSE) print(gpoly@overlaps$rna) ##  class       : SpatVector  ##  geometry    : points  ##  dimensions  : 79761, 3  (geometries, attributes) ##  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       : poly_ID feat_ID feat_ID_uniq ##  type        :   <chr>   <chr>        <int> ##  values      :      NA    Mlc1            1 ##                     NA  Gprc5b            2 ##                     NA    Gfap            3 print(gpoly@overlaps$intensity) ## $dapi_z0 ##                                          poly_ID mini_dataset_dapi_z0 ##                                           <char>                <num> ##       1: 100210519278873141813371229408401071444                    8 ##       2: 100210519278873141813371229408401071444                    8 ##       3: 100210519278873141813371229408401071444                    8 ##       4: 100210519278873141813371229408401071444                    8 ##       5: 100210519278873141813371229408401071444                    8 ##      ---                                                              ## 3170620:  98561957902191275233320065611022298397                   58 ## 3170621:  98561957902191275233320065611022298397                   58 ## 3170622:  98561957902191275233320065611022298397                   88 ## 3170623:  98561957902191275233320065611022298397                   88 ## 3170624:  98561957902191275233320065611022298397                   88"},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"overlaps-to-matrix","dir":"Articles","previous_headings":"","what":"6.2 Overlaps to matrix","title":"Giotto spatial geometry classes","text":"Overlap results can converted expression matrices using overlapToMatrix()","code":"# points, rna modality (default) rna_mat <- overlapToMatrix(gpoly) ## Warning: [overlapToMatrix] expected col_names and row_names ##  not provided together. Points aggregation Matrix output ##  may be missing some cols and rows where no detections ##  were found. print(rna_mat[1:3,1:3]) ## 3 x 3 sparse Matrix of class \"dgCMatrix\" ##       100210519278873141813371229408401071444 ## Abcc9                                       . ## Ackr1                                       . ## Ackr3                                       . ##       101161259912191124732236989250178928032 ## Abcc9                                       . ## Ackr1                                       . ## Ackr3                                       . ##       101488859781016188084173008420811094152 ## Abcc9                                       . ## Ackr1                                       . ## Ackr3                                       2 # intensity, dapi_z0 intens_mat <- overlapToMatrix(gpoly, type = \"intensity\", feat_info = \"dapi_z0\") print(intens_mat[1, 1:3, drop = FALSE]) ## 1 x 3 Matrix of class \"dgeMatrix\" ##                      100210519278873141813371229408401071444 ## mini_dataset_dapi_z0                                   80200 ##                      101161259912191124732236989250178928032 ## mini_dataset_dapi_z0                                  369434 ##                      101488859781016188084173008420811094152 ## mini_dataset_dapi_z0                                  220020 sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.5 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        ##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    ##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           ## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] GiottoClass_0.4.0 ##  ## loaded via a namespace (and not attached): ##  [1] tidyselect_1.2.1            dplyr_1.1.4                 ##  [3] fastmap_1.2.0               SingleCellExperiment_1.26.0 ##  [5] digest_0.6.37               lifecycle_1.0.4             ##  [7] sf_1.0-18                   terra_1.7-83                ##  [9] magrittr_2.0.3              exactextractr_0.10.0        ## [11] compiler_4.4.1              rlang_1.1.4                 ## [13] sass_0.4.9                  tools_4.4.1                 ## [15] utf8_1.2.4                  yaml_2.3.10                 ## [17] data.table_1.16.2           knitr_1.48                  ## [19] S4Arrays_1.4.1              htmlwidgets_1.6.4           ## [21] sp_2.1-4                    classInt_0.4-10             ## [23] DelayedArray_0.30.1         KernSmooth_2.23-24          ## [25] abind_1.4-8                 BiocGenerics_0.50.0         ## [27] desc_1.4.3                  grid_4.4.1                  ## [29] stats4_4.4.1                fansi_1.0.6                 ## [31] e1071_1.7-16                colorspace_2.1-1            ## [33] ggplot2_3.5.1               scales_1.3.0                ## [35] gtools_3.9.5                SummarizedExperiment_1.34.0 ## [37] cli_3.6.3                   rmarkdown_2.28              ## [39] crayon_1.5.3                ragg_1.3.3                  ## [41] generics_0.1.3              httr_1.4.7                  ## [43] rjson_0.2.23                DBI_1.2.3                   ## [45] cachem_1.1.0                proxy_0.4-27                ## [47] zlibbioc_1.50.0             XVector_0.44.0              ## [49] matrixStats_1.4.1           vctrs_0.6.5                 ## [51] Matrix_1.7-0                jsonlite_1.8.9              ## [53] GiottoData_0.2.15           IRanges_2.38.1              ## [55] S4Vectors_0.42.1            scattermore_1.2             ## [57] systemfonts_1.1.0           magick_2.8.5                ## [59] GiottoUtils_0.2.0           jquerylib_0.1.4             ## [61] units_0.8-5                 glue_1.8.0                  ## [63] pkgdown_2.1.1               codetools_0.2-20            ## [65] gtable_0.3.6                GenomeInfoDb_1.40.1         ## [67] raster_3.6-30               GenomicRanges_1.56.2        ## [69] UCSC.utils_1.0.0            munsell_0.5.1               ## [71] tibble_3.2.1                pillar_1.9.0                ## [73] htmltools_0.5.8.1           GenomeInfoDbData_1.2.12     ## [75] R6_2.5.1                    textshaping_0.4.0           ## [77] evaluate_1.0.1              lattice_0.22-6              ## [79] Biobase_2.64.0              highr_0.11                  ## [81] backports_1.5.0             SpatialExperiment_1.14.0    ## [83] bslib_0.8.0                 class_7.3-22                ## [85] Rcpp_1.0.13                 SparseArray_1.4.8           ## [87] checkmate_2.3.2             xfun_0.48                   ## [89] fs_1.6.4                    MatrixGenerics_1.16.0       ## [91] pkgconfig_2.0.3"},{"path":"https://drieslab.github.io/GiottoClass/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Ruben Dries. Author, maintainer. Jiaji George Chen. Author. Guo-Cheng Yuan. Author. Matthew O'Brien. Author. Joselyn C. Chávez-Fuentes. Author. Edward Ruiz. Author.","code":""},{"path":"https://drieslab.github.io/GiottoClass/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Dries R, George Chen J, Yuan G, O'Brien M, Chávez-Fuentes J, Ruiz E (2024). GiottoClass: Giotto Suite object definitions framework. R package version 0.4.0, https://drieslab.github.io/GiottoClass/.","code":"@Manual{,   title = {GiottoClass: Giotto Suite object definitions and framework},   author = {Ruben Dries and Jiaji {George Chen} and Guo-Cheng Yuan and Matthew O'Brien and Joselyn C. Chávez-Fuentes and Edward Ruiz},   year = {2024},   note = {R package version 0.4.0},   url = {https://drieslab.github.io/GiottoClass/}, }"},{"path":"https://drieslab.github.io/GiottoClass/index.html","id":"giottoclass-","dir":"","previous_headings":"","what":"Giotto Suite object definitions and framework","title":"Giotto Suite object definitions and framework","text":"package contains Giotto object subobject class definitions frameworks. Functionalities relating data ingestion, basic object creation, data access within Giotto object, generics defined Giotto classes found . Applications framework convenience functions loading specific technologies found base Giotto package.","code":""},{"path":"https://drieslab.github.io/GiottoClass/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Giotto Suite object definitions and framework","text":"can install GiottoClass like:","code":"library(devtools) install_github('drieslab/GiottoClass')"},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4dimObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Dimension reductions — S3toS4dimObj","title":"Dimension reductions — S3toS4dimObj","text":"Convert S3 dimObj S4","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4dimObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dimension reductions — S3toS4dimObj","text":"","code":"S3toS4dimObj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4dimObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dimension reductions — S3toS4dimObj","text":"object S3 dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4dimObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dimension reductions — S3toS4dimObj","text":"S4 dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatGridObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatially Binned Data — S3toS4spatGridObj","title":"Spatially Binned Data — S3toS4spatGridObj","text":"convert S3 spatialGridObj S4","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatGridObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatially Binned Data — S3toS4spatGridObj","text":"","code":"S3toS4spatialGridObj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatGridObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatially Binned Data — S3toS4spatGridObj","text":"object S3 spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatGridObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatially Binned Data — S3toS4spatGridObj","text":"S4 spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial coordinates — XY","title":"Spatial coordinates — XY","text":"Directly get set xy(z) coordinates spatial subobjects (currently spatLocsObj, giottoPoints, giottoPolygon). coordinate values retrieved set matrix.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial coordinates — XY","text":"","code":"# S4 method for class 'spatLocsObj' XY(x, ...)  # S4 method for class 'spatLocsObj,matrix' XY(x) <- value  # S4 method for class 'giottoPoints' XY(x, ...)  # S4 method for class 'giottoPoints,ANY' XY(x, ...) <- value  # S4 method for class 'giottoPolygon' XY(x, ...)  # S4 method for class 'giottoPolygon,ANY' XY(x, ...) <- value  # S4 method for class 'SpatVector' XY(x, include_geom = FALSE, ...)  # S4 method for class 'SpatVector,matrix' XY(x, ...) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial coordinates — XY","text":"x object ... additional args pass value matrix. xy(z) coordinates set include_geom logical. Whether geom, part, hole terra geometry matrix included.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial coordinates — XY","text":"XY() returns matrix. XY<-() returns class x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial coordinates — XY","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  m1 <- XY(sl) plot(sl)  XY(sl) <- m1 + 1000 plot(sl)   m2 <- XY(gpoints) plot(gpoints)  XY(gpoints) <- m2 * 2 + 1000 plot(gpoints)   m3 <- XY(gpoly) plot(gpoly)  XY(gpoly) <- m3 / 2 plot(gpoly)   XY(gpoly[1:10]) # vertices from first 10 polys #>               x         y #>   [1,] 3321.128 -2568.337 #>   [2,] 3321.356 -2568.510 #>   [3,] 3321.525 -2568.731 #>   [4,] 3321.655 -2568.978 #>   [5,] 3321.742 -2569.259 #>   [6,] 3321.794 -2569.596 #>   [7,] 3321.792 -2569.987 #>   [8,] 3321.844 -2570.324 #>   [9,] 3321.902 -2570.663 #>  [10,] 3321.831 -2571.014 #>  [11,] 3321.711 -2571.295 #>  [12,] 3321.740 -2571.389 #>  [13,] 3321.849 -2571.754 #>  [14,] 3321.902 -2572.157 #>  [15,] 3321.792 -2572.625 #>  [16,] 3321.576 -2572.893 #>  [17,] 3321.316 -2573.096 #>  [18,] 3321.015 -2573.233 #>  [19,] 3320.662 -2573.220 #>  [20,] 3320.302 -2573.113 #>  [21,] 3320.001 -2572.997 #>  [22,] 3319.680 -2572.845 #>  [23,] 3319.302 -2572.735 #>  [24,] 3318.940 -2572.772 #>  [25,] 3318.635 -2572.911 #>  [26,] 3318.329 -2572.893 #>  [27,] 3318.060 -2572.677 #>  [28,] 3317.865 -2572.481 #>  [29,] 3317.723 -2572.444 #>  [30,] 3317.379 -2572.356 #>  [31,] 3317.141 -2572.247 #>  [32,] 3316.922 -2572.078 #>  [33,] 3316.693 -2571.904 #>  [34,] 3316.528 -2571.777 #>  [35,] 3316.282 -2571.653 #>  [36,] 3316.034 -2571.461 #>  [37,] 3315.792 -2571.220 #>  [38,] 3315.648 -2570.908 #>  [39,] 3315.574 -2570.556 #>  [40,] 3315.628 -2570.146 #>  [41,] 3315.628 -2569.846 #>  [42,] 3315.680 -2569.540 #>  [43,] 3315.791 -2569.269 #>  [44,] 3315.950 -2569.001 #>  [45,] 3316.137 -2568.817 #>  [46,] 3316.189 -2568.764 #>  [47,] 3316.263 -2568.480 #>  [48,] 3316.222 -2568.074 #>  [49,] 3316.223 -2567.650 #>  [50,] 3316.522 -2567.598 #>  [51,] 3316.881 -2567.653 #>  [52,] 3317.256 -2567.754 #>  [53,] 3317.634 -2567.862 #>  [54,] 3317.995 -2567.863 #>  [55,] 3318.404 -2567.809 #>  [56,] 3318.538 -2567.777 #>  [57,] 3318.599 -2567.753 #>  [58,] 3318.634 -2567.753 #>  [59,] 3318.811 -2567.710 #>  [60,] 3319.109 -2567.599 #>  [61,] 3319.353 -2567.327 #>  [62,] 3319.517 -2567.056 #>  [63,] 3319.802 -2566.959 #>  [64,] 3320.100 -2567.152 #>  [65,] 3320.279 -2567.403 #>  [66,] 3320.443 -2567.705 #>  [67,] 3320.679 -2567.946 #>  [68,] 3320.929 -2568.141 #>  [69,] 3320.989 -2568.233 #>  [70,] 3321.128 -2568.337 #>  [71,] 3237.913 -2438.411 #>  [72,] 3238.208 -2438.540 #>  [73,] 3238.503 -2438.725 #>  [74,] 3238.739 -2438.961 #>  [75,] 3238.902 -2439.197 #>  [76,] 3239.070 -2439.493 #>  [77,] 3239.184 -2439.842 #>  [78,] 3239.284 -2440.183 #>  [79,] 3239.231 -2440.717 #>  [80,] 3239.190 -2441.019 #>  [81,] 3239.176 -2441.185 #>  [82,] 3239.104 -2441.356 #>  [83,] 3239.070 -2441.465 #>  [84,] 3238.996 -2441.610 #>  [85,] 3238.855 -2441.941 #>  [86,] 3238.642 -2442.267 #>  [87,] 3238.610 -2442.336 #>  [88,] 3238.474 -2442.643 #>  [89,] 3238.316 -2442.966 #>  [90,] 3238.113 -2443.211 #>  [91,] 3237.981 -2443.510 #>  [92,] 3237.798 -2443.795 #>  [93,] 3237.616 -2444.089 #>  [94,] 3237.484 -2444.381 #>  [95,] 3237.285 -2444.639 #>  [96,] 3237.062 -2444.862 #>  [97,] 3237.031 -2444.887 #>  [98,] 3237.018 -2444.906 #>  [99,] 3236.755 -2445.124 #> [100,] 3236.421 -2445.346 #> [101,] 3236.013 -2445.474 #> [102,] 3235.935 -2445.490 #> [103,] 3235.881 -2445.508 #> [104,] 3235.781 -2445.522 #> [105,] 3235.592 -2445.561 #> [106,] 3235.537 -2445.554 #> [107,] 3235.492 -2445.561 #> [108,] 3235.165 -2445.513 #> [109,] 3235.114 -2445.507 #> [110,] 3235.108 -2445.505 #> [111,] 3235.093 -2445.502 #> [112,] 3234.745 -2445.398 #> [113,] 3234.450 -2445.231 #> [114,] 3234.157 -2445.071 #> [115,] 3233.922 -2444.900 #> [116,] 3233.708 -2444.639 #> [117,] 3233.604 -2444.314 #> [118,] 3233.513 -2444.023 #> [119,] 3233.493 -2443.982 #> [120,] 3233.234 -2443.673 #> [121,] 3232.758 -2443.616 #> [122,] 3232.317 -2443.728 #> [123,] 3231.971 -2443.905 #> [124,] 3231.713 -2443.721 #> [125,] 3231.878 -2443.390 #> [126,] 3231.876 -2442.860 #> [127,] 3232.082 -2442.543 #> [128,] 3232.507 -2442.472 #> [129,] 3233.042 -2442.472 #> [130,] 3233.444 -2442.420 #> [131,] 3233.604 -2442.259 #> [132,] 3233.684 -2441.916 #> [133,] 3233.712 -2441.460 #> [134,] 3233.766 -2441.058 #> [135,] 3233.820 -2440.884 #> [136,] 3233.820 -2440.665 #> [137,] 3233.898 -2440.244 #> [138,] 3233.981 -2439.774 #> [139,] 3234.143 -2439.398 #> [140,] 3234.362 -2439.078 #> [141,] 3234.618 -2438.817 #> [142,] 3234.938 -2438.610 #> [143,] 3235.281 -2438.420 #> [144,] 3235.728 -2438.360 #> [145,] 3236.143 -2438.210 #> [146,] 3236.572 -2438.155 #> [147,] 3236.991 -2438.044 #> [148,] 3237.393 -2438.148 #> [149,] 3237.730 -2438.336 #> [150,] 3237.825 -2438.386 #> [151,] 3237.913 -2438.411 #> [152,] 3402.663 -2485.171 #> [153,] 3402.779 -2485.447 #> [154,] 3402.983 -2485.644 #> [155,] 3403.289 -2485.755 #> [156,] 3403.472 -2485.921 #> [157,] 3403.294 -2486.144 #> [158,] 3402.906 -2486.140 #> [159,] 3402.795 -2486.185 #> [160,] 3402.672 -2486.251 #> [161,] 3402.654 -2486.241 #> [162,] 3402.626 -2486.252 #> [163,] 3402.239 -2486.253 #> [164,] 3401.955 -2486.143 #> [165,] 3401.730 -2485.983 #> [166,] 3401.482 -2485.940 #> [167,] 3401.271 -2485.984 #> [168,] 3401.010 -2486.036 #> [169,] 3400.748 -2486.091 #> [170,] 3400.691 -2486.090 #> [171,] 3400.498 -2486.200 #> [172,] 3400.223 -2486.306 #> [173,] 3399.889 -2486.291 #> [174,] 3399.499 -2486.271 #> [175,] 3399.257 -2486.418 #> [176,] 3398.942 -2486.468 #> [177,] 3398.709 -2486.355 #> [178,] 3398.601 -2486.074 #> [179,] 3398.790 -2485.902 #> [180,] 3399.067 -2485.810 #> [181,] 3399.400 -2485.719 #> [182,] 3399.627 -2485.809 #> [183,] 3399.789 -2485.606 #> [184,] 3399.741 -2485.552 #> [185,] 3399.615 -2485.425 #> [186,] 3399.614 -2485.424 #> [187,] 3399.411 -2485.223 #> [188,] 3399.405 -2485.219 #> [189,] 3399.249 -2485.114 #> [190,] 3398.995 -2485.008 #> [191,] 3398.786 -2484.920 #> [192,] 3398.602 -2484.792 #> [193,] 3398.496 -2484.617 #> [194,] 3398.438 -2484.350 #> [195,] 3398.496 -2484.137 #> [196,] 3398.645 -2483.935 #> [197,] 3398.764 -2483.761 #> [198,] 3398.927 -2483.597 #> [199,] 3399.102 -2483.477 #> [200,] 3399.256 -2483.323 #> [201,] 3399.369 -2483.210 #> [202,] 3399.409 -2483.111 #> [203,] 3399.550 -2482.874 #> [204,] 3399.678 -2482.628 #> [205,] 3399.893 -2482.416 #> [206,] 3400.066 -2482.243 #> [207,] 3400.289 -2482.087 #> [208,] 3400.633 -2482.030 #> [209,] 3400.684 -2482.052 #> [210,] 3400.796 -2482.030 #> [211,] 3401.111 -2482.030 #> [212,] 3401.372 -2482.044 #> [213,] 3401.582 -2482.144 #> [214,] 3401.842 -2482.247 #> [215,] 3402.052 -2482.357 #> [216,] 3402.172 -2482.516 #> [217,] 3402.251 -2482.651 #> [218,] 3402.286 -2482.679 #> [219,] 3402.394 -2482.950 #> [220,] 3402.403 -2482.975 #> [221,] 3402.495 -2483.164 #> [222,] 3402.495 -2483.210 #> [223,] 3402.499 -2483.220 #> [224,] 3402.496 -2483.234 #> [225,] 3402.497 -2483.389 #> [226,] 3402.428 -2483.552 #> [227,] 3402.391 -2483.888 #> [228,] 3402.432 -2484.165 #> [229,] 3402.442 -2484.215 #> [230,] 3402.551 -2484.417 #> [231,] 3402.556 -2484.444 #> [232,] 3402.588 -2484.504 #> [233,] 3402.595 -2484.624 #> [234,] 3402.607 -2484.682 #> [235,] 3402.607 -2484.837 #> [236,] 3402.663 -2485.171 #> [237,] 3395.458 -2551.178 #> [238,] 3395.699 -2551.123 #> [239,] 3395.996 -2551.123 #> [240,] 3396.184 -2551.216 #> [241,] 3396.317 -2551.347 #> [242,] 3396.368 -2551.590 #> [243,] 3396.309 -2551.806 #> [244,] 3396.202 -2551.945 #> [245,] 3396.044 -2552.036 #> [246,] 3396.044 -2552.230 #> [247,] 3396.044 -2552.461 #> [248,] 3396.025 -2552.549 #> [249,] 3395.992 -2552.751 #> [250,] 3395.933 -2552.915 #> [251,] 3395.867 -2553.087 #> [252,] 3395.778 -2553.236 #> [253,] 3395.664 -2553.345 #> [254,] 3395.548 -2553.460 #> [255,] 3395.368 -2553.510 #> [256,] 3395.139 -2553.546 #> [257,] 3395.125 -2553.560 #> [258,] 3395.082 -2553.577 #> [259,] 3395.012 -2553.618 #> [260,] 3394.931 -2553.641 #> [261,] 3395.010 -2553.877 #> [262,] 3395.122 -2554.007 #> [263,] 3395.236 -2554.204 #> [264,] 3395.338 -2554.380 #> [265,] 3395.435 -2554.627 #> [266,] 3395.452 -2554.858 #> [267,] 3395.340 -2555.025 #> [268,] 3395.112 -2555.082 #> [269,] 3394.872 -2555.130 #> [270,] 3394.633 -2555.074 #> [271,] 3394.439 -2554.963 #> [272,] 3394.258 -2554.860 #> [273,] 3394.069 -2554.778 #> [274,] 3393.882 -2554.647 #> [275,] 3393.750 -2554.515 #> [276,] 3393.617 -2554.325 #> [277,] 3393.552 -2554.137 #> [278,] 3393.504 -2554.054 #> [279,] 3393.494 -2554.050 #> [280,] 3393.483 -2554.018 #> [281,] 3393.439 -2553.940 #> [282,] 3393.336 -2553.769 #> [283,] 3393.224 -2553.562 #> [284,] 3393.172 -2553.340 #> [285,] 3393.135 -2553.159 #> [286,] 3393.087 -2553.037 #> [287,] 3393.066 -2552.869 #> [288,] 3393.063 -2552.856 #> [289,] 3393.061 -2552.847 #> [290,] 3393.010 -2552.682 #> [291,] 3392.995 -2552.547 #> [292,] 3392.957 -2552.382 #> [293,] 3392.912 -2552.272 #> [294,] 3392.859 -2552.197 #> [295,] 3392.952 -2552.043 #> [296,] 3393.009 -2551.882 #> [297,] 3393.063 -2551.667 #> [298,] 3393.141 -2551.543 #> [299,] 3393.230 -2551.356 #> [300,] 3393.333 -2551.237 #> [301,] 3393.389 -2551.181 #> [302,] 3393.390 -2551.181 #> [303,] 3393.477 -2551.093 #> [304,] 3393.552 -2551.018 #> [305,] 3393.661 -2550.906 #> [306,] 3393.668 -2550.904 #> [307,] 3393.692 -2550.879 #> [308,] 3393.882 -2550.797 #> [309,] 3393.917 -2550.790 #> [310,] 3393.983 -2550.743 #> [311,] 3394.192 -2550.704 #> [312,] 3394.371 -2550.691 #> [313,] 3394.603 -2550.691 #> [314,] 3394.782 -2550.748 #> [315,] 3394.960 -2550.799 #> [316,] 3395.072 -2550.911 #> [317,] 3395.213 -2551.001 #> [318,] 3395.335 -2551.122 #> [319,] 3395.418 -2551.170 #> [320,] 3395.458 -2551.178 #> [321,] 3405.306 -2439.104 #> [322,] 3405.702 -2439.289 #> [323,] 3406.003 -2439.585 #> [324,] 3406.140 -2439.997 #> [325,] 3406.005 -2440.572 #> [326,] 3405.909 -2440.595 #> [327,] 3405.955 -2440.751 #> [328,] 3405.955 -2441.196 #> [329,] 3405.884 -2441.656 #> [330,] 3405.742 -2441.970 #> [331,] 3405.575 -2442.280 #> [332,] 3405.469 -2442.617 #> [333,] 3405.384 -2442.883 #> [334,] 3405.417 -2442.996 #> [335,] 3405.200 -2443.372 #> [336,] 3404.986 -2443.696 #> [337,] 3404.814 -2443.808 #> [338,] 3404.632 -2443.991 #> [339,] 3404.343 -2444.169 #> [340,] 3404.065 -2444.342 #> [341,] 3403.780 -2444.456 #> [342,] 3403.442 -2444.563 #> [343,] 3403.045 -2444.658 #> [344,] 3402.759 -2444.783 #> [345,] 3402.480 -2444.942 #> [346,] 3402.342 -2444.922 #> [347,] 3402.335 -2444.940 #> [348,] 3401.967 -2444.996 #> [349,] 3401.681 -2444.725 #> [350,] 3401.518 -2444.359 #> [351,] 3401.745 -2444.115 #> [352,] 3401.713 -2443.940 #> [353,] 3401.624 -2443.603 #> [354,] 3401.624 -2443.157 #> [355,] 3401.677 -2442.774 #> [356,] 3401.757 -2442.516 #> [357,] 3401.679 -2442.308 #> [358,] 3401.733 -2441.790 #> [359,] 3401.937 -2441.444 #> [360,] 3402.161 -2441.101 #> [361,] 3402.425 -2440.794 #> [362,] 3402.560 -2440.387 #> [363,] 3402.704 -2439.966 #> [364,] 3402.734 -2439.930 #> [365,] 3402.744 -2439.826 #> [366,] 3402.865 -2439.486 #> [367,] 3402.973 -2439.145 #> [368,] 3402.972 -2438.784 #> [369,] 3402.920 -2438.415 #> [370,] 3402.866 -2438.023 #> [371,] 3402.921 -2437.627 #> [372,] 3403.025 -2437.320 #> [373,] 3403.191 -2437.051 #> [374,] 3403.259 -2436.984 #> [375,] 3403.321 -2436.868 #> [376,] 3403.676 -2436.672 #> [377,] 3404.003 -2436.671 #> [378,] 3404.151 -2436.637 #> [379,] 3404.544 -2436.616 #> [380,] 3404.821 -2436.781 #> [381,] 3404.925 -2437.079 #> [382,] 3405.038 -2437.418 #> [383,] 3405.145 -2437.755 #> [384,] 3405.145 -2438.203 #> [385,] 3405.090 -2438.600 #> [386,] 3405.092 -2438.940 #> [387,] 3405.131 -2439.058 #> [388,] 3405.306 -2439.104 #> [389,] 3410.722 -2520.655 #> [390,] 3410.774 -2520.453 #> [391,] 3410.885 -2520.293 #> [392,] 3411.039 -2520.140 #> [393,] 3411.268 -2520.127 #> [394,] 3411.548 -2520.127 #> [395,] 3411.774 -2520.186 #> [396,] 3411.970 -2520.232 #> [397,] 3412.121 -2520.388 #> [398,] 3412.235 -2520.501 #> [399,] 3412.240 -2520.503 #> [400,] 3412.404 -2520.610 #> [401,] 3412.583 -2520.726 #> [402,] 3412.781 -2520.773 #> [403,] 3412.942 -2520.882 #> [404,] 3413.053 -2520.995 #> [405,] 3413.200 -2521.143 #> [406,] 3413.269 -2521.296 #> [407,] 3413.324 -2521.502 #> [408,] 3413.324 -2521.769 #> [409,] 3413.324 -2522.030 #> [410,] 3413.276 -2522.176 #> [411,] 3413.272 -2522.403 #> [412,] 3413.184 -2522.588 #> [413,] 3413.112 -2522.781 #> [414,] 3413.003 -2522.943 #> [415,] 3412.893 -2523.104 #> [416,] 3412.835 -2523.269 #> [417,] 3412.728 -2523.473 #> [418,] 3412.639 -2523.619 #> [419,] 3412.540 -2523.779 #> [420,] 3412.403 -2523.916 #> [421,] 3412.287 -2524.032 #> [422,] 3412.136 -2524.183 #> [423,] 3412.026 -2524.294 #> [424,] 3411.823 -2524.350 #> [425,] 3411.556 -2524.349 #> [426,] 3411.371 -2524.298 #> [427,] 3411.278 -2524.236 #> [428,] 3411.062 -2524.188 #> [429,] 3411.057 -2524.186 #> [430,] 3410.941 -2524.189 #> [431,] 3410.863 -2524.135 #> [432,] 3410.680 -2524.185 #> [433,] 3410.565 -2524.368 #> [434,] 3410.424 -2524.484 #> [435,] 3410.203 -2524.512 #> [436,] 3410.076 -2524.404 #> [437,] 3409.962 -2524.233 #> [438,] 3409.861 -2524.064 #> [439,] 3409.747 -2523.862 #> [440,] 3409.750 -2523.607 #> [441,] 3409.798 -2523.381 #> [442,] 3409.857 -2523.154 #> [443,] 3409.911 -2522.937 #> [444,] 3409.931 -2522.854 #> [445,] 3409.929 -2522.846 #> [446,] 3409.912 -2522.639 #> [447,] 3409.911 -2522.379 #> [448,] 3409.964 -2522.171 #> [449,] 3410.019 -2521.961 #> [450,] 3410.074 -2521.753 #> [451,] 3410.156 -2521.629 #> [452,] 3410.180 -2521.533 #> [453,] 3410.220 -2521.475 #> [454,] 3410.238 -2521.425 #> [455,] 3410.349 -2521.233 #> [456,] 3410.458 -2521.081 #> [457,] 3410.563 -2520.939 #> [458,] 3410.675 -2520.828 #> [459,] 3410.685 -2520.817 #> [460,] 3410.722 -2520.655 #> [461,] 3354.402 -2544.060 #> [462,] 3354.294 -2544.061 #> [463,] 3354.217 -2544.001 #> [464,] 3354.099 -2544.006 #> [465,] 3353.980 -2544.006 #> [466,] 3353.864 -2544.006 #> [467,] 3353.805 -2543.948 #> [468,] 3353.805 -2543.865 #> [469,] 3353.806 -2543.743 #> [470,] 3353.855 -2543.684 #> [471,] 3353.860 -2543.563 #> [472,] 3353.878 -2543.500 #> [473,] 3353.912 -2543.381 #> [474,] 3353.912 -2543.296 #> [475,] 3353.969 -2543.196 #> [476,] 3353.967 -2543.081 #> [477,] 3354.026 -2543.011 #> [478,] 3354.022 -2542.894 #> [479,] 3354.021 -2542.810 #> [480,] 3354.076 -2542.710 #> [481,] 3354.086 -2542.642 #> [482,] 3354.100 -2542.605 #> [483,] 3354.074 -2542.546 #> [484,] 3353.973 -2542.145 #> [485,] 3353.752 -2541.790 #> [486,] 3353.644 -2541.417 #> [487,] 3353.757 -2540.995 #> [488,] 3353.981 -2540.755 #> [489,] 3354.401 -2540.756 #> [490,] 3354.788 -2540.844 #> [491,] 3354.734 -2541.318 #> [492,] 3354.788 -2541.787 #> [493,] 3354.845 -2542.269 #> [494,] 3355.134 -2542.543 #> [495,] 3355.545 -2542.642 #> [496,] 3355.906 -2542.442 #> [497,] 3356.103 -2542.141 #> [498,] 3356.287 -2541.784 #> [499,] 3356.398 -2541.361 #> [500,] 3356.398 -2540.838 #> [501,] 3356.469 -2540.423 #> [502,] 3356.667 -2540.060 #> [503,] 3356.920 -2539.843 #> [504,] 3357.287 -2539.679 #> [505,] 3357.694 -2539.517 #> [506,] 3358.117 -2539.464 #> [507,] 3358.528 -2539.352 #> [508,] 3359.003 -2539.404 #> [509,] 3359.308 -2539.614 #> [510,] 3359.614 -2539.815 #> [511,] 3359.979 -2539.960 #> [512,] 3360.397 -2540.107 #> [513,] 3360.815 -2540.216 #> [514,] 3360.944 -2540.561 #> [515,] 3360.832 -2541.182 #> [516,] 3360.672 -2541.520 #> [517,] 3360.232 -2541.576 #> [518,] 3359.810 -2541.725 #> [519,] 3359.759 -2542.167 #> [520,] 3359.541 -2542.499 #> [521,] 3359.376 -2542.863 #> [522,] 3359.072 -2543.034 #> [523,] 3358.708 -2543.083 #> [524,] 3358.403 -2542.873 #> [525,] 3358.183 -2542.600 #> [526,] 3357.951 -2542.305 #> [527,] 3357.589 -2542.440 #> [528,] 3357.270 -2542.653 #> [529,] 3356.999 -2542.924 #> [530,] 3356.723 -2543.146 #> [531,] 3356.359 -2543.346 #> [532,] 3356.106 -2543.599 #> [533,] 3355.855 -2543.851 #> [534,] 3355.548 -2544.105 #> [535,] 3355.273 -2544.332 #> [536,] 3354.833 -2544.278 #> [537,] 3354.513 -2544.060 #> [538,] 3354.513 -2544.060 #> [539,] 3354.402 -2544.060 #> [540,] 3449.139 -2505.144 #> [541,] 3449.139 -2505.540 #> [542,] 3449.139 -2505.935 #> [543,] 3449.139 -2506.330 #> [544,] 3449.139 -2506.726 #> [545,] 3449.139 -2507.121 #> [546,] 3449.086 -2507.520 #> [547,] 3448.979 -2507.790 #> [548,] 3448.816 -2508.055 #> [549,] 3448.688 -2508.290 #> [550,] 3448.556 -2508.462 #> [551,] 3448.468 -2508.613 #> [552,] 3448.326 -2508.869 #> [553,] 3448.218 -2509.086 #> [554,] 3448.055 -2509.342 #> [555,] 3447.894 -2509.517 #> [556,] 3447.679 -2509.680 #> [557,] 3447.457 -2509.791 #> [558,] 3447.201 -2509.899 #> [559,] 3447.167 -2509.908 #> [560,] 3447.139 -2509.943 #> [561,] 3447.087 -2510.281 #> [562,] 3447.082 -2510.569 #> [563,] 3446.976 -2510.817 #> [564,] 3446.699 -2510.705 #> [565,] 3446.568 -2510.457 #> [566,] 3446.430 -2510.220 #> [567,] 3446.156 -2510.061 #> [568,] 3445.890 -2509.955 #> [569,] 3445.631 -2509.787 #> [570,] 3445.568 -2509.742 #> [571,] 3445.429 -2509.676 #> [572,] 3445.228 -2509.556 #> [573,] 3445.028 -2509.357 #> [574,] 3444.865 -2509.193 #> [575,] 3444.724 -2508.939 #> [576,] 3444.647 -2508.688 #> [577,] 3444.646 -2508.317 #> [578,] 3444.599 -2507.955 #> [579,] 3444.537 -2507.696 #> [580,] 3444.428 -2507.412 #> [581,] 3444.430 -2507.069 #> [582,] 3444.486 -2506.757 #> [583,] 3444.539 -2506.487 #> [584,] 3444.684 -2506.242 #> [585,] 3444.752 -2505.947 #> [586,] 3444.876 -2505.722 #> [587,] 3445.029 -2505.514 #> [588,] 3445.230 -2505.313 #> [589,] 3445.405 -2505.138 #> [590,] 3445.582 -2504.960 #> [591,] 3445.782 -2504.760 #> [592,] 3445.992 -2504.653 #> [593,] 3446.214 -2504.484 #> [594,] 3446.451 -2504.384 #> [595,] 3446.710 -2504.272 #> [596,] 3447.026 -2504.217 #> [597,] 3447.118 -2504.201 #> [598,] 3447.373 -2504.110 #> [599,] 3447.719 -2504.014 #> [600,] 3447.897 -2504.014 #> [601,] 3448.058 -2504.274 #> [602,] 3448.273 -2504.435 #> [603,] 3448.494 -2504.604 #> [604,] 3448.706 -2504.814 #> [605,] 3448.973 -2504.919 #> [606,] 3448.984 -2504.934 #> [607,] 3448.986 -2504.934 #> [608,] 3448.986 -2504.936 #> [609,] 3449.139 -2505.144 #> [610,] 3277.795 -2513.815 #> [611,] 3278.047 -2513.923 #> [612,] 3278.234 -2514.048 #> [613,] 3278.439 -2514.194 #> [614,] 3278.630 -2514.385 #> [615,] 3278.771 -2514.584 #> [616,] 3278.872 -2514.829 #> [617,] 3278.872 -2515.188 #> [618,] 3278.818 -2515.529 #> [619,] 3278.696 -2515.721 #> [620,] 3278.500 -2515.870 #> [621,] 3278.276 -2516.038 #> [622,] 3278.000 -2516.091 #> [623,] 3277.643 -2516.091 #> [624,] 3277.337 -2516.036 #> [625,] 3277.088 -2515.927 #> [626,] 3276.893 -2515.791 #> [627,] 3276.704 -2515.603 #> [628,] 3276.536 -2515.440 #> [629,] 3276.379 -2515.223 #> [630,] 3276.313 -2515.197 #> [631,] 3276.293 -2515.204 #> [632,] 3276.044 -2515.224 #> [633,] 3275.791 -2515.281 #> [634,] 3275.539 -2515.223 #> [635,] 3275.299 -2515.175 #> [636,] 3275.137 -2515.061 #> [637,] 3274.976 -2514.900 #> [638,] 3274.810 -2514.737 #> [639,] 3274.702 -2514.575 #> [640,] 3274.592 -2514.361 #> [641,] 3274.532 -2514.127 #> [642,] 3274.487 -2513.877 #> [643,] 3274.487 -2513.571 #> [644,] 3274.487 -2513.266 #> [645,] 3274.541 -2513.014 #> [646,] 3274.595 -2512.757 #> [647,] 3274.648 -2512.518 #> [648,] 3274.758 -2512.313 #> [649,] 3274.843 -2512.118 #> [650,] 3274.905 -2511.978 #> [651,] 3274.920 -2511.897 #> [652,] 3275.030 -2511.652 #> [653,] 3275.174 -2511.496 #> [654,] 3275.226 -2511.459 #> [655,] 3275.295 -2511.331 #> [656,] 3275.405 -2511.169 #> [657,] 3275.544 -2510.980 #> [658,] 3275.678 -2510.791 #> [659,] 3275.830 -2510.638 #> [660,] 3275.973 -2510.497 #> [661,] 3276.164 -2510.357 #> [662,] 3276.372 -2510.262 #> [663,] 3276.420 -2510.259 #> [664,] 3276.436 -2510.247 #> [665,] 3276.703 -2510.138 #> [666,] 3276.987 -2510.198 #> [667,] 3277.240 -2510.305 #> [668,] 3277.380 -2510.495 #> [669,] 3277.522 -2510.686 #> [670,] 3277.625 -2510.935 #> [671,] 3277.737 -2511.180 #> [672,] 3277.738 -2511.535 #> [673,] 3277.794 -2511.816 #> [674,] 3277.792 -2512.093 #> [675,] 3277.793 -2512.399 #> [676,] 3277.846 -2512.650 #> [677,] 3277.846 -2512.954 #> [678,] 3277.792 -2513.208 #> [679,] 3277.733 -2513.460 #> [680,] 3277.731 -2513.715 #> [681,] 3277.731 -2513.721 #> [682,] 3277.795 -2513.815 #> [683,] 3410.037 -2453.522 #> [684,] 3409.858 -2453.624 #> [685,] 3409.686 -2453.790 #> [686,] 3409.405 -2453.733 #> [687,] 3409.129 -2453.692 #> [688,] 3408.849 -2453.629 #> [689,] 3408.629 -2453.522 #> [690,] 3408.411 -2453.415 #> [691,] 3408.178 -2453.306 #> [692,] 3407.952 -2453.191 #> [693,] 3407.765 -2453.092 #> [694,] 3407.602 -2452.925 #> [695,] 3407.396 -2452.771 #> [696,] 3407.395 -2451.343 #> [697,] 3407.602 -2451.241 #> [698,] 3407.600 -2451.035 #> [699,] 3407.462 -2450.781 #> [700,] 3407.548 -2450.596 #> [701,] 3407.702 -2450.389 #> [702,] 3407.879 -2450.260 #> [703,] 3407.916 -2450.174 #> [704,] 3408.083 -2450.007 #> [705,] 3408.249 -2449.841 #> [706,] 3408.423 -2449.722 #> [707,] 3408.629 -2449.565 #> [708,] 3408.813 -2449.466 #> [709,] 3409.040 -2449.322 #> [710,] 3409.074 -2449.304 #> [711,] 3409.076 -2449.303 #> [712,] 3409.327 -2449.141 #> [713,] 3409.544 -2449.027 #> [714,] 3409.815 -2448.919 #> [715,] 3410.085 -2448.867 #> [716,] 3410.332 -2448.759 #> [717,] 3410.640 -2448.704 #> [718,] 3410.946 -2448.650 #> [719,] 3411.251 -2448.709 #> [720,] 3411.549 -2448.757 #> [721,] 3411.765 -2448.866 #> [722,] 3411.981 -2449.031 #> [723,] 3412.090 -2449.252 #> [724,] 3412.238 -2449.507 #> [725,] 3412.415 -2449.680 #> [726,] 3412.579 -2449.846 #> [727,] 3412.736 -2450.055 #> [728,] 3412.899 -2450.272 #> [729,] 3413.009 -2450.489 #> [730,] 3412.917 -2450.708 #> [731,] 3412.735 -2450.938 #> [732,] 3412.739 -2451.296 #> [733,] 3412.706 -2451.602 #> [734,] 3412.526 -2451.790 #> [735,] 3412.358 -2451.956 #> [736,] 3412.077 -2452.001 #> [737,] 3411.990 -2452.065 #> [738,] 3411.866 -2452.175 #> [739,] 3411.657 -2452.330 #> [740,] 3411.473 -2452.514 #> [741,] 3411.328 -2452.713 #> [742,] 3411.176 -2452.923 #> [743,] 3411.008 -2453.141 #> [744,] 3410.791 -2453.251 #> [745,] 3410.433 -2453.245 #> [746,] 3410.200 -2453.411 #> [747,] 3410.146 -2453.438 #> [748,] 3410.037 -2453.522"},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Active feature type — activeFeatType-generic","title":"Active feature type — activeFeatType-generic","text":"Retrieve set active feature type. value default feature type giotto object uses.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Active feature type — activeFeatType-generic","text":"","code":"# S4 method for class 'giotto' activeFeatType(gobject)  # S4 method for class 'giotto,character' activeFeatType(gobject) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Active feature type — activeFeatType-generic","text":"gobject giotto object value feat_type set default","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Active feature type — activeFeatType-generic","text":"active feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Active feature type — activeFeatType-generic","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" activeFeatType(g) #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Active spatial unit — activeSpatUnit-generic","title":"Active spatial unit — activeSpatUnit-generic","text":"Retrieve set active spatial unit. value default spatial unit giotto object uses.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Active spatial unit — activeSpatUnit-generic","text":"","code":"# S4 method for class 'giotto' activeSpatUnit(gobject)  # S4 method for class 'giotto,character' activeSpatUnit(gobject) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Active spatial unit — activeSpatUnit-generic","text":"gobject giotto object value spat_unit set default","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Active spatial unit — activeSpatUnit-generic","text":"active spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Active spatial unit — activeSpatUnit-generic","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" activeSpatUnit(g) #> [1] \"cell\""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Add cell metadata — addCellMetadata","title":"Add cell metadata — addCellMetadata","text":"Adds cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add cell metadata — addCellMetadata","text":"","code":"addCellMetadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   new_metadata,   vector_name = NULL,   by_column = FALSE,   column_cell_ID = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add cell metadata — addCellMetadata","text":"gobject giotto object spat_unit spatial unit feat_type feature type new_metadata new cell metadata use (data.table, data.frame, vector, factor, ...) vector_name (optional) custom name new metadata column single vector factor provided by_column merge metadata based cell_ID column pDataDT (default = FALSE) column_cell_ID column name new metadata use by_column = TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add cell metadata — addCellMetadata","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add cell metadata — addCellMetadata","text":"can add additional cell metadata several manners: 1. Provide data.frame-like object, vector, factor cell annotations order cell_ID column pDataDT(gobject). bit risky recommended. 2. Provide data.frame-like object cell annotations specify column contains cell IDs, cell IDs need match cell_ID column pDataDT(gobject) 3. Provide vector factor named cell IDs correspond . names matched cell_ID column pDataDT(gobject).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add cell metadata — addCellMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  m <- pDataDT(g) m <- m[, c(\"cell_ID\", \"leiden_clus\")] m$cell_type <- paste0(\"cell_type_\", m$leiden_clus) m <- m[, c(\"cell_ID\", \"cell_type\")]  g <- addCellMetadata(     g,     new_metadata = m,     by_column = TRUE,     column_cell_ID = \"cell_ID\" )  pDataDT(g) #>                 cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                  <char>     <int>    <int>      <num>      <num>       <num> #>   1: AACTCGATGGCGCAGT-1         1      265   41.79811  1057.9308           2 #>   2: GGCTGGCTAGCTTAAA-1         1      279   44.00631  1064.7493           5 #>   3: GACGCCTGTTGCAGGG-1         1      219   34.54259   964.9294           2 #>   4: GAGGGCATCGCGTATC-1         1      294   46.37224  1142.7664           2 #>   5: TCAACACATTGGGTAA-1         1      261   41.16719  1063.3517           2 #>  ---                                                                         #> 620: GGTAGTGCTCGCACCA-1         1      179   28.23344   768.4749           5 #> 621: AAGCTCGTGCCAAGTC-1         1      195   30.75710   756.0675           5 #> 622: TATTCAATTCTAATCC-1         1      247   38.95899   921.8264           5 #> 623: TTCAAAGTCTCTAGCC-1         1      384   60.56782   916.5929           6 #> 624: TTGAATATGGACTTTC-1         1      380   59.93691   912.3051           6 #>      custom_leiden   cell_type #>              <num>      <char> #>   1:             4 cell_type_2 #>   2:             3 cell_type_5 #>   3:             3 cell_type_2 #>   4:             3 cell_type_2 #>   5:             3 cell_type_2 #>  ---                           #> 620:             4 cell_type_5 #> 621:             4 cell_type_5 #> 622:             4 cell_type_5 #> 623:             7 cell_type_6 #> 624:             4 cell_type_6"},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Add feature metadata — addFeatMetadata","title":"Add feature metadata — addFeatMetadata","text":"Adds feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add feature metadata — addFeatMetadata","text":"","code":"addFeatMetadata(   gobject,   feat_type = NULL,   spat_unit = NULL,   new_metadata,   vector_name = NULL,   by_column = FALSE,   column_feat_ID = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add feature metadata — addFeatMetadata","text":"gobject giotto object feat_type feature type spat_unit spatial unit new_metadata new metadata use) vector_name (optional) custom name provide single vector by_column merge metadata based feat_ID column fDataDT column_feat_ID column name new metadata use by_column = TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add feature metadata — addFeatMetadata","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add feature metadata — addFeatMetadata","text":"can add additional feature metadata several manners: 1. Provide data.table data.frame feature annotations order feat_ID column fDataDT(gobject) bit risky recommended. 2. Provide data.table data.frame feature annotations specify column contains feature IDs, feature IDs need match feat_ID column fDataDT(gobject) 3. Provide vector factor named feature IDs correspond . names matched feat_ID column fDataDT(gobject).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add feature metadata — addFeatMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  m <- fDataDT(g) m <- m[, \"feat_ID\"] m$new_feat_ID <- paste0(\"gene_\", m$feat_ID)  g <- addFeatMetadata(     g,     new_metadata = m,     by_column = TRUE,     column_feat_ID = \"feat_ID\" )  fDataDT(g) #>            feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det #>             <char>    <int>      <num>      <num>     <num>         <num> #>   1:         Gna12      502  80.448718  1987.1333 3.1845085      3.958433 #>   2:         Ccnd2      357  57.211538  1254.4730 2.0103734      3.513930 #>   3:        Btbd17      252  40.384615   781.9747 1.2531645      3.103074 #>   4:          Sox9      309  49.519231  1019.7255 1.6341755      3.300083 #>   5:          Sez6      504  80.769231  2177.4740 3.4895416      4.320385 #>  ---                                                                      #> 630:        Lhfpl3      235  37.660256   732.3595 1.1736530      3.116423 #> 631: C030029H02Rik       72  11.538462   203.0811 0.3254506      2.820572 #> 632:       Gm19935       57   9.134615   172.1079 0.2758139      3.019436 #> 633: 9630013A20Rik       52   8.333333   157.2602 0.2520196      3.024235 #> 634: 2900040C04Rik       61   9.775641   179.7015 0.2879831      2.945926 #>         hvf        new_feat_ID #>      <char>             <char> #>   1:     no         gene_Gna12 #>   2:     no         gene_Ccnd2 #>   3:     no        gene_Btbd17 #>   4:     no          gene_Sox9 #>   5:     no          gene_Sez6 #>  ---                           #> 630:     no        gene_Lhfpl3 #> 631:     no gene_C030029H02Rik #> 632:     no       gene_Gm19935 #> 633:     no gene_9630013A20Rik #> 634:     no gene_2900040C04Rik"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"addGiottoImage — addGiottoImage","title":"addGiottoImage — addGiottoImage","text":"Adds lists giottoImages giottoLargeImages gobjects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addGiottoImage — addGiottoImage","text":"","code":"addGiottoImage(   gobject = NULL,   images = NULL,   largeImages = NULL,   spat_loc_name = NULL,   scale_factor = NULL,   negative_y = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addGiottoImage — addGiottoImage","text":"gobject gobject add images objects images list giotto images add largeImages deprecated spat_loc_name provide spatial location slot Giotto align giottoImages. Defaults first one scale_factor provide scale image pixel dimensions relative spatial coordinates. negative_y Map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addGiottoImage — addGiottoImage","text":"updated Giotto object access list images","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addGiottoImage — addGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  addGiottoImage(g, largeImages = list(g_image)) #> Warning: The `largeImages` argument of `addGiottoImage()` is deprecated as of #> GiottoClass 0.3.0. #> ℹ Please use the `images` argument instead. #> ℹ All images should be supplied to `images` instead #> ℹ Names of images may not overlap #>  #> alignment has already been used, will be overwritten #> > image 'alignment' already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":null,"dir":"Reference","previous_headings":"","what":"addGiottoImageMG — addGiottoImageMG","title":"addGiottoImageMG — addGiottoImageMG","text":"Adds giotto image objects giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addGiottoImageMG — addGiottoImageMG","text":"","code":"addGiottoImageMG(   gobject,   images,   spat_unit = NULL,   spat_loc_name = NULL,   scale_factor = NULL,   negative_y = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addGiottoImageMG — addGiottoImageMG","text":"gobject giotto object images list giotto image objects, see createGiottoImage spat_unit spatial unit spat_loc_name provide spatial location slot Giotto align images. Defaults first one scale_factor provide scale image pixel dimensions relative spatial coordinates. negative_y Map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addGiottoImageMG — addGiottoImageMG","text":"updated Giotto object access list images","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addGiottoImageMG — addGiottoImageMG","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  addGiottoImageMG(g, images = list(g_image)) #> Warning: image [1] is not a giotto image object #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"addGiottoLargeImage — addGiottoLargeImage","title":"addGiottoLargeImage — addGiottoLargeImage","text":"Add giotto image objects giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addGiottoLargeImage — addGiottoLargeImage","text":"","code":"addGiottoLargeImage(   gobject = NULL,   largeImages = NULL,   spat_loc_name = NULL,   scale_factor = NULL,   negative_y = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addGiottoLargeImage — addGiottoLargeImage","text":"gobject giotto object largeImages list giottoLargeImage objects spat_loc_name provide spatial location slot Giotto align images. (optional) scale_factor provide scale image pixel dimensions relative spatial coordinates. negative_y map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left. verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addGiottoLargeImage — addGiottoLargeImage","text":"updated Giotto object access list images","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addGiottoLargeImage — addGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  addGiottoLargeImage(g, largeImages = list(g_image)) #>  #> alignment has already been used, will be overwritten #> > image 'alignment' already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Add subcellular giotto points object to giotto object — addGiottoPoints","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"Adds Giotto points existing Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"","code":"addGiottoPoints(gobject, gpoints)  addGiottoPoints3D(gobject, coords, feat_type = \"rna\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"gobject giotto object gpoints list giotto point objects, see createGiottoPoints coords data.frame spatVector least xyz coordinates feature ids. feat_type character. feat_type must previously exist Giotto object. Default = \"rna\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"","code":"x_points <- GiottoData::loadSubObjectMini(\"giottoPoints\") x_expression <- matrix(seq_len(337 * 2), nrow = 337) rownames(x_expression) <- unique(x_points$feat_ID) g <- createGiottoObject(expression = x_expression) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed  g <- addGiottoPoints(gobject = g, gpoints = list(x_points))"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Add giotto polygons to giotto object — addGiottoPolygons","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"Adds Giotto polygon existing Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"","code":"addGiottoPolygons(gobject, gpolygons)"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"gobject giotto object gpolygons list giotto polygon objects, see createGiottoPolygonsFromMask createGiottoPolygonsFromDfr","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"","code":"x <- GiottoData::loadSubObjectMini(\"giottoPolygon\") g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  g <- addGiottoPolygons(gobject = g, gpolygons = list(x))"},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":null,"dir":"Reference","previous_headings":"","what":"addNetworkLayout — addNetworkLayout","title":"addNetworkLayout — addNetworkLayout","text":"Add network layout selected nearest neighbor network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addNetworkLayout — addNetworkLayout","text":"","code":"addNetworkLayout(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_network_to_use = \"sNN\",   network_name = \"sNN.pca\",   layout_type = c(\"drl\"),   options_list = NULL,   layout_name = \"layout\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addNetworkLayout — addNetworkLayout","text":"gobject giotto object spat_unit spatial unit feat_type feature type nn_network_to_use kNN sNN network_name name NN network used layout_type layout algorithm use options_list list options selected layout layout_name name layout return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addNetworkLayout — addNetworkLayout","text":"giotto object updated layout selected NN network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"addNetworkLayout — addNetworkLayout","text":"function creates layout coordinates based provided kNN sNN. Currently force-directed graph layout \"drl\", see layout_with_drl, implemented. provides alternative tSNE UMAP based visualizations.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addNetworkLayout — addNetworkLayout","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  addNetworkLayout(g) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":null,"dir":"Reference","previous_headings":"","what":"addSpatialCentroidLocations — addSpatialCentroidLocations","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"Calculates centroid locations polygons within one selected layers","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"","code":"addSpatialCentroidLocations(   gobject,   poly_info = \"cell\",   feat_type = NULL,   spat_loc_name = \"raw\",   provenance = poly_info,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"gobject giotto object poly_info polygon information feat_type feature type spat_loc_name name give created spatial locations provenance (optional) provenance assign generated spatLocsObj. provided, provenance default poly_info return_gobject return giotto object (default: TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"return_gobject = TRUE giotto object containing calculated polygon centroids returned. return_gobject = FALSE generated polygon centroids returned spatLocObj.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  addSpatialCentroidLocations(g, poly_info = \"aggregate\") #> Start centroid calculation for polygon information #>  layer: aggregate #> > spatial locations for polygon information layer \" aggregate \" and name \" raw #>  \" already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":null,"dir":"Reference","previous_headings":"","what":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"Calculates centroid locations polygons within one selected layer","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"","code":"addSpatialCentroidLocationsLayer(   gobject,   poly_info = \"cell\",   feat_type = NULL,   provenance = poly_info,   spat_loc_name = \"raw\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"gobject giotto object poly_info polygon information feat_type feature type provenance (optional) provenance assign generated spatLocsObj. provided, provenance default poly_info spat_loc_name name give created spatial locations return_gobject return giotto object (default: TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"return_gobject = TRUE giotto object containing calculated polygon centroids returned. return_gobject = FALSE generated polygon centroids returned spatLocsObj.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  addSpatialCentroidLocationsLayer(g, poly_info = \"aggregate\") #> > spatial locations for polygon information layer \" aggregate \" and name \" raw #>  \" already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":null,"dir":"Reference","previous_headings":"","what":"Add alpha channel to image array — add_img_array_alpha","title":"Add alpha channel to image array — add_img_array_alpha","text":"Add alpha channel image array","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add alpha channel to image array — add_img_array_alpha","text":"","code":"add_img_array_alpha(x, alpha)"},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add alpha channel to image array — add_img_array_alpha","text":"x image array use alpha global alpha value use. Numeric. Scales 0 1, 0 fully transparent 1 fully visible","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add alpha channel to image array — add_img_array_alpha","text":"image array 4th channel transparency","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add alpha channel to image array — add_img_array_alpha","text":"Add 4th alpha channel 3 channel RGB image arrays","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add alpha channel to image array — add_img_array_alpha","text":"","code":"x <- matrix(rnorm(4), nrow = 2)  add_img_array_alpha(x, alpha = 0.1) #> , , 1 #>  #>            [,1]       [,2] #> [1,] -0.8289657 -0.8621887 #> [2,] -0.8413987  0.6702333 #>  #> , , 2 #>  #>            [,1]       [,2] #> [1,] -0.8289657 -0.8621887 #> [2,] -0.8413987  0.6702333 #>  #> , , 3 #>  #>            [,1]       [,2] #> [1,] -0.8289657 -0.8621887 #> [2,] -0.8413987  0.6702333 #>  #> , , 4 #>  #>      [,1] [,2] #> [1,]  0.1  0.1 #> [2,]  0.1  0.1 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":null,"dir":"Reference","previous_headings":"","what":"Affine transformations — affine","title":"Affine transformations — affine","text":"Apply affine transformation matrix spatial object. Currently works 2D transforms.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Affine transformations — affine","text":"","code":"# S4 method for class 'giotto,matrix' affine(   x,   y,   inv = FALSE,   spat_unit = \":all:\",   feat_type = \":all:\",   images = \":all:\",   ... )  # S4 method for class 'missing,missing' affine(x)  # S4 method for class 'ANY,missing' affine(x)  # S4 method for class 'ANY,affine2d' affine(x, y, ...)  # S4 method for class 'SpatVector,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'giottoPoints,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'giottoPolygon,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'spatLocsObj,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'giottoLargeImage,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'giottoAffineImage,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'affine2d,matrix' affine(x, y, inv = FALSE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Affine transformations — affine","text":"x object affine transform matrix y matrix coercible matrix (affine2d). matrix either 2 3 columns (linear affine). inv logical. Whether inverse affine transform applied. spat_unit character vector. spatial units affect. :: token affect can used. feat_type character vector. feature types affect. :: token affect can used. images character vector. Images affect. :: token affect can used. ... additional args pass (none implemented)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Affine transformations — affine","text":"affine transformed object affine2d matrix passed x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Affine transformations — affine","text":"","code":"m <- diag(rep(1, 3)) trans_m <- matrix(c(1, 0, 0, 0, 1, 0, 200, 300, 1), nrow = 3) scale_m <- matrix(c(2, 0, 0, 0, 3, 0, 0, 0, 1), nrow = 3) aff_m <- matrix(c(2, 3, 0, 0.2, 3, 0, 100, 29, 1), nrow = 3)  gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\") gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  # creation of affine2d aff <- affine(m) aff <- spin(flip(shear(aff, fx = 0.2)), 45) plot(aff) # blue is start, red is end   # giottoPoints ############################################## plot(gpoints)  plot(affine(gpoints, trans_m))   # giottoPolygon ############################################# plot(gpoly)  plot(affine(gpoly, scale_m))  plot(affine(gpoly, aff)) # affine() with `affine2d`   # spatLocsObj ############################################### plot(affine(sl, m))  plot(affine(sl, trans_m))  plot(affine(sl, scale_m))  # this transformation can be inverted aff_sl <- affine(sl, aff_m) plot(aff_sl)  plot(affine(aff_sl, aff_m, inv = TRUE))"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacks — aggregateStacks","title":"aggregateStacks — aggregateStacks","text":"aggregate expression matrices different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacks — aggregateStacks","text":"","code":"aggregateStacks(   gobject,   spat_units,   feat_type,   values,   summarize_expression = \"sum\",   summarize_locations = \"mean\",   for_loop = FALSE,   for_loop_group_size = 100,   new_spat_unit = \"aggregate\",   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacks — aggregateStacks","text":"gobject giotto object spat_units spatial units aggregate feat_type feature type values values use summarize_expression method summarize expression information summarize_locations method summarize spatial location information for_loop aggregate polygons loop (default = FALSE) for_loop_group_size size polygon groups aggregate loop new_spat_unit new name aggregated spatial unit verbose verbosity","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacks — aggregateStacks","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"aggregateStacks — aggregateStacks","text":"Combines aggregateStacksExpression aggregateStacksLocations","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacks — aggregateStacks","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacks(g,     spat_units = c(\"z0\", \"z1\"), feat_type = \"rna\",     values = \"raw\" ) #> 1. Start aggregating expression data #> > raw already exists and will be replaced with new values #> > Cell metadata for spat_unit \" aggregate \" and feat_type \" rna \" already #>  exists and will be replaced with new metadata. #> Setting cell metadata [aggregate][rna] #> > Feat metadata for spat_unit \" aggregate \" and feat_type \" rna \" already #>  exists and will be replaced with new metadata. #> Setting feature metadata [aggregate][rna] #> 1. Aggregating expression data completed #> 2. Start aggregating Polygon data #> 2. Aggregating polygon data completed #> 3. Start aggregating centroid location data #> Start centroid calculation for polygon information #>  layer: aggregate #> > spatial locations for polygon information layer \" aggregate \" and name \" raw #>  \" already exists and will be replaced #> 3. Aggregating centroid location data completed #> 4. Start aggregating polygon overlap data #> 4. Aggregating polygon overlap data completed #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksExpression — aggregateStacksExpression","title":"aggregateStacksExpression — aggregateStacksExpression","text":"aggregate expression matrices different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksExpression — aggregateStacksExpression","text":"","code":"aggregateStacksExpression(   gobject,   spat_units,   feat_type,   values = \"raw\",   summarize = \"sum\",   new_spat_unit = \"aggregate\",   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksExpression — aggregateStacksExpression","text":"gobject giotto object spat_units spatial units aggregate feat_type feature type values values use summarize method summarize expression information new_spat_unit new name aggregated spatial unit verbose verbosity","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksExpression — aggregateStacksExpression","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacksExpression — aggregateStacksExpression","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacksExpression(g, spat_units = c(\"z0\", \"z1\"), feat_type = \"rna\") #> > raw already exists and will be replaced with new values #> > Cell metadata for spat_unit \" aggregate \" and feat_type \" rna \" already #>  exists and will be replaced with new metadata. #> Setting cell metadata [aggregate][rna] #> > Feat metadata for spat_unit \" aggregate \" and feat_type \" rna \" already #>  exists and will be replaced with new metadata. #> Setting feature metadata [aggregate][rna] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksLocations — aggregateStacksLocations","title":"aggregateStacksLocations — aggregateStacksLocations","text":"aggregate expression matrices different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksLocations — aggregateStacksLocations","text":"","code":"aggregateStacksLocations(   gobject,   spat_units,   values = \"raw\",   summarize = \"mean\",   new_spat_unit = \"aggregate\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksLocations — aggregateStacksLocations","text":"gobject giotto object spat_units spatial units aggregate values values use summarize method summarize spatial location information new_spat_unit new name aggregated spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksLocations — aggregateStacksLocations","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacksLocations — aggregateStacksLocations","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacksLocations(g, spat_units = c(\"z0\", \"z1\")) #> > raw already exists and will be replaced with new spatial #>  locations #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"aggregate polygons overlap information different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"","code":"aggregateStacksPolygonOverlaps(   gobject,   spat_units,   feat_type,   new_spat_unit = \"aggregate\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"gobject giotto object spat_units spatial units aggregate feat_type feature type used overlap calculations new_spat_unit new name aggregated spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacksPolygonOverlaps(g,     spat_units = c(\"z0\", \"z1\"),     feat_type = \"rna\" ) #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksPolygons — aggregateStacksPolygons","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"aggregate polygons different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"","code":"aggregateStacksPolygons(   gobject,   spat_units,   new_spat_unit = \"aggregate\",   for_loop = FALSE,   for_loop_group_size = 100 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"gobject giotto object spat_units spatial units aggregate new_spat_unit new name aggregated spatial unit for_loop aggregate polygons loop (default = FALSE) for_loop_group_size size polygon groups aggregate loop","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacksPolygons(g, spat_units = c(\"z0\", \"z1\")) #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert anndata to Giotto — anndataToGiotto","title":"Convert anndata to Giotto — anndataToGiotto","text":"Converts spatial anndata (e.g. scanpy) .h5ad file Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert anndata to Giotto — anndataToGiotto","text":"","code":"anndataToGiotto(   anndata_path = NULL,   n_key_added = NULL,   spatial_n_key_added = NULL,   delaunay_spat_net = TRUE,   spat_unit = NULL,   feat_type = NULL,   h5_file = NULL,   python_path = NULL,   env_name = \"giotto_env\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert anndata to Giotto — anndataToGiotto","text":"anndata_path path .h5ad file n_key_added equivalent \"key_added\" argument scanpy.pp. neighbors(). multiple spatial networks anndata object, list key_added terms may provided. converting anndata object giottoToAnnData, .txt file may provided, generated function, .e. {spat_unit}_{feat_type}_nn_network_keys_added.txt. \"spatial\". becomes name nearest network gobject. spatial_n_key_added equivalent \"key_added\" argument squidpy.gr.spatial_neighbors. multiple spatial networks anndata object, list key_added terms may provided. converting anndata object giottoToAnnData, .txt file may provided, generated function, .e. {spat_unit}_{feat_type}_spatial_network_keys_added.txt n_key_added. delaunay_spat_net binary parameter spatial network. TRUE, spatial network delaunay network. spat_unit desired spatial unit use conversion, default NULL feat_type desired feature type use conversion, default NULL h5_file name create -disk HDF5 file python_path path python executable within conda/miniconda environment env_name name environment containing python_path executable","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert anndata to Giotto — anndataToGiotto","text":"Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert anndata to Giotto — anndataToGiotto","text":"Function beta. Converts .h5ad file Giotto object. returned Giotto Object take default instructions exception python path, may customized. See changeGiottoInstructions modify instructions creation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate Giotto object — annotateGiotto","title":"Annotate Giotto object — annotateGiotto","text":"Map user provided annotations/labels based another existing metadata column (usually clustering labels)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate Giotto object — annotateGiotto","text":"","code":"annotateGiotto(   gobject,   spat_unit = NULL,   feat_type = NULL,   annotation_vector = NULL,   cluster_column = NULL,   name = \"cell_types\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate Giotto object — annotateGiotto","text":"gobject giotto object spat_unit spatial unit feat_type feature type annotation_vector named character vector. Vector names labels cluster column. Labels assign vector values. cluster_column character. Cell metaadata column map annotation values based . name new name annotation column","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotate Giotto object — annotateGiotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Annotate Giotto object — annotateGiotto","text":"need specify (cluster) column want annotate need provide annotation vector like : 1. identify cell type cluster 2. create vector cell types, e.g. cell_types =  c('T-cell', 'B-cell', 'Stromal') 3. provide original cluster names previous vector, e.g. names(cell_types) = c(2, 1, 3)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Annotate Giotto object — annotateGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  annotation <- c(     \"1\" = \"cell_type_1\",     \"2\" = \"cell_type_2\",     \"3\" = \"cell_type_3\",     \"4\" = \"cell_type_4\",     \"5\" = \"cell_type_5\",     \"6\" = \"cell_type_6\",     \"7\" = \"cell_type_7\",     \"8\" = \"cell_type_8\" )  g <- annotateGiotto(g,     annotation_vector = annotation,     cluster_column = \"leiden_clus\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"annotateSpatialGrid — annotateSpatialGrid","title":"annotateSpatialGrid — annotateSpatialGrid","text":"annotate spatial grid cell ID cell metadata (optional)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"annotateSpatialGrid — annotateSpatialGrid","text":"","code":"annotateSpatialGrid(   gobject,   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = \"raw\",   spatial_grid_name = \"spatial_grid\",   cluster_columns = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"annotateSpatialGrid — annotateSpatialGrid","text":"gobject Giotto object spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations spatial_grid_name name spatial grid, see showGiottoSpatGrids cluster_columns names cell metadata, see pDataDT","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"annotateSpatialGrid — annotateSpatialGrid","text":"annotated spatial grid data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"annotateSpatialGrid — annotateSpatialGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  annotateSpatialGrid(g) #>      sdimx sdimy            cell_ID gr_x_loc gr_y_loc    gr_loc #>      <int> <int>             <char>   <char>   <char>    <char> #>   1:  5477 -4125 AAAGGGATGTAGCAAG-1 gr_x_482 gr_y_264 gr_178007 #>   2:  5959 -2808 AAATGGCATGTCTTGT-1 gr_x_579 gr_y_528 gr_356304 #>   3:  4720 -5202 AAATGGTCAATGTGCC-1 gr_x_331  gr_y_49  gr_32731 #>   4:  5202 -5322 AAATTAACGGGTAGCT-1 gr_x_427  gr_y_25  gr_16627 #>   5:  4101 -4604 AACAACTGGTAGTTGC-1 gr_x_207 gr_y_169 gr_113607 #>  ---                                                            #> 620:  4996 -5442 TTGTAATCCGTACTCG-1 gr_x_386   gr_y_1    gr_386 #> 621:  6303 -2688 TTGTATCACACAGAAT-1 gr_x_648 gr_y_552 gr_372573 #> 622:  5202 -3885 TTGTCGTTCAGTTACC-1 gr_x_427 gr_y_312 gr_210352 #> 623:  5340 -3406 TTGTGGCCCTGACAGT-1 gr_x_455 gr_y_408 gr_275180 #> 624:  5615 -4125 TTGTTCAGTGTGCTAC-1 gr_x_510 gr_y_264 gr_178035"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"annotateSpatialNetwork — annotateSpatialNetwork","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"Annotate spatial network cell metadata information.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"","code":"annotateSpatialNetwork(   gobject,   spat_unit = NULL,   feat_type = NULL,   spatial_network_name = \"Delaunay_network\",   cluster_column,   create_full_network = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"gobject giotto object spat_unit spatial unit feat_type feature type spatial_network_name name spatial network use cluster_column name column use clusters create_full_network convert reduced full network representation","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"annotated network data.table format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  annotateSpatialNetwork(g, cluster_column = \"leiden_clus\") #>                     from                 to sdimx_begin sdimy_begin sdimx_end #>                   <char>             <char>       <num>       <num>     <num> #>    1: AAAGGGATGTAGCAAG-1 TCAAACAACCGCGTCG-1        5477       -4125      5340 #>    2: AAAGGGATGTAGCAAG-1 ACGATCATACATAGAG-1        5477       -4125      5546 #>    3: AAAGGGATGTAGCAAG-1 TATGCTCCCTACTTAC-1        5477       -4125      5408 #>    4: AAAGGGATGTAGCAAG-1 TTGTTCAGTGTGCTAC-1        5477       -4125      5615 #>    5: AAAGGGATGTAGCAAG-1 ATCGACTCTTTCCGTT-1        5477       -4125      5408 #>   ---                                                                         #> 1766: TTCAAGCCGAGCTGAG-1 TTGTATCACACAGAAT-1        6372       -2808      6303 #> 1767: TTCGACGGGAAGGGCG-1 TTCGCACTCGCGTGCT-1        4239       -4125      4308 #> 1768: TTCTTAGTGGCTCAGA-1 TTGTGGCCCTGACAGT-1        5408       -3287      5340 #> 1769: TTCTTGTAACCTAATG-1 TTGGCTCGCATGAGAC-1        3620       -4005      3757 #> 1770: TTGCACGGAGCAGCAC-1 TTGTCGTTCAGTTACC-1        5271       -3766      5202 #>       sdimy_end distance      weight to_cell_type from_cell_type type_int #>           <num>    <num>       <num>       <char>         <char>   <char> #>    1:     -4125 137.0000 0.007299270            5              1   hetero #>    2:     -4244 137.5573 0.007269700            1              1     homo #>    3:     -4244 137.5573 0.007269700            1              1     homo #>    4:     -4125 138.0000 0.007246377            1              1     homo #>    5:     -4005 138.4233 0.007224219            1              1     homo #>   ---                                                                     #> 1766:     -2688 138.4233 0.007224219            2              2     homo #> 1767:     -4245 138.4233 0.007224219            3              3     homo #> 1768:     -3406 137.0584 0.007296161            5              5     homo #> 1769:     -4005 137.0000 0.007299270            1              1     homo #> 1770:     -3885 137.5573 0.007269700            1              3   hetero #>       from_to unified_int #>        <char>      <char> #>    1:     1-5        1--5 #>    2:     1-1        1--1 #>    3:     1-1        1--1 #>    4:     1-1        1--1 #>    5:     1-1        1--1 #>   ---                     #> 1766:     2-2        2--2 #> 1767:     3-3        3--3 #> 1768:     5-5        5--5 #> 1769:     1-1        1--1 #> 1770:     3-1        1--3"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":null,"dir":"Reference","previous_headings":"","what":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"annotate spatial locations 2D spatial grid information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"","code":"annotate_spatlocs_with_spatgrid_2D(spatloc, spatgrid)"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"spatloc spatial_locs slot giotto object spatgrid selected spatial_grid slot giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"annotated spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5) g_spatloc <- getSpatialLocations(g, output = \"data.table\") g_spatgrid <- getSpatialGrid(g) #> The grid name was not specified, default to the first: \"spatial_grid\"  annotate_spatlocs_with_spatgrid_2D(     spatloc = g_spatloc,     spatgrid = g_spatgrid ) #>      sdimx sdimy            cell_ID gr_x_loc gr_y_loc    gr_loc #>      <int> <int>             <char>   <char>   <char>    <char> #>   1:  5477 -4125 AAAGGGATGTAGCAAG-1 gr_x_482 gr_y_264 gr_178007 #>   2:  5959 -2808 AAATGGCATGTCTTGT-1 gr_x_579 gr_y_528 gr_356304 #>   3:  4720 -5202 AAATGGTCAATGTGCC-1 gr_x_331  gr_y_49  gr_32731 #>   4:  5202 -5322 AAATTAACGGGTAGCT-1 gr_x_427  gr_y_25  gr_16627 #>   5:  4101 -4604 AACAACTGGTAGTTGC-1 gr_x_207 gr_y_169 gr_113607 #>  ---                                                            #> 620:  4996 -5442 TTGTAATCCGTACTCG-1 gr_x_386   gr_y_1    gr_386 #> 621:  6303 -2688 TTGTATCACACAGAAT-1 gr_x_648 gr_y_552 gr_372573 #> 622:  5202 -3885 TTGTCGTTCAGTTACC-1 gr_x_427 gr_y_312 gr_210352 #> 623:  5340 -3406 TTGTGGCCCTGACAGT-1 gr_x_455 gr_y_408 gr_275180 #> 624:  5615 -4125 TTGTTCAGTGTGCTAC-1 gr_x_510 gr_y_264 gr_178035"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":null,"dir":"Reference","previous_headings":"","what":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"annotate spatial locations 3D spatial grid information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"","code":"annotate_spatlocs_with_spatgrid_3D(spatloc, spatgrid)"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"spatloc spatial_locs slot giotto object spatgrid selected spatial_grid slot giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"annotated spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"","code":"g <- GiottoData::loadGiottoMini(\"starmap\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_spatloc <- getSpatialLocations(g, output = \"data.table\") g_spatgrid <- getSpatialGrid(g) #> The grid name was not specified, default to the first: \"spatial_grid\"  annotate_spatlocs_with_spatgrid_3D(     spatloc = g_spatloc,     spatgrid = g_spatgrid ) #>       sdimx sdimy sdimz    cell_ID gr_x_loc gr_y_loc gr_z_loc gr_loc #>       <int> <int> <int>     <char>   <char>   <char>   <char> <char> #>    1:   270   212    19  cell_2944   gr_x_2   gr_y_2   gr_z_2  gr_83 #>    2:  1389  1215    54 cell_17523   gr_x_7   gr_y_7   gr_z_4 gr_277 #>    3:  1051   360    89 cell_30080   gr_x_6   gr_y_2   gr_z_5 gr_303 #>    4:   592   777    10   cell_941   gr_x_3   gr_y_5   gr_z_1  gr_39 #>    5:  1058   223    84 cell_28514   gr_x_6   gr_y_2   gr_z_5 gr_303 #>   ---                                                                #> 3901:   348  1383    78 cell_26011   gr_x_2   gr_y_8   gr_z_5 gr_353 #> 3902:   674  1080    89 cell_31539   gr_x_4   gr_y_6   gr_z_5 gr_337 #> 3903:   919   532    22  cell_4185   gr_x_5   gr_y_3   gr_z_2  gr_95 #> 3904:   947   885    23  cell_3851   gr_x_5   gr_y_5   gr_z_2 gr_113 #> 3905:   144   439    60 cell_21337   gr_x_1   gr_y_3   gr_z_4 gr_235"},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the area of individual polygons — area","title":"Get the area of individual polygons — area","text":"Compute area covered polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the area of individual polygons — area","text":"","code":"# S4 method for class 'giottoPolygon' area(x, ...)  # S4 method for class 'SpatVector' area(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the area of individual polygons — area","text":"x giottoPolygon ... additional args pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the area of individual polygons — area","text":"numeric vector spatial area","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the area of individual polygons — area","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  # area of polygons area(gpoly) #>   [1] 115.382156 137.699592  56.258785  40.229395  97.002577  45.332848 #>   [7]  71.292382  88.371522  66.422317  79.931111 127.027294  95.667698 #>  [13]  68.893156  34.568123  44.002485  28.509585 108.275150  73.819729 #>  [19]  78.608663 145.048538  20.719544  28.778835  54.980361  57.290988 #>  [25]  61.593386  39.112532  52.105403  51.045881  81.704714 168.285559 #>  [31]  42.937577 141.422443 164.660053  88.381279  77.152979  43.167074 #>  [37]  44.652023  49.536357  74.097684  93.333373 108.649889   3.625382 #>  [43]  32.388099 116.489993  57.535530  92.338288  52.509047  41.150838 #>  [49]  47.593223  57.158546  70.455928  25.063070  57.779990  47.941342 #>  [55]  42.424001  53.835541  41.876606  55.195710 137.303108  69.164203 #>  [61]  41.795739  67.310060  44.371163  46.254949  19.546489  81.625242 #>  [67] 118.715161  82.471018  87.892114  69.612346 103.555573  88.695051 #>  [73]  93.962734  19.435281 105.202436 152.572181  47.933664 156.543998 #>  [79]  64.170943  63.638421  66.326260 106.778907 112.661813 112.902630 #>  [85]  53.136703  39.287410  44.853020  78.877723  56.053503  46.070249 #>  [91] 113.380182  25.782623 157.828400  65.594372 171.872443  27.492766 #>  [97]  52.454251  92.875400  40.546921  80.775562  17.990194  48.474324 #> [103]  13.770289 115.135690  24.315644  97.226983  68.116633 101.073033 #> [109]  15.995823  43.848299  94.734965  78.376501  74.425205 119.146342 #> [115]  82.297781 101.410965 121.705213  30.474723  17.119168 151.719441 #> [121]  43.829745 191.541382 126.260435  36.689881  69.020409  54.050307 #> [127] 185.517103 101.842157  56.174526 121.983821  62.215237 159.424280 #> [133] 132.573959  42.641755  39.443430  29.879557 247.246029 121.401552 #> [139]  25.106711  38.583762 105.001640  74.286747  35.445152 139.179936 #> [145]  46.361149  60.738068  91.896979 129.837339  22.904326  33.473557 #> [151] 130.753727  53.185364 149.418428 132.050815  12.792682  78.129115 #> [157]  70.328907  33.537418  90.686201  19.452148  32.440515  90.376179 #> [163] 219.310104 101.376410  81.311602  45.864517 122.496632  54.147531 #> [169]  27.897431 126.962657  52.160437  81.601298  87.474158 122.075417 #> [175]  38.124635  62.559769 200.075231  76.312474 107.187281 189.431723 #> [181]  61.075352  44.449498  23.821415  38.340378 111.967876  95.682535 #> [187]  40.150629 150.355333 158.018954  70.179077  43.838012  29.885799 #> [193] 129.266905 137.371563  87.088326 103.063248  57.474822  61.101909 #> [199]  33.657407  38.653428  57.924050 177.706024  15.250413  36.841646 #> [205]  48.513825  87.425664 132.978824  66.737607 157.029775  54.854626 #> [211] 132.416601  37.131024  90.288613  35.586162  59.038520  95.582097 #> [217]  32.162960 100.569991 116.654919  28.754218  60.072974 102.246471 #> [223]  81.471684  20.977006  64.997885  54.027689  17.416627  67.521147 #> [229]  69.259391  75.810748  95.765004  25.195225 100.951886  44.630761 #> [235] 160.643637 179.393657  97.423910 215.156341  58.553909  29.777089 #> [241]  58.746361 121.143932  55.699201  89.429782 160.979431 145.446617 #> [247]  93.233779  83.193754  35.647268 158.733011 116.032780 124.781295 #> [253] 117.895490  22.248638  56.941543  62.493490  95.618526 112.839798 #> [259]  61.189989 148.845224  74.224374  80.251044  39.901354  66.450440 #> [265]  75.327080  43.292625 147.586155  38.198580  81.429289  67.505694 #> [271]  69.769232 119.652217 105.853346 101.714301  30.890972  87.606791 #> [277]  65.124539  27.064328  38.120760  40.075655  62.308542  80.001513 #> [283] 103.832092 142.686465  24.557224  64.228162  41.272696  58.873217 #> [289]  72.104235   6.660052  96.070015 145.968844  90.020228  37.489668 #> [295] 129.927467 134.536297  36.758667  20.868081  35.585220  70.229709 #> [301] 105.964373  25.159487  61.289897  78.716248  74.899171  17.922789 #> [307]  76.998708  75.030590  27.077454  51.461024  66.444366  71.757876 #> [313]  24.097374  62.408624  84.651353  57.801908 141.544944  65.071704 #> [319]  29.312598 108.802794  55.070164 254.011504 108.318436  97.225920 #> [325]  76.222028 219.411328  46.441821  83.046394  28.717752  24.335424 #> [331]  55.846265  99.011556  20.737471  70.343241  75.132632  19.092044 #> [337]  58.283696  63.382027  74.342376 114.644585  30.219673  26.280021 #> [343] 170.236248  63.422589 116.251979  48.900846  90.521441  60.011770 #> [349]  75.488249  54.209468  37.091655  84.761878  31.721098  97.065126 #> [355]  47.004961  32.547595 139.575862  11.718641  91.200086  62.877798 #> [361]  92.867375   9.942683 111.628109  46.906968 126.742572 146.659695 #> [367] 121.516530 128.993617  49.814376 159.781874 105.119283  76.190982 #> [373]  64.170765  74.998533  60.373170  54.510092  74.993138  74.356919 #> [379] 141.118014  65.791923  72.891288 139.330262  54.700658  20.005007 #> [385]  94.911861  91.686109  94.647883 147.515935 122.057396  39.560030 #> [391]  92.092400 163.831117  61.586632 117.874102  40.784218  39.639844 #> [397]  30.144736  66.180669  11.170534  56.022100 120.455304 157.455917 #> [403]  99.923896 176.239903  53.023597  36.134329  71.485715 113.977649 #> [409]  54.369377  65.763036  38.420173  66.186141 108.683300  49.961911 #> [415]  55.405510 109.453060  17.935675  76.790187 123.710744  31.263041 #> [421]  75.685700  40.072969  55.842580  44.135987  36.906334  96.058841 #> [427] 112.879696  35.377052 209.891465  58.217434 156.125202  83.515929 #> [433]  51.581023  89.286940  78.399934 103.823589  86.643317  64.811750 #> [439] 141.296392  89.394817  53.750554  53.189547  54.276573 100.814926 #> [445]  66.101887 179.872754  26.422177  59.277010 141.781207  65.796310 #> [451]  45.170500  71.155894  48.213360 243.277797  24.620358  99.923534 #> [457]  72.348473  82.358683 137.263692 151.990487  46.179693  73.811876  # area of the convex hull area(convHull(sl)) #> [1] 199333.6 feature_hulls <- convHull(gpoints, by = \"feat_ID\") area(feature_hulls) #>   [1] 144798.7133 187046.0487 188143.6215 210427.1860 180407.1047 179525.7058 #>   [7] 185662.0149 208822.2997 197475.9826 157464.4008  65313.8619  40607.1830 #>  [13] 158307.8761 195539.8183  56624.3065  85995.6127  63041.4641 209879.3008 #>  [19] 176481.9921 192658.6919 169032.8309 116820.7911 195495.3261 101153.2271 #>  [25] 120653.8204 137286.5447  93245.5725 128522.5729 193111.8414  49353.5278 #>  [31] 180804.6322 128139.1086 153051.7259 206020.5245 145642.8480 152505.7430 #>  [37] 186224.4956  50800.2600 209040.3709 187270.9635 166411.3041 169683.5130 #>  [43]   1972.2428 205098.5718 182544.5109  64448.4509  28331.9230  42322.6394 #>  [49]   3610.8130   8799.0106  23195.2945   3214.9414  10412.5134  72053.1368 #>  [55] 120626.5302  60738.7859  48229.3741  30282.2113   8911.4632  71181.9991 #>  [61]  22419.9289  53298.6136  84628.9170 200054.0014 200119.6959 102787.5843 #>  [67]  63361.1134  75000.6474 176626.0357  99097.9212  53069.9237  40702.9997 #>  [73]  61487.3084 127273.3633  57111.5701 133841.2571 144324.4832 210716.6701 #>  [79] 132207.5176  86146.5232 164093.7710 135874.2413  70953.2062  89728.6380 #>  [85] 180253.5931 165995.3587 108063.6174 150159.6246  35185.9014 183489.9072 #>  [91] 211191.0325 197805.1203 189662.1234 192889.5422 132440.8011  53443.2281 #>  [97] 203189.7307 157742.8703 157844.6759  78470.3163  42891.5510  33821.5507 #> [103] 151184.7287 205357.6787 153044.4755 186157.1746 144661.6144  67245.9256 #> [109]  99891.9217 130342.7695  55284.9318 165055.3305 190797.7633 123425.4347 #> [115] 170244.0299 158858.8945  68438.8563 181164.1319 147125.4539 176707.4455 #> [121] 196670.1410 129951.9862  56130.7498 194884.0727 130921.8166   8993.5075 #> [127] 184007.4069 204508.4589 163390.4550 175138.2561  85618.0998 108852.5692 #> [133] 178291.7166   5948.7906 189553.4023  33288.5603 187546.3609 193721.1221 #> [139] 187099.2455 111544.1916 169824.2427 182629.6453 153842.1615 114206.2984 #> [145] 210911.4279 199411.5661 193496.9836  52124.3816 111671.8368 217143.9693 #> [151]  52638.6489  61229.5578 149112.6940 140657.9052  43442.4975  60706.2032 #> [157]  38551.4045   2329.5772 123530.9205  13703.5970 185190.5158 146101.2328 #> [163] 149941.5042  97188.3608 127516.2228 148946.6473 149625.0486 197629.5924 #> [169] 153144.4427 168436.2364 130075.8993 134149.9173  72193.2872  26787.0221 #> [175] 119519.3617 156183.6477 134593.0607 163399.9948 131526.4735  47804.8863 #> [181] 205492.3323 157232.1028 121197.4900 163845.3479  40083.6591  18312.2989 #> [187]  85655.4469 153123.9948 174196.8676 121804.4182  52461.4857 171899.3641 #> [193] 211979.5539 105152.9139 192142.5217 159105.8015 150004.0432 141338.8031 #> [199] 188608.9360 145140.7287 199286.2949 154735.2345  31732.1041  53209.3025 #> [205]   6561.2860 115700.7475  89303.6690 134584.2116 133917.3126  96030.7518 #> [211]  10813.7838 155653.7377  67531.9731  33505.7382  95789.7497 106343.2921 #> [217] 207077.8986 190364.0199  17068.4872 143526.0469 183880.8817 162583.8700 #> [223] 154264.8404 195784.6299  77803.8483  59291.6180 102642.3201 207911.3473 #> [229] 180587.5670  88490.0306 169056.4974 132544.9566 164847.8773  83523.8146 #> [235]  76820.7102  24476.6428  20017.6829 193958.7959 206867.3557 127181.7507 #> [241]  69722.6199 111911.0138  80652.9708  26613.0416 160175.1586  94516.3283 #> [247] 197760.0457 171974.4749 213712.1538 200998.7761 210189.2502 205158.0394 #> [253]  53200.8816  21555.2591 129052.4588  45379.0769 132356.6424 189415.9034 #> [259] 152804.3918  23989.4458  30160.6806 127681.6720 125866.3606 171379.6925 #> [265] 160560.9106 181577.2311 170110.4521  62959.7269 135522.6912  82161.7389 #> [271]  64709.6904 120428.2414  51760.3808  29019.6612  92957.8966  67643.3438 #> [277]  79745.5991 162345.8387 177205.7244  64956.2263  73614.0551 170299.4173 #> [283]  47351.9062  18947.1547 165440.5822 115384.7093 206734.0143 209733.3384 #> [289] 128636.3201 137608.9949  26458.9509 117258.2422  40426.2985 176406.4456 #> [295] 169647.3954 154982.2534  41851.6406 187780.5956  38591.3468 205377.0827 #> [301] 175768.2754  56946.4078 162984.3471 208281.3627 196120.1871 207955.2629 #> [307] 166788.0597  58235.4575 123962.0055 147825.7471 153163.2194  38223.7941 #> [313]  53137.2779  15907.0189    696.8923 120960.3162   5148.3261  14033.1056 #> [319]  63886.6932 120026.6378  88685.3133 163816.3287 128323.9647 206332.1977 #> [325] 173391.6733 185103.9587 170731.6459  94495.2530 188002.2522  68231.3765 #> [331]  93176.2753  93399.5022  71158.8974 115309.0944  95269.5287    731.8556 #> [337]  84537.1417"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a text representation of an object — as.character","title":"Create a text representation of an object — as.character","text":"Create text representation object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a text representation of an object — as.character","text":"","code":"# S4 method for class 'giottoImage' as.character(x, ...)  # S4 method for class 'giottoLargeImage' as.character(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a text representation of an object — as.character","text":"x object ... additional params pass (none implemented)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a text representation of an object — as.character","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a text representation of an object — as.character","text":"","code":"img <- GiottoData::loadSubObjectMini(\"giottoLargeImage\") as.character(img) #> [1] \"<giottoLargeImage> dapi_z0\""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to data.table — as.data.table","title":"Coerce to data.table — as.data.table","text":"Coerce data.table possible","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to data.table — as.data.table","text":"","code":"# S3 method for class 'SpatVector' as.data.table(   x,   keep.rownames = FALSE,   geom = NULL,   include_values = TRUE,   ... )  # S3 method for class 'giottoPolygon' as.data.table(x, ...)  # S3 method for class 'giottoPoints' as.data.table(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to data.table — as.data.table","text":"x object coerce keep.rownames argument ignored geom character NULL. NULL, either \"XY\", \"WKT\", \"HEX\", get geometry included coordinates point vertex, Well-Known-Text hexadecimal notation. include_values whether include attributes information geom 'XY' ... additional arguments pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to data.table — as.data.table","text":"data.table","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to data.table — as.data.table","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  data.table::as.data.table(g) #>                                      poly_ID  stack agg_n valid #>                                       <char> <char> <int> <int> #>   1: 100210519278873141813371229408401071444   <NA>     2     1 #>   2: 101161259912191124732236989250178928032   <NA>     2     1 #>   3: 101488859781016188084173008420811094152   <NA>     2     1 #>   4: 101523780333017320796881555775415156847   <NA>     2     1 #>   5: 102184699197574201819246996094734116255   <NA>     2     1 #>  ---                                                            #> 458:   9677424102111816817518421117250891895   <NA>     2     1 #> 459:  97068595823890802071024838798130036179   <NA>     2     1 #> 460:  97411078642927912684859796714759494710   <NA>     2     1 #> 461:   9816437869021910185567097363182418837   <NA>     2     1 #> 462:  98561957902191275233320065611022298397   <NA>     2     1"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to a list — as.list,giotto-method","title":"Coerce to a list — as.list,giotto-method","text":"Generic coerce list possible","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to a list — as.list,giotto-method","text":"","code":"# S4 method for class 'giotto' as.list(x, slots, spat_unit = NULL, feat_type = NULL, name = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to a list — as.list,giotto-method","text":"x object coerce slots character vector. data slots include list. See details spat_unit spatial unit (e.g. \"cell\") feat_type feature type use (e.g. \"rna\", \"protein\") name name elements select slot ... additional arguments","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to a list — as.list,giotto-method","text":"list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerce to a list — as.list,giotto-method","text":"Giotto method - slots argument currently accepts multiple : \"spatial_info\", \"spatial_locs\", \"spatial_network\", \"feat_info\", \"expression\", \"cell_metadata\", \"feat_metadata\", \"spatial_enrichment\", \"nn_network\", \"dimension_reduction\", \"multiomics\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to matrix — as.matrix","title":"Coerce to matrix — as.matrix","text":"Coerce matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to matrix — as.matrix","text":"","code":"# S4 method for class 'spatLocsObj' as.matrix(x, id_rownames = TRUE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to matrix — as.matrix","text":"x object coerce id_rownames logical. Retain spatial IDs rownames ... additional params pass (none implemented)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to matrix — as.matrix","text":"matrix","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to matrix — as.matrix","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") m <- as.matrix(sl)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to SpatVector points — as.points","title":"Coerce to SpatVector points — as.points","text":"Coversion SpatVector points.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to SpatVector points — as.points","text":"","code":"# S4 method for class 'data.frame' as.points(x, include_values = TRUE, specific_values = NULL)  # S4 method for class 'spatLocsObj' as.points(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to SpatVector points — as.points","text":"x SpatRaster, SpatVector, SpatExtent, correctly formatted data.frame include_values logical. Whether include additional columns geometry information SpatVector attributes. Default TRUE. specific_values character. Specific subset columns include attributes include_values = TRUE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to SpatVector points — as.points","text":"SpatVector points","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to SpatVector points — as.points","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  as.points(slot(g, \"spatVector\")) #> Warning: [as.points] returning a copy #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to SpatVector polygons — as.polygons","title":"Coerce to SpatVector polygons — as.polygons","text":"Coversion SpatVector polygons.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to SpatVector polygons — as.polygons","text":"","code":"# S4 method for class 'data.frame' as.polygons(   x,   include_values = TRUE,   specific_values = NULL,   sort_geom = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to SpatVector polygons — as.polygons","text":"x SpatRaster, SpatVector, SpatExtent, correctly formatted data.frame include_values logical. Whether include additional columns geometry information SpatVector attributes. Default TRUE. specific_values character. Specific subset columns include attributes include_values = TRUE. sort_geom logical. Whether sort key data.table input 'geom', 'part', 'hole' columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to SpatVector polygons — as.polygons","text":"SpatVector polygons","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to SpatVector polygons — as.polygons","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  as.polygons(slot(g, \"spatVector\")) #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 480, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateMetaTable — calculateMetaTable","title":"calculateMetaTable — calculateMetaTable","text":"calculates average gene expression one (combined) annotation columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateMetaTable — calculateMetaTable","text":"","code":"calculateMetaTable(   gobject,   spat_unit = NULL,   feat_type = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   metadata_cols = NULL,   selected_feats = NULL,   selected_genes = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateMetaTable — calculateMetaTable","text":"gobject giotto object spat_unit spatial unit feat_type feature type expression_values expression values use metadata_cols annotation columns found pDataDT(gobject) selected_feats subset features use selected_genes subset genes use (deprecated)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateMetaTable — calculateMetaTable","text":"data.table average expression values gene per (combined) annotation","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateMetaTable — calculateMetaTable","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateMetaTable(g, metadata_cols = \"leiden_clus\") #>       leiden_clus uniq_ID      variable      value #>             <num>   <num>        <fctr>      <num> #>    1:           2       2         Gna12 2.95192565 #>    2:           5       5         Gna12 4.41905517 #>    3:           1       1         Gna12 2.51999975 #>    4:           3       3         Gna12 2.60980838 #>    5:           6       6         Gna12 4.18561316 #>   ---                                              #> 4434:           1       1 2900040C04Rik 0.48747773 #> 4435:           3       3 2900040C04Rik 0.21256443 #> 4436:           6       6 2900040C04Rik 0.47596999 #> 4437:           7       7 2900040C04Rik 0.00000000 #> 4438:           4       4 2900040C04Rik 0.04874282"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateMetaTableCells — calculateMetaTableCells","title":"calculateMetaTableCells — calculateMetaTableCells","text":"calculates average metadata values one (combined) annotation columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateMetaTableCells — calculateMetaTableCells","text":"","code":"calculateMetaTableCells(   gobject,   spat_unit = NULL,   feat_type = NULL,   value_cols = NULL,   metadata_cols = NULL,   spat_enr_names = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateMetaTableCells — calculateMetaTableCells","text":"gobject giotto object spat_unit spatial unit feat_type feature type value_cols metadata enrichment value columns use metadata_cols annotation columns found pDataDT(gobject) spat_enr_names spatial enrichment results include","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateMetaTableCells — calculateMetaTableCells","text":"data.table average metadata values per (combined) annotation","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateMetaTableCells — calculateMetaTableCells","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateMetaTableCells(g,     metadata_cols = \"cell_ID\",     value_cols = \"leiden_clus\" ) #>                 cell_ID    variable value #>                  <char>      <fctr> <num> #>   1: AAAGGGATGTAGCAAG-1 leiden_clus     1 #>   2: AAATGGCATGTCTTGT-1 leiden_clus     2 #>   3: AAATGGTCAATGTGCC-1 leiden_clus     4 #>   4: AAATTAACGGGTAGCT-1 leiden_clus     4 #>   5: AACAACTGGTAGTTGC-1 leiden_clus     6 #>  ---                                      #> 620: TTGTAATCCGTACTCG-1 leiden_clus     4 #> 621: TTGTATCACACAGAAT-1 leiden_clus     2 #> 622: TTGTCGTTCAGTTACC-1 leiden_clus     1 #> 623: TTGTGGCCCTGACAGT-1 leiden_clus     5 #> 624: TTGTTCAGTGTGCTAC-1 leiden_clus     1"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate features overlapped by polygons — calculateOverlap","title":"Calculate features overlapped by polygons — calculateOverlap","text":"Calculate subcellular points/feature info image values overlapped polygon annotations. provides summary spatial data overlapped polygon can processed become expression matrix.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate features overlapped by polygons — calculateOverlap","text":"","code":"# S4 method for class 'giotto,missing' calculateOverlap(   x,   name_overlap = NULL,   spatial_info = NULL,   feat_info = NULL,   image_names = NULL,   poly_subset_ids = NULL,   return_gobject = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'giottoPolygon,giottoPoints' calculateOverlap(   x,   y,   name_overlap = NULL,   poly_subset_ids = NULL,   feat_subset_column = NULL,   feat_subset_ids = NULL,   count_info_column = NULL,   return_gpolygon = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'giottoPolygon,giottoLargeImage' calculateOverlap(   x,   y,   name_overlap = NULL,   poly_subset_ids = NULL,   return_gpolygon = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'giottoPolygon,SpatRaster' calculateOverlap(   x,   y,   name_overlap = NULL,   poly_subset_ids = NULL,   return_gpolygon = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'SpatVector,SpatRaster' calculateOverlap(x, y, poly_subset_ids = NULL, verbose = TRUE, ...)  # S4 method for class 'SpatVector,SpatVector' calculateOverlap(   x,   y,   poly_subset_ids = NULL,   feat_subset_column = NULL,   feat_subset_ids = NULL,   count_info_column = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate features overlapped by polygons — calculateOverlap","text":"x Object spatial annotations: giottoPolygon, SpatVector polygons. Can also giotto object name_overlap name overlap results (default feat_info parameter) spatial_info character. Name polygon information feat_info character. Name vector feature information overlap image_names character vector. Name(s) image feature information overlap poly_subset_ids character vector. (optional) Specific poly_IDs use return_gobject return giotto object (default: TRUE) verbose verbose ... additional params pass methods. y Object features overlap: giottoPoints, giottoLargeImage, SpatVector points SpatRaster feat_subset_column character. (optional) feature info attribute subset feature points performing overlap calculation. feat_subset_ids (optional) values matched feat_subset_column order subset feature points performing overlap calculation. count_info_column character. (optional) column count information. Useful cases one detection reported per point. return_gpolygon default = TRUE. Whether return entire giottoPolygon provided x, overlaps information appended bare terra SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate features overlapped by polygons — calculateOverlap","text":"Usually object class x, overlaps information appended. return_* logical params usually allow return lower-level representation results instead. SpatVector,SpatRaster method different returns data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate features overlapped by polygons — calculateOverlap","text":"feat_subset_column, feat_subset_ids, count_info_column specific overlaps feature points info, provided overlapping image data. three params can also passed giotto method ... param working overlaps feature points info.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate features overlapped by polygons — calculateOverlap","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" gpoly <- getPolygonInfo(g,     polygon_name = \"aggregate\",     return_giottoPolygon = TRUE ) gpoints <- getFeatureInfo(g, return_giottoPoints = TRUE) gimg <- getGiottoImage(g, image_type = \"largeImage\")  slot(gpoly, \"overlaps\") <- NULL overlaps(gpoly) # Should now be NULL #> NULL  # detections from 2 z-layers are provided table(gpoints$global_z) #>  #>     0     1  #> 35889 43872   # calculate all transcripts overlapped out_all <- calculateOverlap(gpoly, gpoints) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information overlaps_all <- overlaps(out_all) overlaps_all$rna #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : poly_ID feat_ID feat_ID_uniq #>  type        :   <chr>   <chr>        <int> #>  values      :      NA    Mlc1            1 #>                     NA  Gprc5b            2 #>                     NA    Gfap            3  # calculate z1 only out_z1 <- calculateOverlap(gpoly, gpoints,     feat_subset_column = \"global_z\",     feat_subset_ids = c(1) ) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information overlaps_z1 <- overlaps(out_z1) overlaps_z1$rna #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 43872, 3  (geometries, attributes) #>  extent      : 6400.043, 6900.03, -5149.983, -4699.984  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : poly_ID feat_ID feat_ID_uniq #>  type        :   <chr>   <chr>        <int> #>  values      :      NA  Gabbr2        36198 #>                     NA    Gfap        36199 #>                     NA    Gfap        36200  # overlap image to get sum intensities per cell out_img <- calculateOverlap(gpoly, gimg) #> Start image extract #>    |                                                                               |                                                                      |   0%   |                                                                               |                                                                      |   1%   |                                                                               |=                                                                     |   1%   |                                                                               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|======================================================================|  99%   |                                                                               |======================================================================| 100% #> End image extract overlaps_img <- overlaps(out_img) overlaps_img$intensity #> $dapi_z0 #>                                          poly_ID mini_dataset_dapi_z0 #>                                           <char>                <num> #>       1: 100210519278873141813371229408401071444                   18 #>       2: 100210519278873141813371229408401071444                   18 #>       3: 100210519278873141813371229408401071444                   18 #>       4: 100210519278873141813371229408401071444                   18 #>       5: 100210519278873141813371229408401071444                   18 #>      ---                                                              #> 3170620:  98561957902191275233320065611022298397                   98 #> 3170621:  98561957902191275233320065611022298397                   98 #> 3170622:  98561957902191275233320065611022298397                   88 #> 3170623:  98561957902191275233320065611022298397                   88 #> 3170624:  98561957902191275233320065611022298397                   88 #>   # giotto method # calculate z0 overlaps and return as gobject out_g <- calculateOverlap(g,     feat_subset_column = \"global_z\",     feat_subset_ids = 0 ) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information overlaps(getPolygonInfo(out_g, return_giottoPolygon = TRUE)) #> $rna #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 35889, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : poly_ID feat_ID feat_ID_uniq #>  type        :   <chr>   <chr>        <int> #>  values      :      NA    Mlc1            1 #>                     NA  Gprc5b            2 #>                     NA    Gfap            3 #>   # note that z0 and z1 nrows match that from the table of global z values. # With points overlaps, all points are returned, but non-overlapped points # only have an `NA` value for the `poly_ID` column. Overlapped points will # have the `poly_ID` of their overlapping polygon."},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateOverlapParallel — calculateOverlapParallel","title":"calculateOverlapParallel — calculateOverlapParallel","text":"calculate overlap cellular structures (polygons) features (points)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateOverlapParallel — calculateOverlapParallel","text":"","code":"calculateOverlapParallel(   gobject,   name_overlap = NULL,   spatial_info = \"cell\",   feat_info = \"rna\",   poly_ID_names = \"all\",   polygon_group_size = 500,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateOverlapParallel — calculateOverlapParallel","text":"gobject giotto object name_overlap name overlap results (default feat_info parameter) spatial_info polygon information feat_info feature information poly_ID_names list poly_IDs use polygon_group_size number polygons process per parallelization group return_gobject return giotto object (default: TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateOverlapParallel — calculateOverlapParallel","text":"giotto object spatVector overlapping information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"calculateOverlapParallel — calculateOverlapParallel","text":"parallel follows future approach. means plan(multisession) work, since underlying terra objects internal C pointers. plan(multicore) also supported Rstudio users.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateOverlapParallel — calculateOverlapParallel","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateOverlapParallel(g, spatial_info = \"z1\") #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"calculate overlap cellular structures (polygons) images (intensities)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"","code":"calculateOverlapPolygonImages(   gobject,   name_overlap = \"protein\",   spatial_info = \"cell\",   poly_ID_names = NULL,   image_names = NULL,   poly_subset = NULL,   return_gobject = TRUE,   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"gobject giotto object name_overlap name overlap results (default feat_info parameter) spatial_info polygon information poly_ID_names (optional) list poly_IDs use image_names names images raw data poly_subset numerical values subset polygon spatVector return_gobject return giotto object (default: TRUE) verbose verbose ... additional params exact_extract","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"giotto object data.table overlapping information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateOverlapPolygonImages(g,     spatial_info = \"z0\",     image_names = \"dapi_z0\" ) #> [1] \"0. create image list\" #> [1] \"1. start extraction\" #>    |                                                                               |                                                                      |   0%   |                                                                               |                                                                      |   1%   |                                                                               |=                                                                     |   1%   |                                                                               |=                                                                     |   2%   |                                                                               |==                                                                    |   2%   |                                                                               |==                                                                    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|======================================================================|  99%   |                                                                               |======================================================================| 100% #>                                         poly_ID value coverage_fraction #>                                          <char> <num>             <num> #>       1: 40951783403982682273285375368232495429     8      1.420465e-01 #>       2: 40951783403982682273285375368232495429     8      4.332028e-01 #>       3: 40951783403982682273285375368232495429     8      5.996065e-01 #>       4: 40951783403982682273285375368232495429     8      6.887537e-01 #>       5: 40951783403982682273285375368232495429     8      7.144262e-01 #>      ---                                                                #> 2846020:  9677424102111816817518421117250891895     8      3.764088e-01 #> 2846021:  9677424102111816817518421117250891895     8      5.001789e-01 #> 2846022:  9677424102111816817518421117250891895     8      4.812778e-01 #> 2846023:  9677424102111816817518421117250891895     8      1.656012e-01 #> 2846024:  9677424102111816817518421117250891895     8      1.540388e-05 #>                                         poly_ID dapi_z0 #>                                          <char>   <num> #>       1: 40951783403982682273285375368232495429       8 #>       2: 40951783403982682273285375368232495429       8 #>       3: 40951783403982682273285375368232495429       8 #>       4: 40951783403982682273285375368232495429       8 #>       5: 40951783403982682273285375368232495429       8 #>      ---                                                #> 2846020:  9677424102111816817518421117250891895       8 #> 2846021:  9677424102111816817518421117250891895       8 #> 2846022:  9677424102111816817518421117250891895       8 #> 2846023:  9677424102111816817518421117250891895       8 #> 2846024:  9677424102111816817518421117250891895       8 #> > \" z0 \" already exists and will be replaced #>  with new giotto polygon #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateOverlapRaster — calculateOverlapRaster","title":"calculateOverlapRaster — calculateOverlapRaster","text":"calculate overlap cellular structures (polygons) features (points).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateOverlapRaster — calculateOverlapRaster","text":"","code":"calculateOverlapRaster(   gobject,   name_overlap = NULL,   spatial_info = NULL,   poly_ID_names = NULL,   feat_info = NULL,   feat_subset_column = NULL,   feat_subset_ids = NULL,   count_info_column = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateOverlapRaster — calculateOverlapRaster","text":"gobject giotto object name_overlap name overlap results (default feat_info parameter) spatial_info character. name polygon information poly_ID_names (optional) list poly_IDs use feat_info character. name feature information feat_subset_column feature info column subset features feat_subset_ids ids within feature info column use subsetting count_info_column column count information (optional) return_gobject return giotto object (default: TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateOverlapRaster — calculateOverlapRaster","text":"giotto object spatVector overlapping information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"calculateOverlapRaster — calculateOverlapRaster","text":"Serial overlapping function.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateOverlapRaster — calculateOverlapRaster","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateOverlapRaster(g) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateOverlapSerial — calculateOverlapSerial","title":"calculateOverlapSerial — calculateOverlapSerial","text":"calculate overlap cellular structures (polygons) features (points)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateOverlapSerial — calculateOverlapSerial","text":"","code":"calculateOverlapSerial(   gobject,   name_overlap = NULL,   spatial_info = \"cell\",   feat_info = \"rna\",   poly_ID_names = \"all\",   polygon_group_size = 500,   return_gobject = TRUE,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateOverlapSerial — calculateOverlapSerial","text":"gobject giotto object name_overlap name overlap results (default feat_info parameter) spatial_info polygon information feat_info feature information poly_ID_names list poly_IDs use polygon_group_size number polygons process per group return_gobject return giotto object (default: TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateOverlapSerial — calculateOverlapSerial","text":"giotto object spatVector overlapping information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"calculateOverlapSerial — calculateOverlapSerial","text":"Serial overlapping function works groups polygons time. Number polygons per group defined polygon_group_size param","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateOverlapSerial — calculateOverlapSerial","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateOverlapSerial(g, spatial_info = \"z1\") #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"calculates proportion table cell metadata column (e.g. cluster labels) spatial neighbors source cell. words calculates niche composition given annotation cell.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"","code":"calculateSpatCellMetadataProportions(   gobject,   spat_unit = NULL,   feat_type = NULL,   spat_network = NULL,   metadata_column = NULL,   name = \"proportion\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"gobject giotto object spat_unit spatial unit feat_type feature type spat_network spatial network metadata_column metadata column use name descriptive name calculated proportions return_gobject return giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"giotto object (default) enrichment object return_gobject = FALSE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateSpatCellMetadataProportions(g,     spat_network = \"Delaunay_network\", metadata_column = \"leiden_clus\" ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS proportion #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/cellMetaObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 cellMetaObj — cellMetaObj-class","title":"S4 cellMetaObj — cellMetaObj-class","text":"Framework store cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cellMetaObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 cellMetaObj — cellMetaObj-class","text":"cellMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cellMetaObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 cellMetaObj — cellMetaObj-class","text":"metaDT metadata info col_desc (optional) character vector describing columns metadata spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') provenance origin data aggregated expression information (applicable)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cellMetaObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 cellMetaObj — cellMetaObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"cellMetaObj\") #> An object of class cellMetaObj  #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #> dimensions: 462 6  #>  #>                                    cell_ID nr_feats perc_feats total_expr #>                                     <char>    <int>      <num>      <num> #> 1: 240649020551054330404932383065726870513        5   1.483680   49.40986 #> 2: 274176126496863898679934791272921588227       27   8.011869  191.50684 #> 3: 323754550002953984063006506310071917306       23   6.824926  173.86955 #>    leiden_clus louvain_clus #>          <num>        <num> #> 1:           2            0 #> 2:           2            3 #> 3:           4            8"},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"centroids-generic — centroids-generic","title":"centroids-generic — centroids-generic","text":"Access centroids information polygon objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"centroids-generic — centroids-generic","text":"","code":"# S4 method for class 'giottoPolygon' centroids(x, append_gpolygon = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"centroids-generic — centroids-generic","text":"x object append_gpolygon whether append centroids results giottoPolygon instead returning bare SpatVector. Defaults FALSE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"centroids-generic — centroids-generic","text":"spatVectorCentroids spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"centroids-generic — centroids-generic","text":"giottoPolygon, centroids already exist, pulls spatVectorCentroids slot. Otherwise, generates spatVector slot de novo","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"centroids-generic — centroids-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  centroids(g) #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6401.412, 6899.108, -5146.747, -4700.326  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1"},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — changeGiottoInstructions","title":"deprecated — changeGiottoInstructions","text":"Function change one instructions giotto object. one item supplied params new_values, use vector values. call initialize giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — changeGiottoInstructions","text":"","code":"changeGiottoInstructions(   gobject,   params = NULL,   new_values = NULL,   return_gobject = TRUE,   init_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — changeGiottoInstructions","text":"gobject giotto object params parameter(s) change new_values new value(s) parameter(s) return_gobject (boolean, default = TRUE) return giotto object init_gobject (boolean, default = TRUE) initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — changeGiottoInstructions","text":"giotto object one changed instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"deprecated — changeGiottoInstructions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  changeGiottoInstructions(     gobject = g, params = \"save_plot\",     new_values = TRUE ) #> Warning: `changeGiottoInstructions()` was deprecated in GiottoClass 0.3.5. #> ℹ Please use `instructions()` instead. #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":null,"dir":"Reference","previous_headings":"","what":"changeImageBg — changeImageBg","title":"changeImageBg — changeImageBg","text":"Function change background color magick image plot another color","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"changeImageBg — changeImageBg","text":"","code":"changeImageBg(   mg_object,   bg_color,   perc_range = 10,   new_color = \"#FFFFFF\",   new_name = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"changeImageBg — changeImageBg","text":"mg_object magick image giotto image object bg_color estimated current background color perc_range range around estimated background color include (percentage) new_color new background color new_name change name Giotto image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"changeImageBg — changeImageBg","text":"magick image giotto image object updated background color","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"changeImageBg — changeImageBg","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- convertGiottoLargeImageToMG(g,     largeImage_name = \"image\",     return_gobject = FALSE )  changeImageBg(mg_object = g_image, bg_color = \"white\") #> An object of class ' giottoImage ' with name  image  #>   #> Min and max values are:  #>  Max on x-axis:  6790.5  #>  Min on x-axis:  2000.5  #>  Max on y-axis:  -2380.75  #>  Min on y-axis:  -5730.25  #>   #> Boundary adjustment are:  #>  Max adjustment on x-axis:  0  #>  Min adjustment on x-axis:  0  #>  Max adjustment on y-axis:  0  #>  Min adjustment on y-axis:  0  #>   #> Boundaries are:  #>  Image x-axis max boundary:  6790.5  #>  Image x-axis min boundary:  2000.5  #>  Image y-axis max boundary:  -2380.75  #>  Image y-axis min boundary:  -5730.25  #>   #> Scale factor:  #> x y  #> 1 1  #>  #>  Resolution:  #> x y  #> 1 1  #>  #>  File Path:  #> NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Python Package Installation — checkPythonPackage","title":"Check Python Package Installation — checkPythonPackage","text":"checks python environment provided package, installs found.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Python Package Installation — checkPythonPackage","text":"","code":"checkPythonPackage(   package_name = NULL,   github_package_url = NULL,   env_to_use = \"giotto_env\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Python Package Installation — checkPythonPackage","text":"package_name name python package. See details. github_package_url URL linking github repository containing python package may installed pip, e.g. git+https://github.com/TencentAILabHealthcare/pysodb.git; see details. env_to_use name environment python package installed.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Python Package Installation — checkPythonPackage","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check Python Package Installation — checkPythonPackage","text":"Parameter github_package_url takes precedent package_name, .e. provided, github URL installed. function provided one parameter, .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/check_py_for_scanpy.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Scanpy Installation — check_py_for_scanpy","title":"Check Scanpy Installation — check_py_for_scanpy","text":"checks current python environment scanpy 1.9.0","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/check_py_for_scanpy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Scanpy Installation — check_py_for_scanpy","text":"","code":"check_py_for_scanpy()"},{"path":"https://drieslab.github.io/GiottoClass/reference/check_py_for_scanpy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Scanpy Installation — check_py_for_scanpy","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate circle polygon vertices — circleVertices","title":"Generate circle polygon vertices — circleVertices","text":"Generates vertex coordinates circle around (0,0) given radius. Modified packcircles.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate circle polygon vertices — circleVertices","text":"","code":"circleVertices(radius, npoints = 25)"},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate circle polygon vertices — circleVertices","text":"radius radius circle drawn npoints number vertices generate","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate circle polygon vertices — circleVertices","text":"data.table circle vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate circle polygon vertices — circleVertices","text":"","code":"circleVertices(radius = 10) #>              x             y #>          <num>         <num> #>  1: 10.0000000  0.000000e+00 #>  2:  9.6858316  2.486899e+00 #>  3:  8.7630668  4.817537e+00 #>  4:  7.2896863  6.845471e+00 #>  5:  5.3582679  8.443279e+00 #>  6:  3.0901699  9.510565e+00 #>  7:  0.6279052  9.980267e+00 #>  8: -1.8738131  9.822873e+00 #>  9: -4.2577929  9.048271e+00 #> 10: -6.3742399  7.705132e+00 #> 11: -8.0901699  5.877853e+00 #> 12: -9.2977649  3.681246e+00 #> 13: -9.9211470  1.253332e+00 #> 14: -9.9211470 -1.253332e+00 #> 15: -9.2977649 -3.681246e+00 #> 16: -8.0901699 -5.877853e+00 #> 17: -6.3742399 -7.705132e+00 #> 18: -4.2577929 -9.048271e+00 #> 19: -1.8738131 -9.822873e+00 #> 20:  0.6279052 -9.980267e+00 #> 21:  3.0901699 -9.510565e+00 #> 22:  5.3582679 -8.443279e+00 #> 23:  7.2896863 -6.845471e+00 #> 24:  8.7630668 -4.817537e+00 #> 25:  9.6858316 -2.486899e+00 #> 26: 10.0000000 -2.449294e-15 #>              x             y"},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"colMeans_flex — colMeans_flex","title":"colMeans_flex — colMeans_flex","text":"colMeans_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"colMeans_flex — colMeans_flex","text":"","code":"colMeans_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"colMeans_flex — colMeans_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"colMeans_flex — colMeans_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"colMeans_flex — colMeans_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  colMeans_flex(m) #>  [1] -0.33020071 -0.14415435  0.13720593  0.38627780 -0.15823532 -0.21262668 #>  [7] -0.04357001  0.35755432 -0.45103539  0.06068702"},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"colSums_flex — colSums_flex","title":"colSums_flex — colSums_flex","text":"colSums_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"colSums_flex — colSums_flex","text":"","code":"colSums_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"colSums_flex — colSums_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"colSums_flex — colSums_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"colSums_flex — colSums_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  colSums_flex(m) #>  [1]   1.3396257   4.9253110 -11.5121833  -1.9314278   3.6286812  -0.6779535 #>  [7]  -4.7705262  -1.3051013   5.4512605  -0.7708679"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":null,"dir":"Reference","previous_headings":"","what":"combineCellData — combineCellData","title":"combineCellData — combineCellData","text":"combine cell data information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineCellData — combineCellData","text":"","code":"combineCellData(   gobject,   feat_type = \"rna\",   include_spat_locs = TRUE,   spat_loc_name = \"raw\",   include_poly_info = TRUE,   poly_info = \"cell\",   include_spat_enr = TRUE,   spat_enr_names = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineCellData — combineCellData","text":"gobject giotto object feat_type feature type include_spat_locs include information spatial locations spat_loc_name spatial location name include_poly_info include information polygon poly_info polygon information name include_spat_enr include information spatial enrichment spat_enr_names names spatial enrichment results include","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineCellData — combineCellData","text":"data.table combined spatial information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineCellData — combineCellData","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineCellData(g, poly_info = \"aggregate\") #> $rna #> Key: <cell_ID> #>                                        cell_ID    sdimx     sdimy  geom  part #>                                         <char>    <num>     <num> <int> <num> #>     1: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>     2: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>     3: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>     4: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>     5: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>    ---                                                                        #> 35971:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #> 35972:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #> 35973:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #> 35974:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #> 35975:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #>               x         y  hole  stack agg_n valid nr_feats perc_feats #>           <num>     <num> <num> <char> <int> <int>    <int>      <num> #>     1: 6642.257 -5136.674     0   <NA>     2     1       22    6.52819 #>     2: 6642.711 -5137.020     0   <NA>     2     1       22    6.52819 #>     3: 6643.050 -5137.462     0   <NA>     2     1       22    6.52819 #>     4: 6643.310 -5137.956     0   <NA>     2     1       22    6.52819 #>     5: 6643.484 -5138.518     0   <NA>     2     1       22    6.52819 #>    ---                                                                 #> 35971: 6788.764 -4942.998     0   <NA>     2     1       53   15.72700 #> 35972: 6788.905 -4942.999     0   <NA>     2     1       53   15.72700 #> 35973: 6789.575 -4942.999     0   <NA>     2     1       53   15.72700 #> 35974: 6789.576 -4943.000     0   <NA>     2     1       53   15.72700 #> 35975: 6789.695 -4943.000     0   <NA>     2     1       53   15.72700 #>        total_expr leiden_clus louvain_clus   feat #>             <num>       <num>        <num> <char> #>     1:   163.6923           4           15    rna #>     2:   163.6923           4           15    rna #>     3:   163.6923           4           15    rna #>     4:   163.6923           4           15    rna #>     5:   163.6923           4           15    rna #>    ---                                            #> 35971:   326.0539           1           26    rna #> 35972:   326.0539           1           26    rna #> 35973:   326.0539           1           26    rna #> 35974:   326.0539           1           26    rna #> 35975:   326.0539           1           26    rna #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":null,"dir":"Reference","previous_headings":"","what":"combineFeatureData — combineFeatureData","title":"combineFeatureData — combineFeatureData","text":"combine feature data information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineFeatureData — combineFeatureData","text":"","code":"combineFeatureData(   gobject,   feat_type = NULL,   spat_unit = NULL,   sel_feats = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineFeatureData — combineFeatureData","text":"gobject giotto object feat_type feature type spat_unit spatial unit sel_feats selected features (default: NULL selection)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineFeatureData — combineFeatureData","text":"data.table combined spatial feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineFeatureData — combineFeatureData","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineFeatureData(g, spat_unit = \"aggregate\", feat_type = \"rna\") #> $rna #> Key: <feat_ID> #>        feat_ID nr_cells perc_cells total_expr  mean_expr mean_expr_det hvg_orig #>         <char>    <int>      <num>      <num>      <num>         <num>   <char> #>     1:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     2:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     3:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     4:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     5:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>    ---                                                                          #> 79757:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 79758:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 79759:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 79760:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 79761:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #>              var    hvf  geom  part        x         y  hole global_z #>            <num> <char> <int> <num>    <num>     <num> <num>    <int> #>     1: 3.2630074    yes    52     1 6401.822 -5074.172     0        0 #>     2: 3.2630074    yes  1405     1 6434.212 -4994.575     0        0 #>     3: 3.2630074    yes  1524     1 6435.822 -4993.068     0        0 #>     4: 3.2630074    yes  1564     1 6436.190 -4993.599     0        0 #>     5: 3.2630074    yes  1568     1 6436.225 -4994.331     0        0 #>    ---                                                                #> 79757: 0.9765725     no 55606     1 6755.787 -4842.521     0        1 #> 79758: 0.9765725     no 64289     1 6788.817 -4766.861     0        1 #> 79759: 0.9765725     no 64391     1 6789.242 -4927.838     0        1 #> 79760: 0.9765725     no 65159     1 6792.122 -4894.507     0        1 #> 79761: 0.9765725     no 77586     1 6876.786 -5032.958     0        1 #>        feat_ID_uniq   feat spat_unit #>               <int> <char>    <char> #>     1:           52    rna aggregate #>     2:         1414    rna aggregate #>     3:         1534    rna aggregate #>     4:         1574    rna aggregate #>     5:         1578    rna aggregate #>    ---                               #> 79757:        56040    rna aggregate #> 79758:        64767    rna aggregate #> 79759:        64870    rna aggregate #> 79760:        65645    rna aggregate #> 79761:        78156    rna aggregate #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":null,"dir":"Reference","previous_headings":"","what":"combineFeatureOverlapData — combineFeatureOverlapData","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"combine feature data information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"","code":"combineFeatureOverlapData(   gobject,   feat_type = \"rna\",   sel_feats = NULL,   poly_info = \"cell\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"gobject giotto object feat_type feature type sel_feats selected features (default: NULL selection) poly_info polygon information name","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"data.table combined spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineFeatureOverlapData(g, poly_info = \"aggregate\") #> $rna #> Key: <feat_ID> #>        feat_ID nr_cells perc_cells total_expr  mean_expr mean_expr_det hvg_orig #>         <char>    <int>      <num>      <num>      <num>         <num>   <char> #>     1:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     2:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     3:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     4:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     5:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>    ---                                                                          #> 32067:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 32068:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 32069:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 32070:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 32071:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #>              var    hvf  geom  part        x         y  hole #>            <num> <char> <int> <num>    <num>     <num> <num> #>     1: 3.2630074    yes   327     1 6434.212 -4994.575     0 #>     2: 3.2630074    yes   372     1 6435.822 -4993.068     0 #>     3: 3.2630074    yes   387     1 6436.190 -4993.599     0 #>     4: 3.2630074    yes   389     1 6436.225 -4994.331     0 #>     5: 3.2630074    yes  3476     1 6583.026 -5109.118     0 #>    ---                                                       #> 32067: 0.9765725     no 12671     1 6835.198 -4821.361     0 #> 32068: 0.9765725     no 13128     1 6850.250 -4791.958     0 #> 32069: 0.9765725     no 15407     1 6432.064 -5016.469     0 #> 32070: 0.9765725     no 21939     1 6742.455 -4972.980     0 #> 32071: 0.9765725     no 31289     1 6876.786 -5032.958     0 #>                                        poly_ID feat_ID_uniq stack poly_info #>                                         <char>        <int> <int>    <char> #>     1: 304842190541754537761816256358565562302         1414     1 aggregate #>     2: 304842190541754537761816256358565562302         1534     1 aggregate #>     3: 304842190541754537761816256358565562302         1574     1 aggregate #>     4: 304842190541754537761816256358565562302         1578     1 aggregate #>     5: 183227745956657225549068107012033843521         8860     1 aggregate #>    ---                                                                      #> 32067: 134146760472988945324695838070256730703        30405     1 aggregate #> 32068: 248026342734562151407765229569772513183        31685     1 aggregate #> 32069:  21934936165997373583174173761929761438        37793     2 aggregate #> 32070: 293490979527928845906184572736930005899        53817     2 aggregate #> 32071: 236938169420664432126575547704304293443        78156     2 aggregate #>          feat #>        <char> #>     1:    rna #>     2:    rna #>     3:    rna #>     4:    rna #>     5:    rna #>    ---        #> 32067:    rna #> 32068:    rna #> 32069:    rna #> 32070:    rna #> 32071:    rna #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"combineMetadata — combineMetadata","title":"combineMetadata — combineMetadata","text":"function combines cell metadata spatial locations enrichment results runSpatialEnrich.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineMetadata — combineMetadata","text":"","code":"combineMetadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = \"raw\",   spat_enr_names = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineMetadata — combineMetadata","text":"gobject Giotto object spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations include spat_enr_names names spatial enrichment results include verbose verbosity","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineMetadata — combineMetadata","text":"Extended cell metadata data.table format.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineMetadata — combineMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineMetadata(g) #> Key: <cell_ID> #>                 cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                  <char>     <int>    <int>      <num>      <num>       <num> #>   1: AAAGGGATGTAGCAAG-1         1      227   35.80442   995.1491           1 #>   2: AAATGGCATGTCTTGT-1         1      283   44.63722  1123.8751           2 #>   3: AAATGGTCAATGTGCC-1         1      248   39.11672  1027.6322           4 #>   4: AAATTAACGGGTAGCT-1         1      222   35.01577   974.3766           4 #>   5: AACAACTGGTAGTTGC-1         1      313   49.36909  1174.4881           6 #>  ---                                                                         #> 620: TTGTAATCCGTACTCG-1         1      315   49.68454  1184.0178           4 #> 621: TTGTATCACACAGAAT-1         1      240   37.85489   999.6419           2 #> 622: TTGTCGTTCAGTTACC-1         1      220   34.70032   994.6648           1 #> 623: TTGTGGCCCTGACAGT-1         1      204   32.17666   930.5489           5 #> 624: TTGTTCAGTGTGCTAC-1         1      237   37.38170  1034.8893           1 #>      custom_leiden sdimx sdimy #>              <num> <int> <int> #>   1:             1  5477 -4125 #>   2:             3  5959 -2808 #>   3:             2  4720 -5202 #>   4:             2  5202 -5322 #>   5:             2  4101 -4604 #>  ---                           #> 620:             2  4996 -5442 #> 621:             3  6303 -2688 #> 622:             1  5202 -3885 #> 623:             1  5340 -3406 #> 624:             1  5615 -4125"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"Combine cell metadata spatial cell information (e.g. polygon)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"","code":"combineSpatialCellMetadataInfo(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"gobject Giotto object spat_unit spatial unit feat_type feature type(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"list data.table(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"returned data.table following columns: sdimx: spatial feature location x-axis sdimy: spatial feature location y-axis cell_ID: unique cell ID feat: selected feature(s) columns part cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineSpatialCellMetadataInfo(g, spat_unit = \"aggregate\", feat_type = \"rna\") #> $rna #> Key: <cell_ID> #>                                      cell_ID  stack agg_n valid nr_feats #>                                       <char> <char> <int> <int>    <int> #>   1: 100210519278873141813371229408401071444   <NA>     2     1       22 #>   2: 101161259912191124732236989250178928032   <NA>     2     1       36 #>   3: 101488859781016188084173008420811094152   <NA>     2     1       35 #>   4: 101523780333017320796881555775415156847   <NA>     2     1       39 #>   5: 102184699197574201819246996094734116255   <NA>     2     1       44 #>  ---                                                                     #> 458:   9677424102111816817518421117250891895   <NA>     2     1       30 #> 459:  97068595823890802071024838798130036179   <NA>     2     1       46 #> 460:  97411078642927912684859796714759494710   <NA>     2     1       33 #> 461:   9816437869021910185567097363182418837   <NA>     2     1       31 #> 462:  98561957902191275233320065611022298397   <NA>     2     1       53 #>      perc_feats total_expr leiden_clus louvain_clus   feat #>           <num>      <num>       <num>        <num> <char> #>   1:   6.528190   163.6923           4           15    rna #>   2:  10.682493   228.7269           2           10    rna #>   3:  10.385757   242.0458           1           22    rna #>   4:  11.572700   262.3842           1           24    rna #>   5:  13.056380   291.5877           2            0    rna #>  ---                                                       #> 458:   8.902077   211.7179           2            3    rna #> 459:  13.649852   279.5605           2            5    rna #> 460:   9.792285   226.7092           4           15    rna #> 461:   9.198813   220.4129           3           13    rna #> 462:  15.727003   326.0539           1           26    rna #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine giottoPolygon geometries — combineToMultiPolygon","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"Combine multiple giottoPolygon geometries set multipolygons. Note attributes kept","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"","code":"combineToMultiPolygon(x, groups, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"x giottoPolygon groups data.frame columns 'poly_ID' 'group_ID' relates polygons now combined group_ID name (optional) name giottoPolygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"","code":"gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") groups <- data.table::data.table(     poly_ID = gpoly$poly_ID,     group_ID = sort(rep(LETTERS[seq_len(5)], length.out = nrow(gpoly)))     # make 5 groups )  multi_gp <- combineToMultiPolygon(gpoly, groups)  plot(multi_gp[\"A\"])"},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Compatible spatial network — compatible_spatial_network","title":"Compatible spatial network — compatible_spatial_network","text":"Function evaluate spatial network compatible provided expression matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compatible spatial network — compatible_spatial_network","text":"","code":"compatible_spatial_network(spatial_network, expression_matrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compatible spatial network — compatible_spatial_network","text":"spatial_network spatial network evaluate expression_matrix expression compare ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compatible spatial network — compatible_spatial_network","text":"TRUE character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compatible spatial network — compatible_spatial_network","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spat_net <- getSpatialNetwork(g, output = \"networkDT\") expr_m <- getExpression(g)  compatible_spatial_network(spat_net, expr_m) #> [1] TRUE"},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":null,"dir":"Reference","previous_headings":"","what":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"Get convex hull, minimal bounding rotated rectangle, minimal bounding circle Giotto spatial object terra SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"","code":"# S4 method for class 'spatLocsObj' convHull(x, by = \"\", ...)  # S4 method for class 'giottoSpatial' convHull(x, by = \"\", ...)  # S4 method for class 'spatLocsObj' minRect(x, by = \"\", ...)  # S4 method for class 'giottoSpatial' minRect(x, by = \"\", ...)  # S4 method for class 'spatLocsObj' minCircle(x, by = \"\", ...)  # S4 method for class 'giottoSpatial' minCircle(x, by = \"\", ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"x giotto image, giottoPolygon, giottoPoints, spatLocsObj, SpatVector character (variable name), get new geometry groups input geometries ... additional parameters pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  h <- convHull(sl) plot(h)   r <- minRect(sl) plot(r)   circ <- minCircle(gpoints, by = \"feat_ID\") plot(circ, border = rainbow(100))"},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":null,"dir":"Reference","previous_headings":"","what":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"convert giottoLargeImage downsampling normal magick based giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"","code":"convertGiottoLargeImageToMG(   gobject = NULL,   largeImage_name = NULL,   giottoLargeImage = NULL,   mg_name = NULL,   spat_unit = NULL,   spat_loc_name = NULL,   crop_extent = NULL,   xmax_crop = NULL,   xmin_crop = NULL,   ymax_crop = NULL,   ymin_crop = NULL,   resample_size = 5e+05,   max_intensity = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"gobject gobject containing giottoLargeImage largeImage_name name giottoLargeImage giottoLargeImage alternative input param using giottoLargeImage object instead gobject largeImage_name params mg_name name assign converted magick image based giottoImage. Defaults name giottoLargeImage spat_unit spatial unit spat_loc_name gobject spatial location name map giottoImage (optional) crop_extent extent object focus specific region image xmax_crop assign crop boundary xmin_crop assign crop boundary ymax_crop assign crop boundary ymin_crop assign crop boundary resample_size maximum number pixels use resampling max_intensity value treat maximum intensity color scale return_gobject return giotto object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"giotto object return_gobject = TRUE updated giotto image object return_gobject = FALSE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  convertGiottoLargeImageToMG(g, largeImage_name = \"image\") #> image has already been used, will be overwritten #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":null,"dir":"Reference","previous_headings":"","what":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"converts magick image object data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"","code":"convert_mgImage_to_array_DT(mg_object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"mg_object magick image Giotto image object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"data.table image pixel information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, name = \"image\") mgimg <- as(g_image, \"giottoImage\")  a <- convert_mgImage_to_array_DT(mgimg) force(a) #> Key: <x, y> #>            x     y       c.1       c.2       c.3     4     RGB #>        <int> <int>     <num>     <num>     <num> <num>  <char> #>     1:     1     1 0.5098039 0.5215686 0.5019608     1 #828580 #>     2:     1     2 0.5098039 0.5176471 0.5019608     1 #828480 #>     3:     1     3 0.5098039 0.5176471 0.5019608     1 #828480 #>     4:     1     4 0.5098039 0.5176471 0.4980392     1 #82847F #>     5:     1     5 0.5098039 0.5176471 0.4980392     1 #82847F #>    ---                                                         #> 41792:   172   239 0.3803922 0.3058824 0.4313725     1 #614E6E #> 41793:   172   240 0.4313725 0.3372549 0.4509804     1 #6E5673 #> 41794:   172   241 0.4196078 0.3215686 0.4392157     1 #6B5270 #> 41795:   172   242 0.4470588 0.3215686 0.4549020     1 #725274 #> 41796:   172   243 0.4392157 0.2941176 0.4470588     1 #704B72 force(a) #> Key: <x, y> #>            x     y       c.1       c.2       c.3     4     RGB #>        <int> <int>     <num>     <num>     <num> <num>  <char> #>     1:     1     1 0.5098039 0.5215686 0.5019608     1 #828580 #>     2:     1     2 0.5098039 0.5176471 0.5019608     1 #828480 #>     3:     1     3 0.5098039 0.5176471 0.5019608     1 #828480 #>     4:     1     4 0.5098039 0.5176471 0.4980392     1 #82847F #>     5:     1     5 0.5098039 0.5176471 0.4980392     1 #82847F #>    ---                                                         #> 41792:   172   239 0.3803922 0.3058824 0.4313725     1 #614E6E #> 41793:   172   240 0.4313725 0.3372549 0.4509804     1 #6E5673 #> 41794:   172   241 0.4196078 0.3215686 0.4392157     1 #6B5270 #> 41795:   172   242 0.4470588 0.3215686 0.4549020     1 #725274 #> 41796:   172   243 0.4392157 0.2941176 0.4470588     1 #704B72"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":null,"dir":"Reference","previous_headings":"","what":"convert_to_full_spatial_network — convert_to_full_spatial_network","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"Convert full spatial network, ie ensuring edges may currently represented \\(\\) -> \\(b\\) also reverse \\(b\\) -> \\(\\). entries made unique, interactions ranked distance, rank increases smaller larger distances. rank appended data.table rank_int column. Another rnk_src_trgt column added IDs \\(\\) \\(b\\) pasted together","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"","code":"convert_to_full_spatial_network(reduced_spatial_network_DT)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"reduced_spatial_network_DT reduced spatial network data.table format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spat_net <- getSpatialNetwork(g, output = \"networkDT\")  spat_net_full <- convert_to_full_spatial_network(spat_net)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":null,"dir":"Reference","previous_headings":"","what":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"Convert reduced spatial network. Specifically, removes duplicated connections \\(\\) -> \\(b\\) interactions remain.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"","code":"convert_to_reduced_spatial_network(full_spatial_network_DT)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"full_spatial_network_DT full spatial network data.table format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spat_net <- getSpatialNetwork(g, output = \"networkDT\") spat_net_full <- convert_to_full_spatial_network(spat_net)  convert_to_reduced_spatial_network(spat_net_full) #>                     from                 to sdimx_begin sdimy_begin sdimx_end #>                   <char>             <char>       <num>       <num>     <num> #>    1: AAAGGGATGTAGCAAG-1 TCAAACAACCGCGTCG-1        5477       -4125      5340 #>    2: AAAGGGATGTAGCAAG-1 ACGATCATACATAGAG-1        5477       -4125      5546 #>    3: AAAGGGATGTAGCAAG-1 TATGCTCCCTACTTAC-1        5477       -4125      5408 #>    4: AAAGGGATGTAGCAAG-1 TTGTTCAGTGTGCTAC-1        5477       -4125      5615 #>    5: AAAGGGATGTAGCAAG-1 ATCGACTCTTTCCGTT-1        5477       -4125      5408 #>   ---                                                                         #> 1766: TTCAAGCCGAGCTGAG-1 TTGTATCACACAGAAT-1        6372       -2808      6303 #> 1767: TTCGACGGGAAGGGCG-1 TTCGCACTCGCGTGCT-1        4239       -4125      4308 #> 1768: TTCTTAGTGGCTCAGA-1 TTGTGGCCCTGACAGT-1        5408       -3287      5340 #> 1769: TTCTTGTAACCTAATG-1 TTGGCTCGCATGAGAC-1        3620       -4005      3757 #> 1770: TTGCACGGAGCAGCAC-1 TTGTCGTTCAGTTACC-1        5271       -3766      5202 #>       sdimy_end distance      weight #>           <num>    <num>       <num> #>    1:     -4125 137.0000 0.007299270 #>    2:     -4244 137.5573 0.007269700 #>    3:     -4244 137.5573 0.007269700 #>    4:     -4125 138.0000 0.007246377 #>    5:     -4005 138.4233 0.007224219 #>   ---                                #> 1766:     -2688 138.4233 0.007224219 #> 1767:     -4245 138.4233 0.007224219 #> 1768:     -3406 137.0584 0.007296161 #> 1769:     -4005 137.0000 0.007299270 #> 1770:     -3885 137.5573 0.007269700"},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy an entire object — copy","title":"Copy an entire object — copy","text":"S4 generic Giotto's S4 subobjects return full copies certain subobjects usually return referenced information.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy an entire object — copy","text":"","code":"# S4 method for class 'coordDataDT' copy(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy an entire object — copy","text":"x Giotto S4 class subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy an entire object — copy","text":"giotto subobjects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Copy an entire object — copy","text":"copy(coordDataDT): Copy data.table-based spatial locations object.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Copy an entire object — copy","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  copy(g) #> An object of class exprObj : \"normalized\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                                                                           #> Mlc1    .       .        .        .        . .  5.291601 . .        5.821597 . .        . #> Gprc5b  .       6.398031 .        7.454658 . .  6.273066 . 7.680054 6.808785 . 5.082989 . #> Gfap   10.48137 .        7.901442 5.886051 . . 10.746982 . 5.701006 5.821597 . .        . #>               #> Mlc1   ...... #> Gprc5b ...... #> Gfap   ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"cor_flex — cor_flex","title":"cor_flex — cor_flex","text":"cor_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cor_flex — cor_flex","text":"","code":"cor_flex(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"cor_flex — cor_flex","text":"x data use ... arguments passed stats::cor()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"cor_flex — cor_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"cor_flex — cor_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  cor_flex(m) #>              [,1]        [,2]       [,3]        [,4]        [,5]        [,6] #>  [1,]  1.00000000  0.16620711 -0.8131547  0.61575948 -0.33493205 -0.11683719 #>  [2,]  0.16620711  1.00000000 -0.1017779 -0.28227526 -0.12280489 -0.69807239 #>  [3,] -0.81315474 -0.10177789  1.0000000 -0.37518400  0.16724480  0.24837238 #>  [4,]  0.61575948 -0.28227526 -0.3751840  1.00000000 -0.30441692 -0.08505474 #>  [5,] -0.33493205 -0.12280489  0.1672448 -0.30441692  1.00000000  0.31606004 #>  [6,] -0.11683719 -0.69807239  0.2483724 -0.08505474  0.31606004  1.00000000 #>  [7,] -0.25438824  0.06612684  0.1753142 -0.36953253 -0.29526718  0.10431025 #>  [8,] -0.06386097  0.22412738  0.4751030  0.16334164 -0.02844134  0.06738725 #>  [9,]  0.36653910 -0.50689849 -0.1461906  0.65778248 -0.27050220  0.32750529 #> [10,]  0.11525415 -0.32583704 -0.1610563 -0.13885239 -0.48178336  0.43514813 #>              [,7]        [,8]        [,9]       [,10] #>  [1,] -0.25438824 -0.06386097  0.36653910  0.11525415 #>  [2,]  0.06612684  0.22412738 -0.50689849 -0.32583704 #>  [3,]  0.17531418  0.47510298 -0.14619059 -0.16105627 #>  [4,] -0.36953253  0.16334164  0.65778248 -0.13885239 #>  [5,] -0.29526718 -0.02844134 -0.27050220 -0.48178336 #>  [6,]  0.10431025  0.06738725  0.32750529  0.43514813 #>  [7,]  1.00000000 -0.09626645 -0.45177865  0.69848177 #>  [8,] -0.09626645  1.00000000  0.27557036 -0.31735424 #>  [9,] -0.45177865  0.27557036  1.00000000  0.07936429 #> [10,]  0.69848177 -0.31735424  0.07936429  1.00000000"},{"path":"https://drieslab.github.io/GiottoClass/reference/createBentoAdata.html","id":null,"dir":"Reference","previous_headings":"","what":"Create bento adata object from gobject — createBentoAdata","title":"Create bento adata object from gobject — createBentoAdata","text":"Create bento adata object gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createBentoAdata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create bento adata object from gobject — createBentoAdata","text":"","code":"createBentoAdata(gobject = NULL, env_to_use = \"giotto_env\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/createBentoAdata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create bento adata object from gobject — createBentoAdata","text":"gobject Giotto object env_to_use Python environment within bento installed. already installed, user prompted install bento-tools DEFAULT: \"giotto_env\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createBentoAdata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create bento adata object from gobject — createBentoAdata","text":"bento_adata bento adata object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 cellMetaObj — createCellMetaObj","title":"Create S4 cellMetaObj — createCellMetaObj","text":"Create S4 cellMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 cellMetaObj — createCellMetaObj","text":"","code":"createCellMetaObj(   metadata,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   col_desc = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 cellMetaObj — createCellMetaObj","text":"metadata metadata info spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') provenance origin data aggregated expression information (applicable) col_desc (optional) character vector describing columns metadata verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 cellMetaObj — createCellMetaObj","text":"cellMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 cellMetaObj — createCellMetaObj","text":"","code":"df <- data.frame(cell_ID = c(\"cell_1\", \"cell_2\", \"cell_3\"))  createCellMetaObj(metadata = df) #> An object of class cellMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #> dimensions: 3 1  #>  #>    cell_ID #>     <char> #> 1:  cell_1 #> 2:  cell_2 #> 3:  cell_3"},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 dimObj — createDimObj","title":"Create S4 dimObj — createDimObj","text":"Create S4 dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 dimObj — createDimObj","text":"","code":"createDimObj(   coordinates,   name = \"test\",   spat_unit = \"cell\",   feat_type = \"rna\",   method = NULL,   reduction = \"cells\",   provenance = NULL,   misc = NULL,   my_rownames = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 dimObj — createDimObj","text":"coordinates embedding coordinates name name dimObj spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') method method used generate dimension reduction reduction reduction columns (e.g. cells) rows (e.g. features) provenance origin data aggregated expression information (applicable) misc misc my_rownames (optional) needed, set coordinates rowname values ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 dimObj — createDimObj","text":"dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 dimObj — createDimObj","text":"","code":"x <- matrix(c(2.81, 5.59, 10.54, 2.25, 5.12, 2.79), nrow = 3) rownames(x) <- c(\"cell_1\", \"cell_2\", \"cell_3\") colnames(x) <- c(\"Dim.1\", \"Dim.2\")  createDimObj(coordinates = x, name = \"pca\", method = \"pca\") #> An object of class dimObj : \"pca\" #> --| Contains dimension reduction generated with: pca  #> ----| for feat_type: rna  #> ----|     spat_unit: cell  #>  #>    2 dimensions for 3 data points #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 exprObj — createExprObj","title":"Create S4 exprObj — createExprObj","text":"Create S4 exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 exprObj — createExprObj","text":"","code":"createExprObj(   expression_data,   name = \"test\",   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL,   expression_matrix_class = c(\"dgCMatrix\", \"DelayedArray\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 exprObj — createExprObj","text":"expression_data expression data name name exprObj spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance origin data expression information (applicable) misc misc expression_matrix_class class expression matrix use (e.g. 'dgCMatrix', 'DelayedArray')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 exprObj — createExprObj","text":"exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 exprObj — createExprObj","text":"","code":"x_expr <- readRDS(system.file(\"extdata/toy_matrix.RDS\",     package = \"GiottoClass\" ))  createExprObj(expression_data = x_expr) #> An object of class exprObj : \"test\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #>  #> contains: #> 10 x 10 sparse Matrix of class \"dgCMatrix\" #>                       #> a . . . . . . . . . . #> b . . . . 1 . . . . . #> c . . . . . . 1 . . . #> d . . . . . . . . . 1 #>  #>  ........suppressing 2 rows in show(); maybe adjust options(max.print=, width=) #>                       #> g 1 . . . . . . . . . #> h 1 . . . . . . . . 1 #> i . . . . . . . . . . #> j . . . 1 . 1 . . . . #>  #>  First four colnames: #>  A B C D"},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 featMetaObj — createFeatMetaObj","title":"Create S4 featMetaObj — createFeatMetaObj","text":"Create S4 featMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 featMetaObj — createFeatMetaObj","text":"","code":"createFeatMetaObj(   metadata,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   col_desc = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 featMetaObj — createFeatMetaObj","text":"metadata metadata info spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') provenance origin data aggregated expression information (applicable) col_desc (optional) character vector describing columns metadata verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 featMetaObj — createFeatMetaObj","text":"featMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 featMetaObj — createFeatMetaObj","text":"","code":"x <- data.frame(     feat_ID = c(\"Mlc1\", \"Gprc5b\", \"Gfap\"),     nr_cells = c(80, 138, 151) )  createFeatMetaObj(metadata = x) #> An object of class featMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #>  #>    feat_ID nr_cells #>     <char>    <num> #> 1:    Mlc1       80 #> 2:  Gprc5b      138 #> 3:    Gfap      151"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"createGiottoImage — createGiottoImage","title":"createGiottoImage — createGiottoImage","text":"Creates giotto image can added Giotto object /used add image spatial plotting functions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createGiottoImage — createGiottoImage","text":"","code":"createGiottoImage(   gobject = NULL,   spat_unit = NULL,   spatial_locs = NULL,   spat_loc_name = NULL,   mg_object,   name = \"image\",   image_transformations = NULL,   negative_y = TRUE,   do_manual_adj = FALSE,   xmax_adj = 0,   xmin_adj = 0,   ymax_adj = 0,   ymin_adj = 0,   scale_factor = 1,   x_shift = NULL,   y_shift = NULL,   scale_x = NULL,   scale_y = NULL,   order = c(\"first_scale\", \"first_adj\"),   xmin_set = NULL,   xmax_set = NULL,   ymin_set = NULL,   ymax_set = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createGiottoImage — createGiottoImage","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") spatial_locs spatial locations (alternative gobject = NULL) spat_loc_name name spatial locations within gobject mg_object magick image object name name image image_transformations vector sequential image transformations negative_y Map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left. do_manual_adj (default = FALSE) flag use manual adj values instead automatic alignment given gobject spatlocs xmax_adj, xmin_adj, ymax_adj, ymin_adj adjustment maximum maximum x y-value align image scale_factor scaling image dimensions relative spatial coordinates x_shift, y_shift shift image along x y axes scale_x, scale_y independently scale image x y direction order perform scaling adjustments shifts first xmin_set, xmax_set, ymin_set, ymax_set values override image minmax spatial anchors adjustments verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createGiottoImage — createGiottoImage","text":"giottoImage object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createGiottoImage — createGiottoImage","text":"image_transformations: transformation options magick library [flip_x_axis] flip x-axis (image_flop) [flip_y_axis] flip y-axis (image_flip) Example: image_transformations = c(flip_x_axis, flip_y_axis); first flip x-axis y-axis","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createGiottoImage — createGiottoImage","text":"","code":"image_test <- system.file(\"extdata/toy_intensity.tif\",     package = \"GiottoClass\" )  createGiottoImage(mg_object = image_test) #> Warning: gobject or spatial locations are not provided  #> Arbitrary values will be given  #> An object of class ' giottoImage ' with name  image  #>   #> Min and max values are:  #>  Max on x-axis:  10  #>  Min on x-axis:  0  #>  Max on y-axis:  10  #>  Min on y-axis:  0  #>   #> Boundary adjustment are:  #>  Max adjustment on x-axis:  0  #>  Min adjustment on x-axis:  0  #>  Max adjustment on y-axis:  0  #>  Min adjustment on y-axis:  0  #>   #> Boundaries are:  #>  Image x-axis max boundary:  10  #>  Image x-axis min boundary:  0  #>  Image y-axis max boundary:  10  #>  Image y-axis min boundary:  0  #>   #> Scale factor:  #> x y  #> 1 1  #>  #>  Resolution:  #> x y  #> 1 1  #>  #>  File Path:  #> [1] \"/home/runner/work/_temp/Library/GiottoClass/extdata/toy_intensity.tif\""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"createGiottoLargeImage — createGiottoLargeImage","title":"createGiottoLargeImage — createGiottoLargeImage","text":"Creates large giotto image can added Giotto subcellular object. Generates deep copy SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createGiottoLargeImage — createGiottoLargeImage","text":"","code":"createGiottoLargeImage(   raster_object,   name = \"image\",   negative_y = TRUE,   extent = NULL,   use_rast_ext = FALSE,   image_transformations = NULL,   flip_vertical = FALSE,   flip_horizontal = FALSE,   xmax_bound = NULL,   xmin_bound = NULL,   ymax_bound = NULL,   ymin_bound = NULL,   scale_factor = 1,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createGiottoLargeImage — createGiottoLargeImage","text":"raster_object filepath image, terra SpatRaster , format openable via terra::rast() name name image negative_y Map image negative y spatial values TRUE. Meaning origin upper left instead lower left. extent SpatExtent object assign spatial extent. Takes priority unless use_rast_ext TRUE. use_rast_ext Use extent input raster object image_transformations vector sequential image transformations - construction flip_vertical flip raster vertical manner flip_horizontal flip raster horizontal manner xmax_bound, xmin_bound, ymax_bound, ymin_bound assign min max x y values image spatial placement scale_factor scaling image dimensions relative spatial coordinates verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createGiottoLargeImage — createGiottoLargeImage","text":"giottoLargeImage object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createGiottoLargeImage — createGiottoLargeImage","text":"","code":"image_test <- system.file(\"extdata/toy_intensity.tif\",     package = \"GiottoClass\" )  createGiottoLargeImage(raster_object = image_test) #> An object of class giottoLargeImage : \"image\" #> Image extent            : 0, 1091, -1107, 0 (xmin, xmax, ymin, ymax) #> Original image extent   : 0, 1091, -1107, 0 (xmin, xmax, ymin, ymax) #> Scale factor            : 1, 1 (x, y) #> Resolution              : 1, 1 (x, y) #> Layers                  : 1  #> Estimated max intensity : 168  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoClass/extdata/toy_intensity.tif'"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":null,"dir":"Reference","previous_headings":"","what":"createGiottoLargeImageList — createGiottoLargeImageList","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"Creates list large giotto images can added Giotto object. Generates deep copy SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"","code":"createGiottoLargeImageList(   raster_objects,   names = \"image\",   negative_y = TRUE,   extent = NULL,   use_rast_ext = FALSE,   image_transformations = NULL,   flip_vertical = FALSE,   flip_horizontal = FALSE,   xmax_bound = NULL,   xmin_bound = NULL,   ymax_bound = NULL,   ymin_bound = NULL,   scale_factor = 1,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"raster_objects vector image paths terra SpatRaster image objects names vector names images negative_y Map image negative y spatial values TRUE. Meaning origin upper left instead lower left. extent SpatExtent object assign spatial extent. Takes priority unless use_rast_ext TRUE. use_rast_ext Use extent input raster object image_transformations vector sequential image transformations - construction flip_vertical flip raster vertical manner flip_horizontal flip raster horizontal manner xmax_bound, xmin_bound, ymax_bound, ymin_bound assign min max x y values image spatial placement scale_factor scaling image dimensions relative spatial coordinates verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"list giottoLargeImage objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"See createGiottoLargeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"","code":"image_test <- system.file(\"extdata/toy_intensity.tif\",     package = \"GiottoClass\" )  createGiottoLargeImageList(raster_objects = image_test) #> [[1]] #> An object of class giottoLargeImage : \"image\" #> Image extent            : 0, 1091, -1107, 0 (xmin, xmax, ymin, ymax) #> Original image extent   : 0, 1091, -1107, 0 (xmin, xmax, ymin, ymax) #> Scale factor            : 1, 1 (x, y) #> Resolution              : 1, 1 (x, y) #> Layers                  : 1  #> Estimated max intensity : 168  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoClass/extdata/toy_intensity.tif' #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a giotto object — createGiottoObject","title":"Create a giotto object — createGiottoObject","text":"Function create giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a giotto object — createGiottoObject","text":"","code":"createGiottoObject(   expression,   expression_feat = \"rna\",   spatial_locs = NULL,   spatial_info = NULL,   calc_poly_centroids = FALSE,   centroids_to_spatlocs = FALSE,   feat_info = NULL,   cell_metadata = NULL,   feat_metadata = NULL,   spatial_network = NULL,   spatial_grid = NULL,   spatial_grid_name = NULL,   spatial_enrichment = NULL,   dimension_reduction = NULL,   nn_network = NULL,   images = NULL,   largeImages = NULL,   offset_file = NULL,   instructions = NULL,   cores = determine_cores(),   raw_exprs = NULL,   expression_matrix_class = c(\"dgCMatrix\", \"DelayedArray\"),   h5_file = NULL,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a giotto object — createGiottoObject","text":"expression expression information expression_feat available features (e.g. rna, protein, ...) spatial_locs data.table data.frame coordinates cell centroids spatial_info list giotto polygon objects spatial information, see createGiottoPolygonsFromMask createGiottoPolygonsFromDfr calc_poly_centroids spatial_info provided, whether also calculate centroids centroids_to_spatlocs spatial_info provided, whether also convert centroids spatial locations feat_info list giotto point objects feature info, see createGiottoPoints cell_metadata cell annotation metadata feat_metadata feature annotation metadata unique feature spatial_network list spatial network(s) spatial_grid list spatial grid(s) spatial_grid_name list spatial grid name(s) spatial_enrichment list spatial enrichment score(s) spatial region dimension_reduction list dimension reduction(s) nn_network list nearest neighbor network(s) images list images largeImages deprecated offset_file file used stitch fields together (optional) instructions list instructions output result createGiottoInstructions cores many cores threads use read data paths provided raw_exprs deprecated, use expression expression_matrix_class class expression matrix use (e.g. 'dgCMatrix', 'DelayedArray') h5_file path h5 file verbose verbose building Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a giotto object — createGiottoObject","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a giotto object — createGiottoObject","text":"See http://giottosuite.com/articles/getting_started_gobject.html details [Requirements] create giotto object need provide least matrix genes row names cells column names. matrix can provided base matrix, sparse Matrix, data.frame, data.table path . include spatial information cells (regions) need provide matrix, data.table data.frame (path ) coordinates spatial dimensions. can 2D (x y) 3D (x, y, x). row order cell coordinates column order provided expression data. [Instructions] Additionally instruction file, generated manually createGiottoInstructions can provided instructions, default instruction file created Giotto object. [Multiple fields] case dataset consists multiple fields, like seqFISH+ example, offset file can provided stitch different fields together. stitchFieldCoordinates can used generate offset file. [Processed data] Processed count data, normalized data, can provided using one different expression slots (norm_expr, norm_scaled_expr, custom_expr). [Metadata] Cell gene metadata can provided using cell gene metadata slots. data can also added afterwards using addFeatMetadata addCellMetadata functions. [information] Additional information can provided appropriate slots: spatial networks spatial grids spatial enrichments dimensions reduction nearest neighbours networks images","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a giotto object — createGiottoObject","text":"","code":"expr_matrix <- readRDS(system.file(\"extdata/toy_matrix.RDS\",     package = \"GiottoClass\" ))  createGiottoObject(expression = expr_matrix) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 10, 10 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw #> spatial locations ---------------- #>   [cell] raw #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"Function create giotto object starting subcellular polygon (e.g. cell) points (e.g. transcripts) information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"","code":"createGiottoObjectSubcellular(   gpolygons = NULL,   polygon_mask_list_params = NULL,   polygon_dfr_list_params = NULL,   gpoints = NULL,   cell_metadata = NULL,   feat_metadata = NULL,   spatial_network = NULL,   spatial_network_name = NULL,   spatial_grid = NULL,   spatial_grid_name = NULL,   spatial_enrichment = NULL,   spatial_enrichment_name = NULL,   dimension_reduction = NULL,   nn_network = NULL,   images = NULL,   largeImages = NULL,   largeImages_list_params = NULL,   instructions = NULL,   cores = NA,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"gpolygons giotto polygons polygon_mask_list_params list parameters createGiottoPolygonsFromMask polygon_dfr_list_params list parameters createGiottoPolygonsFromDfr gpoints giotto points cell_metadata cell annotation metadata feat_metadata feature annotation metadata unique feature spatial_network list spatial network(s) spatial_network_name list spatial network name(s) spatial_grid list spatial grid(s) spatial_grid_name list spatial grid name(s) spatial_enrichment list spatial enrichment score(s) spatial region spatial_enrichment_name list spatial enrichment name(s) dimension_reduction list dimension reduction(s) nn_network list nearest neighbor network(s) images list images largeImages deprecated largeImages_list_params image params loading largeImages list instructions list instructions output result createGiottoInstructions cores many cores threads use read data paths provided verbose verbose building Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"two different ways create Giotto Object subcellular information: Starting polygons (spatial units e.g. cell) represented mask dataframe file giotto points (analyte coordinates e.g. transcripts) Starting polygons (spatial units e.g. cell) represented mask dataframe file raw intensity images (e.g. protein stains)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"","code":"x_gpolygons <- GiottoData::loadSubObjectMini(\"giottoPolygon\") x_gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  createGiottoObjectSubcellular(     gpolygons = x_gpolygons,     gpoints = x_gpoints ) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> polygonlist is not a list #> [ cell ] Process polygon info... #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> Setting spatial locations [aggregate] raw #> pointslist is not a list #> [ rna ] Process point info... #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> An object of class giotto  #> [SUBCELLULAR INFO] #> polygons      : aggregate  #> features      : rna  #> [AGGREGATE INFO] #> spatial locations ---------------- #>   [aggregate] raw #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Create giotto points object — createGiottoPoints","title":"Create giotto points object — createGiottoPoints","text":"Create giottoPoints object used represent subcellular point-type features. main values contained within spatVector slot, contain spatial point data also associated set attributes least feat_ID (name feature described) feat_ID_uniq (unique integer identifier specific point).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create giotto points object — createGiottoPoints","text":"","code":"# S4 method for class 'SpatVector' createGiottoPoints(   x,   feat_type = \"rna\",   verbose = TRUE,   split_keyword = NULL,   unique_IDs = NULL )  # S4 method for class 'data.frame' createGiottoPoints(   x,   x_colname = NULL,   y_colname = NULL,   feat_ID_colname = NULL,   feat_type = \"rna\",   verbose = TRUE,   split_keyword = NULL,   unique_IDs = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create giotto points object — createGiottoPoints","text":"x spatVector data.frame-like object points coordinate information (x, y, feat_ID) feat_type character. feature type. Provide one value using split_keyword param. set keywords split , additional feat_type provided order. verbose verbose split_keyword list character vectors keywords split giottoPoints object based feat_ID. Keywords grepl() matched feature IDs information. unique_IDs (optional) character vector unique IDs present within spatVector data. Provided cacheing purposes x_colname column name x-coordinates y_colname column name y-coordinates feat_ID_colname column name feature ids","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create giotto points object — createGiottoPoints","text":"giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create giotto points object — createGiottoPoints","text":"Using manual option can select names x, y, feat_ID columns compatible data.frame already names x, y, /feat_ID.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create giotto points object — createGiottoPoints","text":"","code":"# data.frame input x <- data.frame(     ID = letters[seq_len(6)],     x = seq_len(6),     y = seq(6, 1) ) gpoints <- createGiottoPoints(x) #>   Selecting col \"ID\" as feat_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(gpoints,     raster = FALSE, # don't plot with rasterization or it will be hard to see     cex = 0.5 )   # with a split_keyword # Use this when values to read in contain multiple sets of information that # should be put into separate objects. gp_list <- createGiottoPoints(x,     feat_type = c(\"feat_a\", \"feat_b\"),     split_keyword = list(c(\"b\", \"c\")) ) #>   Selecting col \"ID\" as feat_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively force(gp_list) #> $feat_a #> An object of class giottoPoints #> feat_type : \"feat_a\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 4, 2  (geometries, attributes) #>  extent      : 1, 6, 1, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      d            4 #>                      e            5 #>  #>  #> $feat_b #> An object of class giottoPoints #> feat_type : \"feat_b\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 2, 2  (geometries, attributes) #>  extent      : 2, 3, 4, 5  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       b            2 #>                      c            3 #>  #>   # subsetting gpoints[c(1, 3)] # numerical #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 2, 2  (geometries, attributes) #>  extent      : 1, 3, 4, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      c            3 #>  gpoints[c(TRUE, FALSE, FALSE)] # logical #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 2, 2  (geometries, attributes) #>  extent      : 1, 4, 3, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      d            4 #>  gpoints[c(\"a\", \"f\")] # character subsetting is keyed on feat_ID attribute #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 2, 2  (geometries, attributes) #>  extent      : 1, 6, 1, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      f            6 #>  gpoints[] # drop to SpatVector #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 6, 2  (geometries, attributes) #>  extent      : 1, 6, 1, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      b            2 #>                      c            3"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Create giotto polygons object — createGiottoPolygon","title":"Create giotto polygons object — createGiottoPolygon","text":"Create giottoPolygon object used represent spatial annotations polygons. Inputs can structured data.frame object three columns correspond x/y vertices polygon ID additional columns set attributes, spatial file wkt, .shp, .GeoJSON, mask file (e.g. segmentation results).  character method file reading dispatch specific methods based kind data file .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create giotto polygons object — createGiottoPolygon","text":"","code":"# S4 method for class 'character' createGiottoPolygon(x, ...)  # S4 method for class 'SpatVector' createGiottoPolygon(x, name = \"cell\", calc_centroids = FALSE, verbose = TRUE)  # S4 method for class 'SpatRaster' createGiottoPolygon(   x,   name = \"cell\",   mask_method = c(\"guess\", \"single\", \"multiple\"),   remove_background_polygon = FALSE,   background_algo = c(\"range\"),   fill_holes = TRUE,   poly_IDs = NULL,   ID_fmt = \"cell_\",   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   remove_unvalid_polygons = TRUE,   calc_centroids = FALSE,   verbose = TRUE )  # S4 method for class 'data.frame' createGiottoPolygon(   x,   name = \"cell\",   calc_centroids = FALSE,   skip_eval_dfr = FALSE,   copy_dt = TRUE,   verbose = TRUE )  createGiottoPolygonsFromMask(   maskfile,   mask_method = c(\"guess\", \"single\", \"multiple\"),   name = \"cell\",   remove_background_polygon = FALSE,   background_algo = c(\"range\"),   fill_holes = TRUE,   poly_IDs = NULL,   ID_fmt = \"cell_\",   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   calc_centroids = FALSE,   remove_unvalid_polygons = TRUE,   verbose = FALSE )  createGiottoPolygonsFromDfr(   segmdfr,   name = \"cell\",   calc_centroids = FALSE,   verbose = TRUE,   skip_eval_dfr = FALSE,   copy_dt = TRUE )  createGiottoPolygonsFromGeoJSON(   GeoJSON,   name = \"cell\",   calc_centroids = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create giotto polygons object — createGiottoPolygon","text":"x input. Filepath .GeoJSON mask image file. Can also data.frame vertex 'x', 'y', 'poly_ID' information. ... additional params pass. character method, params pass SpatRaster SpatVector methods, depending whether x filepath maskfile spatial file (ex: wkt, shp, GeoJSON) respectively. name name giottoPolygon object created calc_centroids (default FALSE) calculate centroids polygons verbose verbose mask_method mask file defines individual segmentation annotations. See mask_method section remove_background_polygon try remove background polygon (default: FALSE) background_algo algorithm remove background polygon fill_holes fill holes within created polygons poly_IDs character vector. Default = NULL. Custom unique names polygon mask file. ID_fmt character. applied poly_IDs = NULL. Naming scheme poly_IDs. Default = \"cell_\". See ID_fmt section. flip_vertical flip mask figure vertical manner shift_vertical_step shift vertical (boolean numerical) flip_horizontal flip mask figure horizontal manner shift_horizontal_step shift horizontal (boolean numerical) remove_unvalid_polygons remove unvalid polygons (default: TRUE) skip_eval_dfr (default FALSE) skip evaluation provided dataframe copy_dt (default TRUE) segmdfr provided dt, determines whether copy made maskfile path mask file, terra SpatRaster, data class readable terra::rast() segmdfr data.frame-like object polygon coordinate information (x, y, poly_ID) x y vertex information polygon referenced poly_ID. See details columns selected coordinate ID information. GeoJSON path .GeoJSON file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create giotto polygons object — createGiottoPolygon","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create giotto polygons object — createGiottoPolygon","text":"determining column within tabular data intended provide polygon information, Giotto first checks column names 'x', 'y', 'poly_ID'. discovered, directly selected. discovered Giotto checks data type columns selects first 'character' type column 'poly_ID' first two 'numeric' columns 'x' 'y' respectively. also unsuccessful poly_ID defaults 3rd column. 'x' 'y' default 1st 2nd columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"mask-method","dir":"Reference","previous_headings":"","what":"mask_method","title":"Create giotto polygons object — createGiottoPolygon","text":"One \"single\", \"multiple\", \"guess\". \"single\" assumes provided mask image binary, polygon vs background distinct values. kind image, expected generated polygons single multipart polygon. \"single\" takes multipart polygon breaks apart individual singlepart polygons. initial simple numeric index 'nth' polygon found mask image applied ID (see ID_fmt section). \"multiple\" assumes provided mask image distinct intensity values specify IDs individual polygons. initial numeric ID applied intensity value pixels made annotation polygon mask image (see ID_fmt section). \"guess\" examines values image pick likely appropriate method \"single\" \"multiple\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"id-fmt","dir":"Reference","previous_headings":"","what":"ID_fmt","title":"Create giotto polygons object — createGiottoPolygon","text":"Defaults applying input prefix (using paste0()) numerical ID values detected  mask_method. (ie: ID_fmt = \"cell_\" produces cell_1, cell_2, cell_3, ...) \"%\" character detected input input treated sprintf() fmt param input instead. (ie: ID_fmt = \"cell_%03d\" produces cell_001, cell_002, cell_003, ...)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create giotto polygons object — createGiottoPolygon","text":"","code":"# ------- create from a mask image ------- # m <- system.file(\"extdata/toy_mask_multi.tif\", package = \"GiottoClass\") plot(terra::rast(m), col = grDevices::hcl.colors(7))  gp <- createGiottoPolygon(     m,     flip_vertical = FALSE, flip_horizontal = FALSE,     shift_horizontal_step = FALSE, shift_vertical_step = FALSE,     ID_fmt = \"id_test_%03d\",     name = \"test\" ) plot(gp, col = grDevices::hcl.colors(7))   # ------- create from an shp file ------- # shp <- system.file(\"extdata/toy_poly.shp\", package = \"GiottoClass\") # vector inputs do not have params for flipping and shifting gp2 <- createGiottoPolygon(shp, name = \"test\") #> Selecting attribute \"poly_ID\" as poly_ID plot(gp2, col = grDevices::hcl.colors(7))   # ------- create from data.frame-like ------- # shp <- system.file(\"extdata/toy_poly.shp\", package = \"GiottoClass\") gpoly <- createGiottoPolygon(shp, name = \"test\") #> Selecting attribute \"poly_ID\" as poly_ID plot(gpoly)  gpoly_dt <- data.table::as.data.table(gpoly, geom = \"XY\") needed_cols_dt <- gpoly_dt[, .(geom, part, x, y, hole, poly_ID)] force(needed_cols_dt) #> Key: <geom> #>       geom  part        x        y  hole poly_ID #>      <int> <num>    <num>    <num> <num>  <char> #>   1:     1     1 7.000000 5.000000     0       a #>   2:     1     1 7.000000 5.000000     0       a #>   3:     1     1 6.937166 4.502620     0       a #>   4:     1     1 6.752613 4.036493     0       a #>   5:     1     1 6.457937 3.630906     0       a #>  ---                                             #> 183:     7     1 7.071654 9.688656     0       g #> 184:     7     1 7.457937 9.369094     0       g #> 185:     7     1 7.752613 8.963507     0       g #> 186:     7     1 7.937166 8.497380     0       g #> 187:     7     1 8.000000 8.000000     0       g  out <- createGiottoPolygon(needed_cols_dt,     name = \"test\" ) #>   Selecting col \"poly_ID\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(out)  mask_multi <- system.file(\"extdata/toy_mask_multi.tif\",     package = \"GiottoClass\" ) mask_single <- system.file(\"extdata/toy_mask_single.tif\",     package = \"GiottoClass\" ) plot(terra::rast(mask_multi), col = grDevices::hcl.colors(7))  plot(terra::rast(mask_single))   gpoly1 <- createGiottoPolygonsFromMask(     mask_multi,     flip_vertical = FALSE, flip_horizontal = FALSE,     shift_horizontal_step = FALSE, shift_vertical_step = FALSE,     ID_fmt = \"id_test_%03d\",     name = \"multi_test\" ) plot(gpoly1, col = grDevices::hcl.colors(7))   gpoly2 <- createGiottoPolygonsFromMask(     mask_single,     flip_vertical = FALSE, flip_horizontal = FALSE,     shift_horizontal_step = FALSE, shift_vertical_step = FALSE,     ID_fmt = \"id_test_%03d\",     name = \"single_test\" ) #>   Selecting col \"part\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(gpoly2, col = grDevices::hcl.colors(5))"},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":null,"dir":"Reference","previous_headings":"","what":"createMetafeats — createMetafeats","title":"createMetafeats — createMetafeats","text":"function creates average metafeat/metagene/module clusters.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createMetafeats — createMetafeats","text":"","code":"createMetafeats(   gobject,   spat_unit = NULL,   feat_type = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   feat_clusters,   stat = c(\"mean\", \"sum\", \"max\", \"min\"),   rescale_to = NULL,   name = paste0(\"metafeat_\", ifelse(is.function(stat), \"custom\", stat)),   return_gobject = TRUE,   verbose = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createMetafeats — createMetafeats","text":"gobject Giotto object spat_unit spatial unit feat_type feature type expression_values expression values use feat_clusters numerical vector features names stat statistical transformation calculate across cluster features per cell get metafeature value. Provided defaults \"mean\", 'sum', \"max\", \"min\". function  supplied instead, run via apply(MARGIN = 2) across expression matrix calculate  metafeature value. rescale_to numeric vector length 2. (optional) New maximum minimum rescale features calculating metafeature score using stat. Values first zeroed setting minimum value 0, rescaled. cases values across feature, rescale produces middle point range specified rescale_to name name metagene results return_gobject return giotto object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createMetafeats — createMetafeats","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createMetafeats — createMetafeats","text":"example 'gene_clusters' like : cluster_vector = c(1, 1, 2, 2) names(cluster_vector) = c('geneA', 'geneB', 'geneC', 'geneD')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createMetafeats — createMetafeats","text":"","code":"# load a dataset g <- GiottoData::loadGiottoMini(\"viz\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" # set a spat unit to use activeSpatUnit(g) <- \"aggregate\"  # define the metafeats # We do this by making a set of annotations. These annotations can be # made as either a vector or data.frame  # 1.1 annotation vector (numeric) feats_to_use <- featIDs(g)[seq_len(6)] clust_to_use1 <- c(1, 1, 1, 2, 2, 2) names(clust_to_use1) <- feats_to_use force(clust_to_use1) #>   Mlc1 Gprc5b   Gfap  Ednrb   Sox9   Aqp4  #>      1      1      1      2      2      2   g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use1,     name = \"metagene_1\" ) #> calculating metafeature: 1 #> calculating metafeature: 2  # 1.2 annotation vector (character) clust_to_use2 <- c(rep(\"sig_a\", 3), rep(\"sig_b\", 3)) names(clust_to_use2) <- feats_to_use force(clust_to_use2) #>    Mlc1  Gprc5b    Gfap   Ednrb    Sox9    Aqp4  #> \"sig_a\" \"sig_a\" \"sig_a\" \"sig_b\" \"sig_b\" \"sig_b\"   g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use2,     name = \"metagene_2\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 2.1 annotation data.frame (no weights) # Cols must be: # `clus` - which metafeature # `feat` - features to assign to this metafeature # `w` - (optional) weight to assign the feature before metafeature score #       calculation clust_to_use3 <- data.frame(     clus = c(rep(\"sig_a\", 3), rep(\"sig_b\", 3)),     feat = feats_to_use ) force(clust_to_use3) #>    clus   feat #> 1 sig_a   Mlc1 #> 2 sig_a Gprc5b #> 3 sig_a   Gfap #> 4 sig_b  Ednrb #> 5 sig_b   Sox9 #> 6 sig_b   Aqp4 g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use3,     name = \"metagene_3\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 2.1 annotation data.frame (weights) clust_to_use4 <- data.frame(     clus = c(rep(\"sig_a\", 3), rep(\"sig_b\", 3)),     feat = feats_to_use,     w = c(1, 1, 1, 2, 3, 4) ) force(clust_to_use4) #>    clus   feat w #> 1 sig_a   Mlc1 1 #> 2 sig_a Gprc5b 1 #> 3 sig_a   Gfap 1 #> 4 sig_b  Ednrb 2 #> 5 sig_b   Sox9 3 #> 6 sig_b   Aqp4 4 g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use4,     name = \"weighted_metagene\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 3. Other statistic transforms can be calculated # The default and what has been used so far is just finding the mean g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use4,     stat = \"sum\",     expression_values = \"raw\", # find summed raw expr for these feats     name = \"raw_sums\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 4. A custom stat function can also be supplied # These custom functions must be summary functions, as in, they must # produce only a single numeric output from many custom_stat <- function(x) {     if (max(x) == 0) {         return(0)     }     return(mean(x / max(x))) } g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use4,     stat = custom_stat,     expression_values = \"raw\",     name = \"raw_custom\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 5. A rescale of the values to a specified numeric range can be applied # before the stat score calculation. g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use4,     stat = \"mean\",     expression_values = \"normalized\",     rescale_to = c(0, 1),     name = \"norm_scaled_mean_metafeat\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b showGiottoSpatEnrichments(g) #> Spatial unit:  aggregate   #>  #> --> Feature type:  rna   #>  #> ----> Name  cluster_metagene :  #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #> 4: 4.093622 0.5886051 0.1962017 0.5886051     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #> 4:  87260224659312905497866017323180367450 #>  #> ----> Name  metagene_1 :  #>           1        2                                 cell_ID #>       <num>    <num>                                  <char> #> 1: 3.493789 3.160792 240649020551054330404932383065726870513 #> 2: 2.132677 2.795048 274176126496863898679934791272921588227 #> 3: 2.633814 7.570115 323754550002953984063006506310071917306 #> 4: 4.446903 3.924034  87260224659312905497866017323180367450 #>  #> ----> Name  metagene_2 :  #>       sig_a    sig_b                                 cell_ID #>       <num>    <num>                                  <char> #> 1: 3.493789 3.160792 240649020551054330404932383065726870513 #> 2: 2.132677 2.795048 274176126496863898679934791272921588227 #> 3: 2.633814 7.570115 323754550002953984063006506310071917306 #> 4: 4.446903 3.924034  87260224659312905497866017323180367450 #>  #> ----> Name  metagene_3 :  #>       sig_a    sig_b                                 cell_ID #>       <num>    <num>                                  <char> #> 1: 3.493789 3.160792 240649020551054330404932383065726870513 #> 2: 2.132677 2.795048 274176126496863898679934791272921588227 #> 3: 2.633814 7.570115 323754550002953984063006506310071917306 #> 4: 4.446903 3.924034  87260224659312905497866017323180367450 #>  #> ----> Name  weighted_metagene :  #>       sig_a     sig_b                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 3.493789  6.321584 240649020551054330404932383065726870513 #> 2: 2.132677  5.590096 274176126496863898679934791272921588227 #> 3: 2.633814 23.041672 323754550002953984063006506310071917306 #> 4: 4.446903 11.772102  87260224659312905497866017323180367450 #>  #> ----> Name  raw_sums :  #>    sig_a sig_b                                 cell_ID #>    <num> <num>                                  <char> #> 1:     2     2 240649020551054330404932383065726870513 #> 2:     1     8 274176126496863898679934791272921588227 #> 3:     2    16 323754550002953984063006506310071917306 #> 4:     4     6  87260224659312905497866017323180367450 #>  #> ----> Name  raw_custom :  #>        sig_a     sig_b                                 cell_ID #>        <num>     <num>                                  <char> #> 1: 0.3333333 0.3333333 240649020551054330404932383065726870513 #> 2: 0.3333333 0.3333333 274176126496863898679934791272921588227 #> 3: 0.3333333 0.6666667 323754550002953984063006506310071917306 #> 4: 0.4444444 0.5000000  87260224659312905497866017323180367450 #>  #> ----> Name  norm_scaled_mean_metafeat :  #>        sig_a     sig_b                                 cell_ID #>        <num>     <num>                                  <char> #> 1: 0.3009266 0.6666667 240649020551054330404932383065726870513 #> 2: 0.2139690 0.5895248 274176126496863898679934791272921588227 #> 3: 0.2268554 2.3591938 323754550002953984063006506310071917306 #> 4: 0.4182979 1.2189606  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 nnNetObj — createNearestNetObj","title":"Create S4 nnNetObj — createNearestNetObj","text":"Create S4 nnNetObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 nnNetObj — createNearestNetObj","text":"","code":"createNearestNetObj(   name = \"test\",   network,   nn_type = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 nnNetObj — createNearestNetObj","text":"name name nnNetObj network igraph object data.frame containing nearest neighbor information (see details) nn_type type nearest neighbor network spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 nnNetObj — createNearestNetObj","text":"nnNetObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create S4 nnNetObj — createNearestNetObj","text":"igraph dataframe-like inputs must include certain information. igraph, must , minimum vertex 'name' attributes 'distance' edge attribute. dataframe-like inputs must '', '', 'distance' columns","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 nnNetObj — createNearestNetObj","text":"","code":"x <- GiottoData::loadSubObjectMini(\"nnNetObj\")  createNearestNetObj(     network = slot(x, \"igraph\"), name = \"sNN\",     nn_type = \"sNN\" ) #> An object of class nnNetObj : \"sNN\" #> --| Contains nearest neighbor network generated with: sNN  #> ----| for feat_type: rna  #> ----|     spat_unit: cell  #> IGRAPH 859f76e DNW- 462 3021 --  #> + attr: name (v/c), weight (e/n), distance (e/n), shared (e/n), rank #> | (e/n) #> + edges from 859f76e (vertex names): #> [1] 240649020551054330404932383065726870513->335295524680090725199231409883288198017 #> [2] 240649020551054330404932383065726870513->77151711298730578178892667721058396928  #> [3] 240649020551054330404932383065726870513->322879686187630160969459793861944841206 #> [4] 240649020551054330404932383065726870513->31072896077757820678000109671990674373  #> [5] 240649020551054330404932383065726870513->102184699197574201819246996094734116255 #> [6] 240649020551054330404932383065726870513->17685062374745280598492217386845129350  #> + ... omitted several edges #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"createNearestNetwork — createNearestNetwork","title":"createNearestNetwork — createNearestNetwork","text":"create nearest neighbour (NN) network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createNearestNetwork — createNearestNetwork","text":"","code":"createNearestNetwork(   gobject,   spat_unit = NULL,   feat_type = NULL,   type = c(\"sNN\", \"kNN\"),   dim_reduction_to_use = \"pca\",   dim_reduction_name = NULL,   dimensions_to_use = seq_len(10),   feats_to_use = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   name = NULL,   return_gobject = TRUE,   k = 30,   minimum_shared = 5,   top_shared = 3,   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createNearestNetwork — createNearestNetwork","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") type sNN kNN dim_reduction_to_use dimension reduction method use dim_reduction_name name dimension reduction set use dimensions_to_use number dimensions use input feats_to_use dim_reduction_to_use = NULL, genes use expression_values expression values use name arbitrary name NN network. Defaults [type].[dim_reduction_to_use] return_gobject boolean: return giotto object (default = TRUE) k number k neighbors use minimum_shared minimum shared neighbors top_shared keep ... verbose verbose ... additional parameters kNN sNN functions dbscan","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createNearestNetwork — createNearestNetwork","text":"giotto object updated NN network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createNearestNetwork — createNearestNetwork","text":"function creates k-nearest neighbour (kNN) shared nearest neighbour (sNN) network based provided dimension reduction space. run directly gene expression matrix set dim_reduction_to_use = NULL. See also kNN sNN information networks created. Output kNN: : cell_ID source cell : cell_ID target cell distance: distance cells weight: \\(1/(1 + distance)\\) Output sNN: : cell_ID source cell : cell_ID target cell distance: distance cells weight: \\(1/(1 + distance)\\) shared: number shared neighbours rank: ranking pairwise cell neighbours sNN networks two additional parameters can set: minimum_shared: minimum number shared neighbours needed top_shared: keep number top shared neighbours, irrespective minimum_shared setting","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createNearestNetwork — createNearestNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createNearestNetwork(g) #> > 'sNN.pca' already exists and will be replaced with #>  new nearest neighbor network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a network — createNetwork","title":"Create a network — createNetwork","text":"Create networks node values. hub function many different methods finding nearest neighbors. See details additional params important generating specific types networks.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a network — createNetwork","text":"","code":"createNetwork(   x,   type = c(\"sNN\", \"kNN\", \"delaunay\"),   method = c(\"dbscan\", \"geometry\", \"RTriangle\", \"deldir\"),   node_ids = NULL,   include_distance = TRUE,   include_weight = TRUE,   as.igraph = TRUE,   verbose = NULL,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a network — createNetwork","text":"x matrix. Data treat nodes. Examples include expression information, PCA matrix, spatial locations xy(z) coordinates. type type network create. Currently: \"sNN\", \"kNN\", \"delaunay\" method method used create type network requested. One \"dbscan\" sNN kNN \"geometry\", \"RTriangle\", \"deldir\" delaunay. node_ids character. Node ID values assign. NULL, integer indices used node IDs. include_distance logical. include edge distance attribute output include_weight logical. include edge weight attribute output .igraph logical. Whether return igraph. Otherwise returns data.table verbose verbose. Default = NULL (uses giotto verbosity option) ... additional params pass. See details section","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a network — createNetwork","text":"Either igraph .igraph = TRUE data.table otherwise.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a network — createNetwork","text":"Additional params described . Items parenthesis refer network types /methods params specific . [k] numeric. (sNN, kNN) number neighbors find. Default 30 [minimum_shared] numeric. (sNN) minimum shared neighbors allowed per edge [top_shared] numeric. (sNN) keep least many edges per node, kept edges top ranked terms number shared neighbors. [filter] logical. (kNN) whether filter unique edges apply minimum_k maximum_distance filters. set TRUE generating spatial kNN network. Default FALSE. [minimum_k] (delaunay, kNN) minimum nearest neighbours maximum_distance != NULL [maximum_distance] (delaunay, kNN) edge maximum euclidean distance allowed [Y] (RTriangle) TRUE prohibits insertion Steiner points mesh boundary. Default TRUE [j] (RTriangle) TRUE jettisons vertices part final triangulation output. Default TRUE [S] (RTriangle) Specifies maximum number added Steiner points. Default 0 [options] (geometry) default \"Pp\". See geometry::delaunayn [weight_fun] function calculate weights based distance include_weight = TRUE. Default \\(weight = 1 / (1 + distance)\\) \"kNN\" \"sNN\" types \\(weight = 1 / distance\\) delaunay type networks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a network — createNetwork","text":"","code":"pca <- GiottoData::loadSubObjectMini(\"dimObj\")[] sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")[]  # Delaunay via geometry::delaunayn() del_geom <- createNetwork(     x = as.matrix(sl[, .(sdimx, sdimy)]),     type = \"delaunay\",     method = \"geometry\",     include_weight = TRUE,     weight_fun = function(d) 1 / d,     as.igraph = FALSE,     node_ids = sl$cell_ID )  # Delaunay via RTriangle::triangulate() del_rt <- createNetwork(     x = as.matrix(sl[, .(sdimx, sdimy)]),     type = \"delaunay\",     method = \"RTriangle\",     include_weight = TRUE,     weight_fun = function(d) 1 / d,     as.igraph = FALSE,     node_ids = sl$cell_ID )  # Delaunay via deldir::deldir() del_dd <- createNetwork(     x = as.matrix(sl[, .(sdimx, sdimy)]),     type = \"delaunay\",     method = \"deldir\",     include_weight = TRUE,     weight_fun = function(d) 1 / d,     as.igraph = FALSE,     node_ids = sl$cell_ID )  # kNN spatial network kNN_spat <- createNetwork(     x = as.matrix(sl[, .(sdimx, sdimy)]),     type = \"kNN\",     method = \"dbscan\",     include_weight = TRUE,     weight_fun = function(d) 1 / d, # not the default     as.igraph = FALSE,     node_ids = sl$cell_ID,     k = 4L,     maximum_distance = NULL,     minimum_k = 0L )  # kNN NN network kNN <- createNetwork(     pca[, seq_len(10)],     type = \"kNN\",     method = \"dbscan\",     node_ids = rownames(pca),     as.igraph = TRUE )  # sNN NN network sNN <- createNetwork(     pca[, seq_len(10)],     type = \"sNN\",     method = \"dbscan\",     node_ids = rownames(pca),     as.igraph = TRUE )  # using defaults for sNN with index IDs to create igraph sNN_idx <- createNetwork(pca[, seq_len(10)])"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 spatEnrObj — createSpatEnrObj","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"Create S4 spatEnrObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"","code":"createSpatEnrObj(   enrichment_data,   name = \"test\",   spat_unit = \"cell\",   feat_type = \"rna\",   method = NULL,   provenance = NULL,   misc = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"enrichment_data spatial enrichment results, provided dataframe-like object name name S4 spatEnrObj spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') method method used generate spatial enrichment information provenance origin data aggregated expression information (applicable) misc misc additional information spatial enrichment generated verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"spatEnrObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatEnrObj\")  createSpatEnrObj(     enrichment_data = slot(x, \"enrichDT\"),     name = \"cluster_metagene\" ) #> There are non numeric or integer columns for the spatial #>  enrichment input at column position(s): 6 #>  The first non-numeric column will be considered as a cell ID to test for #>  consistency with the expression matrix. #>  Other non-numeric columns will be removed. #> An object of class spatEnrObj : \"cluster_metagene\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #>    ------------------------ #>  #> preview: #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #>  #> ...first 20 remaining colnames: #>  #>    #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 spatLocsObj — createSpatLocsObj","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"Create S4 spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"","code":"createSpatLocsObj(   coordinates,   name = \"test\",   spat_unit = \"cell\",   provenance = NULL,   misc = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"coordinates spatial coordinates name name spatLocsObj spat_unit spatial unit aggregated expression (e.g. 'cell') provenance origin data aggregated expression information (applicable) misc misc verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"","code":"x <- data.frame(     cell_ID = c(\"cell_1\", \"cell_2\", \"cell_3\"),     sdimx = c(6637.881, 6471.978, 6801.610),     sdimy = c(-5140.465, -4883.541, -4968.685) )  createSpatLocsObj(coordinates = x, name = \"raw\") #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"cell\" #> dimensions: 3 3  #> preview   : #>       sdimx     sdimy cell_ID #>       <num>     <num>  <char> #> 1: 6637.881 -5140.465  cell_1 #> 2: 6471.978 -4883.541  cell_2 #> 3: 6801.610 -4968.685  cell_3 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6471.978 -5140.465 #> [2,] 6801.610 -4883.541 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 spatialNetworkObj — createSpatNetObj","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"Create S4 spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"","code":"createSpatNetObj(   network,   name = \"test\",   networkDT_before_filter = NULL,   method = NULL,   spat_unit = \"cell\",   provenance = NULL,   parameters = NULL,   outputObj = NULL,   cellShapeObj = NULL,   crossSectionObjects = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"network network data connections, distances, weightings name name spatialNetworkObj networkDT_before_filter (optional) unfiltered data.table  network connections, distances, weightings method method used generate spatial network spat_unit spatial unit tag provenance (optional) origin aggregated information (applicable) parameters (optional) additional method-specific parameters used spatial network generation outputObj (optional) network geometry object cellShapeObj (optional) network cell shape information crossSectionObjects (optional) crossSectionObjects misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatialNetworkObj\")  createSpatNetObj(network = slot(x, \"networkDT\"), name = \"Delaunay_network\") #> An object of class spatialNetworkObj : \"Delaunay_network\" #> spat_unit : \"cell\" #>    1275 connections (filtered)"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"createSpatialDefaultGrid — createSpatialDefaultGrid","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"Create spatial grid using default method","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"","code":"createSpatialDefaultGrid(   gobject,   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = \"raw\",   sdimx_stepsize = NULL,   sdimy_stepsize = NULL,   sdimz_stepsize = NULL,   minimum_padding = 1,   name = NULL,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"gobject giotto object spat_unit spatial unit feat_type feature type spat_loc_name spatial location name sdimx_stepsize stepsize along x-axis sdimy_stepsize stepsize along y-axis sdimz_stepsize stepsize along z-axis minimum_padding minimum padding edges name name spatial grid (default = 'spatial_grid') return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"giotto object updated spatial grid slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"Creates spatial grid defined x, y (z) dimensions. dimension units based provided spatial location units.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialDefaultGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"Create spatial Delaunay network based cell centroid physical distances.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"","code":"createSpatialDelaunayNetwork(   gobject,   name = \"Delaunay_network\",   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = NULL,   method = c(\"deldir\", \"delaunayn_geometry\", \"RTriangle\"),   dimensions = \"all\",   maximum_distance = \"auto\",   minimum_k = 0,   options = \"Pp\",   Y = TRUE,   j = TRUE,   S = 0,   verbose = TRUE,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"gobject giotto object name name spatial network (default = 'delaunay_network') spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations method package use create Delaunay network dimensions spatial dimensions use. Use \"sdimx\" (spatial dimension x), \"sdimy\", \"sdimz\" respectively refer X (1st), Y (2nd) Z(3rd) dimension, see details. (default = ) maximum_distance distance cuttof Delaunay neighbors consider. \"auto\", \"upper whisker\" value distance vector neighbors used; see graphics::boxplot() documentation details.(default = \"auto\") minimum_k minimum number neighbours maximum_distance != NULL options (geometry) String containing extra control options underlying Qhull command; see Qhull documentation available options. (default = 'Pp', report precision problems) Y (RTriangle) TRUE prohibits insertion Steiner points mesh boundary. j (RTriangle) TRUE jettisons vertices part final triangulation output. S (RTriangle) Specifies maximum number added Steiner points. verbose verbose return_gobject logical. return giotto object (default = TRUE) output character. Object type return spatial network return_gobject = FALSE. (default: 'spatialNetworkObj') ... additional parameters","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"giotto object updated spatial network slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"Creates spatial Delaunay network explained delaunayn (default), deldir, triangulate.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialDelaunayNetwork(g) #> Delaunay_network has already been used, will be overwritten #> > \" Delaunay_network \" already exists and will be replaced with new spatial #>  network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"Calculates centroid locations giotto polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"","code":"createSpatialFeaturesKNNnetwork(   gobject,   method = \"dbscan\",   feat_type = NULL,   name = \"knn_feats_network\",   k = 4,   maximum_distance = NULL,   minimum_k = 0,   add_feat_ids = FALSE,   verbose = TRUE,   return_gobject = TRUE,   toplevel_params = 2,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"gobject giotto object method kNN algorithm method feat_type feature type build feature network name name network k number neighbors maximum_distance maximum distance bewteen features minimum_k minimum number neighbors find add_feat_ids add feature id names (default = FALSE, increases object size) verbose verbose return_gobject return giotto object (default: TRUE) toplevel_params toplevel value pass updating giotto params ... additional parameters pass kNN","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"return_gobject = TRUE giotto object containing network returned. return_gobject = FALSE network returned datatable.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialFeaturesKNNnetwork(g) #> Convert feature spatial info to matrix #> Create kNN network with dbscan #> Filter output for distance and minimum neighbours #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork_dbscan.html","id":null,"dir":"Reference","previous_headings":"","what":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","title":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","text":"create feature kNN spatial network using dbscan","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork_dbscan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","text":"","code":"createSpatialFeaturesKNNnetwork_dbscan(   gobject,   feat_type = NULL,   name = \"knn_feats_network\",   k = 4,   maximum_distance = NULL,   minimum_k = 0,   add_feat_ids = FALSE,   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork_dbscan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","text":"gobject giotto object feat_type feature type name name assign generated feature network k number neighbors kNN find maximum_distance network maximum distance allowed minimum_k minimum neighbors allowed add_feat_ids boolean. whether add feature information verbose verbose ... additional parameters pass kNN","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork_dbscan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","text":"kNN spatial feature network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"createSpatialGrid — createSpatialGrid","title":"createSpatialGrid — createSpatialGrid","text":"Create spatial grid using default method","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createSpatialGrid — createSpatialGrid","text":"","code":"createSpatialGrid(   gobject,   spat_unit = NULL,   spat_loc_name = \"raw\",   name = NULL,   method = c(\"default\"),   sdimx_stepsize = NULL,   sdimy_stepsize = NULL,   sdimz_stepsize = NULL,   minimum_padding = 1,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createSpatialGrid — createSpatialGrid","text":"gobject giotto object spat_unit spatial unit spat_loc_name spatial location name name name spatial grid method method create spatial grid sdimx_stepsize stepsize along x-axis sdimy_stepsize stepsize along y-axis sdimz_stepsize stepsize along z-axis minimum_padding minimum padding edges return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createSpatialGrid — createSpatialGrid","text":"giotto object updated spatial grid slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createSpatialGrid — createSpatialGrid","text":"Creates spatial grid defined x, y (z) dimensions. dimension units based provided spatial location units. default method: createSpatialDefaultGrid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createSpatialGrid — createSpatialGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"createSpatialKNNnetwork — createSpatialKNNnetwork","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"Create spatial knn network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"","code":"createSpatialKNNnetwork(   gobject,   method = \"dbscan\",   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = NULL,   dimensions = \"all\",   name = \"knn_network\",   k = 4,   maximum_distance = NULL,   minimum_k = 0,   verbose = FALSE,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"gobject giotto object method method create kNN network spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations dimensions spatial dimensions use (default = ) name name spatial network (default = 'spatial_network') k number nearest neighbors based physical distance maximum_distance distance cuttof nearest neighbors consider kNN network minimum_k minimum nearest neigbhours maximum_distance != NULL verbose verbose return_gobject boolean: return giotto object (default = TRUE) output character. Object type return spatial network return_gobject = FALSE. (default: 'spatialNetworkObj') ... additional arguments selected method function","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"giotto object updated spatial network slot dimensions:  default = '' takes possible dimensions. Alternatively can provide character vector specififies spatial dimensions use, e.g. c(\"sdimx', \"sdimy\") numerical vector, e.g. 2:3 maximum_distance:  create network based maximum distance , also need set k high value, e.g. k = 100","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialKNNnetwork(g) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network knn_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Create spatial network — createSpatialNetwork","title":"Create spatial network — createSpatialNetwork","text":"Create spatial network based cell centroids. networks often used determining cell-cell connectivities spatial relationships. several types spatial networks multiple methods generate . Method-specific params labeled name method within parentheses descriptions.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create spatial network — createSpatialNetwork","text":"","code":"createSpatialNetwork(   gobject,   name = NULL,   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = NULL,   dimensions = \"all\",   method = c(\"Delaunay\", \"kNN\"),   delaunay_method = c(\"deldir\", \"delaunayn_geometry\", \"RTriangle\"),   maximum_distance_delaunay = \"auto\",   options = \"Pp\",   Y = TRUE,   j = TRUE,   S = 0,   minimum_k = 0,   knn_method = \"dbscan\",   k = 4,   maximum_distance_knn = NULL,   verbose = FALSE,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create spatial network — createSpatialNetwork","text":"gobject giotto object name name spatial network (default = 'spatial_network') spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations use dimensions spatial dimensions use (default = ) method method use create spatial network. (default = Delaunay) delaunay_method method use generate Delaunay network maximum_distance_delaunay distance cutoff nearest neighbors consider Delaunay network. \"auto\", \"upper whisker\" value distance vector neighbors used; see grDevices::boxplot.stats documentation details.(default = \"auto\") options (geometry) String containing extra control options underlying Qhull command; see Qhull documentation available options. (default = 'Pp', report precision problems) Y (RTriangle) TRUE prohibits insertion Steiner points mesh boundary. j (RTriangle) TRUE jettisons vertices part final triangulation output. S (RTriangle) Specifies maximum number added Steiner points. minimum_k minimum nearest neighbours maximum_distance != NULL knn_method method create kNN network k number nearest neighbors based physical distance maximum_distance_knn distance cutoff nearest neighbors consider kNN network verbose verbose return_gobject logical. return giotto object (default = TRUE) output character. Object type return spatial network return_gobject = FALSE. (default: 'spatialNetworkObj') ... Additional parameters selected function","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create spatial network — createSpatialNetwork","text":"giotto object updated spatial network slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create spatial network — createSpatialNetwork","text":"Creates spatial network connecting single-cells based physical distance . Delaunay method, neighbors decided Delaunay triangulation maximum distance criteria. kNN method, number neighbors can determined k, maximum distance cell without setting minimum k cell. **dimensions: ** default = '' takes possible dimensions. Alternatively can provide character vector specifies spatial dimensions use, e.g. c(\"sdimx', \"sdimy\") numerical vector, e.g. 2:3","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create spatial network — createSpatialNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialNetwork(g) #> Delaunay_network has already been used, will be overwritten #> > \" Delaunay_network \" already exists and will be replaced with new spatial #>  network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a spatial weight matrix — createSpatialWeightMatrix","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"Generate spatial weight matrix based strength spatial interactions nodes. Requires spatial networks first generated.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"","code":"createSpatialWeightMatrix(   gobject,   spat_unit = NULL,   spatial_network_to_use = \"kNN_network\",   method = c(\"distance\", \"adjacency\"),   wm_name = \"spat_weights\",   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"gobject giotto object spat_unit spatial unit spatial_network_to_use spatial network information use method type weighted matrix generate. See details wm_name name assign weight matrix values return_gobject (default = TRUE) whether return giotto object attached results bare weighted matrix verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"spatial weight matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"\"distance\" method calculated using 1/(1+distance) create inverse weighting based distance nodes. \"adjacency\" method binary matrix 1 signifying two nodes connected spatial network 0 indicating .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialWeightMatrix(g, spatial_network_to_use = \"spatial_network\") #> Attaching weight matrix to spatial_network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_KNNnetwork_dbscan.html","id":null,"dir":"Reference","previous_headings":"","what":"create_KNNnetwork_dbscan — create_KNNnetwork_dbscan","title":"create_KNNnetwork_dbscan — create_KNNnetwork_dbscan","text":"Create spatial knn network dbscan","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_KNNnetwork_dbscan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_KNNnetwork_dbscan — create_KNNnetwork_dbscan","text":"","code":"create_KNNnetwork_dbscan(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   sdimz = \"sdimz\",   k = 4,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_KNNnetwork_dbscan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_KNNnetwork_dbscan — create_KNNnetwork_dbscan","text":"spatial knn network dbscan","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":null,"dir":"Reference","previous_headings":"","what":"create_average_DT — create_average_DT","title":"create_average_DT — create_average_DT","text":"calculates average gene expression cell metadata factor (e.g. cluster)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_average_DT — create_average_DT","text":"","code":"create_average_DT(   gobject,   spat_unit = NULL,   feat_type = NULL,   meta_data_name,   expression_values = c(\"normalized\", \"scaled\", \"custom\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"create_average_DT — create_average_DT","text":"gobject giotto object spat_unit spatial unit feat_type feature type meta_data_name name metadata column use expression_values expression values use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_average_DT — create_average_DT","text":"data.table average gene expression values factor","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"create_average_DT — create_average_DT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  create_average_DT(g, meta_data_name = \"leiden_clus\") #>                cluster_2  cluster_5  cluster_1  cluster_3  cluster_6 cluster_7 #> Gna12         3.30737745 3.34082808 3.26309190 3.23263758 3.30171653 3.4313574 #> Ccnd2         1.94201357 2.05141093 2.18616953 2.02323861 1.91616817 2.3163818 #> Btbd17        1.18729607 1.29867174 1.21794661 1.43198694 1.25581641 0.7594994 #> Sox9          1.52919580 1.82629178 1.73707493 1.30671993 2.10794802 0.8765589 #> Sez6          3.45947190 3.30180445 3.77961671 3.45034173 3.07211639 3.7882936 #> Serpinf1      0.49689128 0.67245412 0.40614711 0.52461938 0.31016114 0.1371682 #> S100a6        2.42891377 2.33734168 2.42540182 2.09391026 2.41906585 1.8676702 #> Col1a1        0.22421466 0.10226721 0.10783051 0.29432743 0.15596186 0.3703106 #> Vwf           0.73980288 1.02125057 0.93244909 0.92739552 1.11699965 0.4919525 #> Esam          0.81955988 0.70087106 1.01971007 1.15689072 1.34596491 0.7461961 #> Npas1         0.33784649 0.56748473 0.53158683 0.63813928 0.44098006 0.7215881 #> Tiam1         2.04082965 1.80812107 1.72900493 2.00111715 1.35007867 1.2827112 #> Bcam          0.55274955 0.46173183 0.45044757 0.95543213 0.93821439 0.2666210 #> Hmgn2         2.06603581 2.04159933 1.99690865 1.76837367 1.84263924 2.1922319 #> Rab3b         1.77459139 1.75638043 1.64899950 1.56796461 1.60138382 1.6748753 #> Inmt          0.13863241 0.05262011 0.10527864 0.03996412 0.00000000 0.0000000 #> Ddr1          2.30055485 2.04984165 2.16648979 2.02195473 2.26367690 1.2358701 #> Homer3        1.26643552 1.15517582 1.11972968 1.01678407 0.71873936 1.6754294 #> Cp            0.22881160 0.39256404 0.21860348 0.25071201 0.00000000 0.2504086 #> Calb2         1.41862992 1.32679445 1.12525518 1.48135851 0.98242852 1.9040701 #> Man1a         1.17187286 1.31869487 1.24676725 1.17223778 0.97405462 2.2950651 #> Efnb3         3.00627172 3.13310020 2.69940050 2.74742453 3.06518311 3.0503625 #> Hlf           3.24839637 3.18753475 3.31310560 3.16226642 3.13612021 3.0091062 #> Gstm7         1.48500928 1.42703276 1.16225013 1.19766905 1.33959392 1.6747068 #> Cavin1        0.76178584 0.74779708 0.85791117 0.71491635 0.47148173 0.7352277 #> Sst           3.73684749 3.66376591 4.00841752 3.75201838 4.13871179 3.5194932 #> Hapln2        0.97869249 0.59951972 0.77294983 0.71085218 0.94971053 0.6425065 #> Hspb1         0.52971873 0.70520439 0.61274014 0.46869655 0.57186807 0.0000000 #> Ndrg1         3.13863431 2.61730487 3.02006093 2.98727188 3.46588636 1.8026284 #> Nid1          0.21553865 0.17652907 0.19669062 0.21101093 0.57025089 0.0000000 #> Kit           0.56833963 0.53109779 0.81175354 0.88306169 0.87098881 0.6870762 #> Pvalb         3.28835059 3.07327787 3.23604114 3.04990097 3.21770290 2.9380384 #> Tmbim1        2.37754522 2.08368796 1.92791556 1.88812870 1.74852239 1.1152814 #> Crip1         1.41009971 1.25450326 1.39849965 1.15120273 1.20854459 1.0925703 #> Tek           0.58846075 0.33380651 0.52905848 0.28965068 0.56496634 0.5935108 #> Elovl1        1.85542908 1.68257937 1.39440717 1.26707570 1.48335618 1.3114013 #> Cyba          1.03626710 1.15289251 0.86405628 1.23125127 0.63976179 1.2564585 #> Itih3         1.13630590 1.27197529 1.23250522 1.54389062 0.89307587 0.7474588 #> Cnp           6.03778097 5.82455446 5.72610313 5.77702510 6.08723395 5.0034797 #> Hap1          1.59121288 1.59382394 1.22734443 1.28449310 0.83700513 2.0214657 #> Clic1         1.00898108 0.61047121 0.60289933 0.76176127 0.55957882 0.6369316 #> Stx1a         2.43108017 2.42823381 2.88334873 2.45917900 2.37738140 2.2308187 #> Arpp19        4.42595642 4.35163328 4.80397850 3.89752350 4.45562164 3.9427566 #> Dio2          0.96343624 1.01739656 0.91295021 0.76877531 0.96959609 0.3908687 #> Id3           2.94529544 3.10331664 2.78821879 2.78836190 3.03403342 2.3991619 #> Crlf1         0.68633559 0.92119629 0.62912246 0.71898084 0.58334100 1.0250248 #> Ttc9b         4.29092470 4.57642934 4.57666226 4.01245305 4.26698811 4.2923582 #> Carhsp1       2.55785092 2.19549855 2.04605615 2.27045522 2.17840332 1.8752942 #> Cabp7         2.26141511 2.44514004 2.33171046 2.61207654 3.16472283 1.9179897 #> Fam163b       2.33735544 2.69302626 2.28224543 1.98406086 2.14181837 2.2600349 #> Rarres2       1.15314942 0.79457001 0.76443331 0.97133349 1.13558301 0.7671321 #> Syn2          4.48304876 4.69086545 4.68289652 4.49762071 4.61898034 4.2666136 #> Ick           1.33976866 1.21525841 1.35199145 0.94688793 0.97359053 0.6602028 #> Prox1         1.12087834 1.34728136 0.86501440 1.33385558 0.96045485 1.0248782 #> Adssl1        1.22683731 1.36701339 1.20495704 1.03050662 1.38292753 0.8528214 #> Vipr2         0.41622431 0.36140341 0.35658828 0.46596769 0.22133447 0.6305185 #> Gltp          2.15804351 1.84663313 2.04223111 1.76176658 2.14830600 1.9952998 #> Amotl1        1.59141088 1.52206874 1.67265575 1.88453192 1.80460555 1.5660657 #> Bcas1         3.64879117 3.22084650 3.42773536 3.41097031 3.13603555 2.8217151 #> Aldh1a2       0.12766617 0.06700689 0.09847394 0.30442144 0.00000000 0.3474831 #> Tppp3         2.60248409 2.12178859 2.28050208 2.27905129 2.24382333 2.2492398 #> Sirt2         4.50161397 4.42130053 4.35249062 4.42498751 4.26085093 4.2228421 #> Lpl           0.74898467 0.73794230 0.84582531 0.73030980 0.96083767 0.6531023 #> Cers2         2.35272710 2.57746727 2.31978260 2.28481964 2.52422789 3.1972147 #> Qdpr          5.23889427 4.77963136 4.90730301 4.97703997 5.36660249 4.9643569 #> Stk32c        2.43264753 2.31827006 2.27191999 2.16800239 2.11622851 1.1254119 #> Lbp           0.21986917 0.28440076 0.23720866 0.31418215 0.25051624 0.0000000 #> Hsd11b1       1.26986044 1.47931030 1.35631908 1.65409190 1.51951132 1.7326963 #> Vtn           2.72627600 2.74226687 2.48487479 2.41757776 2.62731419 1.6681123 #> Stac2         1.37615453 1.44983037 1.68280224 1.10862295 1.67586917 0.9597937 #> Plxdc1        1.22437375 1.44472440 1.42370524 1.50672610 1.12087763 0.8329171 #> Igfbp4        2.56466752 2.20266690 2.60079633 2.39337399 2.70624219 3.0103030 #> Dbndd2        2.48931976 2.38269055 2.34673722 2.41390483 2.46122731 2.5249243 #> Pltp          2.21518165 2.02049597 2.09493581 1.95665173 2.49435424 1.3305275 #> Slc12a4       0.98062041 0.87515793 0.89853208 0.65237371 0.98230366 0.9809346 #> Cadps2        1.66298140 1.79355599 1.70677869 1.60769029 1.55996625 1.4189812 #> Erbb3         0.41722543 0.37231331 0.41477667 0.49706419 0.60270594 0.9611556 #> Pmp22         1.47344250 1.44434883 1.32383976 1.40805034 1.14008930 1.1259126 #> Kcnab3        1.30572178 1.20773147 1.52367819 1.07447598 0.74673275 0.4728139 #> Myh11         0.19846986 0.24588139 0.22678101 0.26793807 0.10543429 0.4196490 #> Plod1         1.12228671 1.27754944 1.09295150 1.23896140 1.13073327 1.2264941 #> Etnppl        0.79577091 0.73976180 1.07222053 1.11998472 0.75859382 0.7478169 #> Arhgef25      3.32395185 3.23853885 3.39800246 3.38567462 2.97064593 3.5291598 #> Rcn3          0.41078586 0.24734435 0.67825434 0.56174438 0.25650623 0.5212264 #> Vip           0.83348717 0.73252192 0.69218987 0.83135659 0.52756790 0.5780129 #> Utrn          1.12996068 1.24445634 1.24669304 1.33442974 1.35301345 0.9244398 #> Grm1          1.67262407 1.55697786 1.67076335 2.15167949 1.61600199 1.3251047 #> Reep3         1.45149503 1.30521540 1.63704715 0.88291932 1.55062552 2.0238562 #> Fabp7         1.70844146 1.67648177 1.53028626 1.74460669 1.56617051 1.2506639 #> Dcn           0.47717856 0.33911219 0.31729641 0.46515059 0.30710267 0.6245136 #> Slc17a8       0.17280684 0.10455841 0.28782050 0.04330752 0.17635608 0.0000000 #> Dusp6         1.25874421 1.07733803 1.23134055 1.17891621 1.18342817 1.2890468 #> Kitl          1.41888612 1.55266742 1.57897181 1.31670195 1.02985082 1.0221684 #> Ccn2          0.64678980 1.03034906 0.93286268 0.51762328 1.18479178 0.6489568 #> Timp3         2.23409432 2.05459679 2.16335370 2.15665627 2.37840741 2.4935373 #> Ascl1         0.42848925 0.46801984 0.49010822 0.23662938 0.52055771 0.0000000 #> Unc5b         1.12443275 0.97559247 0.74116499 1.14892392 0.91670574 0.6871979 #> Vsir          1.00682289 0.86527542 0.84954259 0.77101413 1.46413962 0.4970584 #> Gamt          2.33360093 2.02585528 2.10745674 2.14681391 2.43994362 2.0382807 #> Ptprb         0.78607075 0.42205639 0.82417310 0.58637400 0.96141466 1.2463021 #> Csrp2         0.59065362 0.63314040 0.47274840 0.39455994 0.51584406 0.8911345 #> Adarb1        3.53550700 3.30058022 3.38098627 3.46216432 2.58062282 3.0655697 #> Rnf130        1.98574201 2.22208533 2.13350127 1.94480595 2.01370330 2.0420282 #> Nefh          2.05418571 2.14532273 2.08433434 2.32932866 1.89647811 2.7000541 #> Aebp1         0.47659104 0.35614418 0.44012339 0.36315284 0.27892980 0.0000000 #> Sept4         4.72125229 4.40519236 4.25235384 4.46364870 4.96708134 3.8270092 #> Gria1         4.12795684 4.34492850 4.29095060 4.17984545 4.00398837 4.2329121 #> Sypl          2.06287982 1.84444490 2.16063146 2.07372883 2.56105551 3.2220890 #> Arsg          1.27517546 1.23375248 0.99465993 1.03370270 1.58670989 0.2504086 #> Cacng4        1.53992884 1.49452708 1.76753612 1.58747283 1.01433516 1.1549710 #> Rab37         0.90145605 0.52665608 0.58522806 0.49870197 0.47213690 0.2564135 #> Itgb4         0.65964180 0.92831686 0.63561418 0.75968338 0.75914514 0.5053382 #> Aspa          1.87909375 1.45680189 1.53833872 1.72369905 1.46958193 2.5777761 #> Cygb          1.56224133 1.62942100 1.54136833 1.74061875 1.27509267 1.2047964 #> Rflnb         0.73297921 0.58146422 1.01514315 1.03543508 0.54574352 0.9564919 #> Doc2b         0.85036485 0.79605063 0.64340435 0.67876817 0.88942003 0.5897834 #> Gfap          3.12155168 3.24198121 3.03211737 2.75172258 3.35167866 3.7201425 #> Npas3         0.72428750 0.61893080 0.75975639 0.67456185 1.19424107 0.0000000 #> Serpina3n     1.23737941 1.38114731 1.07596381 1.15230991 0.81359560 1.8331696 #> Clmn          2.16643116 1.82939053 2.08910818 2.32066560 2.04461206 1.5499308 #> Prkch         0.47655716 0.50607402 0.56185862 0.61083942 0.73205288 0.6261503 #> Fbln5         0.27933271 0.16453232 0.30820530 0.23993262 0.27045984 0.0000000 #> Akr1c18       0.25486892 0.10717964 0.18107542 0.29201268 0.00000000 0.1371682 #> Gng4          0.93611513 0.72142584 0.89823297 0.87199592 0.72353001 1.9499755 #> Sema4d        2.03092581 1.86271608 1.89149412 1.77346033 1.74305382 1.3499372 #> Cxcl14        2.70461369 3.01340845 2.61703676 2.92785002 2.96684799 3.2410235 #> Hexb          3.00911612 3.37099821 3.18495493 3.30895148 3.64220022 2.5958016 #> Iqgap2        0.90895923 0.78908630 0.98281143 0.83299641 0.98028629 1.0300316 #> Crhbp         0.50371639 0.62988919 0.69393968 0.55015138 1.07634777 0.1371682 #> Rab3c         3.43988290 3.25891694 3.48259901 3.36089800 3.40901135 3.1297855 #> Thbs4         0.49765351 0.59669414 0.52533895 0.45375515 1.01070198 0.0000000 #> Serinc5       1.85389862 1.76190306 1.80870776 2.08593379 1.58414402 1.5293168 #> Erbin         2.45095864 1.96542277 2.62172379 2.34742867 2.29976160 2.4205313 #> Prkcd         2.57324385 2.61354668 2.38756697 2.87293417 2.13261309 2.2796092 #> Pdlim2        2.64100657 2.03304145 2.19677138 2.17522177 2.62607356 1.1154087 #> Ednrb         1.74214831 2.06030247 1.98828402 1.88385559 1.81672934 1.8173021 #> Cpne6         2.98364077 3.20817015 3.18107406 3.40839997 2.72992785 3.3275147 #> Sema5a        1.74619383 1.75016526 1.40190974 1.65337013 1.00666994 2.4115971 #> Matn2         1.02592291 1.31043133 1.24722461 1.06996228 1.28397813 1.0234107 #> Nptxr         3.98905107 4.10408925 4.54218333 4.02744883 3.77647703 4.0245328 #> Enpp2         4.43558458 4.31703048 4.29793558 4.11931597 4.59425832 3.7667837 #> Efcab6        0.31995630 0.44039143 0.53089320 0.32225920 0.43844731 0.8746874 #> Ppp1r1a       4.01406097 4.69827590 4.31408620 4.26538646 4.36988396 4.3554185 #> Litaf         1.76599530 1.58304036 1.59402701 1.46871417 1.80087344 1.7484272 #> Il1rap        1.83932810 1.47409370 1.46592131 1.65888997 1.58001808 1.2359937 #> Apod          5.11956478 5.00724135 4.93962837 4.96219926 5.42790752 3.9966022 #> Cpox          1.88485507 1.55457452 1.67161441 1.48853842 1.68145051 1.2664507 #> Grik1         0.55123294 0.54706355 0.40812361 0.55433660 0.31160914 1.1483943 #> Clic6         0.26628334 0.18558083 0.33574166 0.53274505 0.32058596 0.3474831 #> Nr4a1         0.64554738 0.73686764 0.99578525 0.71031972 0.25864240 0.2526861 #> Igfbp6        1.65030632 1.57194646 1.75294453 1.63411478 1.10892966 0.8347239 #> Sncg          0.40304031 0.28474379 0.38255750 0.38044514 0.42697491 0.0000000 #> Gzma          0.07190143 0.11410847 0.08815679 0.16416438 0.15574311 0.2504086 #> Grm2          0.96663539 0.96544707 1.11083722 0.84242663 0.70178515 0.6245136 #> Prph          0.17354909 0.25141501 0.14536617 0.34584096 0.00000000 0.3242240 #> Rsph1         0.27474608 0.16513017 0.23973773 0.20146095 0.31590239 0.6090279 #> Sox8          1.05032952 1.22311243 1.03490994 0.88191218 1.22329141 1.1165167 #> Fam234a       0.87158086 1.01867176 1.00146330 0.90913099 0.92536879 1.2068740 #> Lims2         1.27731649 1.25909487 1.00587185 1.06166966 1.35833723 1.0815706 #> Aqp4          2.67431922 2.75917648 2.54629507 2.82003279 2.84498269 2.9813845 #> Slc12a2       2.61481381 2.48155481 2.45199470 2.58709031 2.28611363 2.7799110 #> Cd74          0.16323129 0.28640037 0.16826600 0.26490651 0.08241013 0.0000000 #> Pdgfrb        0.53134815 0.69153085 0.59398354 0.55032243 0.82027150 0.2666210 #> Csf1r         2.66955319 2.53276487 2.42293815 2.23872947 2.61373883 2.8836846 #> Cbln2         0.85233400 0.44056965 0.53927191 0.76469578 0.74219937 0.1371682 #> Frmd8         1.46489626 1.19688364 1.45831748 1.18313898 1.21407728 1.1267537 #> Gldc          0.80769231 0.98218429 0.87414267 0.99385658 0.84366451 0.6635751 #> Tcf7l2        1.92964955 1.89001198 1.74476682 2.08429611 1.88492371 1.6457028 #> Bhlhe22       1.26730535 1.57124430 1.63385086 1.27426865 1.07416336 1.8132305 #> Kcnip2        2.25376431 2.23553466 2.76070190 2.34762087 2.53952800 3.1093760 #> Alas2         1.24029336 1.11196961 1.15905023 0.92345850 0.83743496 1.5693706 #> Gdf11         0.89456013 0.78694878 0.85317097 0.80486474 1.06354474 0.5940782 #> Baiap2        3.31778256 3.47637866 3.33135191 2.99228394 2.89563373 3.2529838 #> Ifitm3        1.66376351 1.90122708 1.56203622 1.98765479 2.12591695 1.2725191 #> Phkg1         0.85701198 0.92818993 0.80632925 0.91264376 1.24705822 0.0000000 #> Nptx1         3.44951987 3.60426494 3.51022093 3.32857508 3.53222106 3.4367115 #> Pde8a         0.95549842 0.97877848 0.91299388 1.06086870 1.00052882 0.0000000 #> Itih5         0.66908579 0.61358907 0.66298569 0.88788154 0.66934306 0.2564135 #> Homer2        1.96389655 2.22129055 1.81406114 1.84286080 2.66051456 1.6458791 #> Fam20c        2.02595270 2.06933668 1.66449848 1.96555317 1.41006144 2.5059174 #> Cplx2         4.84253940 5.22427279 4.94190933 4.76831409 4.92894758 5.1011530 #> Myo5b         1.08991437 1.30942463 1.27752362 1.23667112 1.09982000 1.0071975 #> Snca          4.62706705 4.73126980 4.85586143 4.61241596 4.60789463 5.0600640 #> Col3a1        0.10335846 0.09522224 0.14714881 0.21914560 0.13701240 0.0000000 #> Ecrg4         0.45018284 0.32103283 0.61516957 0.49927573 0.82417133 0.3875768 #> Map4k4        2.32223513 2.05759704 2.32236026 2.17313011 2.14955074 2.3387905 #> 2010300C02Rik 2.95949381 3.37786454 3.14329561 2.84124569 3.02035452 3.4352495 #> Ogfrl1        4.06706884 4.06803553 4.44373436 4.29416184 4.30641033 4.0158758 #> Fn1           1.10491890 0.98838442 1.10338559 0.92355011 1.00517314 0.6760625 #> Efhd1         1.68085370 1.43353602 1.55741521 1.35112243 1.69179593 0.8484207 #> Ngef          2.91242099 2.74592475 3.24004763 2.67797217 2.64117361 2.4591740 #> Bok           2.71366296 2.47116725 2.82089779 2.77238677 2.50119762 2.6689739 #> Tmem163       1.33074915 1.18819754 1.27391290 1.38626655 1.19782563 2.0900730 #> Lct           0.55087056 0.90609934 0.47985112 0.37742620 0.63297348 1.2735187 #> Cfh           0.88970003 0.91487359 0.72403399 0.65726992 0.53960703 1.0474544 #> Ptpn4         2.95295578 2.77964915 2.93667271 2.84916240 2.78932644 3.1403560 #> Tnni1         0.78849723 0.56909482 0.59023884 0.60013499 0.99522997 0.2824807 #> Csrp1         5.01572073 4.68519528 4.78446126 4.80670914 5.05684827 5.1119679 #> Nfasc         3.34835525 3.13436419 3.45235108 3.13689334 2.88211743 3.9146409 #> Syt2          0.66474670 0.55319344 0.69937910 0.56156080 0.27321902 0.2666210 #> Atp2b4        1.84269558 1.15386024 1.80429076 1.41293692 1.27377631 1.2427699 #> Rgs16         0.95357582 0.77241859 0.79247107 1.00855874 0.53107269 0.4951308 #> Ncf2          0.19577536 0.30744226 0.28517955 0.04401388 0.22083523 0.0000000 #> Cnih3         1.37787878 1.91073139 1.86309495 1.51923394 0.95664556 2.2298451 #> Tmem63a       1.59770579 1.66244580 1.57718404 1.76645489 1.62173987 0.8654414 #> Cfap126       0.22972328 0.20822942 0.17732501 0.33723331 0.34625506 0.0000000 #> Meig1         0.29109497 0.27586998 0.35000531 0.26306041 0.28185530 0.5090908 #> Ccdc3         0.78413847 0.73650858 0.63024330 0.68680921 0.59021747 1.1575822 #> Rgs5          2.02183992 2.33216198 2.25644205 2.17722922 2.79744251 2.4141827 #> Enkur         0.19258484 0.16684621 0.19068893 0.19143594 0.27889672 0.0000000 #> Myoc          0.58313508 0.62531156 0.54259460 0.46842173 0.37242729 0.2564135 #> Vim           1.63777758 1.87228319 1.50567183 1.96622246 1.92367017 1.2362695 #> Prkcq         0.57988915 0.51531037 0.72080768 0.76230445 0.99688914 0.6372650 #> Gad2          2.58905667 2.66586350 2.23435549 2.35198533 2.70805407 1.8277225 #> Lcn2          0.11001342 0.23756140 0.08109622 0.07181696 0.23086015 0.0000000 #> Nr4a2         1.22250797 0.88546766 1.12822732 0.84090078 1.14285461 1.1404969 #> Ermn          2.49706251 2.35035913 2.53116196 2.23101740 2.34756426 1.6429710 #> Fibcd1        1.06700564 1.12347821 1.12803125 1.14066428 1.31491645 2.0072588 #> Gsn           3.53057502 3.09333206 3.24377538 3.28817732 3.30329127 2.3946310 #> Grb14         3.42052836 3.36173213 2.77046062 3.08122822 3.00375570 2.9427657 #> Notch1        0.73795047 0.57299505 0.76784734 0.79697664 0.79244038 0.3703106 #> Ube2l6        0.79318618 0.71995881 0.73357527 0.72603253 0.68412857 0.7306790 #> Gatm          3.55985522 2.98305682 3.24247224 3.01039727 3.50364606 3.8087241 #> Cd82          1.49922529 1.58499533 1.36301618 1.50503499 1.30925932 1.4534073 #> Mdk           1.58694084 1.61605846 1.61063336 1.68377010 1.44990012 1.1585555 #> Lamp5         1.72564609 1.84724258 2.09268336 1.37732734 1.24490303 2.3696344 #> Itpka         3.38790169 3.77027935 3.64104099 3.56730816 3.20722970 3.6555564 #> Chgb          4.88863946 4.69165476 5.02117029 4.85742016 4.98184272 5.0368354 #> Mal           5.52489949 5.32136589 5.25246346 5.50360680 5.67157535 5.4366287 #> Pdyn          0.79158555 0.59079410 0.58304153 0.54279423 0.19734941 0.5758145 #> Nkx2-2        0.56734724 0.56550690 0.48407154 0.49525147 0.43224503 0.0000000 #> Edn3          0.13911894 0.05176152 0.10439934 0.24100412 0.17549881 0.0000000 #> Car2          4.79559426 4.66259955 4.63408113 4.92886903 4.97714175 5.0083894 #> Col9a3        0.73807814 0.71699776 0.55312249 0.70748193 0.83754395 1.2497755 #> Chrna4        1.65844964 1.85245203 1.94891048 1.54787324 1.42590930 1.1898229 #> Gss           1.23676224 0.97623337 1.16285378 1.02848915 1.06035712 0.2504086 #> Slc7a11       0.64926494 0.63902218 0.68024411 0.86961091 0.64560305 1.0871200 #> Tm4sf1        0.91410376 0.73984987 0.86342619 0.75260177 0.92873579 0.2666210 #> Kcnab1        2.77547276 2.98507524 2.92440955 2.70075041 2.18772552 3.4374489 #> Shox2         0.82458200 0.67605161 0.75661388 0.85502706 0.76525942 0.4929982 #> Serpini1      3.30040994 3.29933835 3.60183670 3.19300777 3.26845870 3.4041277 #> Tspan2        4.21697788 3.63807510 3.87527630 4.09312839 3.90853413 4.3763411 #> S100a11       0.55821875 0.46909211 0.50687831 0.66359584 0.74313723 0.0000000 #> Vcam1         0.90264419 1.11631737 0.91089476 0.85585352 1.14136059 1.0918987 #> Lef1          0.78796878 0.76062726 0.78915342 0.78366249 0.47511347 0.2564135 #> Npy2r         0.57723444 0.84627539 0.80665137 0.67953308 0.73797688 0.4196490 #> F3            1.17849759 1.49972532 1.29002259 1.29397785 1.59195340 0.0000000 #> Calb1         2.75161481 2.64565739 2.66071371 2.35304449 2.24703356 2.8503507 #> Epha7         2.07360225 1.93747690 2.12807952 2.16424935 1.78071038 2.7985356 #> Slc44a1       3.03127766 2.73384982 2.76202669 2.62223174 2.91734606 2.2830737 #> 1110017D15Rik 0.44254321 0.42104894 0.38350624 0.19568207 0.28069313 0.3703106 #> Tpm2          0.47347063 0.28035363 0.43004655 0.65260676 0.53526026 0.2564135 #> Slc6a9        1.76829554 1.79664252 1.68823316 1.74618441 2.14463735 1.3979006 #> Laptm5        1.75628277 1.68232228 1.38838393 1.44405341 1.98893577 2.1105590 #> Sema3c        0.79138634 0.46456785 0.85844214 0.52721566 0.30380740 0.6305185 #> Hpca          5.42154696 5.77634500 5.65291624 5.30758332 5.48050058 6.0249872 #> Padi2         1.47837486 1.10605178 1.07137082 0.92795207 1.38944203 0.4613923 #> Slc4a2        1.39994031 1.55371697 1.29468289 1.37431593 1.41444369 0.6038967 #> Gabrd         2.41994887 2.39963813 2.38924771 2.08800067 2.15819546 2.3539306 #> Rgs12         1.22645589 1.21384074 1.12066235 1.14204164 1.11072187 1.1780739 #> Slc30a3       1.89363523 1.69620000 1.88026617 1.62812203 1.71538297 1.7453630 #> Emilin1       0.15988581 0.06982516 0.02383032 0.08950430 0.19240122 0.0000000 #> 1700001C02Rik 0.18927101 0.05728738 0.07733503 0.01839425 0.15710555 0.0000000 #> Gabra4        2.60497866 2.43929779 2.57947094 2.71908436 2.31227760 2.8052710 #> Pdgfra        0.78804945 0.93572625 1.03361028 1.15029471 0.90386397 0.7194057 #> Epha5         2.38930589 2.35544274 2.31345803 1.94187464 2.14475995 2.2749732 #> Tesc          2.30027805 1.98764453 2.43810163 2.14169984 2.12836973 2.4553152 #> Pitpnm2       2.15711440 2.59388505 2.21222659 1.94021692 2.44767598 2.7039998 #> Mmp17         2.44647351 2.48596867 2.83821830 2.60643100 2.31549141 1.9436145 #> Cit           2.54506390 2.26660798 2.68180498 2.55911909 2.31233140 2.5188545 #> Foxp2         0.98678529 1.02917465 1.17179142 1.19784971 0.73538372 0.3436696 #> Arpc1b        1.62470466 1.29123387 1.73839998 1.34042337 1.61413436 1.7838762 #> Col1a2        0.68218467 0.49410901 0.33255629 0.40645615 0.51822386 0.0000000 #> Eln           0.09061027 0.12437313 0.18921346 0.15069912 0.28733407 0.0000000 #> Pcolce        0.40835217 0.17567545 0.31943003 0.44060403 0.47988101 0.0000000 #> Tsc22d4       4.68481739 4.87820011 4.58044772 4.72661026 4.51677143 4.2072991 #> Cald1         1.00831433 1.09999147 0.96943989 0.73670233 0.93050467 0.8055152 #> Ccdc136       3.19733978 2.90704090 2.90717882 3.07481517 2.32147603 2.3319452 #> Npy           2.70571597 2.42263758 2.73864823 2.31508768 2.82614785 1.9942862 #> Slc13a4       0.32992903 0.09337211 0.14992969 0.18884589 0.12359795 0.0000000 #> Gkn3          0.61270038 0.38462317 0.52145131 0.66694451 0.19017267 0.0000000 #> Slc6a13       0.33661496 0.22670062 0.23966019 0.37448920 0.20501486 0.0000000 #> Mgp           1.66148784 0.78793329 1.50269980 1.41650584 1.02778485 0.3436696 #> Lmo3          2.42932341 2.62194967 2.67226522 2.35574188 2.40708808 2.5245086 #> Slco1c1       1.54177117 2.06311666 2.01561258 1.99786085 1.87544335 2.5707408 #> Cpne9         1.35270330 0.85277249 1.42153976 1.27506722 1.41430820 0.8109540 #> Itpr2         0.68257703 0.50138653 0.75204281 0.89185105 0.91117434 0.3474831 #> Slc6a11       2.61604162 2.62012288 2.50593623 2.66856608 2.30484151 2.5784086 #> Vamp1         2.48963304 2.49782797 2.57893644 2.89025235 2.48330459 2.1890445 #> Cd9           3.11862023 3.00308144 2.84786535 2.72844377 2.86524077 2.3690098 #> Pglyrp1       0.88571095 0.96683044 0.80009758 0.93906298 1.21806059 0.5068221 #> Slc17a6       1.62291007 1.66658407 1.77797658 1.80386313 1.27191228 1.6023952 #> Sipa1l3       1.46441270 1.87109964 1.53637225 1.57753377 1.71206764 1.7216736 #> Sh3gl3        2.42227350 2.18739040 1.96729858 2.11239853 2.11841189 2.1834760 #> Plekhb1       5.26989022 5.08766180 5.33292848 5.29172376 5.43168172 5.4000485 #> Nupr1         0.34593129 0.60897633 0.28826812 0.43127770 0.34710384 0.0000000 #> Dkk3          3.43279965 3.25478191 3.65911228 3.12123621 3.00627044 3.6254150 #> Cox6a2        1.53223212 1.20097966 1.34653532 1.53161448 1.02634977 1.0002553 #> Dkkl1         0.84140367 0.69790200 1.07608973 0.75568738 0.97585842 0.0000000 #> Fgfr2         1.78640295 1.47183801 1.58647443 1.62810292 1.71937644 1.4072603 #> Crym          2.59338157 2.77401687 2.90799042 2.55813201 2.23842391 2.8514304 #> Slc38a5       0.21605026 0.17444448 0.20752276 0.34937317 0.55424647 0.0000000 #> Flna          1.09557690 1.29788690 1.28178968 1.09731220 0.93128353 0.8206811 #> Bgn           0.55339634 0.55505453 0.52065451 0.54507218 0.63729383 0.2564135 #> Col4a1        1.02425466 0.93547399 1.18324437 1.02022529 1.15861721 1.8394679 #> Plat          1.14540299 1.24250895 1.21317463 0.99302566 1.10865702 0.9816925 #> Nr3c2         1.74298171 1.99898592 1.65044180 1.59818056 1.15467732 2.5707193 #> Cbln1         0.50677361 0.56843914 0.49778664 0.67986802 0.53191317 0.7215881 #> Gab1          1.50292378 1.59756945 1.69453646 1.46556971 1.69383067 1.0986573 #> Pllp          3.22415451 3.21743067 3.01274890 3.03544285 2.74681104 2.5136211 #> Necab2        2.21168530 1.90715240 2.26504854 2.39376640 2.30668914 1.1476453 #> Dbndd1        1.15359092 1.34742373 1.27477861 1.35473435 1.17078218 0.7872716 #> Agt           2.58344953 2.65131727 2.23244375 2.66909410 2.54067049 2.9915034 #> Cryab         5.18551692 4.86790348 4.88570189 4.82335774 4.79686080 4.3052533 #> Tagln         0.33838878 0.37546179 0.46356002 0.56298326 0.21107501 0.0000000 #> Mcam          1.17115913 0.82098156 0.95253117 0.80677507 0.93344433 0.9827394 #> Olfm2         2.16938520 2.03888319 2.31740773 1.92146082 2.15946392 2.4801375 #> Icam5         2.81103374 2.98606878 2.87476056 2.66370075 3.01691101 3.2118431 #> Anxa2         0.57179514 0.34788829 0.50720952 0.70967632 0.45995659 0.6369316 #> Rora          2.72090769 3.14506075 2.91905783 2.85151295 2.69507749 1.8534747 #> Calml4        0.17812836 0.24026338 0.21439030 0.26489800 0.12279855 0.2564135 #> Htr3a         0.20623614 0.25779001 0.21562203 0.29249946 0.51795632 0.0000000 #> Paqr5         0.28548196 0.34937823 0.26226962 0.31439479 0.41305397 0.1371682 #> Rasgrf1       4.15342599 4.27961595 4.33009229 4.13530341 4.16508849 4.5934711 #> Zic1          1.47768397 1.44655695 1.39423152 1.80648344 1.34917327 2.0632232 #> Mobp          6.59632749 6.31520717 6.49676468 6.46728343 6.69364109 6.2946899 #> Hhatl         0.93681733 1.06462245 0.98033459 1.11457753 1.24083725 1.0382275 #> Trf           5.45009365 5.02241912 5.14522113 4.95783218 5.58619057 5.1389024 #> Cpne4         1.77621294 1.63315095 1.92080522 1.89454150 1.47925758 1.1136211 #> Cdhr4         0.10169997 0.12003410 0.12457179 0.06082551 0.00000000 0.0000000 #> Cd59a         1.09204790 1.27182310 1.17265850 0.83537412 0.89930350 1.3773815 #> Gng11         2.51158658 2.82844009 2.39374372 2.58329008 2.65677985 2.6251262 #> Chrm1         2.58901145 2.56080761 2.84557636 2.32416159 2.60370776 2.0795552 #> Prr5l         0.82610324 0.76269196 0.57957434 0.65938983 0.55913009 0.6862699 #> Ugt8a         2.78339796 2.44413871 2.53914210 2.46467594 2.32760436 0.9639957 #> Rims3         2.76819976 2.12361322 2.58159429 2.79867693 2.35592738 2.2271525 #> Sgpp2         0.93686313 0.51241116 0.76483544 0.87672988 1.07059811 0.9898886 #> Camkv         4.44530499 4.39151834 4.74003800 4.44649869 4.41698046 5.4369734 #> Sox10         1.87523360 1.68483776 1.86954113 1.71488287 1.81402802 1.9575917 #> Micall1       1.05263096 1.00082961 1.24536063 1.03367055 1.12657206 1.6637881 #> Tie1          0.34054619 0.32802029 0.30334945 0.33701117 0.32710426 0.2824807 #> Fa2h          2.70702598 2.15260925 2.41984825 2.42349903 2.22907359 1.7402922 #> Ucp2          0.79834906 0.75259766 1.12235205 1.13314304 1.32931986 1.5159634 #> Vav3          0.98378113 0.76786652 0.63515849 0.75285785 0.26584800 0.5328893 #> Ccp110        2.29732034 2.19807779 2.47177250 1.90358959 1.82606217 2.4110374 #> Gria2         4.59242525 4.64033571 4.81893386 4.40964277 4.66819325 5.2594264 #> Rasl10a       1.54192423 1.73460468 1.60630631 1.35696467 1.33128251 1.7335148 #> Foxj1         0.58587705 0.65336904 0.39514923 0.46595485 0.55686934 0.0000000 #> Trim59        0.87326383 1.06343482 1.05911906 0.80614020 1.19515684 0.7928307 #> Dynlrb2       0.26238060 0.21789545 0.17695090 0.13195426 0.24472416 0.0000000 #> Gjc1          0.25997653 0.40032750 0.38944777 0.32112771 0.39605926 0.9215004 #> Neurod1       0.67678261 0.81565899 0.80869242 0.72888077 0.64958901 0.9152128 #> Ttyh2         2.00867858 1.61856659 1.52483405 1.73481250 1.94563902 1.9251238 #> Cpne7         1.83558011 1.68264494 1.91383742 1.91205820 1.96437175 1.6219654 #> Nrip3         2.86404839 2.54543673 2.89416401 2.69424073 2.64936601 2.2236894 #> Tbr1          1.98502173 1.94914444 2.35409038 1.89777057 1.66296620 1.6540140 #> Lcat          1.48401002 1.79499129 1.41899153 1.42503144 1.49609368 1.4704056 #> Tmem98        0.84876609 0.78400162 0.76138953 0.85510839 1.28831323 0.6518838 #> Myo1d         0.62446089 0.40878407 0.64095163 0.47877072 0.52474848 0.6478262 #> Prdm8         1.04292224 1.27702526 1.13657692 0.83121952 0.77800741 1.6912317 #> Tgfbi         0.16242251 0.10086874 0.11706610 0.33153366 0.28952068 0.0000000 #> Kcnc2         2.85238527 2.59184448 2.80120583 2.81393417 1.82541417 3.5675709 #> Thrsp         1.66670187 2.09722949 1.64618163 2.02629276 1.75051207 2.3582313 #> Isg15         0.66931028 0.84537077 0.61051327 0.68058352 0.64991891 0.3935818 #> Acta2         0.57752461 0.54501809 0.56501864 0.64096745 0.69354224 0.0000000 #> H2-Q4         0.12644221 0.13312345 0.13251285 0.13326698 0.36279216 0.0000000 #> Dock4         2.29163340 2.21266447 2.43823628 1.83282468 1.96590270 2.4823942 #> Myrf          1.68052605 1.50964521 1.51786885 1.71116937 1.51161493 2.7020055 #> Lmo1          1.68561146 2.17490628 1.99279555 2.00818965 1.59998363 2.9855520 #> Igfbp7        1.77284339 1.99886593 1.93657362 2.05040476 2.33193718 1.0121604 #> P2ry12        1.37878842 1.24887876 1.19884558 1.45998888 1.78452703 1.7301314 #> Pcdh8         1.16073414 1.37681956 1.02213157 1.29615729 0.97496592 1.6198937 #> Lgi4          1.28584162 1.08700341 1.11107934 1.17937170 1.69896078 0.5068221 #> Fxyd1         3.14185573 3.03257244 3.09423916 3.31509575 3.39728196 3.1929004 #> Fxyd7         4.24985766 4.36743132 4.51523820 4.11282865 3.66635135 3.9561871 #> Mag           5.12500474 4.67191908 4.65072225 4.92307953 4.78339942 5.0692949 #> Zcchc12       1.52902191 1.75238761 1.50205089 1.30837531 1.18592398 2.1019134 #> Anln          1.06438290 1.22290140 1.02662252 0.75448601 1.21465958 0.6797875 #> Wnt4          1.07266316 1.11076790 1.04697232 1.19598207 0.44986225 0.8317029 #> C1ql2         0.63756061 0.83656585 0.55546037 0.74039217 0.42425309 1.4792838 #> Unc93b1       0.65399313 0.72501458 0.64464940 0.57091079 1.05917378 1.2411060 #> Tspan15       1.48416997 1.31211576 1.53793806 1.15584722 1.17124980 1.5972370 #> Ppp1r14a      3.34120410 2.99944064 2.85879699 2.91610667 3.11068072 3.0766945 #> Clic4         2.58666667 2.36671046 2.12576758 2.38873272 2.69836201 2.0664659 #> Galnt6        0.79259003 0.86166055 0.59304957 0.62816013 0.94087487 0.3242240 #> Ccn3          1.69445080 1.82519651 2.02261190 1.50804077 2.07883176 2.2958439 #> Rims2         2.29191029 2.32112167 2.29767291 2.16756388 1.45935355 1.7251028 #> Zmat4         1.55506361 1.57574686 1.53556433 1.42295301 1.05790010 1.4843569 #> Cldn11        5.12673269 4.91747338 4.91391632 4.85413605 4.93278681 5.2484757 #> Ccdc33        0.15646381 0.08911464 0.06165821 0.03512126 0.14687971 0.0000000 #> Slc32a1       1.59437851 1.52183497 1.70916749 1.78111100 1.95042305 1.1983679 #> Tgm2          0.39655722 0.24013140 0.25795652 0.33902515 0.57609405 0.0000000 #> Vstm2l        2.22098701 2.38136884 2.51948666 2.11308075 2.07506678 2.2089450 #> Neurod6       2.63428566 2.50013668 2.77025341 2.64586781 2.55916111 2.4965476 #> Crygn         0.16837963 0.15891147 0.11078299 0.02585192 0.25634860 0.0000000 #> Enpp6         0.61638331 0.76178677 0.88997335 0.67357231 0.41861134 0.2387173 #> Neurod2       2.39954962 2.38922135 2.53563564 2.49431276 1.92186944 2.1457090 #> Satb2         0.99178482 0.81658359 1.09482562 0.50963007 1.03455500 0.7250296 #> Pcp4l1        2.97992708 2.96077966 2.92023724 3.06136601 2.54141375 2.1498052 #> Txnip         0.81687069 0.55199932 0.77762053 0.82753556 1.02713336 0.4566015 #> Egr1          2.14886893 1.96359869 2.38581323 2.15333255 2.12058191 2.9450464 #> Otud7b        1.54728064 1.44846861 1.72710033 1.37022748 1.55159842 1.0621922 #> Car14         1.24424269 1.11343694 1.07236797 1.21006471 1.11457941 0.5862004 #> Rgs4          3.46613950 3.57801726 3.66691030 3.69097731 3.26991343 2.2863177 #> Dock10        1.28970847 1.57049487 1.14562505 1.29309427 1.52662939 1.1203111 #> Lpar1         2.09900245 1.58915403 1.77779593 2.03084932 1.87624640 1.6533343 #> Trps1         0.88635242 1.09999999 0.96537691 0.70914548 0.77885897 0.6262941 #> Ptpn3         2.03505854 1.71841934 2.02237954 2.18976046 1.75715473 1.6801179 #> Lefty1        0.53841045 0.66308465 0.78954952 0.70686947 0.71217809 0.8436765 #> Zfhx3         1.01463614 0.96580755 1.05374459 1.16390482 1.05445715 0.8927713 #> St6galnac5    2.16976535 2.53073593 2.28547222 2.07026295 2.41378148 2.3171005 #> Ak5           2.81209723 2.96793488 2.67339895 2.68978028 2.65212379 2.2315317 #> Hrh3          2.26063005 1.67483898 2.03100649 2.01218617 1.34537819 1.2703098 #> Nexn          0.56948760 0.48736435 0.47581899 0.49945862 0.27890296 0.2564135 #> Adgrl4        1.04985868 0.90483970 0.92898229 0.97800088 1.06809182 0.5068221 #> Rlbp1         0.77307162 1.09270069 0.79549368 0.85825563 0.41168285 0.7177937 #> Igfbp2        1.50043225 1.40823846 1.38463073 1.42376461 1.60911510 0.8100896 #> Wfs1          2.18927867 2.30295460 2.32184235 2.44810454 2.92937818 2.1068153 #> Cplx3         0.89687539 0.93155993 1.02811878 0.55739109 1.14881459 1.1910550 #> Orai2         1.69283039 2.08994082 1.92667785 1.68048975 1.55877682 1.6261425 #> Olig2         1.60203185 1.34909962 1.26060560 1.09819003 1.39070009 2.4657778 #> Gpr37         3.10942139 2.62248215 2.73938171 2.69477256 2.76208140 3.3843659 #> Plcb4         2.21541850 2.22112223 2.19114756 2.49093229 1.48135714 1.5824280 #> Nxph4         0.22263899 0.21444872 0.23321410 0.21511268 0.21381214 0.5123107 #> Ndufa4l2      0.76029564 0.59436411 0.42263532 0.59691739 0.75663938 0.2564135 #> Cacng5        0.75850207 1.10563582 0.59535977 0.80880499 0.67086059 0.4663389 #> Plekhg1       1.63237476 1.45942596 1.58926683 1.67521499 1.07618807 0.9779528 #> Cmtm5         3.59912609 3.09342087 3.27582574 3.38148577 3.24189183 4.0948043 #> Gpr161        0.61508999 0.70157514 0.60472709 0.51476430 0.53725598 1.3769960 #> Rfx3          1.19477919 1.18544260 0.89180005 1.05139857 0.66943743 0.8861989 #> Igsf21        1.68603070 1.22147136 1.83816298 1.36185664 1.39103066 1.7312896 #> Ramp3         2.10765261 2.07922426 1.91348009 2.04867784 2.03535612 1.8926492 #> Arhgap12      1.31951502 1.16740918 1.43679667 1.47682701 1.25994916 1.6957406 #> Nkx6-2        1.90055006 1.39579282 1.44117547 1.54679054 1.80681039 1.7592271 #> Ninj2         0.44872324 0.37088683 0.60350690 0.38235840 0.30128077 0.3758855 #> Cldn5         2.05797803 2.16118255 2.01543084 2.15157241 2.88085137 1.9432223 #> Htr2c         0.72402001 0.71674657 0.94921040 0.83540190 0.72370414 1.3014022 #> Hspb8         0.65264924 0.53639950 0.44501817 0.53386240 0.82568828 0.3703106 #> Fmod          0.16746162 0.12864624 0.12528572 0.18129535 0.13869958 0.0000000 #> Prelp         0.89738015 0.60641398 0.70944223 0.79762136 0.64964328 0.9521178 #> Mpped1        2.61638152 2.52593116 2.79221724 2.09534555 2.49422851 2.6844707 #> Rapgef5       1.96906516 2.42593863 2.26278751 1.91891904 1.81402583 1.9696632 #> Vwa1          1.13226660 1.31113787 1.04354593 1.31549050 1.40072163 2.2643882 #> Stab1         0.43845358 0.42299714 0.40552315 0.36719874 0.45872728 0.2504086 #> Arl15         1.26545235 1.28025241 1.37925059 1.28053546 0.71570803 1.4224155 #> Reln          0.86476575 0.83080429 1.00051023 0.96892689 0.77288492 0.1371682 #> Mustn1        0.26758770 0.09690683 0.16914040 0.12959606 0.00000000 0.0000000 #> Pbxip1        1.34938308 1.33038450 1.52504316 1.15143540 1.19436056 2.3029478 #> Dnali1        0.11444348 0.09526922 0.10768508 0.11466140 0.20920214 0.0000000 #> Id1           1.62154126 1.37257775 1.28516523 1.47026285 1.89182064 1.2202405 #> Lrrtm3        1.33048713 1.24589537 1.37982293 1.11962727 0.75626311 1.0594517 #> Tmem212       0.26257481 0.14465794 0.17697560 0.18815656 0.16627582 0.3741050 #> Epop          1.70575981 2.20123934 2.11031292 1.70178432 1.65954865 2.0015656 #> Gjc2          1.50615090 1.47433026 1.34343557 1.24223850 1.31123383 2.0603772 #> 1190005I06Rik 1.35043254 1.35570109 1.12952302 1.02266077 1.17287740 1.8616339 #> Ctla2a        1.24079344 0.98451329 1.06031270 1.13176646 0.99305478 0.3547843 #> Cnr1          1.99177163 2.19292993 2.33292360 2.01669127 2.45104316 2.1977566 #> Gpr4          0.32994338 0.38349617 0.51193651 0.56655929 0.48262546 0.5230345 #> Sowaha        2.11056381 2.81955510 2.20716759 2.34804256 2.87009279 2.6319992 #> Tent5c        0.51357553 0.52555080 0.38222326 0.34015465 0.31439325 0.3976548 #> Serpinb1a     1.16808584 0.95532207 0.97708237 1.03182567 1.20150453 0.5758145 #> S1pr5         1.28460786 0.98366694 0.86736555 0.86549324 0.81975136 0.7280132 #> Penk          1.28150874 1.48804379 1.37118419 1.07752180 1.50500529 1.8658537 #> Cdc42ep2      1.31112799 1.03877484 1.33480677 1.30032413 1.17369038 0.6871979 #> Slitrk6       0.42813022 0.21470071 0.48738984 0.42940442 0.22577354 0.0000000 #> Hpcal4        4.41959519 4.53852396 4.64722880 3.90770677 4.57671568 4.6085595 #> Olig1         4.59979138 4.17669248 4.25667919 4.33405253 4.42979786 2.9726222 #> Rprml         3.07675148 2.89096108 3.24192141 3.01097068 3.15841849 3.0885792 #> Stxbp6        1.68982961 1.67759145 1.49422978 1.59922746 1.34631155 1.6554338 #> Hs3st2        1.12198006 1.02177563 1.24062153 0.97789314 0.88637304 0.5769102 #> Rbp1          1.36164224 1.36587083 1.21432986 1.38511940 1.12779742 0.5328893 #> Ppm1e         3.14150738 3.06855235 3.37154134 3.05397217 3.21361904 3.4547617 #> Sox18         0.55977904 0.81528063 0.42582977 0.60139038 0.38481028 0.6037182 #> Kctd4         1.22576360 1.28181598 0.87460770 1.13942354 0.62521228 1.2614962 #> Nxph3         0.98709456 0.70831593 1.11105497 0.66187736 0.85333024 0.4936364 #> Vat1l         0.90595201 0.84805180 0.70829763 0.71705645 1.05167716 0.3474831 #> Cd24a         0.83585240 0.66717923 0.63308184 0.42952765 0.77319714 0.3935818 #> Odf3b         0.19472127 0.11610201 0.15056997 0.05604758 0.14914976 0.3703106 #> Gjb1          1.63349091 1.24850559 1.23920304 1.25310596 1.40097070 1.0983238 #> Selplg        1.46198870 0.95436411 1.26787210 1.27829013 1.58337965 0.8879271 #> Bcl11b        2.08720626 2.64724695 2.35003951 1.99581744 2.15090413 2.5578504 #> Lhfp          1.30109693 1.69313788 1.63660291 1.29043961 1.15576850 1.9859031 #> Ranbp3l       0.03242664 0.27743058 0.04010778 0.11302941 0.00000000 0.2824807 #> Msx1          0.27092155 0.36375093 0.21662745 0.36830708 0.12867615 0.2564135 #> Zdhhc22       1.89107607 1.70658932 1.55754351 1.79296320 1.68515227 1.1714144 #> Phldb1        2.72674466 2.28226498 2.33404266 2.08710097 2.45410574 2.9918993 #> Ctxn1         4.63620134 4.70894211 4.78510560 4.55425034 4.60291026 4.9102322 #> Tprn          1.75470671 1.39721522 1.28822863 1.36993821 1.31152137 1.3917156 #> Vstm2a        2.28073151 2.26633071 2.15393733 2.28636983 2.22163146 2.1500628 #> Ndnf          0.51310409 0.58195774 0.38392762 0.50161323 0.43649448 0.3875768 #> Pdp1          3.01037972 2.98742459 3.06598155 3.05666212 2.75897253 2.8148635 #> Scn3b         2.40820926 2.84722996 2.85438349 2.75251782 2.69454073 3.5098934 #> Cdc42ep1      1.25933372 1.34260246 0.99908397 1.00464598 1.27408659 0.7373906 #> Gal3st1       1.58753819 1.44401350 1.29638097 1.31334863 1.32980736 1.8481187 #> Rasd1         1.29763417 1.41015801 1.31560461 1.43060189 1.44304974 1.1781116 #> Spink8        1.27139206 1.48848462 1.41945551 1.55335746 1.84664197 1.9907929 #> Opalin        3.34713558 3.25712117 2.96589080 2.98397388 3.26812150 3.1494090 #> Gja4          0.12059199 0.22431300 0.18452209 0.26626134 0.32685198 0.0000000 #> Synpo2        1.30381698 1.05201536 1.04885488 1.25656357 1.22006726 1.5780861 #> Pcdh20        1.02000367 1.35575835 1.33769133 1.26211034 0.83403675 1.7809842 #> Adra1b        1.27403000 1.02719137 1.28061157 0.99103440 1.14741183 1.1441730 #> Fam131a       3.58531575 3.79288244 3.59295331 3.26990512 2.77153982 3.6632339 #> Tmem125       1.06154618 0.77941710 0.91822041 1.19434335 0.92088619 1.2462929 #> Mb21d2        1.88319470 1.57101132 1.53801536 1.78219219 1.39135704 1.3609037 #> Lingo3        1.08347499 1.27753513 1.01662036 1.12567323 0.70963331 1.2846233 #> Ncald         4.47619030 4.63623903 4.66581202 4.35115584 4.38541089 4.7700048 #> Siglech       0.82944635 0.65626474 0.78482842 0.55325551 1.51082291 1.0615638 #> Rgs14         1.49998504 1.67943201 1.31174597 1.36534501 1.12748511 1.3400020 #> Gm14964       0.50914628 0.24641944 0.35409220 0.44864513 0.24150887 0.0000000 #> Gpr17         0.95594366 0.75231028 0.93072472 0.95879073 1.21728945 0.6845804 #> Cx3cr1        1.02819592 1.13498291 0.84360013 1.02390163 1.29212364 0.7194057 #> Ezr           1.70220561 1.86477689 1.47255180 1.38241032 1.93366439 1.1799208 #> Adarb2        0.75636302 0.75530304 0.86623663 0.88371980 0.80480183 0.3976548 #> Cpne8         0.80722610 0.75749844 0.77400170 0.72723726 0.63598534 0.8251990 #> Plekhg3       0.93540440 0.69588822 0.70566064 0.88679433 0.85559176 1.0493189 #> Lamb2         0.89661890 1.11155264 0.88756112 1.02605030 1.13427781 1.4909428 #> Creb5         0.61650207 0.41841136 0.38959639 0.45888483 0.47775179 0.6407260 #> Cntn2         2.19769046 1.98853482 2.31129249 1.83212021 2.27929936 1.2398097 #> Aldh1a1       2.29817855 2.52563080 2.35379228 2.65641791 2.47922311 1.5909304 #> Phgdh         3.16186234 3.45444131 3.10165196 3.33673834 3.61300815 3.2276782 #> Tnfaip6       1.30991237 1.27427386 0.99731184 1.03838146 0.58299791 0.3775465 #> Camk2d        1.91013264 1.75440216 2.22769858 1.77491542 1.64604388 1.5496669 #> Shisa6        1.40168284 1.60698652 1.61333210 1.72421787 1.27669855 2.1950510 #> Cthrc1        0.75791455 0.78019177 0.73432917 0.85975193 0.59578985 0.5068221 #> Tmem119       1.01709217 0.81441820 0.77017322 1.08834503 1.01649421 1.1748484 #> Hmgb2         1.00275853 0.66241499 0.74258912 0.52707685 0.40160431 0.6541978 #> Tmem158       2.27830361 2.23153622 2.33674527 2.00456458 1.79358921 2.6565355 #> Dsp           0.32584473 0.34822123 0.15779537 0.13951865 0.04866590 0.8175892 #> Lrtm2         1.78561984 1.62725178 1.82437791 1.91200291 1.25072335 1.0239489 #> Gabra5        2.08271045 2.19042809 2.35036426 2.17363466 1.86402028 2.8035044 #> Tns1          0.86826741 0.57209402 0.76665670 0.99855609 0.51350110 0.6067047 #> Nell1         1.84269481 1.74220880 1.68494960 1.88827253 1.65591025 0.9011789 #> Slain1        2.82831747 2.25443731 2.49507274 2.66298154 2.19900915 2.3975510 #> Prr18         2.69529293 2.32592581 2.10526236 1.93626405 2.62882326 1.7417281 #> S100a8        0.39841914 0.31742352 0.40403127 0.53159406 0.58116865 0.3474831 #> S100a9        0.45259758 0.22712797 0.47389134 0.48781378 0.40056456 0.1371682 #> Col8a2        0.06717989 0.05587790 0.09922726 0.10487230 0.42155426 0.0000000 #> Synpr         2.06776280 2.30042058 2.13497232 2.36693755 2.13873900 1.8655386 #> Sertm1        1.35580865 1.46341900 1.25682736 1.08935281 1.13479998 2.0082069 #> Adgrf5        0.89756501 0.66877532 1.13318007 1.20908964 0.95886855 1.1535245 #> Capg          0.38903655 0.35245856 0.21153810 0.28855782 0.27376925 0.0000000 #> Gjc3          2.05012612 2.15068339 1.93199599 1.85360953 2.02416301 0.9383281 #> Fcer1g        1.31521853 1.40151280 1.16901605 1.22187509 1.33067651 2.1634638 #> Pde1a         2.60443179 2.51600334 3.10065238 2.33133041 2.97094728 2.2677380 #> Tafa1         1.43448588 1.38764327 1.53188164 0.93793749 0.83074187 1.2099745 #> Ddn           4.74116866 5.10769279 4.80497790 4.76725155 4.88958648 5.7241280 #> Hopx          2.84716359 2.93676383 2.80524269 2.57688789 3.64036484 2.4846092 #> Ptk2b         4.25083755 4.58330163 4.44088016 4.56974541 4.09386716 3.4133443 #> Rgs3          1.48949093 1.63216949 1.50739170 1.75153065 1.47722520 1.1313837 #> Kcng2         0.81096094 0.99894463 0.76329563 0.97884792 0.37033260 0.9943758 #> Ntng1         1.66959193 1.52111510 1.55641161 1.78292903 1.47126781 1.4775886 #> H2-Q7         0.07293258 0.07103938 0.11838827 0.19723209 0.14273118 0.0000000 #> Ifitm2        0.96906880 1.09064416 0.90269673 0.95391429 1.21353976 1.4021251 #> Plaat3        2.50487243 2.51184225 2.66509723 2.22563314 3.00090855 2.8468772 #> Plekhh1       1.74894875 1.68160253 1.50615974 1.50661273 1.58905469 1.2009855 #> Myl4          1.18020420 1.28964125 1.57277445 0.96930487 1.49492177 0.9777995 #> H2-K1         1.33428078 1.59535735 1.74512473 1.78442778 2.14500032 1.5905231 #> Dpp6          3.17192427 3.06393903 3.25492974 3.23346631 2.74675531 3.3143334 #> Tmem91        0.91325311 1.01976509 0.90439258 0.71761435 0.98623491 0.6407260 #> Cyp2d22       1.12801427 1.03854008 1.18972937 1.23368207 1.79398667 0.3935818 #> Ttr           6.19462776 6.26366576 6.08356036 6.07872249 6.84390319 5.7097158 #> Suclg2        0.71876825 1.05265778 0.79135694 0.56916264 0.62196847 1.2940937 #> Patj          0.94550036 0.73674309 0.75330778 0.87271454 0.90792393 1.0548719 #> Btbd3         3.23569186 3.66107529 3.30479961 3.62928422 2.70333505 4.1914698 #> Unc13c        1.12647624 0.85563289 0.83457482 0.82026022 0.60663106 1.3103061 #> Syt9          0.73252808 0.66269409 0.74731851 0.70257922 0.30197116 0.9660008 #> Shisal1       1.63781235 1.58658496 1.63079867 1.72592166 1.27391482 1.8356435 #> Grm4          0.82379382 0.55970502 0.91102293 0.77318015 0.76956595 0.9669871 #> Sox11         0.72569496 0.98116963 0.90692982 0.91801201 0.78341938 1.3880737 #> Slc22a8       0.62010027 0.65232266 0.44280445 0.57180855 0.71534210 0.7740998 #> Slc24a3       3.34455169 3.06058189 3.38792495 3.35547202 2.89063604 2.6629890 #> Klk8          1.14965101 1.48560121 1.13405184 1.37458564 1.32795052 1.4736128 #> Ipcef1        1.55486089 1.28809917 1.90560329 1.18308943 1.57157324 2.0242319 #> Tnnt1         1.85088086 1.54993758 1.34763068 1.57888624 0.78988791 1.3366398 #> Hhip          0.30280717 0.48120264 0.35418673 0.58559193 0.56028980 0.2666210 #> Spag8         0.07313899 0.11994541 0.07826858 0.07973453 0.24626610 0.0000000 #> Fxyd6         2.76320510 2.76118346 2.82867431 2.47509575 3.00110702 1.6754807 #> Ppp1r3c       1.24356108 1.19575277 1.30680502 1.07985846 0.81875439 0.2666210 #> Cbln4         0.65457753 0.56382202 0.54803959 0.66918493 0.58515336 0.3758855 #> Nnat          4.39845107 3.86182696 4.01859780 4.37346434 4.21748417 4.5339505 #> Myl9          1.26493377 1.38354292 1.03635801 1.13510805 1.44268258 0.6635751 #> Vxn           3.53117569 3.31903989 3.47201305 3.21175235 3.32323417 3.4741524 #> Lgals1        1.43037952 1.64432200 1.67221114 1.58771425 1.82899585 0.3436696 #> Gpr88         0.93007302 0.57660156 0.74518927 0.68161931 0.74959412 0.0000000 #> Ctxn3         0.36793834 0.44103903 0.31762107 0.54951397 0.33353101 0.0000000 #> Lyz2          0.64063495 0.29592774 0.40658358 0.50297824 0.68417195 0.3474831 #> Tmem100       0.72780347 0.76122785 0.83235817 0.73586833 0.72919557 0.8543052 #> Wfdc17        0.03592151 0.03125994 0.10073253 0.10269814 0.25262848 0.0000000 #> Ahnak         0.87442210 0.76469206 0.79734451 0.91531682 1.40794558 0.7167474 #> Hba-a2        6.31671961 6.30178206 6.17605155 6.06596014 6.26167421 6.2308667 #> Hba-a1        6.77230847 6.68048781 6.62388866 6.48718732 6.78048518 6.7279361 #> Ccdc153       0.36423938 0.18890700 0.24146879 0.32301029 0.36814199 0.0000000 #> Ccnd1         1.49172433 1.43781973 1.87903187 1.67180559 1.71349654 1.6711655 #> Serpinh1      0.77813139 1.16936908 0.77033088 0.75731999 0.68906297 0.2824807 #> Gad1          3.11135615 2.86412058 3.21870359 3.36647334 2.93370810 2.2695200 #> Arhgef10      1.30399703 1.11347707 1.43731120 1.03112802 0.99866752 1.5000659 #> 2410004P03Rik 0.14404681 0.17406545 0.08321509 0.08717661 0.17331548 0.0000000 #> Nt5dc2        0.71051009 0.77568089 0.64458904 0.80447504 0.71280335 1.2502371 #> Cebpd         0.91772180 1.20032716 0.86517644 0.93989122 1.13127334 1.5196409 #> Sod3          0.71522440 0.61108203 0.37187077 0.72537202 0.70488595 0.7834772 #> H2-D1         2.26112351 2.59192070 2.24441472 2.23564957 2.31971537 2.4143860 #> C4b           1.20912580 1.07666214 1.08784349 0.97983734 1.23896846 0.6141041 #> Tmem88b       3.07189636 2.53557020 2.75820730 2.74813759 2.36238987 1.9045927 #> Hbb-bt        5.73427869 5.85482772 5.61558173 5.57224388 5.69711546 6.0253158 #> Rhog          2.06081008 2.00638986 2.06360270 2.08136653 1.95855083 1.2839779 #> Rprm          1.75743433 1.72853508 1.58142372 1.53667923 1.82211970 1.8632513 #> Ly6a          2.45182370 2.27519555 2.34222985 2.60751217 2.75894028 2.0413342 #> Mog           3.85434500 3.66219244 3.74512123 3.72785284 4.14058242 2.8615374 #> Trbc2         1.20583296 1.28703415 1.50146442 1.22354779 1.38336445 0.6090279 #> Igkc          0.13555940 0.24448284 0.20547536 0.14835237 0.10338205 0.2504086 #> Smim1         1.09552768 0.96792008 1.05119351 1.16738202 1.91408576 1.7977655 #> Hs3st4        2.39012844 2.20126636 2.49203687 2.68146833 2.47900039 2.7906412 #> Evi2a         2.06586106 2.00947394 1.94122254 1.99571269 2.67085999 1.9128370 #> Prkcg         4.14188600 4.17863055 4.46934041 4.14347947 3.94561260 4.3279904 #> Ly6c1         2.47782910 2.71577070 2.59802701 2.53117760 2.70659596 2.7301925 #> Gbp4          0.14737745 0.05765225 0.07565243 0.32623728 0.05709014 0.2666210 #> Wipf3         2.55544936 2.96123354 2.99511897 3.11271141 2.75874347 3.3429219 #> BC039966      0.08464373 0.07695937 0.13722385 0.10447754 0.34869164 0.0000000 #> Gm13889       1.46735997 1.54319311 1.51447377 1.42448664 1.08310793 0.7766758 #> Plcxd2        1.64210575 1.30250470 1.60803209 1.32447479 0.56780985 0.4196490 #> Mia           0.26367437 0.31952226 0.25723706 0.29690062 0.26626194 0.0000000 #> Pou3f1        1.86305306 2.03310718 1.83260238 1.72681881 1.72651282 3.0430671 #> Lrrc10b       1.20742881 1.61461967 1.26439875 1.45805132 1.47514670 1.9429702 #> Apol11b       0.35929836 0.24092320 0.20236074 0.27629799 0.17705447 0.2564135 #> Gpr62         1.17578799 1.10082468 1.17761935 1.16650569 1.15881284 0.6983290 #> Shisa8        0.41727316 0.26971254 0.31966186 0.31993890 0.47023109 0.8756489 #> Gm2115        0.82234763 1.22818773 1.03188783 1.23356153 1.12760221 1.2121439 #> Kctd12        2.20413606 2.03580757 2.30484518 2.27816759 2.13535177 2.3238084 #> 1700047M11Rik 0.95685380 0.88367167 0.76632284 0.86813679 0.55009271 0.8187913 #> Lhfpl3        1.20532422 1.39255353 1.12989133 1.16122852 0.66136299 1.4522671 #> C030029H02Rik 0.37708569 0.39173442 0.28273725 0.26811175 0.29861244 0.3741050 #> Gm19935       0.35745016 0.29221866 0.23263621 0.21978974 0.42931808 0.0000000 #> 9630013A20Rik 0.17597264 0.29575033 0.28874834 0.26833691 0.09952757 0.0000000 #> 2900040C04Rik 0.32757163 0.28457067 0.32113707 0.17356740 0.32761432 0.0000000 #>                cluster_4 #> Gna12         2.60609824 #> Ccnd2         1.75449691 #> Btbd17        1.20395106 #> Sox9          1.65161246 #> Sez6          3.40864347 #> Serpinf1      0.61207785 #> S100a6        1.92737468 #> Col1a1        0.16085927 #> Vwf           0.77167716 #> Esam          0.85819635 #> Npas1         0.61792941 #> Tiam1         2.08517521 #> Bcam          0.78622815 #> Hmgn2         1.82635952 #> Rab3b         1.46259667 #> Inmt          0.12421173 #> Ddr1          1.94713727 #> Homer3        1.57341038 #> Cp            0.28275109 #> Calb2         1.44793211 #> Man1a         1.23827535 #> Efnb3         2.65042930 #> Hlf           3.09046018 #> Gstm7         1.46685037 #> Cavin1        0.70230817 #> Sst           3.66156380 #> Hapln2        0.76712800 #> Hspb1         0.66489715 #> Ndrg1         2.73408497 #> Nid1          0.04243022 #> Kit           0.77771411 #> Pvalb         3.09893154 #> Tmbim1        1.79891682 #> Crip1         1.57047760 #> Tek           0.62410035 #> Elovl1        1.46954470 #> Cyba          1.07571205 #> Itih3         0.95701386 #> Cnp           5.39410872 #> Hap1          1.61910843 #> Clic1         0.51866093 #> Stx1a         2.57695025 #> Arpp19        4.54109612 #> Dio2          0.79573740 #> Id3           2.79703382 #> Crlf1         1.15496768 #> Ttc9b         4.45687988 #> Carhsp1       1.57075592 #> Cabp7         2.48792771 #> Fam163b       2.60011746 #> Rarres2       0.60835906 #> Syn2          4.69831340 #> Ick           0.92748210 #> Prox1         1.02388754 #> Adssl1        0.83671153 #> Vipr2         0.32945893 #> Gltp          1.76140268 #> Amotl1        1.47332766 #> Bcas1         2.79866172 #> Aldh1a2       0.06307203 #> Tppp3         2.18130652 #> Sirt2         4.27459459 #> Lpl           1.07121408 #> Cers2         2.43882985 #> Qdpr          4.73326809 #> Stk32c        2.22177632 #> Lbp           0.19627608 #> Hsd11b1       1.52920468 #> Vtn           2.53775487 #> Stac2         1.29603399 #> Plxdc1        1.00394069 #> Igfbp4        2.18737537 #> Dbndd2        2.03506595 #> Pltp          2.01247707 #> Slc12a4       0.85628245 #> Cadps2        1.81067037 #> Erbb3         0.51423124 #> Pmp22         1.22235809 #> Kcnab3        1.11418182 #> Myh11         0.14259988 #> Plod1         1.01513955 #> Etnppl        0.77888619 #> Arhgef25      3.50954343 #> Rcn3          0.75698657 #> Vip           0.61427950 #> Utrn          1.01510328 #> Grm1          1.93235928 #> Reep3         1.57246606 #> Fabp7         1.74874429 #> Dcn           0.43218827 #> Slc17a8       0.11292223 #> Dusp6         1.53022592 #> Kitl          1.58339868 #> Ccn2          0.56396116 #> Timp3         2.12169068 #> Ascl1         0.42467991 #> Unc5b         0.88591120 #> Vsir          0.62922846 #> Gamt          1.93081585 #> Ptprb         0.95638887 #> Csrp2         0.61034920 #> Adarb1        3.34622701 #> Rnf130        1.79891419 #> Nefh          1.89682064 #> Aebp1         0.30265744 #> Sept4         4.18425152 #> Gria1         4.44084827 #> Sypl          2.28179773 #> Arsg          0.85763161 #> Cacng4        1.43833695 #> Rab37         0.52556290 #> Itgb4         0.52681245 #> Aspa          1.43052716 #> Cygb          2.20674896 #> Rflnb         0.86553427 #> Doc2b         0.59824740 #> Gfap          2.78027907 #> Npas3         0.82203709 #> Serpina3n     1.34144027 #> Clmn          2.33553604 #> Prkch         0.49976063 #> Fbln5         0.43630675 #> Akr1c18       0.10277605 #> Gng4          1.09385812 #> Sema4d        1.68305206 #> Cxcl14        3.03239260 #> Hexb          3.27353577 #> Iqgap2        1.20430675 #> Crhbp         0.49109958 #> Rab3c         3.27239312 #> Thbs4         0.61252956 #> Serinc5       1.99901133 #> Erbin         1.98244265 #> Prkcd         2.14637020 #> Pdlim2        2.33042211 #> Ednrb         1.59033225 #> Cpne6         3.56585260 #> Sema5a        1.87068636 #> Matn2         1.35789783 #> Nptxr         4.61099196 #> Enpp2         4.51135587 #> Efcab6        0.43987268 #> Ppp1r1a       4.59851094 #> Litaf         1.79792102 #> Il1rap        1.40773267 #> Apod          4.62594045 #> Cpox          1.27439556 #> Grik1         0.52200308 #> Clic6         0.42591897 #> Nr4a1         0.85403244 #> Igfbp6        1.55487402 #> Sncg          0.39717035 #> Gzma          0.01537066 #> Grm2          1.19803763 #> Prph          0.26203379 #> Rsph1         0.26057185 #> Sox8          1.07632871 #> Fam234a       0.93518603 #> Lims2         0.98938857 #> Aqp4          2.39931394 #> Slc12a2       2.10404227 #> Cd74          0.10955569 #> Pdgfrb        0.56980162 #> Csf1r         2.53418697 #> Cbln2         0.53026081 #> Frmd8         1.45107637 #> Gldc          0.81997077 #> Tcf7l2        1.78881915 #> Bhlhe22       1.69768308 #> Kcnip2        2.85003650 #> Alas2         0.98245807 #> Gdf11         0.85765670 #> Baiap2        3.57025234 #> Ifitm3        1.65475491 #> Phkg1         0.95307076 #> Nptx1         3.83192513 #> Pde8a         0.48703240 #> Itih5         1.08149119 #> Homer2        2.19581914 #> Fam20c        1.76695203 #> Cplx2         5.27754568 #> Myo5b         1.38504287 #> Snca          4.82591434 #> Col3a1        0.13151465 #> Ecrg4         0.59745978 #> Map4k4        2.08664581 #> 2010300C02Rik 3.16523944 #> Ogfrl1        4.14079304 #> Fn1           1.07906684 #> Efhd1         1.06229685 #> Ngef          2.75647904 #> Bok           2.78164079 #> Tmem163       1.34780537 #> Lct           0.85846186 #> Cfh           0.71937055 #> Ptpn4         3.05481348 #> Tnni1         0.63957991 #> Csrp1         4.62308151 #> Nfasc         3.34781941 #> Syt2          0.45448942 #> Atp2b4        1.76384060 #> Rgs16         0.82849384 #> Ncf2          0.09961637 #> Cnih3         1.78926516 #> Tmem63a       1.60914217 #> Cfap126       0.21236296 #> Meig1         0.43572822 #> Ccdc3         0.53051383 #> Rgs5          2.22307367 #> Enkur         0.16460524 #> Myoc          0.35233935 #> Vim           1.55448093 #> Prkcq         0.53553084 #> Gad2          2.50678278 #> Lcn2          0.12253289 #> Nr4a2         0.95915164 #> Ermn          2.25647105 #> Fibcd1        1.39882457 #> Gsn           3.05493280 #> Grb14         2.61113828 #> Notch1        0.58981274 #> Ube2l6        0.73267755 #> Gatm          3.15793713 #> Cd82          1.39403665 #> Mdk           1.53376080 #> Lamp5         1.81610150 #> Itpka         3.73740983 #> Chgb          4.89580590 #> Mal           5.04683942 #> Pdyn          0.83021815 #> Nkx2-2        0.38872638 #> Edn3          0.10673408 #> Car2          4.83859775 #> Col9a3        0.93330550 #> Chrna4        1.63380471 #> Gss           1.63093165 #> Slc7a11       0.85798499 #> Tm4sf1        0.89917395 #> Kcnab1        3.04226008 #> Shox2         0.74921670 #> Serpini1      2.94974436 #> Tspan2        3.66338603 #> S100a11       0.55417837 #> Vcam1         0.90587290 #> Lef1          0.82801917 #> Npy2r         1.04472256 #> F3            1.34499351 #> Calb1         3.10570843 #> Epha7         2.52694235 #> Slc44a1       2.59962787 #> 1110017D15Rik 0.25822164 #> Tpm2          0.37449563 #> Slc6a9        1.73057613 #> Laptm5        1.38439411 #> Sema3c        0.66432371 #> Hpca          5.92641822 #> Padi2         0.79418108 #> Slc4a2        1.22137346 #> Gabrd         2.14254530 #> Rgs12         1.37988885 #> Slc30a3       1.95904506 #> Emilin1       0.27462874 #> 1700001C02Rik 0.08247050 #> Gabra4        2.73396239 #> Pdgfra        0.91472515 #> Epha5         2.46494758 #> Tesc          2.63279774 #> Pitpnm2       2.26748973 #> Mmp17         2.76300035 #> Cit           2.09743659 #> Foxp2         1.05428719 #> Arpc1b        1.56174316 #> Col1a2        0.27025654 #> Eln           0.23647582 #> Pcolce        0.29688338 #> Tsc22d4       4.38214380 #> Cald1         1.05283005 #> Ccdc136       3.18618838 #> Npy           2.51459626 #> Slc13a4       0.11711368 #> Gkn3          0.32377812 #> Slc6a13       0.34682235 #> Mgp           1.36713519 #> Lmo3          2.63058172 #> Slco1c1       1.79393540 #> Cpne9         1.15978487 #> Itpr2         0.70815555 #> Slc6a11       2.31871251 #> Vamp1         2.87882461 #> Cd9           2.77532732 #> Pglyrp1       0.83805061 #> Slc17a6       1.74404575 #> Sipa1l3       1.97744447 #> Sh3gl3        2.10938506 #> Plekhb1       5.03052367 #> Nupr1         0.35617664 #> Dkk3          3.32926588 #> Cox6a2        1.13090877 #> Dkkl1         0.54054309 #> Fgfr2         1.71329354 #> Crym          2.53876400 #> Slc38a5       0.52886519 #> Flna          0.96571296 #> Bgn           0.35033806 #> Col4a1        1.08994227 #> Plat          1.16879670 #> Nr3c2         1.81639594 #> Cbln1         0.64719536 #> Gab1          1.46719706 #> Pllp          2.83929320 #> Necab2        2.37856283 #> Dbndd1        1.20736269 #> Agt           2.30986060 #> Cryab         4.66577168 #> Tagln         0.42281179 #> Mcam          1.09629339 #> Olfm2         2.26084825 #> Icam5         3.07895079 #> Anxa2         0.38974761 #> Rora          2.58959747 #> Calml4        0.13459022 #> Htr3a         0.44621075 #> Paqr5         0.26346143 #> Rasgrf1       4.38499536 #> Zic1          1.45860493 #> Mobp          6.10458192 #> Hhatl         0.81980020 #> Trf           4.77173848 #> Cpne4         2.20413776 #> Cdhr4         0.06342928 #> Cd59a         1.43861027 #> Gng11         2.19151279 #> Chrm1         2.95772818 #> Prr5l         0.60336929 #> Ugt8a         2.00153051 #> Rims3         2.55188402 #> Sgpp2         0.57907461 #> Camkv         4.70088986 #> Sox10         1.65921654 #> Micall1       1.19040089 #> Tie1          0.30998037 #> Fa2h          2.11498241 #> Ucp2          0.83585966 #> Vav3          0.62844713 #> Ccp110        2.09204511 #> Gria2         4.68558326 #> Rasl10a       1.80985928 #> Foxj1         0.22307537 #> Trim59        0.99786278 #> Dynlrb2       0.07137860 #> Gjc1          0.34064045 #> Neurod1       0.84668834 #> Ttyh2         1.58859307 #> Cpne7         1.93052451 #> Nrip3         2.77075058 #> Tbr1          1.78988837 #> Lcat          1.41763369 #> Tmem98        0.56123415 #> Myo1d         0.66978023 #> Prdm8         1.25861063 #> Tgfbi         0.09177186 #> Kcnc2         2.67091282 #> Thrsp         2.06264951 #> Isg15         0.68267050 #> Acta2         0.53759005 #> H2-Q4         0.04403270 #> Dock4         2.45605205 #> Myrf          1.21563347 #> Lmo1          2.14353738 #> Igfbp7        2.07693868 #> P2ry12        1.54083467 #> Pcdh8         1.79334980 #> Lgi4          1.04604672 #> Fxyd1         3.12197726 #> Fxyd7         4.06784836 #> Mag           4.67393619 #> Zcchc12       1.52071335 #> Anln          0.68573737 #> Wnt4          0.90331411 #> C1ql2         1.16794137 #> Unc93b1       0.81959434 #> Tspan15       1.26549944 #> Ppp1r14a      2.58835889 #> Clic4         2.12422161 #> Galnt6        0.30211407 #> Ccn3          1.54742610 #> Rims2         2.28915772 #> Zmat4         1.49254831 #> Cldn11        4.78456149 #> Ccdc33        0.07363270 #> Slc32a1       1.83410423 #> Tgm2          0.40593632 #> Vstm2l        2.75978563 #> Neurod6       2.82060410 #> Crygn         0.09798658 #> Enpp6         0.58768814 #> Neurod2       2.71342401 #> Satb2         0.79402893 #> Pcp4l1        2.57535473 #> Txnip         0.68700917 #> Egr1          2.50492310 #> Otud7b        1.59728173 #> Car14         1.08944666 #> Rgs4          3.33547592 #> Dock10        1.73507733 #> Lpar1         1.60370465 #> Trps1         0.78861445 #> Ptpn3         2.00909251 #> Lefty1        0.81134858 #> Zfhx3         1.09077552 #> St6galnac5    2.56250778 #> Ak5           3.13566196 #> Hrh3          1.86482080 #> Nexn          0.48396001 #> Adgrl4        1.00117125 #> Rlbp1         0.99467230 #> Igfbp2        1.39985479 #> Wfs1          2.73229161 #> Cplx3         0.50906013 #> Orai2         2.26748066 #> Olig2         1.08102009 #> Gpr37         2.62296320 #> Plcb4         2.11957165 #> Nxph4         0.16686809 #> Ndufa4l2      0.68493998 #> Cacng5        0.73174308 #> Plekhg1       1.30868528 #> Cmtm5         3.15469470 #> Gpr161        0.70486753 #> Rfx3          1.26658762 #> Igsf21        1.76647020 #> Ramp3         1.81952795 #> Arhgap12      1.51450516 #> Nkx6-2        1.37399409 #> Ninj2         0.49197601 #> Cldn5         2.20681530 #> Htr2c         0.89371813 #> Hspb8         0.63868671 #> Fmod          0.04236641 #> Prelp         0.65903079 #> Mpped1        2.39482943 #> Rapgef5       2.40123292 #> Vwa1          1.17900956 #> Stab1         0.41544093 #> Arl15         1.13171031 #> Reln          0.89969889 #> Mustn1        0.05434083 #> Pbxip1        1.45561696 #> Dnali1        0.08601687 #> Id1           1.51472412 #> Lrrtm3        1.11618629 #> Tmem212       0.15113993 #> Epop          1.81153342 #> Gjc2          1.29166595 #> 1190005I06Rik 1.04935507 #> Ctla2a        1.32362644 #> Cnr1          2.12160609 #> Gpr4          0.48872287 #> Sowaha        2.97280378 #> Tent5c        0.25759204 #> Serpinb1a     0.95503066 #> S1pr5         0.68336274 #> Penk          1.45336436 #> Cdc42ep2      1.28679455 #> Slitrk6       0.18711931 #> Hpcal4        4.76118084 #> Olig1         4.10287912 #> Rprml         3.49550568 #> Stxbp6        1.80627634 #> Hs3st2        0.83422411 #> Rbp1          1.30611288 #> Ppm1e         3.21338301 #> Sox18         0.68029097 #> Kctd4         1.38510172 #> Nxph3         0.54103846 #> Vat1l         0.74698880 #> Cd24a         0.40742449 #> Odf3b         0.11363113 #> Gjb1          1.30976978 #> Selplg        1.18755362 #> Bcl11b        2.09150675 #> Lhfp          1.57670266 #> Ranbp3l       0.11161922 #> Msx1          0.15696548 #> Zdhhc22       1.49991394 #> Phldb1        2.21834915 #> Ctxn1         4.74797145 #> Tprn          0.99384427 #> Vstm2a        2.31470010 #> Ndnf          0.54665309 #> Pdp1          3.07130792 #> Scn3b         2.98404777 #> Cdc42ep1      0.92909667 #> Gal3st1       1.13100658 #> Rasd1         1.67572621 #> Spink8        1.68685087 #> Opalin        2.79718795 #> Gja4          0.18769692 #> Synpo2        1.01374359 #> Pcdh20        1.45659664 #> Adra1b        0.93910023 #> Fam131a       3.82104523 #> Tmem125       0.81514353 #> Mb21d2        1.76973253 #> Lingo3        0.92482011 #> Ncald         4.46018666 #> Siglech       0.87621547 #> Rgs14         1.48359693 #> Gm14964       0.23881197 #> Gpr17         0.73653293 #> Cx3cr1        0.95719342 #> Ezr           1.61193468 #> Adarb2        0.49534891 #> Cpne8         0.72932689 #> Plekhg3       0.58116792 #> Lamb2         0.91230505 #> Creb5         0.34033447 #> Cntn2         1.59843273 #> Aldh1a1       2.13762657 #> Phgdh         3.40225383 #> Tnfaip6       1.11901813 #> Camk2d        1.69034013 #> Shisa6        1.88370870 #> Cthrc1        0.86122853 #> Tmem119       0.96813052 #> Hmgb2         0.75379922 #> Tmem158       2.33485916 #> Dsp           0.56496508 #> Lrtm2         1.70069660 #> Gabra5        2.35473191 #> Tns1          0.68278002 #> Nell1         1.98912213 #> Slain1        2.70259995 #> Prr18         1.92474592 #> S100a8        0.35740871 #> S100a9        0.44543463 #> Col8a2        0.18741821 #> Synpr         2.65502986 #> Sertm1        1.18622154 #> Adgrf5        1.03373000 #> Capg          0.21266618 #> Gjc3          1.77287650 #> Fcer1g        1.07990094 #> Pde1a         2.36702109 #> Tafa1         1.26002983 #> Ddn           4.90921841 #> Hopx          2.98504911 #> Ptk2b         4.41025426 #> Rgs3          1.29883300 #> Kcng2         0.97869316 #> Ntng1         1.71046729 #> H2-Q7         0.09426609 #> Ifitm2        1.19277954 #> Plaat3        2.39613452 #> Plekhh1       1.42694370 #> Myl4          0.98021372 #> H2-K1         2.01438048 #> Dpp6          3.32538357 #> Tmem91        1.03303378 #> Cyp2d22       1.30268039 #> Ttr           6.25632335 #> Suclg2        0.47537351 #> Patj          0.59129471 #> Btbd3         3.54003655 #> Unc13c        0.76560805 #> Syt9          0.73367694 #> Shisal1       1.50139458 #> Grm4          0.67044200 #> Sox11         0.94133413 #> Slc22a8       0.74498851 #> Slc24a3       3.24439184 #> Klk8          1.46881306 #> Ipcef1        1.28184953 #> Tnnt1         1.17970564 #> Hhip          0.38943212 #> Spag8         0.05630185 #> Fxyd6         2.51761650 #> Ppp1r3c       1.32238705 #> Cbln4         0.72890041 #> Nnat          4.37366824 #> Myl9          1.25803289 #> Vxn           3.31594192 #> Lgals1        1.50991492 #> Gpr88         0.57929201 #> Ctxn3         0.39628055 #> Lyz2          0.46364032 #> Tmem100       0.65813793 #> Wfdc17        0.12579889 #> Ahnak         0.91869843 #> Hba-a2        5.95260496 #> Hba-a1        6.42665658 #> Ccdc153       0.15608004 #> Ccnd1         1.45258705 #> Serpinh1      0.88895100 #> Gad1          3.20243518 #> Arhgef10      1.14429536 #> 2410004P03Rik 0.17949586 #> Nt5dc2        1.11648381 #> Cebpd         1.09991152 #> Sod3          0.77167033 #> H2-D1         2.08413405 #> C4b           0.92330880 #> Tmem88b       2.17385844 #> Hbb-bt        5.36616636 #> Rhog          1.83048241 #> Rprm          1.73507034 #> Ly6a          2.50538847 #> Mog           3.46300407 #> Trbc2         1.23305101 #> Igkc          0.08856211 #> Smim1         1.01101079 #> Hs3st4        2.55684519 #> Evi2a         2.17418067 #> Prkcg         4.29179503 #> Ly6c1         2.71720127 #> Gbp4          0.11760288 #> Wipf3         3.44832475 #> BC039966      0.05227336 #> Gm13889       1.59952540 #> Plcxd2        1.35893527 #> Mia           0.17050296 #> Pou3f1        1.50999422 #> Lrrc10b       1.53819465 #> Apol11b       0.32937402 #> Gpr62         1.13247697 #> Shisa8        0.27554714 #> Gm2115        1.40123238 #> Kctd12        2.25485833 #> 1700047M11Rik 0.64729410 #> Lhfpl3        1.24297124 #> C030029H02Rik 0.34659023 #> Gm19935       0.24955801 #> 9630013A20Rik 0.33023852 #> 2900040C04Rik 0.32603957"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":null,"dir":"Reference","previous_headings":"","what":"create_average_detection_DT — create_average_detection_DT","title":"create_average_detection_DT — create_average_detection_DT","text":"calculates average gene detection cell metadata factor (e.g. cluster)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_average_detection_DT — create_average_detection_DT","text":"","code":"create_average_detection_DT(   gobject,   feat_type = NULL,   spat_unit = NULL,   meta_data_name,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   detection_threshold = 0 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"create_average_detection_DT — create_average_detection_DT","text":"gobject giotto object feat_type feature type spat_unit spatial unit meta_data_name name metadata column use expression_values expression values use detection_threshold detection threshold consider gene detected","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_average_detection_DT — create_average_detection_DT","text":"data.table average gene epression values factor","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"create_average_detection_DT — create_average_detection_DT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  create_average_detection_DT(g, meta_data_name = \"leiden_clus\") #>                cluster_2  cluster_5  cluster_1   cluster_3  cluster_6 cluster_7 #> Gna12         0.83606557 0.83333333 0.82716049 0.787037037 0.80000000       0.8 #> Ccnd2         0.57377049 0.59523810 0.61728395 0.564814815 0.51111111       0.7 #> Btbd17        0.41803279 0.41666667 0.40123457 0.416666667 0.35555556       0.3 #> Sox9          0.47540984 0.52380952 0.52469136 0.388888889 0.57777778       0.3 #> Sez6          0.81147541 0.78571429 0.85802469 0.787037037 0.71111111       0.8 #> Serpinf1      0.16393443 0.21428571 0.13580247 0.166666667 0.08888889       0.1 #> S100a6        0.67213115 0.66666667 0.66666667 0.583333333 0.64444444       0.6 #> Col1a1        0.07377049 0.03571429 0.03703704 0.083333333 0.04444444       0.1 #> Vwf           0.23770492 0.33333333 0.27777778 0.268518519 0.31111111       0.2 #> Esam          0.28688525 0.26190476 0.34567901 0.361111111 0.35555556       0.3 #> Npas1         0.11475410 0.16666667 0.16049383 0.203703704 0.11111111       0.2 #> Tiam1         0.58196721 0.52380952 0.49382716 0.555555556 0.40000000       0.4 #> Bcam          0.19672131 0.16666667 0.14814815 0.305555556 0.28888889       0.1 #> Hmgn2         0.59016393 0.59523810 0.59259259 0.500000000 0.55555556       0.6 #> Rab3b         0.50819672 0.48809524 0.47530864 0.416666667 0.40000000       0.5 #> Inmt          0.04918033 0.01190476 0.03703704 0.018518519 0.00000000       0.0 #> Ddr1          0.63934426 0.60714286 0.62962963 0.592592593 0.60000000       0.3 #> Homer3        0.42622951 0.35714286 0.34567901 0.296296296 0.22222222       0.6 #> Cp            0.08196721 0.13095238 0.08024691 0.083333333 0.00000000       0.1 #> Calb2         0.40163934 0.39285714 0.31481481 0.379629630 0.24444444       0.5 #> Man1a         0.36885246 0.39285714 0.37654321 0.351851852 0.28888889       0.7 #> Efnb3         0.75409836 0.77380952 0.67901235 0.703703704 0.80000000       0.7 #> Hlf           0.82786885 0.78571429 0.81481481 0.750000000 0.77777778       0.8 #> Gstm7         0.48360656 0.41666667 0.38888889 0.388888889 0.40000000       0.5 #> Cavin1        0.25409836 0.25000000 0.26543210 0.231481481 0.17777778       0.2 #> Sst           0.79508197 0.79761905 0.87037037 0.814814815 0.86666667       0.8 #> Hapln2        0.31967213 0.21428571 0.24691358 0.250000000 0.28888889       0.3 #> Hspb1         0.16393443 0.21428571 0.20370370 0.157407407 0.20000000       0.0 #> Ndrg1         0.77049180 0.67857143 0.74691358 0.768518519 0.77777778       0.4 #> Nid1          0.07377049 0.05952381 0.06790123 0.064814815 0.17777778       0.0 #> Kit           0.17213115 0.16666667 0.27160494 0.259259259 0.24444444       0.2 #> Pvalb         0.77049180 0.77380952 0.77777778 0.731481481 0.77777778       0.7 #> Tmbim1        0.68852459 0.60714286 0.56790123 0.555555556 0.51111111       0.3 #> Crip1         0.43442623 0.36904762 0.43209877 0.333333333 0.37777778       0.4 #> Tek           0.21311475 0.10714286 0.17901235 0.101851852 0.17777778       0.2 #> Elovl1        0.56557377 0.52380952 0.44444444 0.398148148 0.44444444       0.4 #> Cyba          0.33606557 0.39285714 0.28395062 0.388888889 0.17777778       0.3 #> Itih3         0.38524590 0.41666667 0.38888889 0.453703704 0.31111111       0.3 #> Cnp           0.99180328 0.98809524 0.98148148 0.981481481 1.00000000       0.9 #> Hap1          0.50000000 0.48809524 0.38888889 0.398148148 0.26666667       0.6 #> Clic1         0.35245902 0.21428571 0.20987654 0.250000000 0.17777778       0.2 #> Stx1a         0.58196721 0.63095238 0.65432099 0.611111111 0.57777778       0.6 #> Arpp19        0.90983607 0.89285714 0.96913580 0.851851852 0.95555556       0.9 #> Dio2          0.31147541 0.32142857 0.32098765 0.240740741 0.31111111       0.1 #> Id3           0.77868852 0.79761905 0.72222222 0.731481481 0.75555556       0.7 #> Crlf1         0.19672131 0.26190476 0.20987654 0.203703704 0.17777778       0.3 #> Ttc9b         0.88524590 0.94047619 0.89506173 0.814814815 0.86666667       0.9 #> Carhsp1       0.74590164 0.63095238 0.59259259 0.638888889 0.60000000       0.5 #> Cabp7         0.53278689 0.59523810 0.57407407 0.601851852 0.73333333       0.5 #> Fam163b       0.61475410 0.65476190 0.62345679 0.518518519 0.53333333       0.5 #> Rarres2       0.37704918 0.25000000 0.24074074 0.296296296 0.35555556       0.3 #> Syn2          0.92622951 0.92857143 0.90740741 0.907407407 0.95555556       0.9 #> Ick           0.42622951 0.41666667 0.45061728 0.333333333 0.33333333       0.3 #> Prox1         0.34426230 0.41666667 0.27777778 0.398148148 0.31111111       0.3 #> Adssl1        0.40983607 0.42857143 0.37037037 0.351851852 0.42222222       0.3 #> Vipr2         0.12295082 0.11904762 0.11111111 0.138888889 0.06666667       0.2 #> Gltp          0.63934426 0.54761905 0.59259259 0.481481481 0.60000000       0.6 #> Amotl1        0.40983607 0.40476190 0.45679012 0.462962963 0.44444444       0.4 #> Bcas1         0.85245902 0.76190476 0.80246914 0.805555556 0.73333333       0.7 #> Aldh1a2       0.04918033 0.02380952 0.03703704 0.111111111 0.00000000       0.1 #> Tppp3         0.70491803 0.58333333 0.62345679 0.611111111 0.60000000       0.6 #> Sirt2         0.95081967 0.95238095 0.95061728 0.953703704 0.91111111       0.9 #> Lpl           0.25409836 0.20238095 0.25308642 0.212962963 0.31111111       0.2 #> Cers2         0.64754098 0.70238095 0.64814815 0.611111111 0.62222222       0.8 #> Qdpr          0.95901639 0.88095238 0.93209877 0.953703704 0.97777778       1.0 #> Stk32c        0.66393443 0.61904762 0.62962963 0.592592593 0.55555556       0.3 #> Lbp           0.07377049 0.08333333 0.07407407 0.120370370 0.08888889       0.0 #> Hsd11b1       0.40163934 0.46428571 0.42592593 0.481481481 0.42222222       0.5 #> Vtn           0.70491803 0.72619048 0.69135802 0.611111111 0.66666667       0.5 #> Stac2         0.41803279 0.45238095 0.50000000 0.314814815 0.46666667       0.3 #> Plxdc1        0.38524590 0.45238095 0.41975309 0.425925926 0.28888889       0.3 #> Igfbp4        0.63934426 0.55952381 0.64814815 0.592592593 0.64444444       0.7 #> Dbndd2        0.70491803 0.65476190 0.65432099 0.648148148 0.64444444       0.8 #> Pltp          0.65573770 0.58333333 0.59259259 0.564814815 0.62222222       0.4 #> Slc12a4       0.33606557 0.26190476 0.32098765 0.194444444 0.31111111       0.3 #> Cadps2        0.49180328 0.48809524 0.45679012 0.453703704 0.42222222       0.4 #> Erbb3         0.15573770 0.14285714 0.14197531 0.175925926 0.22222222       0.3 #> Pmp22         0.47540984 0.47619048 0.40740741 0.435185185 0.33333333       0.4 #> Kcnab3        0.40163934 0.35714286 0.45679012 0.324074074 0.22222222       0.2 #> Myh11         0.05737705 0.08333333 0.06172840 0.083333333 0.04444444       0.2 #> Plod1         0.40163934 0.42857143 0.36419753 0.398148148 0.33333333       0.4 #> Etnppl        0.27049180 0.23809524 0.35802469 0.333333333 0.24444444       0.3 #> Arhgef25      0.78688525 0.72619048 0.80246914 0.787037037 0.71111111       0.7 #> Rcn3          0.16393443 0.09523810 0.22222222 0.194444444 0.08888889       0.1 #> Vip           0.25409836 0.23809524 0.22222222 0.222222222 0.15555556       0.2 #> Utrn          0.40163934 0.39285714 0.39506173 0.388888889 0.42222222       0.3 #> Grm1          0.49180328 0.42857143 0.47530864 0.592592593 0.44444444       0.4 #> Reep3         0.45901639 0.44047619 0.51234568 0.277777778 0.44444444       0.7 #> Fabp7         0.54098361 0.51190476 0.50617284 0.509259259 0.44444444       0.4 #> Dcn           0.13934426 0.11904762 0.11728395 0.120370370 0.08888889       0.2 #> Slc17a8       0.04918033 0.03571429 0.08024691 0.018518519 0.04444444       0.0 #> Dusp6         0.39344262 0.34523810 0.37037037 0.361111111 0.37777778       0.3 #> Kitl          0.43442623 0.47619048 0.46296296 0.370370370 0.28888889       0.3 #> Ccn2          0.19672131 0.30952381 0.27777778 0.166666667 0.33333333       0.1 #> Timp3         0.67213115 0.58333333 0.61111111 0.574074074 0.64444444       0.7 #> Ascl1         0.17213115 0.15476190 0.16666667 0.083333333 0.15555556       0.0 #> Unc5b         0.36065574 0.32142857 0.24074074 0.370370370 0.28888889       0.2 #> Vsir          0.36065574 0.28571429 0.29012346 0.268518519 0.40000000       0.1 #> Gamt          0.68852459 0.58333333 0.62345679 0.601851852 0.64444444       0.6 #> Ptprb         0.27049180 0.15476190 0.27160494 0.194444444 0.28888889       0.4 #> Csrp2         0.21311475 0.20238095 0.16666667 0.129629630 0.20000000       0.3 #> Adarb1        0.86065574 0.78571429 0.79629630 0.768518519 0.62222222       0.7 #> Rnf130        0.60655738 0.60714286 0.61111111 0.555555556 0.55555556       0.6 #> Nefh          0.59016393 0.58333333 0.57407407 0.620370370 0.48888889       0.8 #> Aebp1         0.15573770 0.11904762 0.15432099 0.111111111 0.11111111       0.0 #> Sept4         0.94262295 0.90476190 0.89506173 0.907407407 0.95555556       0.8 #> Gria1         0.89344262 0.92857143 0.92592593 0.898148148 0.88888889       0.8 #> Sypl          0.63114754 0.53571429 0.61728395 0.592592593 0.64444444       0.9 #> Arsg          0.41803279 0.42857143 0.33950617 0.333333333 0.46666667       0.1 #> Cacng4        0.46721311 0.41666667 0.51234568 0.472222222 0.31111111       0.3 #> Rab37         0.28688525 0.14285714 0.17901235 0.138888889 0.13333333       0.1 #> Itgb4         0.22950820 0.30952381 0.21604938 0.250000000 0.26666667       0.2 #> Aspa          0.54918033 0.44047619 0.46296296 0.500000000 0.44444444       0.7 #> Cygb          0.47540984 0.47619048 0.48148148 0.500000000 0.35555556       0.3 #> Rflnb         0.26229508 0.20238095 0.32716049 0.324074074 0.17777778       0.3 #> Doc2b         0.27049180 0.23809524 0.19753086 0.212962963 0.26666667       0.2 #> Gfap          0.73770492 0.73809524 0.72839506 0.657407407 0.75555556       0.9 #> Npas3         0.23770492 0.21428571 0.25308642 0.212962963 0.35555556       0.0 #> Serpina3n     0.36885246 0.40476190 0.32716049 0.342592593 0.24444444       0.5 #> Clmn          0.64754098 0.54761905 0.59259259 0.648148148 0.55555556       0.5 #> Prkch         0.16393443 0.17857143 0.17901235 0.175925926 0.22222222       0.2 #> Fbln5         0.09836066 0.05952381 0.10493827 0.074074074 0.11111111       0.0 #> Akr1c18       0.08196721 0.03571429 0.06790123 0.083333333 0.00000000       0.1 #> Gng4          0.30327869 0.25000000 0.30246914 0.277777778 0.24444444       0.6 #> Sema4d        0.61475410 0.54761905 0.54938272 0.527777778 0.48888889       0.4 #> Cxcl14        0.72131148 0.79761905 0.70987654 0.759259259 0.75555556       0.9 #> Hexb          0.75409836 0.80952381 0.80864198 0.842592593 0.82222222       0.7 #> Iqgap2        0.27049180 0.26190476 0.29629630 0.250000000 0.28888889       0.3 #> Crhbp         0.16393443 0.19047619 0.22839506 0.166666667 0.28888889       0.1 #> Rab3c         0.80327869 0.75000000 0.83333333 0.768518519 0.80000000       0.8 #> Thbs4         0.17213115 0.19047619 0.15432099 0.120370370 0.28888889       0.0 #> Serinc5       0.58196721 0.54761905 0.55555556 0.601851852 0.44444444       0.5 #> Erbin         0.72950820 0.57142857 0.75308642 0.638888889 0.62222222       0.7 #> Prkcd         0.58196721 0.61904762 0.53086420 0.601851852 0.48888889       0.5 #> Pdlim2        0.69672131 0.55952381 0.59259259 0.555555556 0.66666667       0.3 #> Ednrb         0.55737705 0.61904762 0.58024691 0.564814815 0.51111111       0.6 #> Cpne6         0.73770492 0.75000000 0.72222222 0.759259259 0.64444444       0.7 #> Sema5a        0.53278689 0.50000000 0.43827160 0.481481481 0.31111111       0.7 #> Matn2         0.31967213 0.39285714 0.39506173 0.314814815 0.35555556       0.3 #> Nptxr         0.84426230 0.86904762 0.90740741 0.814814815 0.82222222       0.8 #> Enpp2         0.93442623 0.90476190 0.91975309 0.879629630 0.93333333       0.8 #> Efcab6        0.09836066 0.14285714 0.16666667 0.101851852 0.13333333       0.2 #> Ppp1r1a       0.86885246 0.96428571 0.90123457 0.916666667 0.93333333       0.9 #> Litaf         0.54098361 0.48809524 0.46296296 0.444444444 0.53333333       0.5 #> Il1rap        0.55737705 0.47619048 0.47530864 0.509259259 0.46666667       0.4 #> Apod          0.96721311 0.94047619 0.96913580 0.944444444 0.97777778       0.9 #> Cpox          0.60655738 0.52380952 0.52469136 0.490740741 0.48888889       0.4 #> Grik1         0.19672131 0.17857143 0.14197531 0.175925926 0.11111111       0.3 #> Clic6         0.09016393 0.07142857 0.11111111 0.175925926 0.08888889       0.1 #> Nr4a1         0.20491803 0.25000000 0.32098765 0.222222222 0.08888889       0.1 #> Igfbp6        0.44262295 0.42857143 0.49382716 0.472222222 0.33333333       0.3 #> Sncg          0.12295082 0.09523810 0.12962963 0.129629630 0.13333333       0.0 #> Gzma          0.02459016 0.03571429 0.03086420 0.046296296 0.04444444       0.1 #> Grm2          0.28688525 0.26190476 0.33333333 0.231481481 0.20000000       0.2 #> Prph          0.04918033 0.07142857 0.05555556 0.101851852 0.00000000       0.1 #> Rsph1         0.09836066 0.04761905 0.07407407 0.083333333 0.11111111       0.2 #> Sox8          0.36065574 0.41666667 0.32716049 0.277777778 0.35555556       0.3 #> Fam234a       0.32786885 0.35714286 0.33333333 0.287037037 0.28888889       0.4 #> Lims2         0.43442623 0.40476190 0.33950617 0.351851852 0.40000000       0.3 #> Aqp4          0.72131148 0.73809524 0.71604938 0.759259259 0.71111111       0.9 #> Slc12a2       0.72131148 0.70238095 0.69135802 0.703703704 0.60000000       0.8 #> Cd74          0.05737705 0.10714286 0.06172840 0.074074074 0.02222222       0.0 #> Pdgfrb        0.20491803 0.22619048 0.20370370 0.175925926 0.24444444       0.1 #> Csf1r         0.75409836 0.70238095 0.66666667 0.601851852 0.60000000       0.7 #> Cbln2         0.27868852 0.14285714 0.16049383 0.250000000 0.22222222       0.1 #> Frmd8         0.46721311 0.38095238 0.46296296 0.388888889 0.35555556       0.3 #> Gldc          0.27868852 0.32142857 0.30246914 0.305555556 0.24444444       0.2 #> Tcf7l2        0.45901639 0.46428571 0.41358025 0.453703704 0.42222222       0.3 #> Bhlhe22       0.38524590 0.41666667 0.46913580 0.351851852 0.28888889       0.4 #> Kcnip2        0.54098361 0.54761905 0.69135802 0.555555556 0.66666667       0.7 #> Alas2         0.37704918 0.32142857 0.34567901 0.259259259 0.24444444       0.4 #> Gdf11         0.30327869 0.27380952 0.27160494 0.240740741 0.28888889       0.2 #> Baiap2        0.74590164 0.75000000 0.73456790 0.666666667 0.60000000       0.7 #> Ifitm3        0.50819672 0.57142857 0.46913580 0.564814815 0.55555556       0.4 #> Phkg1         0.31147541 0.29761905 0.27777778 0.268518519 0.35555556       0.0 #> Nptx1         0.72950820 0.76190476 0.75308642 0.675925926 0.80000000       0.7 #> Pde8a         0.31967213 0.30952381 0.30864198 0.342592593 0.35555556       0.0 #> Itih5         0.22950820 0.19047619 0.21604938 0.277777778 0.20000000       0.1 #> Homer2        0.59836066 0.61904762 0.52469136 0.500000000 0.71111111       0.5 #> Fam20c        0.61475410 0.61904762 0.50000000 0.555555556 0.40000000       0.7 #> Cplx2         0.92622951 0.91666667 0.92592593 0.861111111 0.91111111       1.0 #> Myo5b         0.32786885 0.36904762 0.38271605 0.333333333 0.31111111       0.3 #> Snca          0.90163934 0.86904762 0.93209877 0.898148148 0.88888889       1.0 #> Col3a1        0.03278689 0.03571429 0.04320988 0.064814815 0.04444444       0.0 #> Ecrg4         0.16393443 0.10714286 0.19753086 0.157407407 0.26666667       0.2 #> Map4k4        0.68852459 0.63095238 0.67283951 0.629629630 0.60000000       0.7 #> 2010300C02Rik 0.71311475 0.78571429 0.77777778 0.666666667 0.73333333       0.7 #> Ogfrl1        0.87704918 0.86904762 0.93827160 0.879629630 0.91111111       0.8 #> Fn1           0.35245902 0.32142857 0.34567901 0.268518519 0.28888889       0.3 #> Efhd1         0.52459016 0.44047619 0.48148148 0.398148148 0.46666667       0.2 #> Ngef          0.69672131 0.65476190 0.77777778 0.648148148 0.64444444       0.6 #> Bok           0.72131148 0.65476190 0.70987654 0.648148148 0.60000000       0.8 #> Tmem163       0.40163934 0.36904762 0.37654321 0.425925926 0.37777778       0.6 #> Lct           0.17213115 0.23809524 0.15432099 0.111111111 0.17777778       0.4 #> Cfh           0.30327869 0.29761905 0.24691358 0.194444444 0.15555556       0.3 #> Ptpn4         0.76229508 0.71428571 0.73456790 0.703703704 0.68888889       0.8 #> Tnni1         0.29508197 0.21428571 0.20987654 0.194444444 0.31111111       0.1 #> Csrp1         0.98360656 0.92857143 0.96296296 0.944444444 0.95555556       1.0 #> Nfasc         0.84426230 0.78571429 0.84567901 0.777777778 0.75555556       0.9 #> Syt2          0.23770492 0.17857143 0.19135802 0.166666667 0.06666667       0.1 #> Atp2b4        0.53278689 0.36904762 0.51234568 0.416666667 0.33333333       0.3 #> Rgs16         0.30327869 0.25000000 0.21604938 0.277777778 0.13333333       0.2 #> Ncf2          0.07377049 0.09523810 0.09876543 0.009259259 0.06666667       0.0 #> Cnih3         0.43442623 0.55952381 0.54320988 0.435185185 0.33333333       0.7 #> Tmem63a       0.46721311 0.50000000 0.50000000 0.518518519 0.44444444       0.3 #> Cfap126       0.07377049 0.08333333 0.05555556 0.111111111 0.13333333       0.0 #> Meig1         0.10655738 0.09523810 0.10493827 0.101851852 0.11111111       0.2 #> Ccdc3         0.26229508 0.26190476 0.20370370 0.222222222 0.17777778       0.3 #> Rgs5          0.59016393 0.66666667 0.64197531 0.601851852 0.73333333       0.6 #> Enkur         0.06557377 0.04761905 0.06172840 0.064814815 0.11111111       0.0 #> Myoc          0.16393443 0.14285714 0.16666667 0.111111111 0.11111111       0.1 #> Vim           0.45901639 0.55952381 0.45679012 0.546296296 0.55555556       0.4 #> Prkcq         0.20491803 0.17857143 0.25308642 0.259259259 0.31111111       0.2 #> Gad2          0.70491803 0.73809524 0.61111111 0.620370370 0.64444444       0.5 #> Lcn2          0.04098361 0.08333333 0.03086420 0.027777778 0.06666667       0.0 #> Nr4a2         0.40163934 0.30952381 0.37037037 0.268518519 0.35555556       0.3 #> Ermn          0.65573770 0.60714286 0.66049383 0.583333333 0.57777778       0.5 #> Fibcd1        0.28688525 0.28571429 0.29629630 0.287037037 0.35555556       0.5 #> Gsn           0.83606557 0.73809524 0.78395062 0.759259259 0.75555556       0.6 #> Grb14         0.81147541 0.83333333 0.70370370 0.759259259 0.73333333       0.8 #> Notch1        0.27049180 0.22619048 0.25308642 0.268518519 0.24444444       0.1 #> Ube2l6        0.27868852 0.25000000 0.24691358 0.250000000 0.26666667       0.3 #> Gatm          0.84426230 0.72619048 0.79629630 0.759259259 0.82222222       0.9 #> Cd82          0.45901639 0.50000000 0.41975309 0.472222222 0.37777778       0.4 #> Mdk           0.50819672 0.47619048 0.51851852 0.509259259 0.42222222       0.4 #> Lamp5         0.47540984 0.48809524 0.54320988 0.379629630 0.35555556       0.7 #> Itpka         0.77049180 0.82142857 0.79012346 0.777777778 0.71111111       0.7 #> Chgb          0.96721311 0.91666667 0.93827160 0.935185185 0.97777778       1.0 #> Mal           0.95901639 0.95238095 0.95679012 0.972222222 0.95555556       1.0 #> Pdyn          0.25409836 0.17857143 0.19753086 0.157407407 0.08888889       0.2 #> Nkx2-2        0.18852459 0.20238095 0.17283951 0.148148148 0.15555556       0.0 #> Edn3          0.04918033 0.02380952 0.04320988 0.083333333 0.04444444       0.0 #> Car2          0.96721311 0.96428571 0.95061728 0.962962963 0.95555556       1.0 #> Col9a3        0.26229508 0.25000000 0.20370370 0.231481481 0.24444444       0.4 #> Chrna4        0.50000000 0.54761905 0.56172840 0.435185185 0.37777778       0.3 #> Gss           0.42622951 0.35714286 0.38271605 0.342592593 0.33333333       0.1 #> Slc7a11       0.21311475 0.23809524 0.22222222 0.277777778 0.20000000       0.4 #> Tm4sf1        0.28688525 0.22619048 0.27160494 0.259259259 0.28888889       0.1 #> Kcnab1        0.71311475 0.72619048 0.75308642 0.694444444 0.55555556       0.8 #> Shox2         0.22131148 0.17857143 0.21604938 0.203703704 0.20000000       0.1 #> Serpini1      0.77049180 0.77380952 0.80246914 0.712962963 0.75555556       0.8 #> Tspan2        0.90983607 0.82142857 0.85802469 0.879629630 0.82222222       0.9 #> S100a11       0.19672131 0.14285714 0.16666667 0.222222222 0.24444444       0.0 #> Vcam1         0.31147541 0.36904762 0.30864198 0.268518519 0.35555556       0.3 #> Lef1          0.23770492 0.23809524 0.22222222 0.203703704 0.13333333       0.1 #> Npy2r         0.20491803 0.25000000 0.25308642 0.185185185 0.22222222       0.2 #> F3            0.37704918 0.48809524 0.40123457 0.398148148 0.44444444       0.0 #> Calb1         0.73770492 0.67857143 0.70370370 0.611111111 0.60000000       0.6 #> Epha7         0.56557377 0.50000000 0.57407407 0.564814815 0.48888889       0.6 #> Slc44a1       0.78688525 0.70238095 0.74691358 0.685185185 0.71111111       0.6 #> 1110017D15Rik 0.16393443 0.15476190 0.12345679 0.064814815 0.11111111       0.1 #> Tpm2          0.16393443 0.09523810 0.13580247 0.212962963 0.17777778       0.1 #> Slc6a9        0.56557377 0.57142857 0.50000000 0.490740741 0.64444444       0.4 #> Laptm5        0.57377049 0.47619048 0.43209877 0.407407407 0.53333333       0.6 #> Sema3c        0.26229508 0.19047619 0.27160494 0.166666667 0.11111111       0.2 #> Hpca          0.95081967 0.96428571 0.97530864 0.898148148 0.97777778       1.0 #> Padi2         0.47540984 0.34523810 0.35802469 0.277777778 0.44444444       0.2 #> Slc4a2        0.46721311 0.51190476 0.43827160 0.435185185 0.42222222       0.2 #> Gabrd         0.65573770 0.65476190 0.64197531 0.564814815 0.57777778       0.7 #> Rgs12         0.41803279 0.39285714 0.34567901 0.361111111 0.33333333       0.4 #> Slc30a3       0.50819672 0.45238095 0.50617284 0.444444444 0.46666667       0.5 #> Emilin1       0.05737705 0.02380952 0.01234568 0.037037037 0.06666667       0.0 #> 1700001C02Rik 0.05737705 0.02380952 0.03086420 0.009259259 0.06666667       0.0 #> Gabra4        0.66393443 0.63095238 0.69135802 0.685185185 0.60000000       0.8 #> Pdgfra        0.27049180 0.28571429 0.30864198 0.342592593 0.28888889       0.2 #> Epha5         0.65573770 0.63095238 0.61111111 0.500000000 0.57777778       0.6 #> Tesc          0.58196721 0.52380952 0.64814815 0.527777778 0.60000000       0.6 #> Pitpnm2       0.61475410 0.70238095 0.63580247 0.555555556 0.66666667       0.6 #> Mmp17         0.59836066 0.59523810 0.67283951 0.611111111 0.60000000       0.4 #> Cit           0.69672131 0.59523810 0.68518519 0.666666667 0.60000000       0.7 #> Foxp2         0.30327869 0.30952381 0.32716049 0.333333333 0.22222222       0.1 #> Arpc1b        0.52459016 0.41666667 0.53086420 0.407407407 0.46666667       0.6 #> Col1a2        0.22131148 0.19047619 0.10493827 0.120370370 0.17777778       0.0 #> Eln           0.03278689 0.05952381 0.06172840 0.046296296 0.08888889       0.0 #> Pcolce        0.14754098 0.07142857 0.10493827 0.138888889 0.15555556       0.0 #> Tsc22d4       0.95901639 0.97619048 0.96296296 0.962962963 0.93333333       0.9 #> Cald1         0.35245902 0.32142857 0.31481481 0.240740741 0.28888889       0.3 #> Ccdc136       0.78688525 0.72619048 0.73456790 0.731481481 0.55555556       0.6 #> Npy           0.72131148 0.64285714 0.71604938 0.574074074 0.71111111       0.6 #> Slc13a4       0.11475410 0.03571429 0.04938272 0.064814815 0.04444444       0.0 #> Gkn3          0.18032787 0.10714286 0.14814815 0.203703704 0.06666667       0.0 #> Slc6a13       0.12295082 0.08333333 0.08024691 0.120370370 0.06666667       0.0 #> Mgp           0.49180328 0.23809524 0.42592593 0.388888889 0.31111111       0.1 #> Lmo3          0.62295082 0.63095238 0.64814815 0.611111111 0.62222222       0.6 #> Slco1c1       0.46721311 0.57142857 0.59876543 0.583333333 0.51111111       0.8 #> Cpne9         0.40983607 0.26190476 0.40740741 0.351851852 0.35555556       0.2 #> Itpr2         0.23770492 0.17857143 0.25308642 0.277777778 0.28888889       0.1 #> Slc6a11       0.72131148 0.71428571 0.68518519 0.666666667 0.57777778       0.7 #> Vamp1         0.63934426 0.63095238 0.65432099 0.685185185 0.60000000       0.7 #> Cd9           0.77868852 0.78571429 0.74691358 0.648148148 0.68888889       0.6 #> Pglyrp1       0.32786885 0.30952381 0.27160494 0.287037037 0.33333333       0.2 #> Slc17a6       0.41803279 0.44047619 0.46296296 0.407407407 0.31111111       0.3 #> Sipa1l3       0.43442623 0.47619048 0.43827160 0.444444444 0.46666667       0.5 #> Sh3gl3        0.71311475 0.63095238 0.56790123 0.592592593 0.62222222       0.7 #> Plekhb1       0.98360656 0.95238095 0.98148148 0.981481481 0.97777778       1.0 #> Nupr1         0.11475410 0.20238095 0.10493827 0.138888889 0.11111111       0.0 #> Dkk3          0.80327869 0.75000000 0.78395062 0.666666667 0.66666667       0.9 #> Cox6a2        0.47540984 0.34523810 0.38271605 0.435185185 0.31111111       0.3 #> Dkkl1         0.25409836 0.20238095 0.33333333 0.222222222 0.28888889       0.0 #> Fgfr2         0.54918033 0.44047619 0.47530864 0.500000000 0.46666667       0.4 #> Crym          0.63114754 0.64285714 0.70370370 0.574074074 0.55555556       0.7 #> Slc38a5       0.08196721 0.05952381 0.07407407 0.111111111 0.15555556       0.0 #> Flna          0.37704918 0.46428571 0.41358025 0.342592593 0.28888889       0.3 #> Bgn           0.18852459 0.20238095 0.17901235 0.185185185 0.20000000       0.1 #> Col4a1        0.36065574 0.32142857 0.37654321 0.324074074 0.35555556       0.6 #> Plat          0.37704918 0.42857143 0.41358025 0.324074074 0.35555556       0.3 #> Nr3c2         0.48360656 0.57142857 0.46296296 0.453703704 0.31111111       0.6 #> Cbln1         0.18032787 0.17857143 0.17283951 0.203703704 0.17777778       0.2 #> Gab1          0.46721311 0.46428571 0.51234568 0.453703704 0.48888889       0.4 #> Pllp          0.76229508 0.76190476 0.75308642 0.703703704 0.64444444       0.6 #> Necab2        0.61475410 0.51190476 0.60493827 0.583333333 0.62222222       0.4 #> Dbndd1        0.36065574 0.41666667 0.38271605 0.398148148 0.33333333       0.2 #> Agt           0.63934426 0.63095238 0.58024691 0.620370370 0.60000000       0.9 #> Cryab         0.98360656 0.95238095 0.94444444 0.944444444 0.88888889       0.9 #> Tagln         0.09836066 0.11904762 0.14197531 0.157407407 0.08888889       0.0 #> Mcam          0.40163934 0.29761905 0.31481481 0.277777778 0.28888889       0.3 #> Olfm2         0.60655738 0.55952381 0.62962963 0.518518519 0.55555556       0.7 #> Icam5         0.65573770 0.69047619 0.68518519 0.620370370 0.73333333       0.6 #> Anxa2         0.19672131 0.13095238 0.17283951 0.231481481 0.17777778       0.2 #> Rora          0.69672131 0.78571429 0.73456790 0.703703704 0.71111111       0.5 #> Calml4        0.04918033 0.09523810 0.06790123 0.083333333 0.04444444       0.1 #> Htr3a         0.08196721 0.10714286 0.06790123 0.083333333 0.13333333       0.0 #> Paqr5         0.09836066 0.10714286 0.09876543 0.111111111 0.13333333       0.1 #> Rasgrf1       0.87704918 0.92857143 0.88888889 0.898148148 0.88888889       0.9 #> Zic1          0.36885246 0.38095238 0.34567901 0.416666667 0.33333333       0.5 #> Mobp          1.00000000 0.98809524 0.99382716 1.000000000 1.00000000       1.0 #> Hhatl         0.32786885 0.34523810 0.30864198 0.333333333 0.37777778       0.4 #> Trf           0.98360656 0.95238095 0.96296296 0.907407407 0.95555556       1.0 #> Cpne4         0.54098361 0.45238095 0.54320988 0.509259259 0.44444444       0.3 #> Cdhr4         0.03278689 0.03571429 0.04320988 0.027777778 0.00000000       0.0 #> Cd59a         0.35245902 0.42857143 0.37654321 0.277777778 0.26666667       0.5 #> Gng11         0.68032787 0.77380952 0.67283951 0.703703704 0.64444444       0.8 #> Chrm1         0.64754098 0.64285714 0.69135802 0.546296296 0.64444444       0.5 #> Prr5l         0.28688525 0.26190476 0.20370370 0.222222222 0.20000000       0.3 #> Ugt8a         0.72131148 0.63095238 0.68518519 0.666666667 0.55555556       0.3 #> Rims3         0.72950820 0.53571429 0.66049383 0.675925926 0.64444444       0.5 #> Sgpp2         0.31967213 0.16666667 0.24691358 0.268518519 0.31111111       0.3 #> Camkv         0.90163934 0.90476190 0.95061728 0.916666667 0.91111111       1.0 #> Sox10         0.55737705 0.47619048 0.54320988 0.490740741 0.51111111       0.6 #> Micall1       0.37704918 0.35714286 0.41975309 0.342592593 0.40000000       0.5 #> Tie1          0.12295082 0.10714286 0.11111111 0.111111111 0.11111111       0.1 #> Fa2h          0.70491803 0.58333333 0.64814815 0.620370370 0.53333333       0.5 #> Ucp2          0.30327869 0.25000000 0.37037037 0.333333333 0.37777778       0.5 #> Vav3          0.30327869 0.22619048 0.20370370 0.231481481 0.08888889       0.2 #> Ccp110        0.67213115 0.63095238 0.70370370 0.537037037 0.51111111       0.8 #> Gria2         0.92622951 0.91666667 0.94444444 0.898148148 0.93333333       1.0 #> Rasl10a       0.45901639 0.48809524 0.47530864 0.388888889 0.40000000       0.4 #> Foxj1         0.21311475 0.22619048 0.12345679 0.166666667 0.17777778       0.0 #> Trim59        0.31147541 0.35714286 0.35185185 0.287037037 0.37777778       0.2 #> Dynlrb2       0.09016393 0.07142857 0.05555556 0.037037037 0.08888889       0.0 #> Gjc1          0.08196721 0.14285714 0.12962963 0.111111111 0.13333333       0.3 #> Neurod1       0.20491803 0.26190476 0.27777778 0.240740741 0.17777778       0.3 #> Ttyh2         0.58196721 0.48809524 0.44444444 0.462962963 0.53333333       0.5 #> Cpne7         0.50819672 0.46428571 0.51851852 0.490740741 0.55555556       0.4 #> Nrip3         0.73770492 0.67857143 0.72222222 0.638888889 0.62222222       0.7 #> Tbr1          0.51639344 0.51190476 0.58024691 0.481481481 0.44444444       0.5 #> Lcat          0.46721311 0.53571429 0.43827160 0.407407407 0.44444444       0.4 #> Tmem98        0.31147541 0.26190476 0.27160494 0.287037037 0.40000000       0.2 #> Myo1d         0.22131148 0.15476190 0.23456790 0.157407407 0.20000000       0.2 #> Prdm8         0.31967213 0.38095238 0.35185185 0.240740741 0.24444444       0.5 #> Tgfbi         0.05737705 0.04761905 0.03703704 0.120370370 0.11111111       0.0 #> Kcnc2         0.72131148 0.69047619 0.71604938 0.675925926 0.44444444       1.0 #> Thrsp         0.50819672 0.57142857 0.48765432 0.583333333 0.51111111       0.6 #> Isg15         0.24590164 0.27380952 0.20370370 0.212962963 0.22222222       0.2 #> Acta2         0.16393443 0.16666667 0.14197531 0.166666667 0.20000000       0.0 #> H2-Q4         0.04918033 0.04761905 0.04938272 0.037037037 0.11111111       0.0 #> Dock4         0.65573770 0.58333333 0.67901235 0.462962963 0.53333333       0.6 #> Myrf          0.51639344 0.46428571 0.45061728 0.500000000 0.46666667       0.7 #> Lmo1          0.48360656 0.60714286 0.56172840 0.527777778 0.46666667       0.7 #> Igfbp7        0.54918033 0.58333333 0.58641975 0.592592593 0.64444444       0.4 #> P2ry12        0.45081967 0.39285714 0.37037037 0.416666667 0.44444444       0.5 #> Pcdh8         0.34426230 0.39285714 0.31481481 0.370370370 0.28888889       0.5 #> Lgi4          0.44262295 0.33333333 0.37654321 0.361111111 0.53333333       0.2 #> Fxyd1         0.82786885 0.79761905 0.81481481 0.824074074 0.77777778       0.9 #> Fxyd7         0.89344262 0.91666667 0.92592593 0.861111111 0.73333333       0.9 #> Mag           0.96721311 0.90476190 0.93209877 0.953703704 0.88888889       1.0 #> Zcchc12       0.46721311 0.52380952 0.45061728 0.398148148 0.33333333       0.6 #> Anln          0.36065574 0.40476190 0.33950617 0.250000000 0.37777778       0.2 #> Wnt4          0.33606557 0.32142857 0.34567901 0.370370370 0.13333333       0.3 #> C1ql2         0.17213115 0.19047619 0.17283951 0.203703704 0.13333333       0.3 #> Unc93b1       0.23770492 0.25000000 0.21604938 0.185185185 0.33333333       0.3 #> Tspan15       0.50000000 0.41666667 0.48148148 0.351851852 0.37777778       0.5 #> Ppp1r14a      0.81147541 0.73809524 0.72839506 0.740740741 0.73333333       0.8 #> Clic4         0.71311475 0.66666667 0.61111111 0.666666667 0.71111111       0.6 #> Galnt6        0.27868852 0.29761905 0.20987654 0.222222222 0.28888889       0.1 #> Ccn3          0.47540984 0.48809524 0.53086420 0.416666667 0.55555556       0.6 #> Rims2         0.64754098 0.65476190 0.65432099 0.611111111 0.42222222       0.5 #> Zmat4         0.48360656 0.46428571 0.49382716 0.444444444 0.28888889       0.4 #> Cldn11        0.94262295 0.96428571 0.96913580 0.935185185 0.91111111       1.0 #> Ccdc33        0.04918033 0.03571429 0.02469136 0.018518519 0.04444444       0.0 #> Slc32a1       0.44262295 0.45238095 0.48765432 0.472222222 0.48888889       0.4 #> Tgm2          0.13934426 0.09523810 0.09259259 0.120370370 0.15555556       0.0 #> Vstm2l        0.61475410 0.63095238 0.64197531 0.527777778 0.53333333       0.6 #> Neurod6       0.66393443 0.61904762 0.66666667 0.629629630 0.60000000       0.5 #> Crygn         0.05737705 0.05952381 0.04320988 0.009259259 0.06666667       0.0 #> Enpp6         0.20491803 0.25000000 0.29012346 0.222222222 0.15555556       0.1 #> Neurod2       0.59836066 0.57142857 0.62962963 0.592592593 0.46666667       0.5 #> Satb2         0.31147541 0.28571429 0.33333333 0.157407407 0.35555556       0.2 #> Pcp4l1        0.73770492 0.77380952 0.72222222 0.740740741 0.60000000       0.6 #> Txnip         0.30327869 0.19047619 0.25308642 0.268518519 0.33333333       0.2 #> Egr1          0.57377049 0.54761905 0.64197531 0.564814815 0.55555556       0.8 #> Otud7b        0.50819672 0.47619048 0.54938272 0.425925926 0.46666667       0.3 #> Car14         0.39344262 0.38095238 0.34567901 0.370370370 0.35555556       0.2 #> Rgs4          0.79508197 0.83333333 0.79012346 0.833333333 0.75555556       0.6 #> Dock10        0.41803279 0.48809524 0.37037037 0.398148148 0.46666667       0.3 #> Lpar1         0.60655738 0.47619048 0.51851852 0.574074074 0.51111111       0.5 #> Trps1         0.31147541 0.35714286 0.32098765 0.212962963 0.26666667       0.3 #> Ptpn3         0.56557377 0.47619048 0.54938272 0.583333333 0.48888889       0.5 #> Lefty1        0.16393443 0.20238095 0.22839506 0.203703704 0.22222222       0.2 #> Zfhx3         0.28688525 0.28571429 0.29629630 0.296296296 0.28888889       0.3 #> St6galnac5    0.57377049 0.66666667 0.59876543 0.518518519 0.68888889       0.5 #> Ak5           0.73770492 0.76190476 0.67283951 0.685185185 0.66666667       0.5 #> Hrh3          0.64754098 0.48809524 0.56172840 0.537037037 0.40000000       0.4 #> Nexn          0.17213115 0.16666667 0.14197531 0.138888889 0.08888889       0.1 #> Adgrl4        0.31967213 0.29761905 0.30246914 0.287037037 0.33333333       0.2 #> Rlbp1         0.28688525 0.33333333 0.27777778 0.259259259 0.13333333       0.2 #> Igfbp2        0.46721311 0.42857143 0.42592593 0.425925926 0.44444444       0.3 #> Wfs1          0.59836066 0.61904762 0.61111111 0.629629630 0.75555556       0.4 #> Cplx3         0.25409836 0.28571429 0.28395062 0.157407407 0.31111111       0.3 #> Orai2         0.46721311 0.53571429 0.56790123 0.462962963 0.46666667       0.4 #> Olig2         0.50819672 0.44047619 0.39506173 0.342592593 0.42222222       0.7 #> Gpr37         0.77868852 0.64285714 0.70987654 0.703703704 0.68888889       0.8 #> Plcb4         0.59836066 0.60714286 0.59876543 0.629629630 0.40000000       0.5 #> Nxph4         0.07377049 0.07142857 0.07407407 0.064814815 0.06666667       0.1 #> Ndufa4l2      0.25409836 0.20238095 0.13580247 0.185185185 0.22222222       0.1 #> Cacng5        0.26229508 0.33333333 0.19753086 0.231481481 0.17777778       0.1 #> Plekhg1       0.46721311 0.39285714 0.43827160 0.453703704 0.28888889       0.3 #> Cmtm5         0.85245902 0.75000000 0.82098765 0.814814815 0.80000000       1.0 #> Gpr161        0.17213115 0.23809524 0.19135802 0.166666667 0.15555556       0.4 #> Rfx3          0.36885246 0.35714286 0.29012346 0.324074074 0.24444444       0.3 #> Igsf21        0.50000000 0.36904762 0.53086420 0.379629630 0.40000000       0.5 #> Ramp3         0.54918033 0.51190476 0.46913580 0.490740741 0.48888889       0.5 #> Arhgap12      0.39344262 0.35714286 0.43827160 0.453703704 0.35555556       0.5 #> Nkx6-2        0.55737705 0.44047619 0.44444444 0.444444444 0.48888889       0.5 #> Ninj2         0.16393443 0.13095238 0.20987654 0.129629630 0.11111111       0.2 #> Cldn5         0.60655738 0.59523810 0.57407407 0.620370370 0.75555556       0.6 #> Htr2c         0.21311475 0.23809524 0.30864198 0.268518519 0.20000000       0.4 #> Hspb8         0.24590164 0.19047619 0.15432099 0.175925926 0.28888889       0.1 #> Fmod          0.05737705 0.04761905 0.04320988 0.064814815 0.04444444       0.0 #> Prelp         0.30327869 0.20238095 0.23456790 0.259259259 0.20000000       0.3 #> Mpped1        0.66393443 0.61904762 0.66666667 0.481481481 0.55555556       0.6 #> Rapgef5       0.55737705 0.64285714 0.61111111 0.527777778 0.51111111       0.5 #> Vwa1          0.38524590 0.44047619 0.33950617 0.435185185 0.46666667       0.8 #> Stab1         0.15573770 0.14285714 0.14814815 0.129629630 0.13333333       0.1 #> Arl15         0.39344262 0.38095238 0.41358025 0.379629630 0.24444444       0.4 #> Reln          0.30327869 0.26190476 0.32716049 0.277777778 0.22222222       0.1 #> Mustn1        0.09836066 0.03571429 0.06172840 0.046296296 0.00000000       0.0 #> Pbxip1        0.44262295 0.44047619 0.48765432 0.342592593 0.37777778       0.7 #> Dnali1        0.04098361 0.02380952 0.03086420 0.037037037 0.08888889       0.0 #> Id1           0.53278689 0.40476190 0.42592593 0.435185185 0.53333333       0.3 #> Lrrtm3        0.42622951 0.38095238 0.43827160 0.324074074 0.22222222       0.3 #> Tmem212       0.08196721 0.03571429 0.05555556 0.055555556 0.04444444       0.1 #> Epop          0.50000000 0.59523810 0.58641975 0.453703704 0.42222222       0.5 #> Gjc2          0.45901639 0.45238095 0.39506173 0.370370370 0.40000000       0.6 #> 1190005I06Rik 0.45901639 0.41666667 0.37654321 0.324074074 0.33333333       0.6 #> Ctla2a        0.40983607 0.33333333 0.33950617 0.361111111 0.28888889       0.1 #> Cnr1          0.57377049 0.60714286 0.61728395 0.518518519 0.60000000       0.6 #> Gpr4          0.11475410 0.14285714 0.16666667 0.175925926 0.15555556       0.2 #> Sowaha        0.56557377 0.70238095 0.56790123 0.601851852 0.77777778       0.6 #> Tent5c        0.19672131 0.17857143 0.13580247 0.111111111 0.08888889       0.1 #> Serpinb1a     0.38524590 0.29761905 0.32098765 0.314814815 0.33333333       0.2 #> S1pr5         0.42622951 0.33333333 0.29629630 0.287037037 0.26666667       0.3 #> Penk          0.36885246 0.42857143 0.40740741 0.324074074 0.44444444       0.5 #> Cdc42ep2      0.43442623 0.36904762 0.43209877 0.407407407 0.35555556       0.2 #> Slitrk6       0.14754098 0.07142857 0.16049383 0.120370370 0.06666667       0.0 #> Hpcal4        0.92622951 0.89285714 0.93209877 0.805555556 0.91111111       1.0 #> Olig1         0.94262295 0.88095238 0.91358025 0.907407407 0.88888889       0.6 #> Rprml         0.72950820 0.64285714 0.74074074 0.685185185 0.71111111       0.7 #> Stxbp6        0.50000000 0.48809524 0.45679012 0.462962963 0.40000000       0.5 #> Hs3st2        0.31967213 0.28571429 0.35802469 0.277777778 0.24444444       0.2 #> Rbp1          0.43442623 0.42857143 0.40740741 0.425925926 0.33333333       0.2 #> Ppm1e         0.77049180 0.76190476 0.82098765 0.722222222 0.77777778       0.8 #> Sox18         0.18852459 0.23809524 0.14814815 0.212962963 0.11111111       0.2 #> Kctd4         0.36885246 0.39285714 0.26543210 0.324074074 0.22222222       0.3 #> Nxph3         0.29508197 0.21428571 0.32716049 0.203703704 0.20000000       0.1 #> Vat1l         0.31147541 0.30952381 0.23456790 0.203703704 0.31111111       0.1 #> Cd24a         0.29508197 0.21428571 0.21604938 0.129629630 0.24444444       0.2 #> Odf3b         0.07377049 0.03571429 0.04938272 0.018518519 0.04444444       0.1 #> Gjb1          0.52459016 0.38095238 0.37654321 0.361111111 0.40000000       0.4 #> Selplg        0.48360656 0.30952381 0.39506173 0.398148148 0.42222222       0.2 #> Bcl11b        0.56557377 0.66666667 0.62345679 0.518518519 0.51111111       0.6 #> Lhfp          0.42622951 0.51190476 0.47530864 0.370370370 0.35555556       0.6 #> Ranbp3l       0.01639344 0.08333333 0.01234568 0.046296296 0.00000000       0.1 #> Msx1          0.10655738 0.13095238 0.08024691 0.111111111 0.04444444       0.1 #> Zdhhc22       0.54098361 0.44047619 0.40123457 0.462962963 0.44444444       0.3 #> Phldb1        0.76229508 0.66666667 0.62962963 0.611111111 0.66666667       0.8 #> Ctxn1         0.88524590 0.90476190 0.88271605 0.898148148 0.86666667       0.8 #> Tprn          0.55737705 0.47619048 0.41975309 0.398148148 0.40000000       0.5 #> Vstm2a        0.61475410 0.59523810 0.59876543 0.601851852 0.60000000       0.6 #> Ndnf          0.16393443 0.16666667 0.11728395 0.148148148 0.13333333       0.2 #> Pdp1          0.73770492 0.72619048 0.72839506 0.685185185 0.68888889       0.7 #> Scn3b         0.60655738 0.70238095 0.71604938 0.685185185 0.68888889       0.8 #> Cdc42ep1      0.40163934 0.44047619 0.33950617 0.305555556 0.40000000       0.2 #> Gal3st1       0.50819672 0.47619048 0.41358025 0.407407407 0.37777778       0.5 #> Rasd1         0.37704918 0.39285714 0.37654321 0.361111111 0.37777778       0.4 #> Spink8        0.32786885 0.33333333 0.34567901 0.361111111 0.44444444       0.4 #> Opalin        0.77868852 0.78571429 0.72839506 0.712962963 0.75555556       0.7 #> Gja4          0.04918033 0.07142857 0.06790123 0.092592593 0.08888889       0.0 #> Synpo2        0.35245902 0.29761905 0.29012346 0.342592593 0.31111111       0.5 #> Pcdh20        0.29508197 0.35714286 0.38271605 0.351851852 0.24444444       0.4 #> Adra1b        0.37704918 0.34523810 0.38888889 0.305555556 0.31111111       0.3 #> Fam131a       0.79508197 0.83333333 0.78395062 0.694444444 0.66666667       0.7 #> Tmem125       0.34426230 0.25000000 0.30864198 0.370370370 0.28888889       0.4 #> Mb21d2        0.55737705 0.51190476 0.46296296 0.509259259 0.40000000       0.4 #> Lingo3        0.36065574 0.39285714 0.30864198 0.361111111 0.20000000       0.4 #> Ncald         0.92622951 0.95238095 0.93827160 0.888888889 0.88888889       1.0 #> Siglech       0.27868852 0.23809524 0.25925926 0.166666667 0.40000000       0.3 #> Rgs14         0.44262295 0.46428571 0.37037037 0.370370370 0.31111111       0.4 #> Gm14964       0.18852459 0.07142857 0.12962963 0.138888889 0.08888889       0.0 #> Gpr17         0.31147541 0.25000000 0.27777778 0.268518519 0.37777778       0.2 #> Cx3cr1        0.36885246 0.34523810 0.27160494 0.324074074 0.35555556       0.2 #> Ezr           0.54918033 0.53571429 0.45061728 0.425925926 0.51111111       0.4 #> Adarb2        0.24590164 0.23809524 0.27777778 0.287037037 0.22222222       0.1 #> Cpne8         0.27868852 0.22619048 0.24691358 0.231481481 0.20000000       0.2 #> Plekhg3       0.32786885 0.26190476 0.24074074 0.287037037 0.28888889       0.3 #> Lamb2         0.30327869 0.36904762 0.29012346 0.314814815 0.33333333       0.4 #> Creb5         0.20491803 0.14285714 0.14814815 0.166666667 0.15555556       0.2 #> Cntn2         0.64754098 0.55952381 0.66666667 0.555555556 0.62222222       0.4 #> Aldh1a1       0.65573770 0.67857143 0.67283951 0.712962963 0.64444444       0.4 #> Phgdh         0.81967213 0.84523810 0.82098765 0.814814815 0.84444444       0.8 #> Tnfaip6       0.42622951 0.41666667 0.35185185 0.342592593 0.17777778       0.1 #> Camk2d        0.58196721 0.52380952 0.62345679 0.481481481 0.46666667       0.4 #> Shisa6        0.40163934 0.44047619 0.46296296 0.444444444 0.33333333       0.6 #> Cthrc1        0.28688525 0.28571429 0.24074074 0.259259259 0.17777778       0.2 #> Tmem119       0.36065574 0.23809524 0.25308642 0.342592593 0.28888889       0.4 #> Hmgb2         0.33606557 0.20238095 0.24074074 0.185185185 0.13333333       0.3 #> Tmem158       0.63934426 0.59523810 0.62962963 0.555555556 0.46666667       0.7 #> Dsp           0.08196721 0.08333333 0.04938272 0.037037037 0.02222222       0.2 #> Lrtm2         0.51639344 0.47619048 0.54320988 0.537037037 0.35555556       0.4 #> Gabra5        0.54918033 0.57142857 0.61728395 0.537037037 0.48888889       0.6 #> Tns1          0.29508197 0.20238095 0.24691358 0.314814815 0.15555556       0.2 #> Nell1         0.53278689 0.52380952 0.47530864 0.500000000 0.44444444       0.2 #> Slain1        0.77868852 0.63095238 0.69753086 0.712962963 0.57777778       0.7 #> Prr18         0.72950820 0.63095238 0.57407407 0.537037037 0.71111111       0.6 #> S100a8        0.12295082 0.10714286 0.12345679 0.138888889 0.15555556       0.1 #> S100a9        0.15573770 0.07142857 0.14197531 0.148148148 0.11111111       0.1 #> Col8a2        0.02459016 0.02380952 0.03086420 0.046296296 0.13333333       0.0 #> Synpr         0.54918033 0.61904762 0.57407407 0.620370370 0.55555556       0.4 #> Sertm1        0.40163934 0.44047619 0.37037037 0.324074074 0.31111111       0.6 #> Adgrf5        0.31147541 0.23809524 0.36419753 0.379629630 0.33333333       0.3 #> Capg          0.13934426 0.11904762 0.07407407 0.092592593 0.08888889       0.0 #> Gjc3          0.58196721 0.61904762 0.54938272 0.527777778 0.57777778       0.3 #> Fcer1g        0.45081967 0.45238095 0.38888889 0.379629630 0.33333333       0.7 #> Pde1a         0.63114754 0.60714286 0.71604938 0.574074074 0.68888889       0.5 #> Tafa1         0.41803279 0.40476190 0.45679012 0.259259259 0.26666667       0.4 #> Ddn           0.90163934 0.90476190 0.92592593 0.888888889 0.91111111       1.0 #> Hopx          0.75409836 0.73809524 0.72839506 0.657407407 0.82222222       0.6 #> Ptk2b         0.90163934 0.92857143 0.91975309 0.935185185 0.88888889       0.6 #> Rgs3          0.47540984 0.50000000 0.47530864 0.500000000 0.44444444       0.3 #> Kcng2         0.25409836 0.28571429 0.24074074 0.277777778 0.13333333       0.3 #> Ntng1         0.45081967 0.39285714 0.41358025 0.425925926 0.35555556       0.4 #> H2-Q7         0.02459016 0.02380952 0.04320988 0.064814815 0.04444444       0.0 #> Ifitm2        0.31967213 0.36904762 0.31481481 0.296296296 0.35555556       0.5 #> Plaat3        0.66393443 0.69047619 0.72839506 0.629629630 0.77777778       0.8 #> Plekhh1       0.52459016 0.48809524 0.46296296 0.453703704 0.44444444       0.4 #> Myl4          0.32786885 0.34523810 0.40740741 0.277777778 0.40000000       0.4 #> H2-K1         0.41803279 0.47619048 0.53086420 0.537037037 0.60000000       0.5 #> Dpp6          0.77049180 0.73809524 0.77777778 0.740740741 0.66666667       0.7 #> Tmem91        0.28688525 0.32142857 0.31481481 0.222222222 0.28888889       0.2 #> Cyp2d22       0.40163934 0.34523810 0.39506173 0.388888889 0.51111111       0.2 #> Ttr           1.00000000 1.00000000 0.98765432 0.990740741 1.00000000       1.0 #> Suclg2        0.24590164 0.33333333 0.27777778 0.185185185 0.17777778       0.4 #> Patj          0.27049180 0.21428571 0.20987654 0.259259259 0.24444444       0.3 #> Btbd3         0.79508197 0.86904762 0.80864198 0.833333333 0.68888889       0.9 #> Unc13c        0.36065574 0.30952381 0.26543210 0.268518519 0.17777778       0.4 #> Syt9          0.23770492 0.21428571 0.25308642 0.203703704 0.08888889       0.3 #> Shisal1       0.50000000 0.44047619 0.49382716 0.462962963 0.37777778       0.6 #> Grm4          0.25409836 0.19047619 0.28395062 0.203703704 0.20000000       0.2 #> Sox11         0.27049180 0.32142857 0.30246914 0.287037037 0.26666667       0.4 #> Slc22a8       0.22131148 0.21428571 0.15432099 0.185185185 0.22222222       0.3 #> Slc24a3       0.81967213 0.77380952 0.80246914 0.787037037 0.73333333       0.6 #> Klk8          0.32786885 0.44047619 0.31481481 0.379629630 0.35555556       0.4 #> Ipcef1        0.42622951 0.35714286 0.51851852 0.324074074 0.44444444       0.6 #> Tnnt1         0.45901639 0.40476190 0.30864198 0.388888889 0.15555556       0.3 #> Hhip          0.11475410 0.17857143 0.12962963 0.194444444 0.17777778       0.1 #> Spag8         0.02459016 0.03571429 0.03086420 0.027777778 0.08888889       0.0 #> Fxyd6         0.69672131 0.70238095 0.74074074 0.648148148 0.71111111       0.5 #> Ppp1r3c       0.40163934 0.39285714 0.43209877 0.342592593 0.26666667       0.1 #> Cbln4         0.19672131 0.17857143 0.17901235 0.203703704 0.15555556       0.2 #> Nnat          0.96721311 0.86904762 0.90740741 0.888888889 0.88888889       0.9 #> Myl9          0.40163934 0.45238095 0.30864198 0.324074074 0.42222222       0.2 #> Vxn           0.77868852 0.75000000 0.72839506 0.703703704 0.73333333       0.8 #> Lgals1        0.45081967 0.51190476 0.53086420 0.472222222 0.48888889       0.1 #> Gpr88         0.29508197 0.19047619 0.21604938 0.203703704 0.24444444       0.0 #> Ctxn3         0.11475410 0.14285714 0.12345679 0.148148148 0.06666667       0.0 #> Lyz2          0.23770492 0.10714286 0.15432099 0.157407407 0.20000000       0.1 #> Tmem100       0.24590164 0.27380952 0.28395062 0.231481481 0.22222222       0.3 #> Wfdc17        0.01639344 0.01190476 0.02469136 0.037037037 0.08888889       0.0 #> Ahnak         0.29508197 0.26190476 0.26543210 0.314814815 0.42222222       0.2 #> Hba-a2        0.99180328 1.00000000 0.99382716 0.990740741 0.97777778       1.0 #> Hba-a1        1.00000000 0.97619048 1.00000000 0.990740741 1.00000000       1.0 #> Ccdc153       0.12295082 0.04761905 0.06790123 0.101851852 0.11111111       0.0 #> Ccnd1         0.46721311 0.45238095 0.56172840 0.490740741 0.51111111       0.5 #> Serpinh1      0.27868852 0.38095238 0.24691358 0.250000000 0.24444444       0.1 #> Gad1          0.73770492 0.66666667 0.74074074 0.777777778 0.71111111       0.6 #> Arhgef10      0.41803279 0.35714286 0.45061728 0.324074074 0.33333333       0.5 #> 2410004P03Rik 0.04098361 0.08333333 0.03703704 0.027777778 0.04444444       0.0 #> Nt5dc2        0.22950820 0.22619048 0.22222222 0.250000000 0.22222222       0.3 #> Cebpd         0.28688525 0.35714286 0.28395062 0.296296296 0.31111111       0.4 #> Sod3          0.24590164 0.20238095 0.12962963 0.231481481 0.22222222       0.2 #> H2-D1         0.67213115 0.76190476 0.66049383 0.611111111 0.64444444       0.8 #> C4b           0.40163934 0.33333333 0.36419753 0.296296296 0.37777778       0.2 #> Tmem88b       0.78688525 0.66666667 0.72222222 0.703703704 0.60000000       0.6 #> Hbb-bt        0.99180328 1.00000000 0.98148148 0.990740741 0.95555556       1.0 #> Rhog          0.58196721 0.54761905 0.59259259 0.583333333 0.48888889       0.4 #> Rprm          0.48360656 0.45238095 0.39506173 0.407407407 0.44444444       0.6 #> Ly6a          0.70491803 0.63095238 0.64814815 0.703703704 0.73333333       0.7 #> Mog           0.83606557 0.78571429 0.83333333 0.851851852 0.91111111       0.6 #> Trbc2         0.31967213 0.35714286 0.40740741 0.333333333 0.37777778       0.2 #> Igkc          0.04918033 0.07142857 0.04938272 0.037037037 0.02222222       0.1 #> Smim1         0.38524590 0.32142857 0.34567901 0.370370370 0.62222222       0.6 #> Hs3st4        0.63934426 0.55952381 0.62345679 0.657407407 0.66666667       0.7 #> Evi2a         0.60655738 0.55952381 0.57407407 0.574074074 0.71111111       0.6 #> Prkcg         0.86885246 0.86904762 0.90740741 0.833333333 0.80000000       0.8 #> Ly6c1         0.68032787 0.73809524 0.70370370 0.675925926 0.66666667       0.8 #> Gbp4          0.05737705 0.02380952 0.03086420 0.101851852 0.02222222       0.1 #> Wipf3         0.61475410 0.69047619 0.70987654 0.694444444 0.66666667       0.6 #> BC039966      0.03278689 0.03571429 0.04320988 0.027777778 0.08888889       0.0 #> Gm13889       0.46721311 0.47619048 0.48765432 0.444444444 0.33333333       0.2 #> Plcxd2        0.49180328 0.39285714 0.45679012 0.388888889 0.17777778       0.2 #> Mia           0.08196721 0.09523810 0.08641975 0.101851852 0.08888889       0.0 #> Pou3f1        0.53278689 0.57142857 0.50617284 0.481481481 0.42222222       0.7 #> Lrrc10b       0.33606557 0.42857143 0.35802469 0.379629630 0.37777778       0.5 #> Apol11b       0.13114754 0.08333333 0.06790123 0.092592593 0.06666667       0.1 #> Gpr62         0.40163934 0.36904762 0.40740741 0.379629630 0.35555556       0.2 #> Shisa8        0.14754098 0.10714286 0.11111111 0.111111111 0.15555556       0.3 #> Gm2115        0.24590164 0.34523810 0.28395062 0.351851852 0.31111111       0.3 #> Kctd12        0.66393443 0.55952381 0.63580247 0.601851852 0.60000000       0.6 #> 1700047M11Rik 0.32786885 0.29761905 0.25925926 0.277777778 0.22222222       0.2 #> Lhfpl3        0.40163934 0.44047619 0.37654321 0.342592593 0.20000000       0.5 #> C030029H02Rik 0.13114754 0.14285714 0.09876543 0.092592593 0.11111111       0.1 #> Gm19935       0.13114754 0.08333333 0.07407407 0.074074074 0.13333333       0.0 #> 9630013A20Rik 0.05737705 0.09523810 0.09259259 0.083333333 0.04444444       0.0 #> 2900040C04Rik 0.12295082 0.10714286 0.10493827 0.055555556 0.08888889       0.0 #>                cluster_4 #> Gna12         0.72043011 #> Ccnd2         0.49462366 #> Btbd17        0.39784946 #> Sox9          0.54838710 #> Sez6          0.80645161 #> Serpinf1      0.23655914 #> S100a6        0.55913978 #> Col1a1        0.05376344 #> Vwf           0.24731183 #> Esam          0.30107527 #> Npas1         0.19354839 #> Tiam1         0.52688172 #> Bcam          0.27956989 #> Hmgn2         0.55913978 #> Rab3b         0.41935484 #> Inmt          0.04301075 #> Ddr1          0.56989247 #> Homer3        0.48387097 #> Cp            0.08602151 #> Calb2         0.34408602 #> Man1a         0.39784946 #> Efnb3         0.67741935 #> Hlf           0.76344086 #> Gstm7         0.46236559 #> Cavin1        0.25806452 #> Sst           0.79569892 #> Hapln2        0.25806452 #> Hspb1         0.23655914 #> Ndrg1         0.72043011 #> Nid1          0.02150538 #> Kit           0.24731183 #> Pvalb         0.75268817 #> Tmbim1        0.52688172 #> Crip1         0.51612903 #> Tek           0.21505376 #> Elovl1        0.47311828 #> Cyba          0.35483871 #> Itih3         0.29032258 #> Cnp           0.96774194 #> Hap1          0.47311828 #> Clic1         0.20430108 #> Stx1a         0.62365591 #> Arpp19        0.94623656 #> Dio2          0.26881720 #> Id3           0.73118280 #> Crlf1         0.33333333 #> Ttc9b         0.91397849 #> Carhsp1       0.46236559 #> Cabp7         0.56989247 #> Fam163b       0.64516129 #> Rarres2       0.23655914 #> Syn2          0.87096774 #> Ick           0.34408602 #> Prox1         0.27956989 #> Adssl1        0.29032258 #> Vipr2         0.12903226 #> Gltp          0.54838710 #> Amotl1        0.38709677 #> Bcas1         0.70967742 #> Aldh1a2       0.03225806 #> Tppp3         0.62365591 #> Sirt2         0.92473118 #> Lpl           0.34408602 #> Cers2         0.66666667 #> Qdpr          0.94623656 #> Stk32c        0.60215054 #> Lbp           0.07526882 #> Hsd11b1       0.45161290 #> Vtn           0.72043011 #> Stac2         0.39784946 #> Plxdc1        0.31182796 #> Igfbp4        0.59139785 #> Dbndd2        0.59139785 #> Pltp          0.58064516 #> Slc12a4       0.31182796 #> Cadps2        0.50537634 #> Erbb3         0.18279570 #> Pmp22         0.39784946 #> Kcnab3        0.34408602 #> Myh11         0.03225806 #> Plod1         0.36559140 #> Etnppl        0.25806452 #> Arhgef25      0.77419355 #> Rcn3          0.25806452 #> Vip           0.18279570 #> Utrn          0.35483871 #> Grm1          0.54838710 #> Reep3         0.53763441 #> Fabp7         0.53763441 #> Dcn           0.15053763 #> Slc17a8       0.03225806 #> Dusp6         0.46236559 #> Kitl          0.46236559 #> Ccn2          0.17204301 #> Timp3         0.65591398 #> Ascl1         0.16129032 #> Unc5b         0.27956989 #> Vsir          0.22580645 #> Gamt          0.60215054 #> Ptprb         0.32258065 #> Csrp2         0.21505376 #> Adarb1        0.77419355 #> Rnf130        0.54838710 #> Nefh          0.56989247 #> Aebp1         0.11827957 #> Sept4         0.91397849 #> Gria1         0.88172043 #> Sypl          0.65591398 #> Arsg          0.31182796 #> Cacng4        0.43010753 #> Rab37         0.16129032 #> Itgb4         0.18279570 #> Aspa          0.41935484 #> Cygb          0.59139785 #> Rflnb         0.30107527 #> Doc2b         0.21505376 #> Gfap          0.70967742 #> Npas3         0.27956989 #> Serpina3n     0.39784946 #> Clmn          0.66666667 #> Prkch         0.16129032 #> Fbln5         0.15053763 #> Akr1c18       0.03225806 #> Gng4          0.35483871 #> Sema4d        0.52688172 #> Cxcl14        0.79569892 #> Hexb          0.81720430 #> Iqgap2        0.35483871 #> Crhbp         0.13978495 #> Rab3c         0.76344086 #> Thbs4         0.20430108 #> Serinc5       0.59139785 #> Erbin         0.58064516 #> Prkcd         0.46236559 #> Pdlim2        0.65591398 #> Ednrb         0.48387097 #> Cpne6         0.75268817 #> Sema5a        0.51612903 #> Matn2         0.39784946 #> Nptxr         0.91397849 #> Enpp2         0.95698925 #> Efcab6        0.13978495 #> Ppp1r1a       0.91397849 #> Litaf         0.51612903 #> Il1rap        0.40860215 #> Apod          0.92473118 #> Cpox          0.44086022 #> Grik1         0.18279570 #> Clic6         0.13978495 #> Nr4a1         0.29032258 #> Igfbp6        0.45161290 #> Sncg          0.13978495 #> Gzma          0.01075269 #> Grm2          0.34408602 #> Prph          0.08602151 #> Rsph1         0.11827957 #> Sox8          0.37634409 #> Fam234a       0.34408602 #> Lims2         0.35483871 #> Aqp4          0.69892473 #> Slc12a2       0.61290323 #> Cd74          0.05376344 #> Pdgfrb        0.19354839 #> Csf1r         0.68817204 #> Cbln2         0.19354839 #> Frmd8         0.49462366 #> Gldc          0.27956989 #> Tcf7l2        0.44086022 #> Bhlhe22       0.43010753 #> Kcnip2        0.65591398 #> Alas2         0.29032258 #> Gdf11         0.29032258 #> Baiap2        0.77419355 #> Ifitm3        0.50537634 #> Phkg1         0.31182796 #> Nptx1         0.77419355 #> Pde8a         0.19354839 #> Itih5         0.32258065 #> Homer2        0.64516129 #> Fam20c        0.51612903 #> Cplx2         0.96774194 #> Myo5b         0.38709677 #> Snca          0.89247312 #> Col3a1        0.04301075 #> Ecrg4         0.19354839 #> Map4k4        0.63440860 #> 2010300C02Rik 0.73118280 #> Ogfrl1        0.87096774 #> Fn1           0.33333333 #> Efhd1         0.36559140 #> Ngef          0.66666667 #> Bok           0.68817204 #> Tmem163       0.40860215 #> Lct           0.23655914 #> Cfh           0.26881720 #> Ptpn4         0.77419355 #> Tnni1         0.24731183 #> Csrp1         0.97849462 #> Nfasc         0.84946237 #> Syt2          0.13978495 #> Atp2b4        0.52688172 #> Rgs16         0.24731183 #> Ncf2          0.04301075 #> Cnih3         0.50537634 #> Tmem63a       0.50537634 #> Cfap126       0.07526882 #> Meig1         0.17204301 #> Ccdc3         0.19354839 #> Rgs5          0.65591398 #> Enkur         0.08602151 #> Myoc          0.12903226 #> Vim           0.43010753 #> Prkcq         0.20430108 #> Gad2          0.68817204 #> Lcn2          0.04301075 #> Nr4a2         0.30107527 #> Ermn          0.65591398 #> Fibcd1        0.37634409 #> Gsn           0.78494624 #> Grb14         0.68817204 #> Notch1        0.21505376 #> Ube2l6        0.25806452 #> Gatm          0.81720430 #> Cd82          0.45161290 #> Mdk           0.47311828 #> Lamp5         0.47311828 #> Itpka         0.76344086 #> Chgb          0.88172043 #> Mal           0.95698925 #> Pdyn          0.24731183 #> Nkx2-2        0.15053763 #> Edn3          0.04301075 #> Car2          0.97849462 #> Col9a3        0.31182796 #> Chrna4        0.48387097 #> Gss           0.52688172 #> Slc7a11       0.30107527 #> Tm4sf1        0.30107527 #> Kcnab1        0.75268817 #> Shox2         0.18279570 #> Serpini1      0.65591398 #> Tspan2        0.82795699 #> S100a11       0.21505376 #> Vcam1         0.33333333 #> Lef1          0.23655914 #> Npy2r         0.30107527 #> F3            0.43010753 #> Calb1         0.75268817 #> Epha7         0.63440860 #> Slc44a1       0.72043011 #> 1110017D15Rik 0.11827957 #> Tpm2          0.12903226 #> Slc6a9        0.55913978 #> Laptm5        0.45161290 #> Sema3c        0.21505376 #> Hpca          0.95698925 #> Padi2         0.26881720 #> Slc4a2        0.43010753 #> Gabrd         0.60215054 #> Rgs12         0.41935484 #> Slc30a3       0.49462366 #> Emilin1       0.07526882 #> 1700001C02Rik 0.03225806 #> Gabra4        0.69892473 #> Pdgfra        0.30107527 #> Epha5         0.63440860 #> Tesc          0.66666667 #> Pitpnm2       0.62365591 #> Mmp17         0.65591398 #> Cit           0.60215054 #> Foxp2         0.29032258 #> Arpc1b        0.48387097 #> Col1a2        0.09677419 #> Eln           0.09677419 #> Pcolce        0.10752688 #> Tsc22d4       0.93548387 #> Cald1         0.35483871 #> Ccdc136       0.78494624 #> Npy           0.64516129 #> Slc13a4       0.05376344 #> Gkn3          0.09677419 #> Slc6a13       0.09677419 #> Mgp           0.43010753 #> Lmo3          0.62365591 #> Slco1c1       0.52688172 #> Cpne9         0.34408602 #> Itpr2         0.25806452 #> Slc6a11       0.66666667 #> Vamp1         0.74193548 #> Cd9           0.70967742 #> Pglyrp1       0.27956989 #> Slc17a6       0.46236559 #> Sipa1l3       0.51612903 #> Sh3gl3        0.64516129 #> Plekhb1       0.97849462 #> Nupr1         0.12903226 #> Dkk3          0.74193548 #> Cox6a2        0.35483871 #> Dkkl1         0.17204301 #> Fgfr2         0.50537634 #> Crym          0.56989247 #> Slc38a5       0.18279570 #> Flna          0.32258065 #> Bgn           0.12903226 #> Col4a1        0.36559140 #> Plat          0.38709677 #> Nr3c2         0.48387097 #> Cbln1         0.22580645 #> Gab1          0.47311828 #> Pllp          0.73118280 #> Necab2        0.65591398 #> Dbndd1        0.39784946 #> Agt           0.58064516 #> Cryab         0.93548387 #> Tagln         0.11827957 #> Mcam          0.35483871 #> Olfm2         0.62365591 #> Icam5         0.68817204 #> Anxa2         0.15053763 #> Rora          0.66666667 #> Calml4        0.04301075 #> Htr3a         0.13978495 #> Paqr5         0.09677419 #> Rasgrf1       0.87096774 #> Zic1          0.37634409 #> Mobp          0.97849462 #> Hhatl         0.26881720 #> Trf           0.92473118 #> Cpne4         0.60215054 #> Cdhr4         0.03225806 #> Cd59a         0.47311828 #> Gng11         0.61290323 #> Chrm1         0.69892473 #> Prr5l         0.21505376 #> Ugt8a         0.56989247 #> Rims3         0.64516129 #> Sgpp2         0.18279570 #> Camkv         0.92473118 #> Sox10         0.47311828 #> Micall1       0.44086022 #> Tie1          0.11827957 #> Fa2h          0.55913978 #> Ucp2          0.30107527 #> Vav3          0.23655914 #> Ccp110        0.60215054 #> Gria2         0.89247312 #> Rasl10a       0.48387097 #> Foxj1         0.08602151 #> Trim59        0.34408602 #> Dynlrb2       0.03225806 #> Gjc1          0.10752688 #> Neurod1       0.25806452 #> Ttyh2         0.48387097 #> Cpne7         0.50537634 #> Nrip3         0.75268817 #> Tbr1          0.47311828 #> Lcat          0.45161290 #> Tmem98        0.19354839 #> Myo1d         0.23655914 #> Prdm8         0.32258065 #> Tgfbi         0.02150538 #> Kcnc2         0.68817204 #> Thrsp         0.58064516 #> Isg15         0.22580645 #> Acta2         0.17204301 #> H2-Q4         0.02150538 #> Dock4         0.62365591 #> Myrf          0.38709677 #> Lmo1          0.52688172 #> Igfbp7        0.61290323 #> P2ry12        0.49462366 #> Pcdh8         0.50537634 #> Lgi4          0.36559140 #> Fxyd1         0.80645161 #> Fxyd7         0.84946237 #> Mag           0.95698925 #> Zcchc12       0.47311828 #> Anln          0.22580645 #> Wnt4          0.31182796 #> C1ql2         0.25806452 #> Unc93b1       0.27956989 #> Tspan15       0.41935484 #> Ppp1r14a      0.65591398 #> Clic4         0.61290323 #> Galnt6        0.11827957 #> Ccn3          0.44086022 #> Rims2         0.65591398 #> Zmat4         0.49462366 #> Cldn11        0.95698925 #> Ccdc33        0.03225806 #> Slc32a1       0.51612903 #> Tgm2          0.13978495 #> Vstm2l        0.72043011 #> Neurod6       0.63440860 #> Crygn         0.04301075 #> Enpp6         0.18279570 #> Neurod2       0.62365591 #> Satb2         0.25806452 #> Pcp4l1        0.67741935 #> Txnip         0.25806452 #> Egr1          0.67741935 #> Otud7b        0.52688172 #> Car14         0.37634409 #> Rgs4          0.78494624 #> Dock10        0.53763441 #> Lpar1         0.45161290 #> Trps1         0.27956989 #> Ptpn3         0.55913978 #> Lefty1        0.24731183 #> Zfhx3         0.33333333 #> St6galnac5    0.64516129 #> Ak5           0.68817204 #> Hrh3          0.54838710 #> Nexn          0.17204301 #> Adgrl4        0.33333333 #> Rlbp1         0.33333333 #> Igfbp2        0.45161290 #> Wfs1          0.70967742 #> Cplx3         0.16129032 #> Orai2         0.61290323 #> Olig2         0.37634409 #> Gpr37         0.67741935 #> Plcb4         0.60215054 #> Nxph4         0.06451613 #> Ndufa4l2      0.21505376 #> Cacng5        0.25806452 #> Plekhg1       0.40860215 #> Cmtm5         0.80645161 #> Gpr161        0.22580645 #> Rfx3          0.40860215 #> Igsf21        0.52688172 #> Ramp3         0.47311828 #> Arhgap12      0.45161290 #> Nkx6-2        0.41935484 #> Ninj2         0.18279570 #> Cldn5         0.61290323 #> Htr2c         0.29032258 #> Hspb8         0.22580645 #> Fmod          0.02150538 #> Prelp         0.21505376 #> Mpped1        0.62365591 #> Rapgef5       0.64516129 #> Vwa1          0.38709677 #> Stab1         0.12903226 #> Arl15         0.34408602 #> Reln          0.31182796 #> Mustn1        0.02150538 #> Pbxip1        0.50537634 #> Dnali1        0.04301075 #> Id1           0.49462366 #> Lrrtm3        0.37634409 #> Tmem212       0.05376344 #> Epop          0.50537634 #> Gjc2          0.38709677 #> 1190005I06Rik 0.37634409 #> Ctla2a        0.40860215 #> Cnr1          0.58064516 #> Gpr4          0.15053763 #> Sowaha        0.74193548 #> Tent5c        0.10752688 #> Serpinb1a     0.33333333 #> S1pr5         0.23655914 #> Penk          0.38709677 #> Cdc42ep2      0.40860215 #> Slitrk6       0.06451613 #> Hpcal4        0.95698925 #> Olig1         0.91397849 #> Rprml         0.76344086 #> Stxbp6        0.50537634 #> Hs3st2        0.22580645 #> Rbp1          0.41935484 #> Ppm1e         0.76344086 #> Sox18         0.22580645 #> Kctd4         0.40860215 #> Nxph3         0.19354839 #> Vat1l         0.23655914 #> Cd24a         0.15053763 #> Odf3b         0.04301075 #> Gjb1          0.40860215 #> Selplg        0.38709677 #> Bcl11b        0.54838710 #> Lhfp          0.49462366 #> Ranbp3l       0.04301075 #> Msx1          0.05376344 #> Zdhhc22       0.40860215 #> Phldb1        0.61290323 #> Ctxn1         0.88172043 #> Tprn          0.34408602 #> Vstm2a        0.61290323 #> Ndnf          0.16129032 #> Pdp1          0.76344086 #> Scn3b         0.70967742 #> Cdc42ep1      0.31182796 #> Gal3st1       0.37634409 #> Rasd1         0.46236559 #> Spink8        0.43010753 #> Opalin        0.70967742 #> Gja4          0.06451613 #> Synpo2        0.29032258 #> Pcdh20        0.36559140 #> Adra1b        0.31182796 #> Fam131a       0.77419355 #> Tmem125       0.29032258 #> Mb21d2        0.54838710 #> Lingo3        0.31182796 #> Ncald         0.86021505 #> Siglech       0.29032258 #> Rgs14         0.43010753 #> Gm14964       0.08602151 #> Gpr17         0.22580645 #> Cx3cr1        0.33333333 #> Ezr           0.52688172 #> Adarb2        0.16129032 #> Cpne8         0.23655914 #> Plekhg3       0.24731183 #> Lamb2         0.33333333 #> Creb5         0.12903226 #> Cntn2         0.49462366 #> Aldh1a1       0.60215054 #> Phgdh         0.87096774 #> Tnfaip6       0.39784946 #> Camk2d        0.49462366 #> Shisa6        0.50537634 #> Cthrc1        0.27956989 #> Tmem119       0.35483871 #> Hmgb2         0.25806452 #> Tmem158       0.62365591 #> Dsp           0.13978495 #> Lrtm2         0.50537634 #> Gabra5        0.56989247 #> Tns1          0.25806452 #> Nell1         0.56989247 #> Slain1        0.74193548 #> Prr18         0.50537634 #> S100a8        0.10752688 #> S100a9        0.17204301 #> Col8a2        0.06451613 #> Synpr         0.62365591 #> Sertm1        0.35483871 #> Adgrf5        0.31182796 #> Capg          0.08602151 #> Gjc3          0.52688172 #> Fcer1g        0.36559140 #> Pde1a         0.59139785 #> Tafa1         0.34408602 #> Ddn           0.87096774 #> Hopx          0.76344086 #> Ptk2b         0.86021505 #> Rgs3          0.41935484 #> Kcng2         0.30107527 #> Ntng1         0.46236559 #> H2-Q7         0.04301075 #> Ifitm2        0.41935484 #> Plaat3        0.67741935 #> Plekhh1       0.44086022 #> Myl4          0.26881720 #> H2-K1         0.64516129 #> Dpp6          0.75268817 #> Tmem91        0.33333333 #> Cyp2d22       0.45161290 #> Ttr           1.00000000 #> Suclg2        0.15053763 #> Patj          0.18279570 #> Btbd3         0.82795699 #> Unc13c        0.22580645 #> Syt9          0.24731183 #> Shisal1       0.43010753 #> Grm4          0.21505376 #> Sox11         0.31182796 #> Slc22a8       0.23655914 #> Slc24a3       0.77419355 #> Klk8          0.40860215 #> Ipcef1        0.36559140 #> Tnnt1         0.27956989 #> Hhip          0.13978495 #> Spag8         0.02150538 #> Fxyd6         0.66666667 #> Ppp1r3c       0.45161290 #> Cbln4         0.22580645 #> Nnat          0.90322581 #> Myl9          0.40860215 #> Vxn           0.73118280 #> Lgals1        0.48387097 #> Gpr88         0.19354839 #> Ctxn3         0.13978495 #> Lyz2          0.16129032 #> Tmem100       0.21505376 #> Wfdc17        0.05376344 #> Ahnak         0.32258065 #> Hba-a2        1.00000000 #> Hba-a1        1.00000000 #> Ccdc153       0.05376344 #> Ccnd1         0.43010753 #> Serpinh1      0.31182796 #> Gad1          0.74193548 #> Arhgef10      0.37634409 #> 2410004P03Rik 0.06451613 #> Nt5dc2        0.35483871 #> Cebpd         0.31182796 #> Sod3          0.23655914 #> H2-D1         0.59139785 #> C4b           0.30107527 #> Tmem88b       0.56989247 #> Hbb-bt        0.96774194 #> Rhog          0.55913978 #> Rprm          0.45161290 #> Ly6a          0.68817204 #> Mog           0.81720430 #> Trbc2         0.30107527 #> Igkc          0.03225806 #> Smim1         0.33333333 #> Hs3st4        0.64516129 #> Evi2a         0.62365591 #> Prkcg         0.86021505 #> Ly6c1         0.72043011 #> Gbp4          0.04301075 #> Wipf3         0.78494624 #> BC039966      0.02150538 #> Gm13889       0.47311828 #> Plcxd2        0.40860215 #> Mia           0.07526882 #> Pou3f1        0.41935484 #> Lrrc10b       0.39784946 #> Apol11b       0.11827957 #> Gpr62         0.39784946 #> Shisa8        0.10752688 #> Gm2115        0.44086022 #> Kctd12        0.61290323 #> 1700047M11Rik 0.23655914 #> Lhfpl3        0.39784946 #> C030029H02Rik 0.12903226 #> Gm19935       0.08602151 #> 9630013A20Rik 0.11827957 #> 2900040C04Rik 0.10752688"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cell_meta_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_cell_meta_obj — create_cell_meta_obj","title":"create_cell_meta_obj — create_cell_meta_obj","text":"create_cell_meta_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cell_meta_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_cell_meta_obj — create_cell_meta_obj","text":"","code":"create_cell_meta_obj(   metaDT = NULL,   col_desc = NA_character_,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cell_meta_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_cell_meta_obj — create_cell_meta_obj","text":"cell_meta_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"create_cluster_matrix — create_cluster_matrix","title":"create_cluster_matrix — create_cluster_matrix","text":"creates aggregated matrix given clustering column","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_cluster_matrix — create_cluster_matrix","text":"","code":"create_cluster_matrix(   gobject,   spat_unit = NULL,   feat_type = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   cluster_column,   feat_subset = NULL,   gene_subset = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"create_cluster_matrix — create_cluster_matrix","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") expression_values name expression values use cluster_column name cluster column use, feat_subset subset features use gene_subset deprecated use.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_cluster_matrix — create_cluster_matrix","text":"matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"create_cluster_matrix — create_cluster_matrix","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  create_cluster_matrix(g, cluster_column = \"leiden_clus\") #> 634 x 7 Matrix of class \"dgeMatrix\" #>                cluster_2  cluster_5  cluster_1  cluster_3  cluster_6 cluster_7 #> 1110017D15Rik 0.44254321 0.42104894 0.38350624 0.19568207 0.28069313 0.3703106 #> 1190005I06Rik 1.35043254 1.35570109 1.12952302 1.02266077 1.17287740 1.8616339 #> 1700001C02Rik 0.18927101 0.05728738 0.07733503 0.01839425 0.15710555 0.0000000 #> 1700047M11Rik 0.95685380 0.88367167 0.76632284 0.86813679 0.55009271 0.8187913 #> 2010300C02Rik 2.95949381 3.37786454 3.14329561 2.84124569 3.02035452 3.4352495 #> 2410004P03Rik 0.14404681 0.17406545 0.08321509 0.08717661 0.17331548 0.0000000 #> 2900040C04Rik 0.32757163 0.28457067 0.32113707 0.17356740 0.32761432 0.0000000 #> 9630013A20Rik 0.17597264 0.29575033 0.28874834 0.26833691 0.09952757 0.0000000 #> Acta2         0.57752461 0.54501809 0.56501864 0.64096745 0.69354224 0.0000000 #> Adarb1        3.53550700 3.30058022 3.38098627 3.46216432 2.58062282 3.0655697 #> Adarb2        0.75636302 0.75530304 0.86623663 0.88371980 0.80480183 0.3976548 #> Adgrf5        0.89756501 0.66877532 1.13318007 1.20908964 0.95886855 1.1535245 #> Adgrl4        1.04985868 0.90483970 0.92898229 0.97800088 1.06809182 0.5068221 #> Adra1b        1.27403000 1.02719137 1.28061157 0.99103440 1.14741183 1.1441730 #> Adssl1        1.22683731 1.36701339 1.20495704 1.03050662 1.38292753 0.8528214 #> Aebp1         0.47659104 0.35614418 0.44012339 0.36315284 0.27892980 0.0000000 #> Agt           2.58344953 2.65131727 2.23244375 2.66909410 2.54067049 2.9915034 #> Ahnak         0.87442210 0.76469206 0.79734451 0.91531682 1.40794558 0.7167474 #> Ak5           2.81209723 2.96793488 2.67339895 2.68978028 2.65212379 2.2315317 #> Akr1c18       0.25486892 0.10717964 0.18107542 0.29201268 0.00000000 0.1371682 #> Alas2         1.24029336 1.11196961 1.15905023 0.92345850 0.83743496 1.5693706 #> Aldh1a1       2.29817855 2.52563080 2.35379228 2.65641791 2.47922311 1.5909304 #> Aldh1a2       0.12766617 0.06700689 0.09847394 0.30442144 0.00000000 0.3474831 #> Amotl1        1.59141088 1.52206874 1.67265575 1.88453192 1.80460555 1.5660657 #> Anln          1.06438290 1.22290140 1.02662252 0.75448601 1.21465958 0.6797875 #> Anxa2         0.57179514 0.34788829 0.50720952 0.70967632 0.45995659 0.6369316 #> Apod          5.11956478 5.00724135 4.93962837 4.96219926 5.42790752 3.9966022 #> Apol11b       0.35929836 0.24092320 0.20236074 0.27629799 0.17705447 0.2564135 #> Aqp4          2.67431922 2.75917648 2.54629507 2.82003279 2.84498269 2.9813845 #> Arhgap12      1.31951502 1.16740918 1.43679667 1.47682701 1.25994916 1.6957406 #> Arhgef10      1.30399703 1.11347707 1.43731120 1.03112802 0.99866752 1.5000659 #> Arhgef25      3.32395185 3.23853885 3.39800246 3.38567462 2.97064593 3.5291598 #> Arl15         1.26545235 1.28025241 1.37925059 1.28053546 0.71570803 1.4224155 #> Arpc1b        1.62470466 1.29123387 1.73839998 1.34042337 1.61413436 1.7838762 #> Arpp19        4.42595642 4.35163328 4.80397850 3.89752350 4.45562164 3.9427566 #> Arsg          1.27517546 1.23375248 0.99465993 1.03370270 1.58670989 0.2504086 #> Ascl1         0.42848925 0.46801984 0.49010822 0.23662938 0.52055771 0.0000000 #> Aspa          1.87909375 1.45680189 1.53833872 1.72369905 1.46958193 2.5777761 #> Atp2b4        1.84269558 1.15386024 1.80429076 1.41293692 1.27377631 1.2427699 #> BC039966      0.08464373 0.07695937 0.13722385 0.10447754 0.34869164 0.0000000 #> Baiap2        3.31778256 3.47637866 3.33135191 2.99228394 2.89563373 3.2529838 #> Bcam          0.55274955 0.46173183 0.45044757 0.95543213 0.93821439 0.2666210 #> Bcas1         3.64879117 3.22084650 3.42773536 3.41097031 3.13603555 2.8217151 #> Bcl11b        2.08720626 2.64724695 2.35003951 1.99581744 2.15090413 2.5578504 #> Bgn           0.55339634 0.55505453 0.52065451 0.54507218 0.63729383 0.2564135 #> Bhlhe22       1.26730535 1.57124430 1.63385086 1.27426865 1.07416336 1.8132305 #> Bok           2.71366296 2.47116725 2.82089779 2.77238677 2.50119762 2.6689739 #> Btbd17        1.18729607 1.29867174 1.21794661 1.43198694 1.25581641 0.7594994 #> Btbd3         3.23569186 3.66107529 3.30479961 3.62928422 2.70333505 4.1914698 #> C030029H02Rik 0.37708569 0.39173442 0.28273725 0.26811175 0.29861244 0.3741050 #> C1ql2         0.63756061 0.83656585 0.55546037 0.74039217 0.42425309 1.4792838 #> C4b           1.20912580 1.07666214 1.08784349 0.97983734 1.23896846 0.6141041 #> Cabp7         2.26141511 2.44514004 2.33171046 2.61207654 3.16472283 1.9179897 #> Cacng4        1.53992884 1.49452708 1.76753612 1.58747283 1.01433516 1.1549710 #> Cacng5        0.75850207 1.10563582 0.59535977 0.80880499 0.67086059 0.4663389 #> Cadps2        1.66298140 1.79355599 1.70677869 1.60769029 1.55996625 1.4189812 #> Calb1         2.75161481 2.64565739 2.66071371 2.35304449 2.24703356 2.8503507 #> Calb2         1.41862992 1.32679445 1.12525518 1.48135851 0.98242852 1.9040701 #> Cald1         1.00831433 1.09999147 0.96943989 0.73670233 0.93050467 0.8055152 #> Calml4        0.17812836 0.24026338 0.21439030 0.26489800 0.12279855 0.2564135 #> Camk2d        1.91013264 1.75440216 2.22769858 1.77491542 1.64604388 1.5496669 #> Camkv         4.44530499 4.39151834 4.74003800 4.44649869 4.41698046 5.4369734 #> Capg          0.38903655 0.35245856 0.21153810 0.28855782 0.27376925 0.0000000 #> Car14         1.24424269 1.11343694 1.07236797 1.21006471 1.11457941 0.5862004 #> Car2          4.79559426 4.66259955 4.63408113 4.92886903 4.97714175 5.0083894 #> Carhsp1       2.55785092 2.19549855 2.04605615 2.27045522 2.17840332 1.8752942 #> Cavin1        0.76178584 0.74779708 0.85791117 0.71491635 0.47148173 0.7352277 #> Cbln1         0.50677361 0.56843914 0.49778664 0.67986802 0.53191317 0.7215881 #> Cbln2         0.85233400 0.44056965 0.53927191 0.76469578 0.74219937 0.1371682 #> Cbln4         0.65457753 0.56382202 0.54803959 0.66918493 0.58515336 0.3758855 #> Ccdc136       3.19733978 2.90704090 2.90717882 3.07481517 2.32147603 2.3319452 #> Ccdc153       0.36423938 0.18890700 0.24146879 0.32301029 0.36814199 0.0000000 #> Ccdc3         0.78413847 0.73650858 0.63024330 0.68680921 0.59021747 1.1575822 #> Ccdc33        0.15646381 0.08911464 0.06165821 0.03512126 0.14687971 0.0000000 #> Ccn2          0.64678980 1.03034906 0.93286268 0.51762328 1.18479178 0.6489568 #> Ccn3          1.69445080 1.82519651 2.02261190 1.50804077 2.07883176 2.2958439 #> Ccnd1         1.49172433 1.43781973 1.87903187 1.67180559 1.71349654 1.6711655 #> Ccnd2         1.94201357 2.05141093 2.18616953 2.02323861 1.91616817 2.3163818 #> Ccp110        2.29732034 2.19807779 2.47177250 1.90358959 1.82606217 2.4110374 #> Cd24a         0.83585240 0.66717923 0.63308184 0.42952765 0.77319714 0.3935818 #> Cd59a         1.09204790 1.27182310 1.17265850 0.83537412 0.89930350 1.3773815 #> Cd74          0.16323129 0.28640037 0.16826600 0.26490651 0.08241013 0.0000000 #> Cd82          1.49922529 1.58499533 1.36301618 1.50503499 1.30925932 1.4534073 #> Cd9           3.11862023 3.00308144 2.84786535 2.72844377 2.86524077 2.3690098 #> Cdc42ep1      1.25933372 1.34260246 0.99908397 1.00464598 1.27408659 0.7373906 #> Cdc42ep2      1.31112799 1.03877484 1.33480677 1.30032413 1.17369038 0.6871979 #> Cdhr4         0.10169997 0.12003410 0.12457179 0.06082551 0.00000000 0.0000000 #> Cebpd         0.91772180 1.20032716 0.86517644 0.93989122 1.13127334 1.5196409 #> Cers2         2.35272710 2.57746727 2.31978260 2.28481964 2.52422789 3.1972147 #> Cfap126       0.22972328 0.20822942 0.17732501 0.33723331 0.34625506 0.0000000 #> Cfh           0.88970003 0.91487359 0.72403399 0.65726992 0.53960703 1.0474544 #> Chgb          4.88863946 4.69165476 5.02117029 4.85742016 4.98184272 5.0368354 #> Chrm1         2.58901145 2.56080761 2.84557636 2.32416159 2.60370776 2.0795552 #> Chrna4        1.65844964 1.85245203 1.94891048 1.54787324 1.42590930 1.1898229 #> Cit           2.54506390 2.26660798 2.68180498 2.55911909 2.31233140 2.5188545 #> Cldn11        5.12673269 4.91747338 4.91391632 4.85413605 4.93278681 5.2484757 #> Cldn5         2.05797803 2.16118255 2.01543084 2.15157241 2.88085137 1.9432223 #> Clic1         1.00898108 0.61047121 0.60289933 0.76176127 0.55957882 0.6369316 #> Clic4         2.58666667 2.36671046 2.12576758 2.38873272 2.69836201 2.0664659 #> Clic6         0.26628334 0.18558083 0.33574166 0.53274505 0.32058596 0.3474831 #> Clmn          2.16643116 1.82939053 2.08910818 2.32066560 2.04461206 1.5499308 #> Cmtm5         3.59912609 3.09342087 3.27582574 3.38148577 3.24189183 4.0948043 #> Cnih3         1.37787878 1.91073139 1.86309495 1.51923394 0.95664556 2.2298451 #> Cnp           6.03778097 5.82455446 5.72610313 5.77702510 6.08723395 5.0034797 #> Cnr1          1.99177163 2.19292993 2.33292360 2.01669127 2.45104316 2.1977566 #> Cntn2         2.19769046 1.98853482 2.31129249 1.83212021 2.27929936 1.2398097 #> Col1a1        0.22421466 0.10226721 0.10783051 0.29432743 0.15596186 0.3703106 #> Col1a2        0.68218467 0.49410901 0.33255629 0.40645615 0.51822386 0.0000000 #> Col3a1        0.10335846 0.09522224 0.14714881 0.21914560 0.13701240 0.0000000 #> Col4a1        1.02425466 0.93547399 1.18324437 1.02022529 1.15861721 1.8394679 #> Col8a2        0.06717989 0.05587790 0.09922726 0.10487230 0.42155426 0.0000000 #> Col9a3        0.73807814 0.71699776 0.55312249 0.70748193 0.83754395 1.2497755 #> Cox6a2        1.53223212 1.20097966 1.34653532 1.53161448 1.02634977 1.0002553 #> Cp            0.22881160 0.39256404 0.21860348 0.25071201 0.00000000 0.2504086 #> Cplx2         4.84253940 5.22427279 4.94190933 4.76831409 4.92894758 5.1011530 #> Cplx3         0.89687539 0.93155993 1.02811878 0.55739109 1.14881459 1.1910550 #> Cpne4         1.77621294 1.63315095 1.92080522 1.89454150 1.47925758 1.1136211 #> Cpne6         2.98364077 3.20817015 3.18107406 3.40839997 2.72992785 3.3275147 #> Cpne7         1.83558011 1.68264494 1.91383742 1.91205820 1.96437175 1.6219654 #> Cpne8         0.80722610 0.75749844 0.77400170 0.72723726 0.63598534 0.8251990 #> Cpne9         1.35270330 0.85277249 1.42153976 1.27506722 1.41430820 0.8109540 #> Cpox          1.88485507 1.55457452 1.67161441 1.48853842 1.68145051 1.2664507 #> Creb5         0.61650207 0.41841136 0.38959639 0.45888483 0.47775179 0.6407260 #> Crhbp         0.50371639 0.62988919 0.69393968 0.55015138 1.07634777 0.1371682 #> Crip1         1.41009971 1.25450326 1.39849965 1.15120273 1.20854459 1.0925703 #> Crlf1         0.68633559 0.92119629 0.62912246 0.71898084 0.58334100 1.0250248 #> Cryab         5.18551692 4.86790348 4.88570189 4.82335774 4.79686080 4.3052533 #> Crygn         0.16837963 0.15891147 0.11078299 0.02585192 0.25634860 0.0000000 #> Crym          2.59338157 2.77401687 2.90799042 2.55813201 2.23842391 2.8514304 #> Csf1r         2.66955319 2.53276487 2.42293815 2.23872947 2.61373883 2.8836846 #> Csrp1         5.01572073 4.68519528 4.78446126 4.80670914 5.05684827 5.1119679 #> Csrp2         0.59065362 0.63314040 0.47274840 0.39455994 0.51584406 0.8911345 #> Cthrc1        0.75791455 0.78019177 0.73432917 0.85975193 0.59578985 0.5068221 #> Ctla2a        1.24079344 0.98451329 1.06031270 1.13176646 0.99305478 0.3547843 #> Ctxn1         4.63620134 4.70894211 4.78510560 4.55425034 4.60291026 4.9102322 #> Ctxn3         0.36793834 0.44103903 0.31762107 0.54951397 0.33353101 0.0000000 #> Cx3cr1        1.02819592 1.13498291 0.84360013 1.02390163 1.29212364 0.7194057 #> Cxcl14        2.70461369 3.01340845 2.61703676 2.92785002 2.96684799 3.2410235 #> Cyba          1.03626710 1.15289251 0.86405628 1.23125127 0.63976179 1.2564585 #> Cygb          1.56224133 1.62942100 1.54136833 1.74061875 1.27509267 1.2047964 #> Cyp2d22       1.12801427 1.03854008 1.18972937 1.23368207 1.79398667 0.3935818 #> Dbndd1        1.15359092 1.34742373 1.27477861 1.35473435 1.17078218 0.7872716 #> Dbndd2        2.48931976 2.38269055 2.34673722 2.41390483 2.46122731 2.5249243 #> Dcn           0.47717856 0.33911219 0.31729641 0.46515059 0.30710267 0.6245136 #> Ddn           4.74116866 5.10769279 4.80497790 4.76725155 4.88958648 5.7241280 #> Ddr1          2.30055485 2.04984165 2.16648979 2.02195473 2.26367690 1.2358701 #> Dio2          0.96343624 1.01739656 0.91295021 0.76877531 0.96959609 0.3908687 #> Dkk3          3.43279965 3.25478191 3.65911228 3.12123621 3.00627044 3.6254150 #> Dkkl1         0.84140367 0.69790200 1.07608973 0.75568738 0.97585842 0.0000000 #> Dnali1        0.11444348 0.09526922 0.10768508 0.11466140 0.20920214 0.0000000 #> Doc2b         0.85036485 0.79605063 0.64340435 0.67876817 0.88942003 0.5897834 #> Dock10        1.28970847 1.57049487 1.14562505 1.29309427 1.52662939 1.1203111 #> Dock4         2.29163340 2.21266447 2.43823628 1.83282468 1.96590270 2.4823942 #> Dpp6          3.17192427 3.06393903 3.25492974 3.23346631 2.74675531 3.3143334 #> Dsp           0.32584473 0.34822123 0.15779537 0.13951865 0.04866590 0.8175892 #> Dusp6         1.25874421 1.07733803 1.23134055 1.17891621 1.18342817 1.2890468 #> Dynlrb2       0.26238060 0.21789545 0.17695090 0.13195426 0.24472416 0.0000000 #> Ecrg4         0.45018284 0.32103283 0.61516957 0.49927573 0.82417133 0.3875768 #> Edn3          0.13911894 0.05176152 0.10439934 0.24100412 0.17549881 0.0000000 #> Ednrb         1.74214831 2.06030247 1.98828402 1.88385559 1.81672934 1.8173021 #> Efcab6        0.31995630 0.44039143 0.53089320 0.32225920 0.43844731 0.8746874 #> Efhd1         1.68085370 1.43353602 1.55741521 1.35112243 1.69179593 0.8484207 #> Efnb3         3.00627172 3.13310020 2.69940050 2.74742453 3.06518311 3.0503625 #> Egr1          2.14886893 1.96359869 2.38581323 2.15333255 2.12058191 2.9450464 #> Eln           0.09061027 0.12437313 0.18921346 0.15069912 0.28733407 0.0000000 #> Elovl1        1.85542908 1.68257937 1.39440717 1.26707570 1.48335618 1.3114013 #> Emilin1       0.15988581 0.06982516 0.02383032 0.08950430 0.19240122 0.0000000 #> Enkur         0.19258484 0.16684621 0.19068893 0.19143594 0.27889672 0.0000000 #> Enpp2         4.43558458 4.31703048 4.29793558 4.11931597 4.59425832 3.7667837 #> Enpp6         0.61638331 0.76178677 0.88997335 0.67357231 0.41861134 0.2387173 #> Epha5         2.38930589 2.35544274 2.31345803 1.94187464 2.14475995 2.2749732 #> Epha7         2.07360225 1.93747690 2.12807952 2.16424935 1.78071038 2.7985356 #> Epop          1.70575981 2.20123934 2.11031292 1.70178432 1.65954865 2.0015656 #> Erbb3         0.41722543 0.37231331 0.41477667 0.49706419 0.60270594 0.9611556 #> Erbin         2.45095864 1.96542277 2.62172379 2.34742867 2.29976160 2.4205313 #> Ermn          2.49706251 2.35035913 2.53116196 2.23101740 2.34756426 1.6429710 #> Esam          0.81955988 0.70087106 1.01971007 1.15689072 1.34596491 0.7461961 #> Etnppl        0.79577091 0.73976180 1.07222053 1.11998472 0.75859382 0.7478169 #> Evi2a         2.06586106 2.00947394 1.94122254 1.99571269 2.67085999 1.9128370 #> Ezr           1.70220561 1.86477689 1.47255180 1.38241032 1.93366439 1.1799208 #> F3            1.17849759 1.49972532 1.29002259 1.29397785 1.59195340 0.0000000 #> Fa2h          2.70702598 2.15260925 2.41984825 2.42349903 2.22907359 1.7402922 #> Fabp7         1.70844146 1.67648177 1.53028626 1.74460669 1.56617051 1.2506639 #> Fam131a       3.58531575 3.79288244 3.59295331 3.26990512 2.77153982 3.6632339 #> Fam163b       2.33735544 2.69302626 2.28224543 1.98406086 2.14181837 2.2600349 #> Fam20c        2.02595270 2.06933668 1.66449848 1.96555317 1.41006144 2.5059174 #> Fam234a       0.87158086 1.01867176 1.00146330 0.90913099 0.92536879 1.2068740 #> Fbln5         0.27933271 0.16453232 0.30820530 0.23993262 0.27045984 0.0000000 #> Fcer1g        1.31521853 1.40151280 1.16901605 1.22187509 1.33067651 2.1634638 #> Fgfr2         1.78640295 1.47183801 1.58647443 1.62810292 1.71937644 1.4072603 #> Fibcd1        1.06700564 1.12347821 1.12803125 1.14066428 1.31491645 2.0072588 #> Flna          1.09557690 1.29788690 1.28178968 1.09731220 0.93128353 0.8206811 #> Fmod          0.16746162 0.12864624 0.12528572 0.18129535 0.13869958 0.0000000 #> Fn1           1.10491890 0.98838442 1.10338559 0.92355011 1.00517314 0.6760625 #> Foxj1         0.58587705 0.65336904 0.39514923 0.46595485 0.55686934 0.0000000 #> Foxp2         0.98678529 1.02917465 1.17179142 1.19784971 0.73538372 0.3436696 #> Frmd8         1.46489626 1.19688364 1.45831748 1.18313898 1.21407728 1.1267537 #> Fxyd1         3.14185573 3.03257244 3.09423916 3.31509575 3.39728196 3.1929004 #> Fxyd6         2.76320510 2.76118346 2.82867431 2.47509575 3.00110702 1.6754807 #> Fxyd7         4.24985766 4.36743132 4.51523820 4.11282865 3.66635135 3.9561871 #> Gab1          1.50292378 1.59756945 1.69453646 1.46556971 1.69383067 1.0986573 #> Gabra4        2.60497866 2.43929779 2.57947094 2.71908436 2.31227760 2.8052710 #> Gabra5        2.08271045 2.19042809 2.35036426 2.17363466 1.86402028 2.8035044 #> Gabrd         2.41994887 2.39963813 2.38924771 2.08800067 2.15819546 2.3539306 #> Gad1          3.11135615 2.86412058 3.21870359 3.36647334 2.93370810 2.2695200 #> Gad2          2.58905667 2.66586350 2.23435549 2.35198533 2.70805407 1.8277225 #> Gal3st1       1.58753819 1.44401350 1.29638097 1.31334863 1.32980736 1.8481187 #> Galnt6        0.79259003 0.86166055 0.59304957 0.62816013 0.94087487 0.3242240 #> Gamt          2.33360093 2.02585528 2.10745674 2.14681391 2.43994362 2.0382807 #> Gatm          3.55985522 2.98305682 3.24247224 3.01039727 3.50364606 3.8087241 #> Gbp4          0.14737745 0.05765225 0.07565243 0.32623728 0.05709014 0.2666210 #> Gdf11         0.89456013 0.78694878 0.85317097 0.80486474 1.06354474 0.5940782 #> Gfap          3.12155168 3.24198121 3.03211737 2.75172258 3.35167866 3.7201425 #> Gja4          0.12059199 0.22431300 0.18452209 0.26626134 0.32685198 0.0000000 #> Gjb1          1.63349091 1.24850559 1.23920304 1.25310596 1.40097070 1.0983238 #> Gjc1          0.25997653 0.40032750 0.38944777 0.32112771 0.39605926 0.9215004 #> Gjc2          1.50615090 1.47433026 1.34343557 1.24223850 1.31123383 2.0603772 #> Gjc3          2.05012612 2.15068339 1.93199599 1.85360953 2.02416301 0.9383281 #> Gkn3          0.61270038 0.38462317 0.52145131 0.66694451 0.19017267 0.0000000 #> Gldc          0.80769231 0.98218429 0.87414267 0.99385658 0.84366451 0.6635751 #> Gltp          2.15804351 1.84663313 2.04223111 1.76176658 2.14830600 1.9952998 #> Gm13889       1.46735997 1.54319311 1.51447377 1.42448664 1.08310793 0.7766758 #> Gm14964       0.50914628 0.24641944 0.35409220 0.44864513 0.24150887 0.0000000 #> Gm19935       0.35745016 0.29221866 0.23263621 0.21978974 0.42931808 0.0000000 #> Gm2115        0.82234763 1.22818773 1.03188783 1.23356153 1.12760221 1.2121439 #> Gna12         3.30737745 3.34082808 3.26309190 3.23263758 3.30171653 3.4313574 #> Gng11         2.51158658 2.82844009 2.39374372 2.58329008 2.65677985 2.6251262 #> Gng4          0.93611513 0.72142584 0.89823297 0.87199592 0.72353001 1.9499755 #> Gpr161        0.61508999 0.70157514 0.60472709 0.51476430 0.53725598 1.3769960 #> Gpr17         0.95594366 0.75231028 0.93072472 0.95879073 1.21728945 0.6845804 #> Gpr37         3.10942139 2.62248215 2.73938171 2.69477256 2.76208140 3.3843659 #> Gpr4          0.32994338 0.38349617 0.51193651 0.56655929 0.48262546 0.5230345 #> Gpr62         1.17578799 1.10082468 1.17761935 1.16650569 1.15881284 0.6983290 #> Gpr88         0.93007302 0.57660156 0.74518927 0.68161931 0.74959412 0.0000000 #> Grb14         3.42052836 3.36173213 2.77046062 3.08122822 3.00375570 2.9427657 #> Gria1         4.12795684 4.34492850 4.29095060 4.17984545 4.00398837 4.2329121 #> Gria2         4.59242525 4.64033571 4.81893386 4.40964277 4.66819325 5.2594264 #> Grik1         0.55123294 0.54706355 0.40812361 0.55433660 0.31160914 1.1483943 #> Grm1          1.67262407 1.55697786 1.67076335 2.15167949 1.61600199 1.3251047 #> Grm2          0.96663539 0.96544707 1.11083722 0.84242663 0.70178515 0.6245136 #> Grm4          0.82379382 0.55970502 0.91102293 0.77318015 0.76956595 0.9669871 #> Gsn           3.53057502 3.09333206 3.24377538 3.28817732 3.30329127 2.3946310 #> Gss           1.23676224 0.97623337 1.16285378 1.02848915 1.06035712 0.2504086 #> Gstm7         1.48500928 1.42703276 1.16225013 1.19766905 1.33959392 1.6747068 #> Gzma          0.07190143 0.11410847 0.08815679 0.16416438 0.15574311 0.2504086 #> H2-D1         2.26112351 2.59192070 2.24441472 2.23564957 2.31971537 2.4143860 #> H2-K1         1.33428078 1.59535735 1.74512473 1.78442778 2.14500032 1.5905231 #> H2-Q4         0.12644221 0.13312345 0.13251285 0.13326698 0.36279216 0.0000000 #> H2-Q7         0.07293258 0.07103938 0.11838827 0.19723209 0.14273118 0.0000000 #> Hap1          1.59121288 1.59382394 1.22734443 1.28449310 0.83700513 2.0214657 #> Hapln2        0.97869249 0.59951972 0.77294983 0.71085218 0.94971053 0.6425065 #> Hba-a1        6.77230847 6.68048781 6.62388866 6.48718732 6.78048518 6.7279361 #> Hba-a2        6.31671961 6.30178206 6.17605155 6.06596014 6.26167421 6.2308667 #> Hbb-bt        5.73427869 5.85482772 5.61558173 5.57224388 5.69711546 6.0253158 #> Hexb          3.00911612 3.37099821 3.18495493 3.30895148 3.64220022 2.5958016 #> Hhatl         0.93681733 1.06462245 0.98033459 1.11457753 1.24083725 1.0382275 #> Hhip          0.30280717 0.48120264 0.35418673 0.58559193 0.56028980 0.2666210 #> Hlf           3.24839637 3.18753475 3.31310560 3.16226642 3.13612021 3.0091062 #> Hmgb2         1.00275853 0.66241499 0.74258912 0.52707685 0.40160431 0.6541978 #> Hmgn2         2.06603581 2.04159933 1.99690865 1.76837367 1.84263924 2.1922319 #> Homer2        1.96389655 2.22129055 1.81406114 1.84286080 2.66051456 1.6458791 #> Homer3        1.26643552 1.15517582 1.11972968 1.01678407 0.71873936 1.6754294 #> Hopx          2.84716359 2.93676383 2.80524269 2.57688789 3.64036484 2.4846092 #> Hpca          5.42154696 5.77634500 5.65291624 5.30758332 5.48050058 6.0249872 #> Hpcal4        4.41959519 4.53852396 4.64722880 3.90770677 4.57671568 4.6085595 #> Hrh3          2.26063005 1.67483898 2.03100649 2.01218617 1.34537819 1.2703098 #> Hs3st2        1.12198006 1.02177563 1.24062153 0.97789314 0.88637304 0.5769102 #> Hs3st4        2.39012844 2.20126636 2.49203687 2.68146833 2.47900039 2.7906412 #> Hsd11b1       1.26986044 1.47931030 1.35631908 1.65409190 1.51951132 1.7326963 #> Hspb1         0.52971873 0.70520439 0.61274014 0.46869655 0.57186807 0.0000000 #> Hspb8         0.65264924 0.53639950 0.44501817 0.53386240 0.82568828 0.3703106 #> Htr2c         0.72402001 0.71674657 0.94921040 0.83540190 0.72370414 1.3014022 #> Htr3a         0.20623614 0.25779001 0.21562203 0.29249946 0.51795632 0.0000000 #> Icam5         2.81103374 2.98606878 2.87476056 2.66370075 3.01691101 3.2118431 #> Ick           1.33976866 1.21525841 1.35199145 0.94688793 0.97359053 0.6602028 #> Id1           1.62154126 1.37257775 1.28516523 1.47026285 1.89182064 1.2202405 #> Id3           2.94529544 3.10331664 2.78821879 2.78836190 3.03403342 2.3991619 #> Ifitm2        0.96906880 1.09064416 0.90269673 0.95391429 1.21353976 1.4021251 #> Ifitm3        1.66376351 1.90122708 1.56203622 1.98765479 2.12591695 1.2725191 #> Igfbp2        1.50043225 1.40823846 1.38463073 1.42376461 1.60911510 0.8100896 #> Igfbp4        2.56466752 2.20266690 2.60079633 2.39337399 2.70624219 3.0103030 #> Igfbp6        1.65030632 1.57194646 1.75294453 1.63411478 1.10892966 0.8347239 #> Igfbp7        1.77284339 1.99886593 1.93657362 2.05040476 2.33193718 1.0121604 #> Igkc          0.13555940 0.24448284 0.20547536 0.14835237 0.10338205 0.2504086 #> Igsf21        1.68603070 1.22147136 1.83816298 1.36185664 1.39103066 1.7312896 #> Il1rap        1.83932810 1.47409370 1.46592131 1.65888997 1.58001808 1.2359937 #> Inmt          0.13863241 0.05262011 0.10527864 0.03996412 0.00000000 0.0000000 #> Ipcef1        1.55486089 1.28809917 1.90560329 1.18308943 1.57157324 2.0242319 #> Iqgap2        0.90895923 0.78908630 0.98281143 0.83299641 0.98028629 1.0300316 #> Isg15         0.66931028 0.84537077 0.61051327 0.68058352 0.64991891 0.3935818 #> Itgb4         0.65964180 0.92831686 0.63561418 0.75968338 0.75914514 0.5053382 #> Itih3         1.13630590 1.27197529 1.23250522 1.54389062 0.89307587 0.7474588 #> Itih5         0.66908579 0.61358907 0.66298569 0.88788154 0.66934306 0.2564135 #> Itpka         3.38790169 3.77027935 3.64104099 3.56730816 3.20722970 3.6555564 #> Itpr2         0.68257703 0.50138653 0.75204281 0.89185105 0.91117434 0.3474831 #> Kcnab1        2.77547276 2.98507524 2.92440955 2.70075041 2.18772552 3.4374489 #> Kcnab3        1.30572178 1.20773147 1.52367819 1.07447598 0.74673275 0.4728139 #> Kcnc2         2.85238527 2.59184448 2.80120583 2.81393417 1.82541417 3.5675709 #> Kcng2         0.81096094 0.99894463 0.76329563 0.97884792 0.37033260 0.9943758 #> Kcnip2        2.25376431 2.23553466 2.76070190 2.34762087 2.53952800 3.1093760 #> Kctd12        2.20413606 2.03580757 2.30484518 2.27816759 2.13535177 2.3238084 #> Kctd4         1.22576360 1.28181598 0.87460770 1.13942354 0.62521228 1.2614962 #> Kit           0.56833963 0.53109779 0.81175354 0.88306169 0.87098881 0.6870762 #> Kitl          1.41888612 1.55266742 1.57897181 1.31670195 1.02985082 1.0221684 #> Klk8          1.14965101 1.48560121 1.13405184 1.37458564 1.32795052 1.4736128 #> Lamb2         0.89661890 1.11155264 0.88756112 1.02605030 1.13427781 1.4909428 #> Lamp5         1.72564609 1.84724258 2.09268336 1.37732734 1.24490303 2.3696344 #> Laptm5        1.75628277 1.68232228 1.38838393 1.44405341 1.98893577 2.1105590 #> Lbp           0.21986917 0.28440076 0.23720866 0.31418215 0.25051624 0.0000000 #> Lcat          1.48401002 1.79499129 1.41899153 1.42503144 1.49609368 1.4704056 #> Lcn2          0.11001342 0.23756140 0.08109622 0.07181696 0.23086015 0.0000000 #> Lct           0.55087056 0.90609934 0.47985112 0.37742620 0.63297348 1.2735187 #> Lef1          0.78796878 0.76062726 0.78915342 0.78366249 0.47511347 0.2564135 #> Lefty1        0.53841045 0.66308465 0.78954952 0.70686947 0.71217809 0.8436765 #> Lgals1        1.43037952 1.64432200 1.67221114 1.58771425 1.82899585 0.3436696 #> Lgi4          1.28584162 1.08700341 1.11107934 1.17937170 1.69896078 0.5068221 #> Lhfp          1.30109693 1.69313788 1.63660291 1.29043961 1.15576850 1.9859031 #> Lhfpl3        1.20532422 1.39255353 1.12989133 1.16122852 0.66136299 1.4522671 #> Lims2         1.27731649 1.25909487 1.00587185 1.06166966 1.35833723 1.0815706 #> Lingo3        1.08347499 1.27753513 1.01662036 1.12567323 0.70963331 1.2846233 #> Litaf         1.76599530 1.58304036 1.59402701 1.46871417 1.80087344 1.7484272 #> Lmo1          1.68561146 2.17490628 1.99279555 2.00818965 1.59998363 2.9855520 #> Lmo3          2.42932341 2.62194967 2.67226522 2.35574188 2.40708808 2.5245086 #> Lpar1         2.09900245 1.58915403 1.77779593 2.03084932 1.87624640 1.6533343 #> Lpl           0.74898467 0.73794230 0.84582531 0.73030980 0.96083767 0.6531023 #> Lrrc10b       1.20742881 1.61461967 1.26439875 1.45805132 1.47514670 1.9429702 #> Lrrtm3        1.33048713 1.24589537 1.37982293 1.11962727 0.75626311 1.0594517 #> Lrtm2         1.78561984 1.62725178 1.82437791 1.91200291 1.25072335 1.0239489 #> Ly6a          2.45182370 2.27519555 2.34222985 2.60751217 2.75894028 2.0413342 #> Ly6c1         2.47782910 2.71577070 2.59802701 2.53117760 2.70659596 2.7301925 #> Lyz2          0.64063495 0.29592774 0.40658358 0.50297824 0.68417195 0.3474831 #> Mag           5.12500474 4.67191908 4.65072225 4.92307953 4.78339942 5.0692949 #> Mal           5.52489949 5.32136589 5.25246346 5.50360680 5.67157535 5.4366287 #> Man1a         1.17187286 1.31869487 1.24676725 1.17223778 0.97405462 2.2950651 #> Map4k4        2.32223513 2.05759704 2.32236026 2.17313011 2.14955074 2.3387905 #> Matn2         1.02592291 1.31043133 1.24722461 1.06996228 1.28397813 1.0234107 #> Mb21d2        1.88319470 1.57101132 1.53801536 1.78219219 1.39135704 1.3609037 #> Mcam          1.17115913 0.82098156 0.95253117 0.80677507 0.93344433 0.9827394 #> Mdk           1.58694084 1.61605846 1.61063336 1.68377010 1.44990012 1.1585555 #> Meig1         0.29109497 0.27586998 0.35000531 0.26306041 0.28185530 0.5090908 #> Mgp           1.66148784 0.78793329 1.50269980 1.41650584 1.02778485 0.3436696 #> Mia           0.26367437 0.31952226 0.25723706 0.29690062 0.26626194 0.0000000 #> Micall1       1.05263096 1.00082961 1.24536063 1.03367055 1.12657206 1.6637881 #> Mmp17         2.44647351 2.48596867 2.83821830 2.60643100 2.31549141 1.9436145 #> Mobp          6.59632749 6.31520717 6.49676468 6.46728343 6.69364109 6.2946899 #> Mog           3.85434500 3.66219244 3.74512123 3.72785284 4.14058242 2.8615374 #> Mpped1        2.61638152 2.52593116 2.79221724 2.09534555 2.49422851 2.6844707 #> Msx1          0.27092155 0.36375093 0.21662745 0.36830708 0.12867615 0.2564135 #> Mustn1        0.26758770 0.09690683 0.16914040 0.12959606 0.00000000 0.0000000 #> Myh11         0.19846986 0.24588139 0.22678101 0.26793807 0.10543429 0.4196490 #> Myl4          1.18020420 1.28964125 1.57277445 0.96930487 1.49492177 0.9777995 #> Myl9          1.26493377 1.38354292 1.03635801 1.13510805 1.44268258 0.6635751 #> Myo1d         0.62446089 0.40878407 0.64095163 0.47877072 0.52474848 0.6478262 #> Myo5b         1.08991437 1.30942463 1.27752362 1.23667112 1.09982000 1.0071975 #> Myoc          0.58313508 0.62531156 0.54259460 0.46842173 0.37242729 0.2564135 #> Myrf          1.68052605 1.50964521 1.51786885 1.71116937 1.51161493 2.7020055 #> Ncald         4.47619030 4.63623903 4.66581202 4.35115584 4.38541089 4.7700048 #> Ncf2          0.19577536 0.30744226 0.28517955 0.04401388 0.22083523 0.0000000 #> Ndnf          0.51310409 0.58195774 0.38392762 0.50161323 0.43649448 0.3875768 #> Ndrg1         3.13863431 2.61730487 3.02006093 2.98727188 3.46588636 1.8026284 #> Ndufa4l2      0.76029564 0.59436411 0.42263532 0.59691739 0.75663938 0.2564135 #> Necab2        2.21168530 1.90715240 2.26504854 2.39376640 2.30668914 1.1476453 #> Nefh          2.05418571 2.14532273 2.08433434 2.32932866 1.89647811 2.7000541 #> Nell1         1.84269481 1.74220880 1.68494960 1.88827253 1.65591025 0.9011789 #> Neurod1       0.67678261 0.81565899 0.80869242 0.72888077 0.64958901 0.9152128 #> Neurod2       2.39954962 2.38922135 2.53563564 2.49431276 1.92186944 2.1457090 #> Neurod6       2.63428566 2.50013668 2.77025341 2.64586781 2.55916111 2.4965476 #> Nexn          0.56948760 0.48736435 0.47581899 0.49945862 0.27890296 0.2564135 #> Nfasc         3.34835525 3.13436419 3.45235108 3.13689334 2.88211743 3.9146409 #> Ngef          2.91242099 2.74592475 3.24004763 2.67797217 2.64117361 2.4591740 #> Nid1          0.21553865 0.17652907 0.19669062 0.21101093 0.57025089 0.0000000 #> Ninj2         0.44872324 0.37088683 0.60350690 0.38235840 0.30128077 0.3758855 #> Nkx2-2        0.56734724 0.56550690 0.48407154 0.49525147 0.43224503 0.0000000 #> Nkx6-2        1.90055006 1.39579282 1.44117547 1.54679054 1.80681039 1.7592271 #> Nnat          4.39845107 3.86182696 4.01859780 4.37346434 4.21748417 4.5339505 #> Notch1        0.73795047 0.57299505 0.76784734 0.79697664 0.79244038 0.3703106 #> Npas1         0.33784649 0.56748473 0.53158683 0.63813928 0.44098006 0.7215881 #> Npas3         0.72428750 0.61893080 0.75975639 0.67456185 1.19424107 0.0000000 #> Nptx1         3.44951987 3.60426494 3.51022093 3.32857508 3.53222106 3.4367115 #> Nptxr         3.98905107 4.10408925 4.54218333 4.02744883 3.77647703 4.0245328 #> Npy           2.70571597 2.42263758 2.73864823 2.31508768 2.82614785 1.9942862 #> Npy2r         0.57723444 0.84627539 0.80665137 0.67953308 0.73797688 0.4196490 #> Nr3c2         1.74298171 1.99898592 1.65044180 1.59818056 1.15467732 2.5707193 #> Nr4a1         0.64554738 0.73686764 0.99578525 0.71031972 0.25864240 0.2526861 #> Nr4a2         1.22250797 0.88546766 1.12822732 0.84090078 1.14285461 1.1404969 #> Nrip3         2.86404839 2.54543673 2.89416401 2.69424073 2.64936601 2.2236894 #> Nt5dc2        0.71051009 0.77568089 0.64458904 0.80447504 0.71280335 1.2502371 #> Ntng1         1.66959193 1.52111510 1.55641161 1.78292903 1.47126781 1.4775886 #> Nupr1         0.34593129 0.60897633 0.28826812 0.43127770 0.34710384 0.0000000 #> Nxph3         0.98709456 0.70831593 1.11105497 0.66187736 0.85333024 0.4936364 #> Nxph4         0.22263899 0.21444872 0.23321410 0.21511268 0.21381214 0.5123107 #> Odf3b         0.19472127 0.11610201 0.15056997 0.05604758 0.14914976 0.3703106 #> Ogfrl1        4.06706884 4.06803553 4.44373436 4.29416184 4.30641033 4.0158758 #> Olfm2         2.16938520 2.03888319 2.31740773 1.92146082 2.15946392 2.4801375 #> Olig1         4.59979138 4.17669248 4.25667919 4.33405253 4.42979786 2.9726222 #> Olig2         1.60203185 1.34909962 1.26060560 1.09819003 1.39070009 2.4657778 #> Opalin        3.34713558 3.25712117 2.96589080 2.98397388 3.26812150 3.1494090 #> Orai2         1.69283039 2.08994082 1.92667785 1.68048975 1.55877682 1.6261425 #> Otud7b        1.54728064 1.44846861 1.72710033 1.37022748 1.55159842 1.0621922 #> P2ry12        1.37878842 1.24887876 1.19884558 1.45998888 1.78452703 1.7301314 #> Padi2         1.47837486 1.10605178 1.07137082 0.92795207 1.38944203 0.4613923 #> Paqr5         0.28548196 0.34937823 0.26226962 0.31439479 0.41305397 0.1371682 #> Patj          0.94550036 0.73674309 0.75330778 0.87271454 0.90792393 1.0548719 #> Pbxip1        1.34938308 1.33038450 1.52504316 1.15143540 1.19436056 2.3029478 #> Pcdh20        1.02000367 1.35575835 1.33769133 1.26211034 0.83403675 1.7809842 #> Pcdh8         1.16073414 1.37681956 1.02213157 1.29615729 0.97496592 1.6198937 #> Pcolce        0.40835217 0.17567545 0.31943003 0.44060403 0.47988101 0.0000000 #> Pcp4l1        2.97992708 2.96077966 2.92023724 3.06136601 2.54141375 2.1498052 #> Pde1a         2.60443179 2.51600334 3.10065238 2.33133041 2.97094728 2.2677380 #> Pde8a         0.95549842 0.97877848 0.91299388 1.06086870 1.00052882 0.0000000 #> Pdgfra        0.78804945 0.93572625 1.03361028 1.15029471 0.90386397 0.7194057 #> Pdgfrb        0.53134815 0.69153085 0.59398354 0.55032243 0.82027150 0.2666210 #> Pdlim2        2.64100657 2.03304145 2.19677138 2.17522177 2.62607356 1.1154087 #> Pdp1          3.01037972 2.98742459 3.06598155 3.05666212 2.75897253 2.8148635 #> Pdyn          0.79158555 0.59079410 0.58304153 0.54279423 0.19734941 0.5758145 #> Penk          1.28150874 1.48804379 1.37118419 1.07752180 1.50500529 1.8658537 #> Pglyrp1       0.88571095 0.96683044 0.80009758 0.93906298 1.21806059 0.5068221 #> Phgdh         3.16186234 3.45444131 3.10165196 3.33673834 3.61300815 3.2276782 #> Phkg1         0.85701198 0.92818993 0.80632925 0.91264376 1.24705822 0.0000000 #> Phldb1        2.72674466 2.28226498 2.33404266 2.08710097 2.45410574 2.9918993 #> Pitpnm2       2.15711440 2.59388505 2.21222659 1.94021692 2.44767598 2.7039998 #> Plaat3        2.50487243 2.51184225 2.66509723 2.22563314 3.00090855 2.8468772 #> Plat          1.14540299 1.24250895 1.21317463 0.99302566 1.10865702 0.9816925 #> Plcb4         2.21541850 2.22112223 2.19114756 2.49093229 1.48135714 1.5824280 #> Plcxd2        1.64210575 1.30250470 1.60803209 1.32447479 0.56780985 0.4196490 #> Plekhb1       5.26989022 5.08766180 5.33292848 5.29172376 5.43168172 5.4000485 #> Plekhg1       1.63237476 1.45942596 1.58926683 1.67521499 1.07618807 0.9779528 #> Plekhg3       0.93540440 0.69588822 0.70566064 0.88679433 0.85559176 1.0493189 #> Plekhh1       1.74894875 1.68160253 1.50615974 1.50661273 1.58905469 1.2009855 #> Pllp          3.22415451 3.21743067 3.01274890 3.03544285 2.74681104 2.5136211 #> Plod1         1.12228671 1.27754944 1.09295150 1.23896140 1.13073327 1.2264941 #> Pltp          2.21518165 2.02049597 2.09493581 1.95665173 2.49435424 1.3305275 #> Plxdc1        1.22437375 1.44472440 1.42370524 1.50672610 1.12087763 0.8329171 #> Pmp22         1.47344250 1.44434883 1.32383976 1.40805034 1.14008930 1.1259126 #> Pou3f1        1.86305306 2.03310718 1.83260238 1.72681881 1.72651282 3.0430671 #> Ppm1e         3.14150738 3.06855235 3.37154134 3.05397217 3.21361904 3.4547617 #> Ppp1r14a      3.34120410 2.99944064 2.85879699 2.91610667 3.11068072 3.0766945 #> Ppp1r1a       4.01406097 4.69827590 4.31408620 4.26538646 4.36988396 4.3554185 #> Ppp1r3c       1.24356108 1.19575277 1.30680502 1.07985846 0.81875439 0.2666210 #> Prdm8         1.04292224 1.27702526 1.13657692 0.83121952 0.77800741 1.6912317 #> Prelp         0.89738015 0.60641398 0.70944223 0.79762136 0.64964328 0.9521178 #> Prkcd         2.57324385 2.61354668 2.38756697 2.87293417 2.13261309 2.2796092 #> Prkcg         4.14188600 4.17863055 4.46934041 4.14347947 3.94561260 4.3279904 #> Prkch         0.47655716 0.50607402 0.56185862 0.61083942 0.73205288 0.6261503 #> Prkcq         0.57988915 0.51531037 0.72080768 0.76230445 0.99688914 0.6372650 #> Prox1         1.12087834 1.34728136 0.86501440 1.33385558 0.96045485 1.0248782 #> Prph          0.17354909 0.25141501 0.14536617 0.34584096 0.00000000 0.3242240 #> Prr18         2.69529293 2.32592581 2.10526236 1.93626405 2.62882326 1.7417281 #> Prr5l         0.82610324 0.76269196 0.57957434 0.65938983 0.55913009 0.6862699 #> Ptk2b         4.25083755 4.58330163 4.44088016 4.56974541 4.09386716 3.4133443 #> Ptpn3         2.03505854 1.71841934 2.02237954 2.18976046 1.75715473 1.6801179 #> Ptpn4         2.95295578 2.77964915 2.93667271 2.84916240 2.78932644 3.1403560 #> Ptprb         0.78607075 0.42205639 0.82417310 0.58637400 0.96141466 1.2463021 #> Pvalb         3.28835059 3.07327787 3.23604114 3.04990097 3.21770290 2.9380384 #> Qdpr          5.23889427 4.77963136 4.90730301 4.97703997 5.36660249 4.9643569 #> Rab37         0.90145605 0.52665608 0.58522806 0.49870197 0.47213690 0.2564135 #> Rab3b         1.77459139 1.75638043 1.64899950 1.56796461 1.60138382 1.6748753 #> Rab3c         3.43988290 3.25891694 3.48259901 3.36089800 3.40901135 3.1297855 #> Ramp3         2.10765261 2.07922426 1.91348009 2.04867784 2.03535612 1.8926492 #> Ranbp3l       0.03242664 0.27743058 0.04010778 0.11302941 0.00000000 0.2824807 #> Rapgef5       1.96906516 2.42593863 2.26278751 1.91891904 1.81402583 1.9696632 #> Rarres2       1.15314942 0.79457001 0.76443331 0.97133349 1.13558301 0.7671321 #> Rasd1         1.29763417 1.41015801 1.31560461 1.43060189 1.44304974 1.1781116 #> Rasgrf1       4.15342599 4.27961595 4.33009229 4.13530341 4.16508849 4.5934711 #> Rasl10a       1.54192423 1.73460468 1.60630631 1.35696467 1.33128251 1.7335148 #> Rbp1          1.36164224 1.36587083 1.21432986 1.38511940 1.12779742 0.5328893 #> Rcn3          0.41078586 0.24734435 0.67825434 0.56174438 0.25650623 0.5212264 #> Reep3         1.45149503 1.30521540 1.63704715 0.88291932 1.55062552 2.0238562 #> Reln          0.86476575 0.83080429 1.00051023 0.96892689 0.77288492 0.1371682 #> Rflnb         0.73297921 0.58146422 1.01514315 1.03543508 0.54574352 0.9564919 #> Rfx3          1.19477919 1.18544260 0.89180005 1.05139857 0.66943743 0.8861989 #> Rgs12         1.22645589 1.21384074 1.12066235 1.14204164 1.11072187 1.1780739 #> Rgs14         1.49998504 1.67943201 1.31174597 1.36534501 1.12748511 1.3400020 #> Rgs16         0.95357582 0.77241859 0.79247107 1.00855874 0.53107269 0.4951308 #> Rgs3          1.48949093 1.63216949 1.50739170 1.75153065 1.47722520 1.1313837 #> Rgs4          3.46613950 3.57801726 3.66691030 3.69097731 3.26991343 2.2863177 #> Rgs5          2.02183992 2.33216198 2.25644205 2.17722922 2.79744251 2.4141827 #> Rhog          2.06081008 2.00638986 2.06360270 2.08136653 1.95855083 1.2839779 #> Rims2         2.29191029 2.32112167 2.29767291 2.16756388 1.45935355 1.7251028 #> Rims3         2.76819976 2.12361322 2.58159429 2.79867693 2.35592738 2.2271525 #> Rlbp1         0.77307162 1.09270069 0.79549368 0.85825563 0.41168285 0.7177937 #> Rnf130        1.98574201 2.22208533 2.13350127 1.94480595 2.01370330 2.0420282 #> Rora          2.72090769 3.14506075 2.91905783 2.85151295 2.69507749 1.8534747 #> Rprm          1.75743433 1.72853508 1.58142372 1.53667923 1.82211970 1.8632513 #> Rprml         3.07675148 2.89096108 3.24192141 3.01097068 3.15841849 3.0885792 #> Rsph1         0.27474608 0.16513017 0.23973773 0.20146095 0.31590239 0.6090279 #> S100a11       0.55821875 0.46909211 0.50687831 0.66359584 0.74313723 0.0000000 #> S100a6        2.42891377 2.33734168 2.42540182 2.09391026 2.41906585 1.8676702 #> S100a8        0.39841914 0.31742352 0.40403127 0.53159406 0.58116865 0.3474831 #> S100a9        0.45259758 0.22712797 0.47389134 0.48781378 0.40056456 0.1371682 #> S1pr5         1.28460786 0.98366694 0.86736555 0.86549324 0.81975136 0.7280132 #> Satb2         0.99178482 0.81658359 1.09482562 0.50963007 1.03455500 0.7250296 #> Scn3b         2.40820926 2.84722996 2.85438349 2.75251782 2.69454073 3.5098934 #> Selplg        1.46198870 0.95436411 1.26787210 1.27829013 1.58337965 0.8879271 #> Sema3c        0.79138634 0.46456785 0.85844214 0.52721566 0.30380740 0.6305185 #> Sema4d        2.03092581 1.86271608 1.89149412 1.77346033 1.74305382 1.3499372 #> Sema5a        1.74619383 1.75016526 1.40190974 1.65337013 1.00666994 2.4115971 #> Sept4         4.72125229 4.40519236 4.25235384 4.46364870 4.96708134 3.8270092 #> Serinc5       1.85389862 1.76190306 1.80870776 2.08593379 1.58414402 1.5293168 #> Serpina3n     1.23737941 1.38114731 1.07596381 1.15230991 0.81359560 1.8331696 #> Serpinb1a     1.16808584 0.95532207 0.97708237 1.03182567 1.20150453 0.5758145 #> Serpinf1      0.49689128 0.67245412 0.40614711 0.52461938 0.31016114 0.1371682 #> Serpinh1      0.77813139 1.16936908 0.77033088 0.75731999 0.68906297 0.2824807 #> Serpini1      3.30040994 3.29933835 3.60183670 3.19300777 3.26845870 3.4041277 #> Sertm1        1.35580865 1.46341900 1.25682736 1.08935281 1.13479998 2.0082069 #> Sez6          3.45947190 3.30180445 3.77961671 3.45034173 3.07211639 3.7882936 #> Sgpp2         0.93686313 0.51241116 0.76483544 0.87672988 1.07059811 0.9898886 #> Sh3gl3        2.42227350 2.18739040 1.96729858 2.11239853 2.11841189 2.1834760 #> Shisa6        1.40168284 1.60698652 1.61333210 1.72421787 1.27669855 2.1950510 #> Shisa8        0.41727316 0.26971254 0.31966186 0.31993890 0.47023109 0.8756489 #> Shisal1       1.63781235 1.58658496 1.63079867 1.72592166 1.27391482 1.8356435 #> Shox2         0.82458200 0.67605161 0.75661388 0.85502706 0.76525942 0.4929982 #> Siglech       0.82944635 0.65626474 0.78482842 0.55325551 1.51082291 1.0615638 #> Sipa1l3       1.46441270 1.87109964 1.53637225 1.57753377 1.71206764 1.7216736 #> Sirt2         4.50161397 4.42130053 4.35249062 4.42498751 4.26085093 4.2228421 #> Slain1        2.82831747 2.25443731 2.49507274 2.66298154 2.19900915 2.3975510 #> Slc12a2       2.61481381 2.48155481 2.45199470 2.58709031 2.28611363 2.7799110 #> Slc12a4       0.98062041 0.87515793 0.89853208 0.65237371 0.98230366 0.9809346 #> Slc13a4       0.32992903 0.09337211 0.14992969 0.18884589 0.12359795 0.0000000 #> Slc17a6       1.62291007 1.66658407 1.77797658 1.80386313 1.27191228 1.6023952 #> Slc17a8       0.17280684 0.10455841 0.28782050 0.04330752 0.17635608 0.0000000 #> Slc22a8       0.62010027 0.65232266 0.44280445 0.57180855 0.71534210 0.7740998 #> Slc24a3       3.34455169 3.06058189 3.38792495 3.35547202 2.89063604 2.6629890 #> Slc30a3       1.89363523 1.69620000 1.88026617 1.62812203 1.71538297 1.7453630 #> Slc32a1       1.59437851 1.52183497 1.70916749 1.78111100 1.95042305 1.1983679 #> Slc38a5       0.21605026 0.17444448 0.20752276 0.34937317 0.55424647 0.0000000 #> Slc44a1       3.03127766 2.73384982 2.76202669 2.62223174 2.91734606 2.2830737 #> Slc4a2        1.39994031 1.55371697 1.29468289 1.37431593 1.41444369 0.6038967 #> Slc6a11       2.61604162 2.62012288 2.50593623 2.66856608 2.30484151 2.5784086 #> Slc6a13       0.33661496 0.22670062 0.23966019 0.37448920 0.20501486 0.0000000 #> Slc6a9        1.76829554 1.79664252 1.68823316 1.74618441 2.14463735 1.3979006 #> Slc7a11       0.64926494 0.63902218 0.68024411 0.86961091 0.64560305 1.0871200 #> Slco1c1       1.54177117 2.06311666 2.01561258 1.99786085 1.87544335 2.5707408 #> Slitrk6       0.42813022 0.21470071 0.48738984 0.42940442 0.22577354 0.0000000 #> Smim1         1.09552768 0.96792008 1.05119351 1.16738202 1.91408576 1.7977655 #> Snca          4.62706705 4.73126980 4.85586143 4.61241596 4.60789463 5.0600640 #> Sncg          0.40304031 0.28474379 0.38255750 0.38044514 0.42697491 0.0000000 #> Sod3          0.71522440 0.61108203 0.37187077 0.72537202 0.70488595 0.7834772 #> Sowaha        2.11056381 2.81955510 2.20716759 2.34804256 2.87009279 2.6319992 #> Sox10         1.87523360 1.68483776 1.86954113 1.71488287 1.81402802 1.9575917 #> Sox11         0.72569496 0.98116963 0.90692982 0.91801201 0.78341938 1.3880737 #> Sox18         0.55977904 0.81528063 0.42582977 0.60139038 0.38481028 0.6037182 #> Sox8          1.05032952 1.22311243 1.03490994 0.88191218 1.22329141 1.1165167 #> Sox9          1.52919580 1.82629178 1.73707493 1.30671993 2.10794802 0.8765589 #> Spag8         0.07313899 0.11994541 0.07826858 0.07973453 0.24626610 0.0000000 #> Spink8        1.27139206 1.48848462 1.41945551 1.55335746 1.84664197 1.9907929 #> Sst           3.73684749 3.66376591 4.00841752 3.75201838 4.13871179 3.5194932 #> St6galnac5    2.16976535 2.53073593 2.28547222 2.07026295 2.41378148 2.3171005 #> Stab1         0.43845358 0.42299714 0.40552315 0.36719874 0.45872728 0.2504086 #> Stac2         1.37615453 1.44983037 1.68280224 1.10862295 1.67586917 0.9597937 #> Stk32c        2.43264753 2.31827006 2.27191999 2.16800239 2.11622851 1.1254119 #> Stx1a         2.43108017 2.42823381 2.88334873 2.45917900 2.37738140 2.2308187 #> Stxbp6        1.68982961 1.67759145 1.49422978 1.59922746 1.34631155 1.6554338 #> Suclg2        0.71876825 1.05265778 0.79135694 0.56916264 0.62196847 1.2940937 #> Syn2          4.48304876 4.69086545 4.68289652 4.49762071 4.61898034 4.2666136 #> Synpo2        1.30381698 1.05201536 1.04885488 1.25656357 1.22006726 1.5780861 #> Synpr         2.06776280 2.30042058 2.13497232 2.36693755 2.13873900 1.8655386 #> Sypl          2.06287982 1.84444490 2.16063146 2.07372883 2.56105551 3.2220890 #> Syt2          0.66474670 0.55319344 0.69937910 0.56156080 0.27321902 0.2666210 #> Syt9          0.73252808 0.66269409 0.74731851 0.70257922 0.30197116 0.9660008 #> Tafa1         1.43448588 1.38764327 1.53188164 0.93793749 0.83074187 1.2099745 #> Tagln         0.33838878 0.37546179 0.46356002 0.56298326 0.21107501 0.0000000 #> Tbr1          1.98502173 1.94914444 2.35409038 1.89777057 1.66296620 1.6540140 #> Tcf7l2        1.92964955 1.89001198 1.74476682 2.08429611 1.88492371 1.6457028 #> Tek           0.58846075 0.33380651 0.52905848 0.28965068 0.56496634 0.5935108 #> Tent5c        0.51357553 0.52555080 0.38222326 0.34015465 0.31439325 0.3976548 #> Tesc          2.30027805 1.98764453 2.43810163 2.14169984 2.12836973 2.4553152 #> Tgfbi         0.16242251 0.10086874 0.11706610 0.33153366 0.28952068 0.0000000 #> Tgm2          0.39655722 0.24013140 0.25795652 0.33902515 0.57609405 0.0000000 #> Thbs4         0.49765351 0.59669414 0.52533895 0.45375515 1.01070198 0.0000000 #> Thrsp         1.66670187 2.09722949 1.64618163 2.02629276 1.75051207 2.3582313 #> Tiam1         2.04082965 1.80812107 1.72900493 2.00111715 1.35007867 1.2827112 #> Tie1          0.34054619 0.32802029 0.30334945 0.33701117 0.32710426 0.2824807 #> Timp3         2.23409432 2.05459679 2.16335370 2.15665627 2.37840741 2.4935373 #> Tm4sf1        0.91410376 0.73984987 0.86342619 0.75260177 0.92873579 0.2666210 #> Tmbim1        2.37754522 2.08368796 1.92791556 1.88812870 1.74852239 1.1152814 #> Tmem100       0.72780347 0.76122785 0.83235817 0.73586833 0.72919557 0.8543052 #> Tmem119       1.01709217 0.81441820 0.77017322 1.08834503 1.01649421 1.1748484 #> Tmem125       1.06154618 0.77941710 0.91822041 1.19434335 0.92088619 1.2462929 #> Tmem158       2.27830361 2.23153622 2.33674527 2.00456458 1.79358921 2.6565355 #> Tmem163       1.33074915 1.18819754 1.27391290 1.38626655 1.19782563 2.0900730 #> Tmem212       0.26257481 0.14465794 0.17697560 0.18815656 0.16627582 0.3741050 #> Tmem63a       1.59770579 1.66244580 1.57718404 1.76645489 1.62173987 0.8654414 #> Tmem88b       3.07189636 2.53557020 2.75820730 2.74813759 2.36238987 1.9045927 #> Tmem91        0.91325311 1.01976509 0.90439258 0.71761435 0.98623491 0.6407260 #> Tmem98        0.84876609 0.78400162 0.76138953 0.85510839 1.28831323 0.6518838 #> Tnfaip6       1.30991237 1.27427386 0.99731184 1.03838146 0.58299791 0.3775465 #> Tnni1         0.78849723 0.56909482 0.59023884 0.60013499 0.99522997 0.2824807 #> Tnnt1         1.85088086 1.54993758 1.34763068 1.57888624 0.78988791 1.3366398 #> Tns1          0.86826741 0.57209402 0.76665670 0.99855609 0.51350110 0.6067047 #> Tpm2          0.47347063 0.28035363 0.43004655 0.65260676 0.53526026 0.2564135 #> Tppp3         2.60248409 2.12178859 2.28050208 2.27905129 2.24382333 2.2492398 #> Tprn          1.75470671 1.39721522 1.28822863 1.36993821 1.31152137 1.3917156 #> Trbc2         1.20583296 1.28703415 1.50146442 1.22354779 1.38336445 0.6090279 #> Trf           5.45009365 5.02241912 5.14522113 4.95783218 5.58619057 5.1389024 #> Trim59        0.87326383 1.06343482 1.05911906 0.80614020 1.19515684 0.7928307 #> Trps1         0.88635242 1.09999999 0.96537691 0.70914548 0.77885897 0.6262941 #> Tsc22d4       4.68481739 4.87820011 4.58044772 4.72661026 4.51677143 4.2072991 #> Tspan15       1.48416997 1.31211576 1.53793806 1.15584722 1.17124980 1.5972370 #> Tspan2        4.21697788 3.63807510 3.87527630 4.09312839 3.90853413 4.3763411 #> Ttc9b         4.29092470 4.57642934 4.57666226 4.01245305 4.26698811 4.2923582 #> Ttr           6.19462776 6.26366576 6.08356036 6.07872249 6.84390319 5.7097158 #> Ttyh2         2.00867858 1.61856659 1.52483405 1.73481250 1.94563902 1.9251238 #> Txnip         0.81687069 0.55199932 0.77762053 0.82753556 1.02713336 0.4566015 #> Ube2l6        0.79318618 0.71995881 0.73357527 0.72603253 0.68412857 0.7306790 #> Ucp2          0.79834906 0.75259766 1.12235205 1.13314304 1.32931986 1.5159634 #> Ugt8a         2.78339796 2.44413871 2.53914210 2.46467594 2.32760436 0.9639957 #> Unc13c        1.12647624 0.85563289 0.83457482 0.82026022 0.60663106 1.3103061 #> Unc5b         1.12443275 0.97559247 0.74116499 1.14892392 0.91670574 0.6871979 #> Unc93b1       0.65399313 0.72501458 0.64464940 0.57091079 1.05917378 1.2411060 #> Utrn          1.12996068 1.24445634 1.24669304 1.33442974 1.35301345 0.9244398 #> Vamp1         2.48963304 2.49782797 2.57893644 2.89025235 2.48330459 2.1890445 #> Vat1l         0.90595201 0.84805180 0.70829763 0.71705645 1.05167716 0.3474831 #> Vav3          0.98378113 0.76786652 0.63515849 0.75285785 0.26584800 0.5328893 #> Vcam1         0.90264419 1.11631737 0.91089476 0.85585352 1.14136059 1.0918987 #> Vim           1.63777758 1.87228319 1.50567183 1.96622246 1.92367017 1.2362695 #> Vip           0.83348717 0.73252192 0.69218987 0.83135659 0.52756790 0.5780129 #> Vipr2         0.41622431 0.36140341 0.35658828 0.46596769 0.22133447 0.6305185 #> Vsir          1.00682289 0.86527542 0.84954259 0.77101413 1.46413962 0.4970584 #> Vstm2a        2.28073151 2.26633071 2.15393733 2.28636983 2.22163146 2.1500628 #> Vstm2l        2.22098701 2.38136884 2.51948666 2.11308075 2.07506678 2.2089450 #> Vtn           2.72627600 2.74226687 2.48487479 2.41757776 2.62731419 1.6681123 #> Vwa1          1.13226660 1.31113787 1.04354593 1.31549050 1.40072163 2.2643882 #> Vwf           0.73980288 1.02125057 0.93244909 0.92739552 1.11699965 0.4919525 #> Vxn           3.53117569 3.31903989 3.47201305 3.21175235 3.32323417 3.4741524 #> Wfdc17        0.03592151 0.03125994 0.10073253 0.10269814 0.25262848 0.0000000 #> Wfs1          2.18927867 2.30295460 2.32184235 2.44810454 2.92937818 2.1068153 #> Wipf3         2.55544936 2.96123354 2.99511897 3.11271141 2.75874347 3.3429219 #> Wnt4          1.07266316 1.11076790 1.04697232 1.19598207 0.44986225 0.8317029 #> Zcchc12       1.52902191 1.75238761 1.50205089 1.30837531 1.18592398 2.1019134 #> Zdhhc22       1.89107607 1.70658932 1.55754351 1.79296320 1.68515227 1.1714144 #> Zfhx3         1.01463614 0.96580755 1.05374459 1.16390482 1.05445715 0.8927713 #> Zic1          1.47768397 1.44655695 1.39423152 1.80648344 1.34917327 2.0632232 #> Zmat4         1.55506361 1.57574686 1.53556433 1.42295301 1.05790010 1.4843569 #>                cluster_4 #> 1110017D15Rik 0.25822164 #> 1190005I06Rik 1.04935507 #> 1700001C02Rik 0.08247050 #> 1700047M11Rik 0.64729410 #> 2010300C02Rik 3.16523944 #> 2410004P03Rik 0.17949586 #> 2900040C04Rik 0.32603957 #> 9630013A20Rik 0.33023852 #> Acta2         0.53759005 #> Adarb1        3.34622701 #> Adarb2        0.49534891 #> Adgrf5        1.03373000 #> Adgrl4        1.00117125 #> Adra1b        0.93910023 #> Adssl1        0.83671153 #> Aebp1         0.30265744 #> Agt           2.30986060 #> Ahnak         0.91869843 #> Ak5           3.13566196 #> Akr1c18       0.10277605 #> Alas2         0.98245807 #> Aldh1a1       2.13762657 #> Aldh1a2       0.06307203 #> Amotl1        1.47332766 #> Anln          0.68573737 #> Anxa2         0.38974761 #> Apod          4.62594045 #> Apol11b       0.32937402 #> Aqp4          2.39931394 #> Arhgap12      1.51450516 #> Arhgef10      1.14429536 #> Arhgef25      3.50954343 #> Arl15         1.13171031 #> Arpc1b        1.56174316 #> Arpp19        4.54109612 #> Arsg          0.85763161 #> Ascl1         0.42467991 #> Aspa          1.43052716 #> Atp2b4        1.76384060 #> BC039966      0.05227336 #> Baiap2        3.57025234 #> Bcam          0.78622815 #> Bcas1         2.79866172 #> Bcl11b        2.09150675 #> Bgn           0.35033806 #> Bhlhe22       1.69768308 #> Bok           2.78164079 #> Btbd17        1.20395106 #> Btbd3         3.54003655 #> C030029H02Rik 0.34659023 #> C1ql2         1.16794137 #> C4b           0.92330880 #> Cabp7         2.48792771 #> Cacng4        1.43833695 #> Cacng5        0.73174308 #> Cadps2        1.81067037 #> Calb1         3.10570843 #> Calb2         1.44793211 #> Cald1         1.05283005 #> Calml4        0.13459022 #> Camk2d        1.69034013 #> Camkv         4.70088986 #> Capg          0.21266618 #> Car14         1.08944666 #> Car2          4.83859775 #> Carhsp1       1.57075592 #> Cavin1        0.70230817 #> Cbln1         0.64719536 #> Cbln2         0.53026081 #> Cbln4         0.72890041 #> Ccdc136       3.18618838 #> Ccdc153       0.15608004 #> Ccdc3         0.53051383 #> Ccdc33        0.07363270 #> Ccn2          0.56396116 #> Ccn3          1.54742610 #> Ccnd1         1.45258705 #> Ccnd2         1.75449691 #> Ccp110        2.09204511 #> Cd24a         0.40742449 #> Cd59a         1.43861027 #> Cd74          0.10955569 #> Cd82          1.39403665 #> Cd9           2.77532732 #> Cdc42ep1      0.92909667 #> Cdc42ep2      1.28679455 #> Cdhr4         0.06342928 #> Cebpd         1.09991152 #> Cers2         2.43882985 #> Cfap126       0.21236296 #> Cfh           0.71937055 #> Chgb          4.89580590 #> Chrm1         2.95772818 #> Chrna4        1.63380471 #> Cit           2.09743659 #> Cldn11        4.78456149 #> Cldn5         2.20681530 #> Clic1         0.51866093 #> Clic4         2.12422161 #> Clic6         0.42591897 #> Clmn          2.33553604 #> Cmtm5         3.15469470 #> Cnih3         1.78926516 #> Cnp           5.39410872 #> Cnr1          2.12160609 #> Cntn2         1.59843273 #> Col1a1        0.16085927 #> Col1a2        0.27025654 #> Col3a1        0.13151465 #> Col4a1        1.08994227 #> Col8a2        0.18741821 #> Col9a3        0.93330550 #> Cox6a2        1.13090877 #> Cp            0.28275109 #> Cplx2         5.27754568 #> Cplx3         0.50906013 #> Cpne4         2.20413776 #> Cpne6         3.56585260 #> Cpne7         1.93052451 #> Cpne8         0.72932689 #> Cpne9         1.15978487 #> Cpox          1.27439556 #> Creb5         0.34033447 #> Crhbp         0.49109958 #> Crip1         1.57047760 #> Crlf1         1.15496768 #> Cryab         4.66577168 #> Crygn         0.09798658 #> Crym          2.53876400 #> Csf1r         2.53418697 #> Csrp1         4.62308151 #> Csrp2         0.61034920 #> Cthrc1        0.86122853 #> Ctla2a        1.32362644 #> Ctxn1         4.74797145 #> Ctxn3         0.39628055 #> Cx3cr1        0.95719342 #> Cxcl14        3.03239260 #> Cyba          1.07571205 #> Cygb          2.20674896 #> Cyp2d22       1.30268039 #> Dbndd1        1.20736269 #> Dbndd2        2.03506595 #> Dcn           0.43218827 #> Ddn           4.90921841 #> Ddr1          1.94713727 #> Dio2          0.79573740 #> Dkk3          3.32926588 #> Dkkl1         0.54054309 #> Dnali1        0.08601687 #> Doc2b         0.59824740 #> Dock10        1.73507733 #> Dock4         2.45605205 #> Dpp6          3.32538357 #> Dsp           0.56496508 #> Dusp6         1.53022592 #> Dynlrb2       0.07137860 #> Ecrg4         0.59745978 #> Edn3          0.10673408 #> Ednrb         1.59033225 #> Efcab6        0.43987268 #> Efhd1         1.06229685 #> Efnb3         2.65042930 #> Egr1          2.50492310 #> Eln           0.23647582 #> Elovl1        1.46954470 #> Emilin1       0.27462874 #> Enkur         0.16460524 #> Enpp2         4.51135587 #> Enpp6         0.58768814 #> Epha5         2.46494758 #> Epha7         2.52694235 #> Epop          1.81153342 #> Erbb3         0.51423124 #> Erbin         1.98244265 #> Ermn          2.25647105 #> Esam          0.85819635 #> Etnppl        0.77888619 #> Evi2a         2.17418067 #> Ezr           1.61193468 #> F3            1.34499351 #> Fa2h          2.11498241 #> Fabp7         1.74874429 #> Fam131a       3.82104523 #> Fam163b       2.60011746 #> Fam20c        1.76695203 #> Fam234a       0.93518603 #> Fbln5         0.43630675 #> Fcer1g        1.07990094 #> Fgfr2         1.71329354 #> Fibcd1        1.39882457 #> Flna          0.96571296 #> Fmod          0.04236641 #> Fn1           1.07906684 #> Foxj1         0.22307537 #> Foxp2         1.05428719 #> Frmd8         1.45107637 #> Fxyd1         3.12197726 #> Fxyd6         2.51761650 #> Fxyd7         4.06784836 #> Gab1          1.46719706 #> Gabra4        2.73396239 #> Gabra5        2.35473191 #> Gabrd         2.14254530 #> Gad1          3.20243518 #> Gad2          2.50678278 #> Gal3st1       1.13100658 #> Galnt6        0.30211407 #> Gamt          1.93081585 #> Gatm          3.15793713 #> Gbp4          0.11760288 #> Gdf11         0.85765670 #> Gfap          2.78027907 #> Gja4          0.18769692 #> Gjb1          1.30976978 #> Gjc1          0.34064045 #> Gjc2          1.29166595 #> Gjc3          1.77287650 #> Gkn3          0.32377812 #> Gldc          0.81997077 #> Gltp          1.76140268 #> Gm13889       1.59952540 #> Gm14964       0.23881197 #> Gm19935       0.24955801 #> Gm2115        1.40123238 #> Gna12         2.60609824 #> Gng11         2.19151279 #> Gng4          1.09385812 #> Gpr161        0.70486753 #> Gpr17         0.73653293 #> Gpr37         2.62296320 #> Gpr4          0.48872287 #> Gpr62         1.13247697 #> Gpr88         0.57929201 #> Grb14         2.61113828 #> Gria1         4.44084827 #> Gria2         4.68558326 #> Grik1         0.52200308 #> Grm1          1.93235928 #> Grm2          1.19803763 #> Grm4          0.67044200 #> Gsn           3.05493280 #> Gss           1.63093165 #> Gstm7         1.46685037 #> Gzma          0.01537066 #> H2-D1         2.08413405 #> H2-K1         2.01438048 #> H2-Q4         0.04403270 #> H2-Q7         0.09426609 #> Hap1          1.61910843 #> Hapln2        0.76712800 #> Hba-a1        6.42665658 #> Hba-a2        5.95260496 #> Hbb-bt        5.36616636 #> Hexb          3.27353577 #> Hhatl         0.81980020 #> Hhip          0.38943212 #> Hlf           3.09046018 #> Hmgb2         0.75379922 #> Hmgn2         1.82635952 #> Homer2        2.19581914 #> Homer3        1.57341038 #> Hopx          2.98504911 #> Hpca          5.92641822 #> Hpcal4        4.76118084 #> Hrh3          1.86482080 #> Hs3st2        0.83422411 #> Hs3st4        2.55684519 #> Hsd11b1       1.52920468 #> Hspb1         0.66489715 #> Hspb8         0.63868671 #> Htr2c         0.89371813 #> Htr3a         0.44621075 #> Icam5         3.07895079 #> Ick           0.92748210 #> Id1           1.51472412 #> Id3           2.79703382 #> Ifitm2        1.19277954 #> Ifitm3        1.65475491 #> Igfbp2        1.39985479 #> Igfbp4        2.18737537 #> Igfbp6        1.55487402 #> Igfbp7        2.07693868 #> Igkc          0.08856211 #> Igsf21        1.76647020 #> Il1rap        1.40773267 #> Inmt          0.12421173 #> Ipcef1        1.28184953 #> Iqgap2        1.20430675 #> Isg15         0.68267050 #> Itgb4         0.52681245 #> Itih3         0.95701386 #> Itih5         1.08149119 #> Itpka         3.73740983 #> Itpr2         0.70815555 #> Kcnab1        3.04226008 #> Kcnab3        1.11418182 #> Kcnc2         2.67091282 #> Kcng2         0.97869316 #> Kcnip2        2.85003650 #> Kctd12        2.25485833 #> Kctd4         1.38510172 #> Kit           0.77771411 #> Kitl          1.58339868 #> Klk8          1.46881306 #> Lamb2         0.91230505 #> Lamp5         1.81610150 #> Laptm5        1.38439411 #> Lbp           0.19627608 #> Lcat          1.41763369 #> Lcn2          0.12253289 #> Lct           0.85846186 #> Lef1          0.82801917 #> Lefty1        0.81134858 #> Lgals1        1.50991492 #> Lgi4          1.04604672 #> Lhfp          1.57670266 #> Lhfpl3        1.24297124 #> Lims2         0.98938857 #> Lingo3        0.92482011 #> Litaf         1.79792102 #> Lmo1          2.14353738 #> Lmo3          2.63058172 #> Lpar1         1.60370465 #> Lpl           1.07121408 #> Lrrc10b       1.53819465 #> Lrrtm3        1.11618629 #> Lrtm2         1.70069660 #> Ly6a          2.50538847 #> Ly6c1         2.71720127 #> Lyz2          0.46364032 #> Mag           4.67393619 #> Mal           5.04683942 #> Man1a         1.23827535 #> Map4k4        2.08664581 #> Matn2         1.35789783 #> Mb21d2        1.76973253 #> Mcam          1.09629339 #> Mdk           1.53376080 #> Meig1         0.43572822 #> Mgp           1.36713519 #> Mia           0.17050296 #> Micall1       1.19040089 #> Mmp17         2.76300035 #> Mobp          6.10458192 #> Mog           3.46300407 #> Mpped1        2.39482943 #> Msx1          0.15696548 #> Mustn1        0.05434083 #> Myh11         0.14259988 #> Myl4          0.98021372 #> Myl9          1.25803289 #> Myo1d         0.66978023 #> Myo5b         1.38504287 #> Myoc          0.35233935 #> Myrf          1.21563347 #> Ncald         4.46018666 #> Ncf2          0.09961637 #> Ndnf          0.54665309 #> Ndrg1         2.73408497 #> Ndufa4l2      0.68493998 #> Necab2        2.37856283 #> Nefh          1.89682064 #> Nell1         1.98912213 #> Neurod1       0.84668834 #> Neurod2       2.71342401 #> Neurod6       2.82060410 #> Nexn          0.48396001 #> Nfasc         3.34781941 #> Ngef          2.75647904 #> Nid1          0.04243022 #> Ninj2         0.49197601 #> Nkx2-2        0.38872638 #> Nkx6-2        1.37399409 #> Nnat          4.37366824 #> Notch1        0.58981274 #> Npas1         0.61792941 #> Npas3         0.82203709 #> Nptx1         3.83192513 #> Nptxr         4.61099196 #> Npy           2.51459626 #> Npy2r         1.04472256 #> Nr3c2         1.81639594 #> Nr4a1         0.85403244 #> Nr4a2         0.95915164 #> Nrip3         2.77075058 #> Nt5dc2        1.11648381 #> Ntng1         1.71046729 #> Nupr1         0.35617664 #> Nxph3         0.54103846 #> Nxph4         0.16686809 #> Odf3b         0.11363113 #> Ogfrl1        4.14079304 #> Olfm2         2.26084825 #> Olig1         4.10287912 #> Olig2         1.08102009 #> Opalin        2.79718795 #> Orai2         2.26748066 #> Otud7b        1.59728173 #> P2ry12        1.54083467 #> Padi2         0.79418108 #> Paqr5         0.26346143 #> Patj          0.59129471 #> Pbxip1        1.45561696 #> Pcdh20        1.45659664 #> Pcdh8         1.79334980 #> Pcolce        0.29688338 #> Pcp4l1        2.57535473 #> Pde1a         2.36702109 #> Pde8a         0.48703240 #> Pdgfra        0.91472515 #> Pdgfrb        0.56980162 #> Pdlim2        2.33042211 #> Pdp1          3.07130792 #> Pdyn          0.83021815 #> Penk          1.45336436 #> Pglyrp1       0.83805061 #> Phgdh         3.40225383 #> Phkg1         0.95307076 #> Phldb1        2.21834915 #> Pitpnm2       2.26748973 #> Plaat3        2.39613452 #> Plat          1.16879670 #> Plcb4         2.11957165 #> Plcxd2        1.35893527 #> Plekhb1       5.03052367 #> Plekhg1       1.30868528 #> Plekhg3       0.58116792 #> Plekhh1       1.42694370 #> Pllp          2.83929320 #> Plod1         1.01513955 #> Pltp          2.01247707 #> Plxdc1        1.00394069 #> Pmp22         1.22235809 #> Pou3f1        1.50999422 #> Ppm1e         3.21338301 #> Ppp1r14a      2.58835889 #> Ppp1r1a       4.59851094 #> Ppp1r3c       1.32238705 #> Prdm8         1.25861063 #> Prelp         0.65903079 #> Prkcd         2.14637020 #> Prkcg         4.29179503 #> Prkch         0.49976063 #> Prkcq         0.53553084 #> Prox1         1.02388754 #> Prph          0.26203379 #> Prr18         1.92474592 #> Prr5l         0.60336929 #> Ptk2b         4.41025426 #> Ptpn3         2.00909251 #> Ptpn4         3.05481348 #> Ptprb         0.95638887 #> Pvalb         3.09893154 #> Qdpr          4.73326809 #> Rab37         0.52556290 #> Rab3b         1.46259667 #> Rab3c         3.27239312 #> Ramp3         1.81952795 #> Ranbp3l       0.11161922 #> Rapgef5       2.40123292 #> Rarres2       0.60835906 #> Rasd1         1.67572621 #> Rasgrf1       4.38499536 #> Rasl10a       1.80985928 #> Rbp1          1.30611288 #> Rcn3          0.75698657 #> Reep3         1.57246606 #> Reln          0.89969889 #> Rflnb         0.86553427 #> Rfx3          1.26658762 #> Rgs12         1.37988885 #> Rgs14         1.48359693 #> Rgs16         0.82849384 #> Rgs3          1.29883300 #> Rgs4          3.33547592 #> Rgs5          2.22307367 #> Rhog          1.83048241 #> Rims2         2.28915772 #> Rims3         2.55188402 #> Rlbp1         0.99467230 #> Rnf130        1.79891419 #> Rora          2.58959747 #> Rprm          1.73507034 #> Rprml         3.49550568 #> Rsph1         0.26057185 #> S100a11       0.55417837 #> S100a6        1.92737468 #> S100a8        0.35740871 #> S100a9        0.44543463 #> S1pr5         0.68336274 #> Satb2         0.79402893 #> Scn3b         2.98404777 #> Selplg        1.18755362 #> Sema3c        0.66432371 #> Sema4d        1.68305206 #> Sema5a        1.87068636 #> Sept4         4.18425152 #> Serinc5       1.99901133 #> Serpina3n     1.34144027 #> Serpinb1a     0.95503066 #> Serpinf1      0.61207785 #> Serpinh1      0.88895100 #> Serpini1      2.94974436 #> Sertm1        1.18622154 #> Sez6          3.40864347 #> Sgpp2         0.57907461 #> Sh3gl3        2.10938506 #> Shisa6        1.88370870 #> Shisa8        0.27554714 #> Shisal1       1.50139458 #> Shox2         0.74921670 #> Siglech       0.87621547 #> Sipa1l3       1.97744447 #> Sirt2         4.27459459 #> Slain1        2.70259995 #> Slc12a2       2.10404227 #> Slc12a4       0.85628245 #> Slc13a4       0.11711368 #> Slc17a6       1.74404575 #> Slc17a8       0.11292223 #> Slc22a8       0.74498851 #> Slc24a3       3.24439184 #> Slc30a3       1.95904506 #> Slc32a1       1.83410423 #> Slc38a5       0.52886519 #> Slc44a1       2.59962787 #> Slc4a2        1.22137346 #> Slc6a11       2.31871251 #> Slc6a13       0.34682235 #> Slc6a9        1.73057613 #> Slc7a11       0.85798499 #> Slco1c1       1.79393540 #> Slitrk6       0.18711931 #> Smim1         1.01101079 #> Snca          4.82591434 #> Sncg          0.39717035 #> Sod3          0.77167033 #> Sowaha        2.97280378 #> Sox10         1.65921654 #> Sox11         0.94133413 #> Sox18         0.68029097 #> Sox8          1.07632871 #> Sox9          1.65161246 #> Spag8         0.05630185 #> Spink8        1.68685087 #> Sst           3.66156380 #> St6galnac5    2.56250778 #> Stab1         0.41544093 #> Stac2         1.29603399 #> Stk32c        2.22177632 #> Stx1a         2.57695025 #> Stxbp6        1.80627634 #> Suclg2        0.47537351 #> Syn2          4.69831340 #> Synpo2        1.01374359 #> Synpr         2.65502986 #> Sypl          2.28179773 #> Syt2          0.45448942 #> Syt9          0.73367694 #> Tafa1         1.26002983 #> Tagln         0.42281179 #> Tbr1          1.78988837 #> Tcf7l2        1.78881915 #> Tek           0.62410035 #> Tent5c        0.25759204 #> Tesc          2.63279774 #> Tgfbi         0.09177186 #> Tgm2          0.40593632 #> Thbs4         0.61252956 #> Thrsp         2.06264951 #> Tiam1         2.08517521 #> Tie1          0.30998037 #> Timp3         2.12169068 #> Tm4sf1        0.89917395 #> Tmbim1        1.79891682 #> Tmem100       0.65813793 #> Tmem119       0.96813052 #> Tmem125       0.81514353 #> Tmem158       2.33485916 #> Tmem163       1.34780537 #> Tmem212       0.15113993 #> Tmem63a       1.60914217 #> Tmem88b       2.17385844 #> Tmem91        1.03303378 #> Tmem98        0.56123415 #> Tnfaip6       1.11901813 #> Tnni1         0.63957991 #> Tnnt1         1.17970564 #> Tns1          0.68278002 #> Tpm2          0.37449563 #> Tppp3         2.18130652 #> Tprn          0.99384427 #> Trbc2         1.23305101 #> Trf           4.77173848 #> Trim59        0.99786278 #> Trps1         0.78861445 #> Tsc22d4       4.38214380 #> Tspan15       1.26549944 #> Tspan2        3.66338603 #> Ttc9b         4.45687988 #> Ttr           6.25632335 #> Ttyh2         1.58859307 #> Txnip         0.68700917 #> Ube2l6        0.73267755 #> Ucp2          0.83585966 #> Ugt8a         2.00153051 #> Unc13c        0.76560805 #> Unc5b         0.88591120 #> Unc93b1       0.81959434 #> Utrn          1.01510328 #> Vamp1         2.87882461 #> Vat1l         0.74698880 #> Vav3          0.62844713 #> Vcam1         0.90587290 #> Vim           1.55448093 #> Vip           0.61427950 #> Vipr2         0.32945893 #> Vsir          0.62922846 #> Vstm2a        2.31470010 #> Vstm2l        2.75978563 #> Vtn           2.53775487 #> Vwa1          1.17900956 #> Vwf           0.77167716 #> Vxn           3.31594192 #> Wfdc17        0.12579889 #> Wfs1          2.73229161 #> Wipf3         3.44832475 #> Wnt4          0.90331411 #> Zcchc12       1.52071335 #> Zdhhc22       1.49991394 #> Zfhx3         1.09077552 #> Zic1          1.45860493 #> Zmat4         1.49254831"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_dim_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_dim_obj — create_dim_obj","title":"create_dim_obj — create_dim_obj","text":"create_dim_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_dim_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_dim_obj — create_dim_obj","text":"","code":"create_dim_obj(   name = \"test\",   reduction = \"cells\",   reduction_method = NA_character_,   coordinates = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL,   my_rownames = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_dim_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_dim_obj — create_dim_obj","text":"dim_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_expr_obj — create_expr_obj","title":"create_expr_obj — create_expr_obj","text":"create_expr_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_expr_obj — create_expr_obj","text":"","code":"create_expr_obj(   name = \"test\",   exprMat = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"create_expr_obj — create_expr_obj","text":"exprMat matrix expression information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_expr_obj — create_expr_obj","text":"expr_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"create_expr_obj — create_expr_obj","text":"","code":"x_expr <- readRDS(system.file(\"extdata/toy_matrix.RDS\",     package = \"GiottoClass\" ))  create_expr_obj(exprMat = x_expr) #> Warning: `create_expr_obj()` was deprecated in GiottoClass 3.3.0. #> ℹ Please use `createExprObj()` instead. #> An object of class exprObj : \"test\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #>  #> contains: #>   A B C D E F G H I J #> a 0 0 0 0 0 0 0 0 0 0 #> b 0 0 0 0 1 0 0 0 0 0 #> c 0 0 0 0 0 0 1 0 0 0 #> d 0 0 0 0 0 0 0 0 0 1 #> e 0 0 1 0 0 0 0 0 0 0 #> f 0 0 0 0 0 0 0 0 1 0 #> g 1 0 0 0 0 0 0 0 0 0 #> h 1 0 0 0 0 0 0 0 0 1 #> i 0 0 0 0 0 0 0 0 0 0 #> j 0 0 0 1 0 1 0 0 0 0 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_feat_meta_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_feat_meta_obj — create_feat_meta_obj","title":"create_feat_meta_obj — create_feat_meta_obj","text":"create_feat_meta_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_feat_meta_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_feat_meta_obj — create_feat_meta_obj","text":"","code":"create_feat_meta_obj(   metaDT = NULL,   col_desc = NA_character_,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_feat_meta_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_feat_meta_obj — create_feat_meta_obj","text":"feat_meta_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_featureNetwork_object.html","id":null,"dir":"Reference","previous_headings":"","what":"Create feature network object — create_featureNetwork_object","title":"Create feature network object — create_featureNetwork_object","text":"Create feature network object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_featureNetwork_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create feature network object — create_featureNetwork_object","text":"","code":"create_featureNetwork_object(   name = \"feat_network\",   network_datatable = NULL,   network_lookup_id = NULL,   full = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_featureNetwork_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create feature network object — create_featureNetwork_object","text":"name name assign created feature network object network_datatable network data.table object network_lookup_id network lookup id full fully connected status","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_featureNetwork_object.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create feature network object — create_featureNetwork_object","text":"featureNetwork_object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_points_object.html","id":null,"dir":"Reference","previous_headings":"","what":"Create giotto points object — create_giotto_points_object","title":"Create giotto points object — create_giotto_points_object","text":"Create giotto points object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_points_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create giotto points object — create_giotto_points_object","text":"","code":"create_giotto_points_object(   feat_type = \"rna\",   spatVector = NULL,   networks = NULL,   unique_IDs = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_points_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create giotto points object — create_giotto_points_object","text":"feat_type feature type spatVector terra spatVector object containing point data networks (optional) feature network object unique_IDs (optional) unique IDs spatVector cacheing","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_points_object.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create giotto points object — create_giotto_points_object","text":"giotto_points_object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_polygon_object.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a giotto polygon object — create_giotto_polygon_object","title":"Create a giotto polygon object — create_giotto_polygon_object","text":"Create giotto polygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_polygon_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a giotto polygon object — create_giotto_polygon_object","text":"","code":"create_giotto_polygon_object(   name = \"cell\",   spatVector = NULL,   spatVectorCentroids = NULL,   overlaps = NULL,   unique_IDs = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_polygon_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a giotto polygon object — create_giotto_polygon_object","text":"name name polygon object spatVector SpatVector polygons spatVectorCentroids (optional) SpatVector polygon centroids overlaps (optional) feature overlaps polygons unique_IDs unique polygon IDs cacheing","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_polygon_object.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a giotto polygon object — create_giotto_polygon_object","text":"giotto_polygon_object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_nn_net_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_nn_net_obj — create_nn_net_obj","title":"create_nn_net_obj — create_nn_net_obj","text":"create_nn_net_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_nn_net_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_nn_net_obj — create_nn_net_obj","text":"","code":"create_nn_net_obj(   name = \"test\",   nn_type = NA_character_,   igraph = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_nn_net_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_nn_net_obj — create_nn_net_obj","text":"nn_net_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_enr_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_spat_enr_obj — create_spat_enr_obj","title":"create_spat_enr_obj — create_spat_enr_obj","text":"create_spat_enr_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_enr_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_spat_enr_obj — create_spat_enr_obj","text":"","code":"create_spat_enr_obj(   name = \"test\",   method = NA_character_,   enrichDT = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_enr_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_spat_enr_obj — create_spat_enr_obj","text":"spat_enr_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 spatialGridObj — create_spat_grid_obj","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"Create S4 spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"","code":"create_spat_grid_obj(   name = \"test\",   method = NA_character_,   parameters = NULL,   gridDT = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"name name spatialGridObj method method used generate spatial grid parameters additional method-specific parameters used spatial grid generation gridDT data.table holding spatial grid information spat_unit spatial unit feat_type feature type provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatialGridObj\")  create_spat_grid_obj(name = \"test\", gridDT = x) #> An object of class spatialGridObj : \"test\" #> Contains annotations for spatial unit: \"cell\" and feature type: \"rna\" #> Contains spatial grid defined for: #>    5 intervals from x range: 6400.82 to 6900.82  #>    5 intervals from y range: -5173.441 to -4673.441 #>  #> Contains spatial grid generated with: NA  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_locs_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_spat_locs_obj — create_spat_locs_obj","title":"create_spat_locs_obj — create_spat_locs_obj","text":"create_spat_locs_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_locs_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_spat_locs_obj — create_spat_locs_obj","text":"","code":"create_spat_locs_obj(   name = \"test\",   coordinates = NULL,   spat_unit = \"cell\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_locs_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_spat_locs_obj — create_spat_locs_obj","text":"spat_locs_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_net_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_spat_net_obj — create_spat_net_obj","title":"create_spat_net_obj — create_spat_net_obj","text":"create_spat_net_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_net_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_spat_net_obj — create_spat_net_obj","text":"","code":"create_spat_net_obj(   name = \"test\",   method = NA_character_,   parameters = NULL,   outputObj = NULL,   networkDT = NULL,   networkDT_before_filter = NULL,   cellShapeObj = NULL,   crossSectionObjects = NULL,   spat_unit = \"cell\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_net_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_spat_net_obj — create_spat_net_obj","text":"spat_net_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":null,"dir":"Reference","previous_headings":"","what":"Crop to a spatial subset — crop","title":"Crop to a spatial subset — crop","text":"Spatially subset object x using object y. Giotto spatial subobjects respond terra::crop. giottoPoints giottoPolygon, alternative faster crop operation implemented data.table manipulation geometry information used default. mode also allows rectangular subsetting. Additionally, giottoPolygons cropped using centroids entire polygon either present instead default crop behavior keep portion polygon fall within selected crop region. Set DT = FALSE order use default style terra::crop behavior also allows usage additional params ...","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Crop to a spatial subset — crop","text":"","code":"# S4 method for class 'giottoLargeImage' crop(x, y, ...)  # S4 method for class 'giottoAffineImage' crop(x, y, ...)  # S4 method for class 'spatLocsObj' crop(x, y, ...)  # S4 method for class 'spatialNetworkObj' crop(x, y, ...)  # S4 method for class 'giottoPoints' crop(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)  # S4 method for class 'giottoPolygon' crop(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Crop to a spatial subset — crop","text":"x object y object SpatExtent returns SpatExtent ... additional params pass terra::crop DT logical. Use alternative DT subsetting crop operation xmin, xmax, ymin, ymax used DT = TRUE. Set extent bounds independently","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Crop to a spatial subset — crop","text":"SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Crop to a spatial subset — crop","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\") crop(g_image, g_image) #> An object of class giottoLargeImage : \"alignment\" #> Image extent            : 2364.5, 6522.5, -5425.25, -2620.75 (xmin, xmax, ymin, ymax) #> Original image extent   : 2364.5, 6522.5, -5425.25, -2620.75 (xmin, xmax, ymin, ymax) #> Scale factor            : 13.2420382165605, 13.2287735849057 (x, y) #> Resolution              : 0.0755170755170755, 0.0755927972900695 (x, y) #> Layers                  : 4  #> Estimated max intensity : 174  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoData/Mini_datasets/Visium/VisiumObject/Images/alignment_spatRaster'"},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Crop a giotto largeImage object — cropGiottoLargeImage","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"Crop giottoLargeImage based crop_extent argument given values","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"","code":"cropGiottoLargeImage(   gobject = NULL,   largeImage_name = NULL,   giottoLargeImage = NULL,   crop_name = \"image\",   crop_extent = NULL,   xmax_crop = NULL,   xmin_crop = NULL,   ymax_crop = NULL,   ymin_crop = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"gobject gobject holding giottoLargeImage largeImage_name name giottoLargeImage within gobject giottoLargeImage alternative input param using giottoLargeImage object instead gobject largeImage_name params crop_name arbitrary name cropped giottoLargeImage crop_extent terra extent object used crop giottoLargeImage xmax_crop, xmin_crop, ymax_crop, ymin_crop crop min/max x y bounds","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"giottoLargeImage object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  cropGiottoLargeImage(g, largeImage_name = \"image\") #> An object of class giottoLargeImage : \"image\" #> Image extent            : 2000.5, 6790.5, -5730.25, -2380.75 (xmin, xmax, ymin, ymax) #> Original image extent   : 2000.5, 6790.5, -5730.25, -2380.75 (xmin, xmax, ymin, ymax) #> Scale factor            : 19.7119341563786, 19.4738372093023 (x, y) #> Resolution              : 0.0507306889352818, 0.051350947902672 (x, y) #> Layers                  : 4  #> Estimated max intensity : 133  #> Estimated min intensity : 36  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoData/Mini_datasets/Visium/VisiumObject/Images/image_spatRaster'"},{"path":"https://drieslab.github.io/GiottoClass/reference/data_access_params.html","id":null,"dir":"Reference","previous_headings":"","what":"data_access_params — data_access_params","title":"data_access_params — data_access_params","text":"data_access_params","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/data_access_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"data_access_params — data_access_params","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class) output format get information (e.g. \"data.table\") set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. copy_obj whether deep copy/duplicate getting object (default = TRUE) initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/data_access_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"data_access_params — data_access_params","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":null,"dir":"Reference","previous_headings":"","what":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"Affine transforms linear transformations cover scaling, rotation, shearing, translations. can represented matrices 2x3 3x3 values. function reads matrix extracts values needed perform list class affine. Works 2D transforms. Logic https://math.stackexchange.com//3521141","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"","code":".decomp_affine(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"x object coercible matrix 2x3 3x3 affine matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"list transforms information.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"","code":"# load example data sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  # affine transform matrices m <- diag(rep(1, 3)) shear_m <- trans_m <- m trans_m[seq(2), 3] <- c(200, 300) scale_m <- diag(c(2, 3, 1)) shear_m[2, 1] <- 2 aff_m <- matrix(c(     2, 0.5, 1000,     -0.3, 3, 20,     100, 29, 1 ), nrow = 3, byrow = TRUE)  # create affine objects # values are shown in order of operations affine(m) #> <affine2d> #> anchor    : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> rotate    : 0  (rad) #> shear     : 0, 0  (x, y) #> scale     : 1, 1  (x, y) #> translate : 0, 0  (x, y) affine(trans_m) #> <affine2d> #> anchor    : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> rotate    : 0  (rad) #> shear     : 0, 0  (x, y) #> scale     : 1, 1  (x, y) #> translate : 200, 300  (x, y) affine(scale_m) #> <affine2d> #> anchor    : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> rotate    : 0  (rad) #> shear     : 0, 0  (x, y) #> scale     : 2, 3  (x, y) #> translate : 0, 0  (x, y) s <- affine(shear_m) a <- affine(aff_m) force(a) #> <affine2d> #> anchor    : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> rotate    : -0.165148677414627  (rad) #> shear     : 0.016260162601626, 0  (x, y) #> scale     : 2.02210754385589, 3.04138126514911  (x, y) #> translate : 1000, 20  (x, y)  # perform piecewise transforms with decomp  sl_shear_piecewise <- sl |>     spin(GiottoUtils::degrees(s$rotate), x0 = 0, y0 = 0) |>     shear(fx = s$shear[[\"x\"]], fy = s$shear[[\"y\"]], x0 = 0, y0 = 0) |>     rescale(fx = s$scale[[\"x\"]], fy = s$scale[[\"y\"]], x0 = 0, y0 = 0) |>     spatShift(dx = s$translate[[\"x\"]], dy = s$translate[[\"y\"]])  sl_aff_piecewise <- sl |>     spin(GiottoUtils::degrees(a$rotate), x0 = 0, y0 = 0) |>     shear(fx = a$shear[[\"x\"]], fy = a$shear[[\"y\"]], x0 = 0, y0 = 0) |>     rescale(fx = a$scale[[\"x\"]], fy = a$scale[[\"y\"]], x0 = 0, y0 = 0) |>     spatShift(dx = a$translate[[\"x\"]], dy = a$translate[[\"y\"]])  plot(affine(sl, shear_m))  plot(sl_shear_piecewise) plot(affine(sl, aff_m))  plot(sl_aff_piecewise)"},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":null,"dir":"Reference","previous_headings":"","what":"Density plot — density","title":"Density plot — density","text":"Create density plots pixel values giottoLargeImage. Wrapper around terra::density().","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Density plot — density","text":"","code":"# S4 method for class 'giottoLargeImage' density(x, show_max = TRUE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Density plot — density","text":"x giottoLargeImage show_max logical. Plot set max intensity vertical red line ... Arguments passed terra::density","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Density plot — density","text":"density plot","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Density plot — density","text":"","code":"f <- system.file(package = \"GiottoClass\", \"extdata/toy_intensity.tif\") gimg <- createGiottoLargeImage(f, use_rast_ext = TRUE) #> use_rast_ext == TRUE #>  extent from input raster_object will be used.  density(gimg)"},{"path":"https://drieslab.github.io/GiottoClass/reference/density_giottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","title":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","text":"Plot smoothed curve giotto largeImage intensity values","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/density_giottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","text":"","code":".dist_giottolargeimage(   gobject = NULL,   image_name = NULL,   giottoLargeImage = NULL,   method = \"dens\",   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/density_giottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","text":"gobject giotto object giottoLargeImage giotto large image object method method plotting image distribution ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/density_giottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","text":"density histogram plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dimObj Class — dimObj-class","title":"S4 dimObj Class — dimObj-class","text":"Framework store dimension reduction information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 dimObj Class — dimObj-class","text":"dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dimObj Class — dimObj-class","text":"name name dimObject feat_type feature type data spat_unit spatial unit data provenance origin aggregated information (applicable) reduction whether reduction performed 'feats' 'cells' reduction_method method used generate dimension reduction coordinates embedding coordinates misc method-specific additional outputs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 dimObj Class — dimObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"dimObj\") #> An object of class dimObj : \"pca\" #> --| Contains dimension reduction generated with: pca  #> ----| for feat_type: rna  #> ----|     spat_unit: aggregate  #>  #>    100 dimensions for 462 data points #>  #> Additional included info: #> [1] \"eigenvalues\" \"loadings\"    #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":null,"dir":"Reference","previous_headings":"","what":"Dimnames of an object — dimnames","title":"Dimnames of an object — dimnames","text":"Retrieve set dimnames object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dimnames of an object — dimnames","text":"","code":"# S4 method for class 'giotto' dimnames(x)  # S4 method for class 'exprObj' dimnames(x)  # S4 method for class 'dimObj' dimnames(x)  # S4 method for class 'spatLocsObj' dimnames(x)  # S4 method for class 'metaData' dimnames(x)  # S4 method for class 'enrData' dimnames(x)  # S4 method for class 'dimObj' dimnames(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dimnames of an object — dimnames","text":"x object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dimnames of an object — dimnames","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dimnames of an object — dimnames","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  dimnames(g) #> [[1]] #>           1           2           3           4           5           6  #>      \"Mlc1\"    \"Gprc5b\"      \"Gfap\"     \"Ednrb\"      \"Sox9\"      \"Aqp4\"  #>           7           8           9          10          11          12  #>      \"Gjc3\"      \"Sox8\"     \"Ntsr2\" \"Adcyap1r1\"       \"Smo\"    \"Gpr161\"  #>          13          14          15          16          17          18  #>      \"C1qb\"     \"Olig1\"      \"C1qa\"     \"Lmtk2\"     \"Pth1r\"     \"Ephb6\"  #>          19          20          21          22          23          24  #>     \"Gpr26\"    \"Gabbr1\"    \"Adra2a\"    \"Gabbr2\"     \"Timp4\"     \"Abcc9\"  #>          25          26          27          28          29          30  #>     \"Csf1r\"     \"Ntrk2\"    \"Adgrg1\"     \"Ntrk3\"      \"Ddr1\"     \"Erbb4\"  #>          31          32          33          34          35          36  #>    \"Selplg\"     \"Cspg5\"      \"Dlk1\"   \"Gpr37l1\"      \"Fzd1\"     \"Fgfr3\"  #>          37          38          39          40          41          42  #>  \"Slc25a18\"     \"Igf1r\"    \"Adgrl1\"     \"S1pr1\"       \"Ryk\"      \"Grm5\"  #>          43          44          45          46          47          48  #>     \"Eomes\"       \"Axl\"    \"Efemp1\"    \"Adgrb3\"     \"Sstr4\"       \"Fn1\"  #>          49          50          51          52          53          54  #>    \"Adora1\"     \"Erbb2\"     \"Gper1\"    \"Gramd3\"     \"Mertk\"   \"Slc32a1\"  #>          55          56          57          58          59          60  #>    \"Adgra1\"    \"Adgrl2\"     \"Ptgfr\"      \"Fzd2\"   \"Aldh1l1\"    \"Adgrg6\"  #>          61          62          63          64          65          66  #>      \"Egfr\"    \"Gpr162\"     \"Lpar4\"       \"Kit\"     \"Ptgdr\"      \"Gad1\"  #>          68          69          71          72          73          74  #>      \"Lgr4\"     \"Tyro3\"   \"Atp13a5\"      \"Ddr2\"     \"Rspo3\"  \"Arhgap29\"  #>          75          76          77          78          80          82  #>     \"Ackr3\"    \"Gpr146\"      \"Fzd7\"   \"Slc47a1\"      \"Insr\"    \"Ptger3\"  #>          83          84          85          86          87          88  #>    \"Bdkrb1\"     \"Traf4\"    \"Celsr2\"      \"Fzd4\"     \"Fgfr2\"    \"Cx3cr1\"  #>          89          90          91          92          93          94  #>    \"Anxa11\"    \"Adgrb1\"     \"Lpar1\"     \"Gpr17\"    \"Gpr173\"      \"Ror1\"  #>          95          96          97          99         100         101  #>    \"Cxcl12\"    \"Kiss1r\"     \"Epha4\"    \"Gpr182\"     \"Man1a\"      \"Gpr4\"  #>         102         103         104         105         106         107  #>    \"P2ry14\"     \"Hcar1\"     \"Ephb1\"     \"Adrb1\"      \"Grm3\"     \"P2ry1\"  #>         109         110         111         112         113         114  #>      \"Nrp2\"      \"Ptk7\"   \"Slco1a4\"   \"Tmem108\"      \"Hrh3\"     \"Insrr\"  #>         115         116         117         118         119         120  #>    \"Cmklr1\"      \"Opn3\"    \"Adra1b\"     \"Gpr62\"     \"Npy1r\"      \"Nrp1\"  #>         121         122         123         125         126         127  #>      \"Fzd6\"     \"S1pr5\"    \"Pdgfrb\"      \"Flt1\"     \"Chrm3\"    \"Agtr1a\"  #>         128         129         130         132         133         134  #>    \"Adgrl4\"     \"Ephb3\"     \"Lpar6\"     \"Epha6\"      \"Fzd5\"      \"Emcn\"  #>         135         136         137         138         139         140  #>     \"Cldn5\"     \"Sstr1\"      \"Fzd3\"    \"P2ry12\"    \"Adgrl3\"    \"Sema4d\"  #>         141         142         143         144         145         146  #>    \"Adgrf5\"    \"Gpr160\"    \"Mrgpre\"    \"Amigo2\"    \"Adgra3\"    \"P2yr13\"  #>         147         148         149         150         151         152  #>     \"Epha3\"    \"Adgre1\"     \"P2ry6\"    \"Cx3cl1\"    \"Epha10\"     \"Tacr1\"  #>         153         154         155         156         157         158  #>     \"Peg10\"     \"Ednra\"    \"Plxnb3\"      \"Flt4\"   \"Slc17a7\"      \"Drd2\"  #>         159         160         161         162         163         164  #>     \"Tjap1\"      \"Fzd8\"   \"Cd300c2\"      \"Htr4\"     \"Gpr52\"       \"Tek\"  #>         165         166         167         168         170         171  #>     \"S1pr2\"       \"Kdr\"      \"Ror2\"     \"Kcnj8\"      \"Hrh1\"    \"Celsr1\"  #>         172         173         176         177         178         180  #>    \"Gpr153\"     \"S1pr3\"    \"Adgra2\"    \"Fgfrl1\"      \"Tie1\"   \"Slc15a3\"  #>         181         182         183         184         185         186  #>     \"Ccr10\"    \"Pdgfra\"     \"Lhcgr\"    \"Mrgprf\"     \"Ascl1\"    \"Baiap2\"  #>         187         188         189         190         191         193  #>     \"Gpr85\"     \"Gpr22\"      \"Gcgr\"      \"Grm1\"     \"Ptafr\"    \"Calcrl\"  #>         194         195         197         198         199         200  #>     \"Gpr34\"     \"Cenpe\"   \"Adora2b\"     \"Adrb2\"      \"Ccr2\"       \"Alk\"  #>         201         203         204         205         207         208  #>     \"Tacr3\"     \"Chrm5\"     \"Erbb3\"      \"Ccr9\"     \"Gpr21\"     \"Epha7\"  #>         209         210         211         212         214         216  #>    \"Adra2b\"    \"Pcdh15\" \"Blank-104\"   \"Adora2a\"      \"Drd1\"  \"Blank-57\"  #>         218         219         220         221         223         225  #>      \"Grm7\"     \"Htr1b\"      \"Fzd9\"      \"Grm4\" \"Blank-152\"     \"Aplnr\"  #>         226         227         228         229         230         231  #>    \"Gpr176\"       \"F2r\"   \"Vmn1r43\"    \"Gpr156\"     \"Gpr55\" \"Blank-155\"  #>         232         233         234         235         236         237  #>    \"Bdkrb2\"     \"C5ar2\"    \"Gpbar1\"    \"Adgrv1\"    \"Gprc5c\"     \"Lmod1\"  #>         238         240         241         242         243         244  #>    \"Gpr135\"     \"Rxfp3\"    \"Tbxa2r\"     \"Fzd10\"       \"Ret\"  \"Blank-80\"  #>         246         247         248         250         251         253  #>     \"Epha8\"     \"Gpr75\"     \"Ackr1\"    \"Adgrg4\"     \"Chrm1\"     \"Epha1\"  #>         254         255         256         257         259         261  #>    \"Vmn2r1\"      \"Syt4\"  \"Tas2r135\"      \"Ccr1\"     \"Lpar2\"     \"Myh11\"  #>         262         263         267         271         272         274  #>      \"Gipr\"      \"Musk\"    \"Gpr183\"      \"Cnr1\"     \"C3ar1\"     \"S1pr4\"  #>         278         280         281         283         284         285  #>      \"Grm2\"     \"C5ar1\"     \"Ephb2\"      \"Fpr1\"       \"Rho\"     \"Gpr27\"  #>         288         289         290         291         294         296  #>    \"Adra1d\"    \"Gpr157\"    \"Adgrg2\"  \"Blank-45\"     \"Gpr20\"      \"Casr\"  #>         297         298         299         302         305         306  #>     \"Avpr2\"      \"Mc5r\"      \"Sctr\"     \"Epha5\"    \"Gpr158\"     \"Cxcr4\"  #>         313         315         316         321         322         323  #>     \"Vipr1\"      \"Gpr6\" \"Blank-148\"    \"Celsr3\"     \"Uts2r\"      \"Hrh2\"  #>         324         325         328         329         330         331  #>      \"Htr6\"   \"Slc17a6\"      \"Gpr1\"     \"Glp2r\"   \"Ppp1r3g\"     \"V1ra8\"  #>         332         333         334         335         337         339  #>      \"Trhr\"     \"Sstr3\"     \"Gpr63\"     \"Htr1a\"     \"F2rl3\"       \"Pln\"  #>         340         341         347         348         350         351  #>    \"Grin2b\"     \"Gpr37\"     \"Chrm4\"      \"Lgr6\"     \"Gpr61\"    \"Taar7e\"  #>         352         353         354         356         358         360  #>      \"Mas1\"     \"Npy2r\"    \"Ptger2\"     \"P2ry2\"     \"Oprm1\"    \"Prokr2\"  #>         362         364         365         366         369         372  #>    \"Adra1a\"     \"Gpr45\"      \"Mc4r\" \"Blank-128\"     \"Sstr2\"      \"Flt3\"  #>         375         376         381         382         383         387  #>     \"Htr5a\"      \"Ghsr\"     \"Galr1\"  \"Blank-95\"     \"Gpr83\"     \"Crhr1\"  #>         388         389         390         393         396         399  #>      \"Brs3\"      \"Drd5\"    \"Gpr139\"     \"Taar6\"     \"Htr5b\"   \"Vmn1r40\"  #>         401         402         407         410         411         412  #>       \"Rrh\"  \"Blank-83\"     \"Crhr2\" \"Blank-161\"   \"Vmn1r50\"    \"Tas1r3\"  #>         414         417         418         420         428         434  #>     \"Taar2\"     \"P2ry4\"     \"Mchr1\"    \"Tas1r1\"  \"Blank-69\"      \"Htr7\"  #>         436         441         446         448         452         458  #>    \"Hcrtr2\"     \"Htr2a\"   \"Cysltr2\"   \"Vmn1r46\"      \"Grpr\"    \"Adgrf2\"  #>         461         463         464         468         474         475  #> \"Blank-127\"      \"Opn5\"     \"Taar3\"      \"Oxtr\"     \"Cckbr\"      \"Nmbr\"  #>         476         477         481         482         487         492  #>    \"Ptger4\" \"Blank-145\"    \"Gpr101\"   \"Slc17a8\"    \"Adgrf4\"     \"Epha2\"  #>         528  #> \"Blank-139\"  #>  #> [[2]] #>                                         2  #> \"240649020551054330404932383065726870513\"  #>                                         3  #> \"274176126496863898679934791272921588227\"  #>                                         4  #> \"323754550002953984063006506310071917306\"  #>                                         5  #>  \"87260224659312905497866017323180367450\"  #>                                         6  #>  \"17817477728742691260808256980746537959\"  #>                                         7  #> \"182132384503107798660396708280285136358\"  #>                                         9  #> \"316289522368890354495930310222776908199\"  #>                                        10  #> \"318995879282318989627235045690211636294\"  #>                                        11  #> \"104570855383158731814075192607294301741\"  #>                                        12  #> \"115370283894795045523368609208878185314\"  #>                                        13  #> \"123860671559578247432410194986927758864\"  #>                                        14  #> \"126981423897188762239468136959275655616\"  #>                                        15  #> \"134398773695365619188678200952912609063\"  #>                                        16  #>  \"15242486364109501724975900940581726845\"  #>                                        17  #> \"152684748256642370929802439227360458069\"  #>                                        18  #> \"153751792203577791006158581642177087065\"  #>                                        19  #>  \"16326589507615554063401897357427439030\"  #>                                        20  #> \"165786478473465185470745991122188406667\"  #>                                        21  #> \"167710327060928309829388429279250508392\"  #>                                        22  #> \"172181421897607556322673704318102678295\"  #>                                        23  #> \"176844289786228093052039491926955764947\"  #>                                        24  #> \"182235958169292445695483205478317795477\"  #>                                        25  #> \"183227745956657225549068107012033843521\"  #>                                        26  #> \"186988931894710833920932112634285943415\"  #>                                        27  #> \"190687643154627893064711601675234362640\"  #>                                        28  #>  \"20548793658722995878220914240286086757\"  #>                                        29  #> \"206702762285684421190019779213421380201\"  #>                                        30  #> \"216701996099683814512199402223708471323\"  #>                                        31  #>  \"21934936165997373583174173761929761438\"  #>                                        32  #> \"230344318208995342827768566280706457626\"  #>                                        33  #> \"251905496166492083168644493421091558216\"  #>                                        34  #> \"262996653580953175020435707363716649390\"  #>                                        35  #>  \"27666206735695437393204421885258583706\"  #>                                        37  #> \"286906689872367261752702769926754066848\"  #>                                        38  #> \"288822108801800165318171357739905375883\"  #>                                        39  #> \"301054712356664458042996323827909441002\"  #>                                        40  #> \"304842190541754537761816256358565562302\"  #>                                        41  #> \"318439340668767417720582355350205310941\"  #>                                        42  #> \"335295524680090725199231409883288198017\"  #>                                        43  #>  \"35118346554513854436644695033199584696\"  #>                                        44  #>  \"41054036480225512911591384807281320971\"  #>                                        45  #>  \"43731708947199618294982749003938483862\"  #>                                        46  #>  \"48024672048124996997588408479044670509\"  #>                                        47  #>  \"51348907619842676963078202479438175138\"  #>                                        49  #>  \"67532821514617092397935003422482443295\"  #>                                        50  #>  \"77151711298730578178892667721058396928\"  #>                                        51  #>  \"77782228870577724567477221255169934206\"  #>                                        52  #>   \"8777587181320516093160667806451882030\"  #>                                        53  #>  \"95838678880751873613229512065975406368\"  #>                                        54  #>  \"95947958963963707263153541936375959179\"  #>                                        55  #>   \"9668748337336721830701975018211142813\"  #>                                        56  #>  \"97411078642927912684859796714759494710\"  #>                                        57  #> \"101161259912191124732236989250178928032\"  #>                                        58  #> \"110615983935499449765434338770904504245\"  #>                                        59  #> \"110858042010405247711695373195937122852\"  #>                                        60  #> \"110900719814678261966908552089216814729\"  #>                                        61  #>  \"12925323527075390484710711277617599454\"  #>                                        63  #> \"137348923180371322628727011975895485209\"  #>                                        64  #> \"138859376429590720661963324654447571708\"  #>                                        65  #> \"140543565961583233746802451796981444137\"  #>                                        66  #> \"143386081176260440019925196855300710659\"  #>                                        67  #> \"143408196806895889016075556052288734233\"  #>                                        68  #> \"145421744145915784890159499930205641713\"  #>                                        69  #> \"148336156782096202859532636956126767457\"  #>                                        70  #> \"150082699777048696177232440639953146354\"  #>                                        71  #>  \"15247055772869406897093633424720409278\"  #>                                        72  #>  \"15834776842182822801451197571763335013\"  #>                                        73  #> \"170833460535439412738579124041592991444\"  #>                                        74  #> \"173780780834031059819946658163431921979\"  #>                                        75  #> \"174306823762889142173283452439684229948\"  #>                                        76  #> \"175540604452034099044348476236813150837\"  #>                                        77  #> \"177757177666889772027017950398587309639\"  #>                                        78  #>  \"17868848607867654301368031294266874310\"  #>                                        79  #> \"180947508370750255585892730777436680945\"  #>                                        80  #> \"187952627468949069447188707715308813657\"  #>                                        81  #>   \"1900302715660571356090444774019116326\"  #>                                        82  #> \"203192161403397797138670022274582721699\"  #>                                        83  #> \"206016050634629330546630679047044021073\"  #>                                        85  #> \"214394514156259228118188949454902817376\"  #>                                        86  #> \"221669638772738575000116137509912039310\"  #>                                        87  #> \"224458376429228506642398057779371677646\"  #>                                        88  #> \"226912346807310637711937183879196326571\"  #>                                        89  #> \"227232155811404089141823608874580791245\"  #>                                        91  #> \"236677629222667262221261861475728542818\"  #>                                        93  #> \"244015124549889909957742476033146111487\"  #>                                        94  #> \"244247765904337326625465691380839405459\"  #>                                        95  #> \"244448312826260498647079278647004353269\"  #>                                        96  #> \"244840145612854293464477850603474951260\"  #>                                        97  #> \"262797098003740683881650619022037793005\"  #>                                        98  #> \"265185306239991354232232246957204545228\"  #>                                        99  #> \"266413162898429280572455841453688616870\"  #>                                       101  #> \"275784684664527332374777211328350223506\"  #>                                       102  #> \"277057315125198906319398446608128392905\"  #>                                       104  #> \"291975341311453330406711526698967834209\"  #>                                       105  #> \"295193149306421749943849825086053455411\"  #>                                       106  #>  \"30222355550742125173065032035537805062\"  #>                                       107  #> \"304560432600831995659079356647103974886\"  #>                                       108  #>  \"30571638947438619177947320407779261750\"  #>                                       109  #> \"306415949245581212081161219410047325001\"  #>                                       110  #> \"311565496674213535805029947713320284697\"  #>                                       111  #> \"314397389362641167108869069386457433770\"  #>                                       112  #>   \"3188909098022617910378369321966273882\"  #>                                       113  #> \"322879686187630160969459793861944841206\"  #>                                       114  #> \"330850389163886577071114668277958486114\"  #>                                       115  #> \"334199301045926627171760429217123408914\"  #>                                       116  #> \"339814056401091912617621500767389941735\"  #>                                       117  #>  \"36648998424868029072860674954666559763\"  #>                                       118  #>  \"39033692777509843205319060807429911979\"  #>                                       119  #>   \"3942785923272820952395109293003259310\"  #>                                       120  #>  \"47275912178029130797780898068213599096\"  #>                                       121  #>  \"56815638009315000170441964570512336625\"  #>                                       122  #>  \"57203625626451579261315887898923502046\"  #>                                       123  #>  \"62669443199671326763841071380380779477\"  #>                                       124  #>  \"64228015236811922665804882776457047292\"  #>                                       126  #>  \"68418314542386876178693610244900595267\"  #>                                       127  #>  \"70219882915166469874938407731799217344\"  #>                                       128  #>  \"75660428514717127988983246148828583482\"  #>                                       129  #>  \"75682347267697870039469591993208007445\"  #>                                       130  #>  \"87903363874776475366779322866396664731\"  #>                                       131  #>  \"88743795534206169429467675642537392511\"  #>                                       133  #>   \"9538866320245722231901445225545432644\"  #>                                       134  #>  \"96091484747656303270745913028146994621\"  #>                                       135  #> \"116860147088450350976374609398998546737\"  #>                                       136  #> \"133061403473432310288273623600023558748\"  #>                                       137  #> \"137154375879163008723188861204335796821\"  #>                                       138  #> \"185903314401459366597627436588666236388\"  #>                                       139  #> \"217996462208701069168232210617040322639\"  #>                                       140  #> \"226667648171626631993624597360362535576\"  #>                                       141  #> \"254829253202043893331055483138743800247\"  #>                                       142  #> \"271967915636064836314881508293335292245\"  #>                                       143  #> \"273673567134859598195435250950149370161\"  #>                                       144  #> \"305306955532868686456926844192964831687\"  #>                                       145  #> \"307030440204593378842812081935039092344\"  #>                                       146  #> \"311587331826654155209560142756469108973\"  #>                                       147  #>  \"44197902970141946871502798467323259089\"  #>                                       148  #>  \"44721220002773982161418195292536576043\"  #>                                       150  #>  \"65855854848879329159292019718060662708\"  #>                                       151  #>  \"76322781861215450124167009829890606622\"  #>                                       152  #>  \"11065258297873257226330942251431244138\"  #>                                       153  #> \"118071411587380747913796380721014165557\"  #>                                       154  #> \"123540785709544435621019288242840920053\"  #>                                       156  #> \"130428604684362047522418850101908720496\"  #>                                       157  #> \"134509424346276649608483685115101376571\"  #>                                       158  #> \"136341171141277731884608634279863298546\"  #>                                       160  #> \"137356600627014280700323828086313714576\"  #>                                       161  #> \"151798130004305208790801168757831384604\"  #>                                       162  #> \"162684318525520950869468479178769741207\"  #>                                       163  #> \"164424478098970510930576318421517316799\"  #>                                       164  #> \"166456955228473064319115194076209471689\"  #>                                       165  #> 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                         178  #> \"254538897036257180617662178141894962698\"  #>                                       179  #> \"257184545464839903394564555141875300987\"  #>                                       180  #> \"266246243070401825856501948379131507953\"  #>                                       181  #> \"280661554698226730422771895627995747059\"  #>                                       182  #> \"283821893476134729825893155000887153128\"  #>                                       183  #> \"286146294981380023269011675378975275188\"  #>                                       184  #> \"292254379263157279159966458654907155929\"  #>                                       185  #> \"293900582929631255788566880963197704396\"  #>                                       186  #> \"296019945099320175547230863498668480924\"  #>                                       187  #> \"307915098305811968258082436904262060268\"  #>                                       188  #>  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\"44008904762684544698290274594786253864\"  #>                                       483  #>  \"45132055669603860975170270958616474203\"  #>                                       484  #>  \"48397968139053633868743221368648769526\"  #>                                       485  #>   \"5354320566326536115841810233457333218\"  #>                                       486  #>  \"84576212513852183046872073655366585876\"  #>                                       487  #>  \"93224512791273624539716048847627852106\"  #>                                       488  #>  \"94116688659316792325585723413480005969\"  #>                                       489  #>  \"95576868254612369736656993305254629824\"  #>                                       490  #> \"116773984610486768651813739650149729993\"  #>                                       491  #> \"192778585506432744690553563495715115375\"  #>                                       492  #> \"220626094022262894991291197563012916160\"  #>                                       493  #> \"262323915115773877344473192484876459225\"  #>                                       494  #> \"264234489423886906860498828392801290668\"  #>                                       495  #> \"328891726607418454659643302361160567789\"  #>                                       496  #>   \"6380671372744430258754116433861320161\"  #>                                       497  #>  \"75286702783716447443887872812098770697\"  #>                                       498  #>   \"9677424102111816817518421117250891895\"  #>                                       499  #>  \"17685062374745280598492217386845129350\"  #>                                       501  #>  \"32422253415776258079819139802733069941\"  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Dimensions of giotto objects — dims-generic","title":"Dimensions of giotto objects — dims-generic","text":"Find dimensions object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dimensions of giotto objects — dims-generic","text":"","code":"# S4 method for class 'giotto' nrow(x)  # S4 method for class 'giottoPoints' nrow(x)  # S4 method for class 'giottoPolygon' nrow(x)  # S4 method for class 'spatLocsObj' nrow(x)  # S4 method for class 'exprData' nrow(x)  # S4 method for class 'metaData' nrow(x)  # S4 method for class 'spatialNetworkObj' nrow(x)  # S4 method for class 'enrData' nrow(x)  # S4 method for class 'dimObj' nrow(x)  # S4 method for class 'giotto' ncol(x)  # S4 method for class 'exprData' ncol(x)  # S4 method for class 'metaData' ncol(x)  # S4 method for class 'enrData' ncol(x)  # S4 method for class 'dimObj' ncol(x)  # S4 method for class 'giotto' dim(x)  # S4 method for class 'spatLocsObj' dim(x)  # S4 method for class 'exprData' dim(x)  # S4 method for class 'metaData' dim(x)  # S4 method for class 'enrData' dim(x)  # S4 method for class 'giottoLargeImage' dim(x)  # S4 method for class 'giottoPolygon' dim(x)  # S4 method for class 'giottoPoints' dim(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dimensions of giotto objects — dims-generic","text":"x object check dimensions ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dimensions of giotto objects — dims-generic","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dimensions of giotto objects — dims-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  nrow(g) #> [1] 79761"},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot distribution of image intensity values — distGiottoImage","title":"Plot distribution of image intensity values — distGiottoImage","text":"Plot distribution intensity values using either density plot histogram. Useful finding image artefact outliers determining reasonable scaling cutoffs.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot distribution of image intensity values — distGiottoImage","text":"","code":"distGiottoImage(   gobject = NULL,   image_type = \"largeImage\",   image_name = NULL,   giottoLargeImage = NULL,   method = c(\"dens\", \"hist\"),   show_max = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot distribution of image intensity values — distGiottoImage","text":"gobject giotto object image_type image object type (supports largeImage set default) image_name name image object use giottoLargeImage giotto large image object method plot type show image intensity distribution show_max logical. Plot set max intensity vertical red line ... additional params pass terra::hist() terra::density()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot distribution of image intensity values — distGiottoImage","text":"density histogram plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot distribution of image intensity values — distGiottoImage","text":"Plot generated downsampling original image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"plotting-method-dens-","dir":"Reference","previous_headings":"","what":"Plotting method 'dens'","title":"Plot distribution of image intensity values — distGiottoImage","text":"Density plot intensity values image objects. N total values examined. Bandwidth refers curve smoothing value applied.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"plotting-method-hist-","dir":"Reference","previous_headings":"","what":"Plotting method 'hist'","title":"Plot distribution of image intensity values — distGiottoImage","text":"Histogram intensity values image objects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot distribution of image intensity values — distGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  distGiottoImage(g, image_name = \"image\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/doDeferred.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform deferred/lazy operations — doDeferred","title":"Perform deferred/lazy operations — doDeferred","text":"Force deferred/lazy operations.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/doDeferred.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform deferred/lazy operations — doDeferred","text":"","code":"# S4 method for class 'giottoAffineImage' doDeferred(x, size = 5e+05, filename = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/doDeferred.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform deferred/lazy operations — doDeferred","text":"x object force deferred operations size numeric. Minimum number image pixels render evaluating filename character. Full filepath write rendered image . NULL, file tempdir() generated. ... additional args pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/doDeferred.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Perform deferred/lazy operations — doDeferred","text":"","code":"gimg <- GiottoData::loadSubObjectMini(\"giottoLargeImage\") affimg <- spin(gimg, 45) # lazily performs affine  # force the affine operation and render the output with at least 5e5 px gimg2 <- doDeferred(affimg, size = 5e5) # **This is mainly intended for visualization.** # This process saves with image depth of 8. # Spatially transformed raster values are not preferred for analysis"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_mat.html","id":null,"dir":"Reference","previous_headings":"","what":"Print abbreviated matrix — .abbrev_mat","title":"Print abbreviated matrix — .abbrev_mat","text":"print abbreviated matrix exprObj. Works Matrix pkg denseMatrix, matrix, data.frame classes inherit .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_mat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print abbreviated matrix — .abbrev_mat","text":"","code":".abbrev_mat(exprObj, nrows, ncols, header = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_mat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print abbreviated matrix — .abbrev_mat","text":"abbreviated matrix exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_spatlocs.html","id":null,"dir":"Reference","previous_headings":"","what":"Print abbreviated spatlocs — .abbrev_spatlocs","title":"Print abbreviated spatlocs — .abbrev_spatlocs","text":"print abbreviated spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_spatlocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print abbreviated spatlocs — .abbrev_spatlocs","text":"","code":".abbrev_spatlocs(spatLocsObj, nrows)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_spatlocs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print abbreviated spatlocs — .abbrev_spatlocs","text":"abbreviated spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-bitdepth.html","id":null,"dir":"Reference","previous_headings":"","what":"Guess likely bitdepth from value(s) — .bitdepth","title":"Guess likely bitdepth from value(s) — .bitdepth","text":"Guess likely bitdepth value(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-bitdepth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Guess likely bitdepth from value(s) — .bitdepth","text":"","code":".bitdepth(x, return_max = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-bitdepth.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Guess likely bitdepth from value(s) — .bitdepth","text":"x numeric vector. Values representative data assessed bitdepth. usually sampled subset values raster. return_max logical. default FALSE. Whether return maximum possible value detected bitdepth instead bitdepth ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-bitdepth.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Guess likely bitdepth from value(s) — .bitdepth","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_centroids_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate polygon centroids — .calculate_centroids_polygons","title":"Calculate polygon centroids — .calculate_centroids_polygons","text":"calculates centroids selected polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_centroids_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate polygon centroids — .calculate_centroids_polygons","text":"","code":".calculate_centroids_polygons(   gpolygon,   name = \"centroids\",   append_gpolygon = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_centroids_polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate polygon centroids — .calculate_centroids_polygons","text":"SpatVector giotto polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_distance_and_weight.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate spatial network distance and weight — .calculate_distance_and_weight","title":"Calculate spatial network distance and weight — .calculate_distance_and_weight","text":"Calculate distance weight metrics data.table spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_distance_and_weight.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate spatial network distance and weight — .calculate_distance_and_weight","text":"","code":".calculate_distance_and_weight(   networkDT = NULL,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   sdimz = \"sdimz\",   d2_or_d3 = c(2, 3) )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_distance_and_weight.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate spatial network distance and weight — .calculate_distance_and_weight","text":"networkDT spatial network data.table sdimx spatial dimension x sdimy spatial dimension y sdimz spatial dimension z d2_or_d3 number dimensions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_distance_and_weight.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate spatial network distance and weight — .calculate_distance_and_weight","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_overlap_raster.html","id":null,"dir":"Reference","previous_headings":"","what":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","title":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","text":"Core workflow function accepts simple SpatVector inputs, performs rasterization polys checks overlaps.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_overlap_raster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","text":"","code":".calculate_overlap_raster(   spatvec,   pointvec,   count_info_column = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_overlap_raster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","text":"spatvec SpatVector polygon giottoPolygon object pointvec SpatVector points giottoPoints object count_info_column column count information (optional) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_overlap_raster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","text":"SpatVector overlapped points info","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_cell_meta_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check cell metadata object — .check_cell_meta_obj","title":"Check cell metadata object — .check_cell_meta_obj","text":"Function check S4 cellMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_cell_meta_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check cell metadata object — .check_cell_meta_obj","text":"","code":".check_cell_meta_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_cell_meta_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check cell metadata object — .check_cell_meta_obj","text":"object S4 cellMetaObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_cell_meta_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check cell metadata object — .check_cell_meta_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_dim_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check dimObj — .check_dim_obj","title":"Check dimObj — .check_dim_obj","text":"check function S4 dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_dim_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check dimObj — .check_dim_obj","text":"","code":".check_dim_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_dim_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check dimObj — .check_dim_obj","text":"object S4 dimObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_dim_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check dimObj — .check_dim_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_expr_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check exprObj — .check_expr_obj","title":"Check exprObj — .check_expr_obj","text":"Check function S4 exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_expr_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check exprObj — .check_expr_obj","text":"","code":".check_expr_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_expr_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check exprObj — .check_expr_obj","text":"object S4 exprObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_expr_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check exprObj — .check_expr_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_feat_meta_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check feature metadata object — .check_feat_meta_obj","title":"Check feature metadata object — .check_feat_meta_obj","text":"Function check S4 featMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_feat_meta_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check feature metadata object — .check_feat_meta_obj","text":"","code":".check_feat_meta_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_feat_meta_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check feature metadata object — .check_feat_meta_obj","text":"object S4 featMetaObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_feat_meta_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check feature metadata object — .check_feat_meta_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_giotto_python_modules.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","title":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","text":"Check core python packages Giotto uses. internal currently called giotto initialize() method","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_giotto_python_modules.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","text":"","code":".check_giotto_python_modules(my_python_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_giotto_python_modules.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","text":"my_python_path path python environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_giotto_python_modules.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_grid_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check spatialGridObj — .check_spat_grid_obj","title":"Check spatialGridObj — .check_spat_grid_obj","text":"Check function S4 spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_grid_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check spatialGridObj — .check_spat_grid_obj","text":"","code":".check_spat_grid_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_grid_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check spatialGridObj — .check_spat_grid_obj","text":"object S4 spatialGridObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_grid_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check spatialGridObj — .check_spat_grid_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_locs_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check spatLocsObj — .check_spat_locs_obj","title":"Check spatLocsObj — .check_spat_locs_obj","text":"Check function S4 spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_locs_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check spatLocsObj — .check_spat_locs_obj","text":"","code":".check_spat_locs_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_locs_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check spatLocsObj — .check_spat_locs_obj","text":"object S4 spatLocsObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_locs_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check spatLocsObj — .check_spat_locs_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_net_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check spatialNetworkObj — .check_spat_net_obj","title":"Check spatialNetworkObj — .check_spat_net_obj","text":"Check function S4 spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_net_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check spatialNetworkObj — .check_spat_net_obj","text":"","code":".check_spat_net_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_net_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check spatialNetworkObj — .check_spat_net_obj","text":"object S4 spatialNetworkObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_net_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check spatialNetworkObj — .check_spat_net_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spatial_location_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Check spatial location data — .check_spatial_location_data","title":"Check spatial location data — .check_spatial_location_data","text":"check cell ID (spatial unit) names spatial location expression data. look identical IDs sorting.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spatial_location_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check spatial location data — .check_spatial_location_data","text":"","code":".check_spatial_location_data(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spatial_location_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check spatial location data — .check_spatial_location_data","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-combine_stack_spatvectors.html","id":null,"dir":"Reference","previous_headings":"","what":".combine_stack_spatvectors — .combine_stack_spatvectors","title":".combine_stack_spatvectors — .combine_stack_spatvectors","text":"combines/aggregates polygons cell ID different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-combine_stack_spatvectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".combine_stack_spatvectors — .combine_stack_spatvectors","text":"","code":".combine_stack_spatvectors(   gobject,   spat_units,   for_loop = FALSE,   for_loop_group_size = 100 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-combine_stack_spatvectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".combine_stack_spatvectors — .combine_stack_spatvectors","text":"SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_2d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_2d — .create_delaunaynetwork_2d","title":".create_delaunaynetwork_2d — .create_delaunaynetwork_2d","text":"Create spatial 2D Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_2d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_2d — .create_delaunaynetwork_2d","text":"","code":".create_delaunaynetwork_2d(   gobject,   method = c(\"delaunayn_geometry\", \"RTriangle\", \"deldir\"),   spat_unit = NULL,   spat_loc_name = \"raw\",   sdimx = \"sdimx\",   sdimy = \"sdimy\",   name = \"delaunay_network\",   maximum_distance = \"auto\",   minimum_k = 0,   options = \"Pp\",   Y = TRUE,   j = TRUE,   S = 0,   verbose = TRUE,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_2d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_2d — .create_delaunaynetwork_2d","text":"spatial 2D Delaunay network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_3d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_3d — .create_delaunaynetwork_3d","title":".create_delaunaynetwork_3d — .create_delaunaynetwork_3d","text":"Create spatial 3D Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_3d — .create_delaunaynetwork_3d","text":"","code":".create_delaunaynetwork_3d(   gobject,   method = \"delaunayn_geometry\",   spat_unit = NULL,   spat_loc_name = \"raw\",   sdimx = \"sdimx\",   sdimy = \"sdimy\",   sdimz = \"sdimz\",   name = \"delaunay_network_3D\",   maximum_distance = \"auto\",   minimum_k = 0,   options = \"Pp\",   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_3d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_3d — .create_delaunaynetwork_3d","text":"spatial 3D Delaunay network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_RTriangle.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_RTriangle — .create_delaunaynetwork_RTriangle","title":".create_delaunaynetwork_RTriangle — .create_delaunaynetwork_RTriangle","text":"Create spatial Delaunay network RTriangle","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_RTriangle.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_RTriangle — .create_delaunaynetwork_RTriangle","text":"","code":".create_delaunaynetwork_RTriangle(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   Y = TRUE,   j = TRUE,   S = 0,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_RTriangle.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_RTriangle — .create_delaunaynetwork_RTriangle","text":"spatial Delaunay network RTriangle","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_deldir.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_deldir — .create_delaunaynetwork_deldir","title":".create_delaunaynetwork_deldir — .create_delaunaynetwork_deldir","text":"Create spatial Delaunay network deldir","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_deldir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_deldir — .create_delaunaynetwork_deldir","text":"","code":".create_delaunaynetwork_deldir(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_deldir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_deldir — .create_delaunaynetwork_deldir","text":"spatial Delaunay network deldir","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_geometry — .create_delaunaynetwork_geometry","title":".create_delaunaynetwork_geometry — .create_delaunaynetwork_geometry","text":"Create spatial Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_geometry — .create_delaunaynetwork_geometry","text":"","code":".create_delaunaynetwork_geometry(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   options = \"Pp\",   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_geometry — .create_delaunaynetwork_geometry","text":"spatial Delaunay network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry_3d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_geometry_3d — .create_delaunaynetwork_geometry_3d","title":".create_delaunaynetwork_geometry_3d — .create_delaunaynetwork_geometry_3d","text":"Create spatial 3D Delaunay network geometry","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry_3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_geometry_3d — .create_delaunaynetwork_geometry_3d","text":"","code":".create_delaunaynetwork_geometry_3d(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   sdimz = \"sdimz\",   options = options,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry_3d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_geometry_3d — .create_delaunaynetwork_geometry_3d","text":"spatial 3D Delaunay network geometry","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_2d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_spatialgrid_default_2d — .create_spatialgrid_default_2d","title":".create_spatialgrid_default_2d — .create_spatialgrid_default_2d","text":"create 2D spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_2d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_spatialgrid_default_2d — .create_spatialgrid_default_2d","text":"","code":".create_spatialgrid_default_2d(   gobject,   spat_unit = NULL,   spat_loc_name = \"raw\",   sdimx_stepsize = NULL,   sdimy_stepsize = NULL,   minimum_padding = 1 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_2d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_spatialgrid_default_2d — .create_spatialgrid_default_2d","text":"2D spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_3d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_spatialgrid_default_3d — .create_spatialgrid_default_3d","title":".create_spatialgrid_default_3d — .create_spatialgrid_default_3d","text":"create 3D spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_spatialgrid_default_3d — .create_spatialgrid_default_3d","text":"","code":".create_spatialgrid_default_3d(   gobject,   spat_unit = NULL,   spat_loc_name = \"raw\",   sdimx_stepsize = NULL,   sdimy_stepsize = NULL,   sdimz_stepsize = NULL,   minimum_padding = 1 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_3d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_spatialgrid_default_3d — .create_spatialgrid_default_3d","text":"3D spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatvector_object_from_dfr.html","id":null,"dir":"Reference","previous_headings":"","what":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","title":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","text":"create terra spatvector data.frame cols 1 2 must x y coordinates respectively. Additional columns set attributes points first additional (col 3) feat_ID.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatvector_object_from_dfr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","text":"","code":".create_spatvector_object_from_dfr(   x,   x_colname = NULL,   y_colname = NULL,   feat_ID_colname = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatvector_object_from_dfr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","text":"x data.frame object x_colname column name x-coordinates y_colname column name y-coordinates feat_ID_colname column name feature ids verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatvector_object_from_dfr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","text":"SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_terra_spatraster.html","id":null,"dir":"Reference","previous_headings":"","what":"Load image as a terra spatRaster object — .create_terra_spatraster","title":"Load image as a terra spatRaster object — .create_terra_spatraster","text":"Load image terra spatRaster object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_terra_spatraster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load image as a terra spatRaster object — .create_terra_spatraster","text":"","code":".create_terra_spatraster(image_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_terra_spatraster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load image as a terra spatRaster object — .create_terra_spatraster","text":"image_path existing full filepath image loaded terra spatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_terra_spatraster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load image as a terra spatRaster object — .create_terra_spatraster","text":"spatRaster object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-do_gpoly.html","id":null,"dir":"Reference","previous_headings":"","what":"Do giottoPolygon — .do_gpoly","title":"Do giottoPolygon — .do_gpoly","text":"giottoPolygon objects carry 3 pieces spatial information. polygons, centroids, polygon overlapped features. need updated spatial manipulations applied. function simplifies performing functions SpatVector-based slots.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-do_gpoly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Do giottoPolygon — .do_gpoly","text":"","code":".do_gpoly(x, what, args = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-do_gpoly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Do giottoPolygon — .do_gpoly","text":"x giottoPolygon call args list additional args","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-do_gpoly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Do giottoPolygon — .do_gpoly","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_points.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert point data data.table to spatVector — .dt_to_spatvector_points","title":"Convert point data data.table to spatVector — .dt_to_spatvector_points","text":"data.table spatVector points","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_points.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert point data data.table to spatVector — .dt_to_spatvector_points","text":"","code":".dt_to_spatvector_points(dt, include_values = TRUE, specific_values = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_points.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert point data data.table to spatVector — .dt_to_spatvector_points","text":"dt data.table include_values boolean. Include additional values data.table attributes paired created terra spatVector specific_values specific values include attributes include_values == TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_points.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert point data data.table to spatVector — .dt_to_spatvector_points","text":"spatVector points","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","title":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","text":"convert data.table spatVector polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","text":"","code":".dt_to_spatvector_polygon(   dt,   include_values = TRUE,   specific_values = NULL,   sort_geom = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_polygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","text":"dt data.table. terra geometry information include_values logical. Whether include additional columns geometry information SpatVector attributes. Default TRUE. specific_values character. Specific subset columns include attributes include_values = TRUE. sort_geom logical. Whether sort key data.table input 'geom', 'part', 'hole' columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","text":"polygon spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-edge_coords_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Numerical array of edge start and end — .edge_coords_array","title":"Numerical array of edge start and end — .edge_coords_array","text":"Generate \\(2\\) x \\(j\\) x \\(k\\) numerical array edge start end coordinates. Rows correspond  start end. Cols variable ie x, y, (z) whatever variable used measure sample location graph space. third dim sample. layout makes easy iterate across matrix slices array [stats::dist()].","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-edge_coords_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Numerical array of edge start and end — .edge_coords_array","text":"","code":".edge_coords_array(x, y, x_node_ids = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-edge_coords_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Numerical array of edge start and end — .edge_coords_array","text":"x matrix nodes info coords y network data.table cols x_node_ids y indexed character cols, node IDs apply coords x must supplied character vector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-edge_coords_array.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Numerical array of edge start and end — .edge_coords_array","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-filter_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter spatial network — .filter_network","title":"Filter spatial network — .filter_network","text":"Filter spatial network spatial characteristics","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-filter_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter spatial network — .filter_network","text":"","code":".filter_network(networkDT = NULL, maximum_distance = NULL, minimum_k = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-filter_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter spatial network — .filter_network","text":"networkDT spatial network data.table format maximum_distance maximum distance cell centroids minimum_k minimum number neighbors","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-filter_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter spatial network — .filter_network","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_2d.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_2d — .find_grid_2d","title":".find_grid_2d — .find_grid_2d","text":"find grid location 2D","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_2d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_2d — .find_grid_2d","text":"","code":".find_grid_2d(grid_DT, x_loc, y_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_2d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_2d — .find_grid_2d","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_3d.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_3d — .find_grid_3d","title":".find_grid_3d — .find_grid_3d","text":"find grid location 3D","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_3d — .find_grid_3d","text":"","code":".find_grid_3d(grid_DT, x_loc, y_loc, z_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_3d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_3d — .find_grid_3d","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_x.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_x — .find_grid_x","title":".find_grid_x — .find_grid_x","text":"find grid location x-axis","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_x.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_x — .find_grid_x","text":"","code":".find_grid_x(grid_DT, x_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_x.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_x — .find_grid_x","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_y.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_y — .find_grid_y","title":".find_grid_y — .find_grid_y","text":"find grid location y-axis","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_y.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_y — .find_grid_y","text":"","code":".find_grid_y(grid_DT, y_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_y.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_y — .find_grid_y","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_z.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_z — .find_grid_z","title":".find_grid_z — .find_grid_z","text":"find grid location z-axis","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_z.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_z — .find_grid_z","text":"","code":".find_grid_z(grid_DT, z_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_z.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_z — .find_grid_z","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-fix_multipart_geoms.html","id":null,"dir":"Reference","previous_headings":"","what":"Split multi-part polygons — .fix_multipart_geoms","title":"Split multi-part polygons — .fix_multipart_geoms","text":"function split geoms (polygons) multiple parts","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-fix_multipart_geoms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split multi-part polygons — .fix_multipart_geoms","text":"","code":".fix_multipart_geoms(spatVector)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-fix_multipart_geoms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split multi-part polygons — .fix_multipart_geoms","text":"SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-giotto_alloc_dt.html","id":null,"dir":"Reference","previous_headings":"","what":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","title":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","text":"Finds DT based objects, overallocates data.tables, sets objects back giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-giotto_alloc_dt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","text":"","code":".giotto_alloc_dt(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-giotto_alloc_dt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-giotto_alloc_dt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-identify_background_range_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify background range polygons — .identify_background_range_polygons","title":"Identify background range polygons — .identify_background_range_polygons","text":"function remove background polygon comparing individual polygon vertex xy ranges overall SpatVector extent. SpatVector function run MUST contain polygons generated part FOV. individual polygons compared overall extent assumed roughly original mask image.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-identify_background_range_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify background range polygons — .identify_background_range_polygons","text":"","code":".identify_background_range_polygons(spatVector, threshold = 0.9)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-identify_background_range_polygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify background range polygons — .identify_background_range_polygons","text":"spatVector terra polygon spatvector threshold polygon's x y range exceeds fraction overall SpatVector extent, flagged removal.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-identify_background_range_polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify background range polygons — .identify_background_range_polygons","text":"character vector polygon IDs variable length (usually either length 0 .e. background poly remove, 1, background poly remove) used correct threshold.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_giotto_environment.html","id":null,"dir":"Reference","previous_headings":"","what":".install_giotto_environment — .install_giotto_environment","title":".install_giotto_environment — .install_giotto_environment","text":"installation options giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_giotto_environment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".install_giotto_environment — .install_giotto_environment","text":"","code":".install_giotto_environment(   force_environment = FALSE,   packages_to_install = c(\"pandas\", \"networkx\", \"python-igraph\", \"leidenalg\",     \"python-louvain\", \"python.app\", \"scikit-learn\", \"smfishhmrf\", \"session-info\"),   pip_packages = c(\"python-louvain\", \"smfishhmrf\", \"session-info\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   confirm = TRUE,   envname = \"giotto_env\",   conda = \"auto\",   verbose = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_giotto_environment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".install_giotto_environment — .install_giotto_environment","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_github_link_pip.html","id":null,"dir":"Reference","previous_headings":"","what":"Install Package from GitHub Link — .install_github_link_pip","title":"Install Package from GitHub Link — .install_github_link_pip","text":"Installs link python env","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_github_link_pip.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install Package from GitHub Link — .install_github_link_pip","text":"","code":".install_github_link_pip(link = NULL, env = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_github_link_pip.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install Package from GitHub Link — .install_github_link_pip","text":"link link github repository containing python package, e.g. git+https://github.com/TencentAILabHealthcare/pysodb.git env conda environment link installed via pip","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_github_link_pip.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install Package from GitHub Link — .install_github_link_pip","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":null,"dir":"Reference","previous_headings":"","what":"Install Python Package with Reticulate — .install_py_pkg_reticulate","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"Install Python Package Reticulate","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"","code":".install_py_pkg_reticulate(package = NULL, env = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"package name python package env name environment python package installed.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"Installs package python env prompting user. Installation done via py_install reticulate package.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-merge_spatial_enrich_info.html","id":null,"dir":"Reference","previous_headings":"","what":".merge_spatial_enrich_info — .merge_spatial_enrich_info","title":".merge_spatial_enrich_info — .merge_spatial_enrich_info","text":"take combine data.table result append spatial enrichment results.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-merge_spatial_enrich_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".merge_spatial_enrich_info — .merge_spatial_enrich_info","text":"","code":".merge_spatial_enrich_info(   gobject,   comb_dt,   spat_unit,   feat_type,   spat_enr_names = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-merge_spatial_enrich_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".merge_spatial_enrich_info — .merge_spatial_enrich_info","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Overlap points per polgyon — .overlap_points_per_polygon","title":"Overlap points per polgyon — .overlap_points_per_polygon","text":"Loop overlap single polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overlap points per polgyon — .overlap_points_per_polygon","text":"","code":".overlap_points_per_polygon(spatvec, pointvec, poly_ID_names, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overlap points per polgyon — .overlap_points_per_polygon","text":"spatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon_wrapped.html","id":null,"dir":"Reference","previous_headings":"","what":"Overlap points per polygon – wrapped — .overlap_points_per_polygon_wrapped","title":"Overlap points per polygon – wrapped — .overlap_points_per_polygon_wrapped","text":"overlap wrapped polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon_wrapped.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overlap points per polygon – wrapped — .overlap_points_per_polygon_wrapped","text":"","code":".overlap_points_per_polygon_wrapped(   spatvec_wrapped,   pointvec_wrapped,   poly_ID_names )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon_wrapped.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overlap points per polygon – wrapped — .overlap_points_per_polygon_wrapped","text":"Packed object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_single_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Overlap points – single polygon — .overlap_points_single_polygon","title":"Overlap points – single polygon — .overlap_points_single_polygon","text":"overlap single polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_single_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overlap points – single polygon — .overlap_points_single_polygon","text":"","code":".overlap_points_single_polygon(spatvec, poly_ID_name, pointvec_dt)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_single_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overlap points – single polygon — .overlap_points_single_polygon","text":"terra::intersect","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottoimage_mg.html","id":null,"dir":"Reference","previous_headings":"","what":".plot_giottoimage_mg — .plot_giottoimage_mg","title":".plot_giottoimage_mg — .plot_giottoimage_mg","text":"get plot giottoImage either directly giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottoimage_mg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".plot_giottoimage_mg — .plot_giottoimage_mg","text":"","code":".plot_giottoimage_mg(gobject = NULL, image_name = NULL, giottoImage = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottoimage_mg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":".plot_giottoimage_mg — .plot_giottoimage_mg","text":"gobject giotto object image_name name giotto image showGiottoImageNames giottoImage giottoImage object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottoimage_mg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".plot_giottoimage_mg — .plot_giottoimage_mg","text":"plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottolargeimage.html","id":null,"dir":"Reference","previous_headings":"","what":".plot_giottolargeimage — .plot_giottolargeimage","title":".plot_giottolargeimage — .plot_giottolargeimage","text":"Plot downsampled version giottoLargeImage. Cropping can increase plot resolution region interest.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottolargeimage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".plot_giottolargeimage — .plot_giottolargeimage","text":"","code":".plot_giottolargeimage(   gobject = NULL,   largeImage_name = NULL,   giottoLargeImage = NULL,   crop_extent = NULL,   xmax_crop = NULL,   xmin_crop = NULL,   ymax_crop = NULL,   ymin_crop = NULL,   max_intensity = NULL,   asRGB = FALSE,   stretch = NULL,   axes = TRUE,   smooth = TRUE,   mar = c(3, 5, 1.5, 1),   legend = FALSE,   maxcell = 5e+05,   col = grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1),   asp = 1,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottolargeimage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":".plot_giottolargeimage — .plot_giottolargeimage","text":"gobject giotto object largeImage_name name giottoLargeImage giottoLargeImage giottoLargeImage object crop_extent (optional) extent object focus specific region image xmax_crop, xmin_crop, ymax_crop, ymin_crop (optional) crop min/max x y bounds max_intensity (optional) value treat maximum intensity color scale asRGB (optional) logical. Force RGB plotting automatically detected stretch character. Option stretch values increase contrast: \"lin\" linear \"hist\" (histogram) axes boolean. Default = TRUE. Whether draw axes smooth boolean. default = TRUE. whether apply smoothing image mar plot margins default = c(3,5,1.5,1) legend whether plot legend color scale (grayscale ). default = FALSE maxcell positive integer. Maximum number image cells use plot col character. Colors single channel images. default grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1). can also data.frame two columns (value, color) get \"classes\" type legend three columns (, , color) get \"interval\" type legend asp numeric. (default = 1) specific aspect ratio use ... additional params pass terra::plot terra::plotRGB depending depending image type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottolargeimage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".plot_giottolargeimage — .plot_giottolargeimage","text":"plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":null,"dir":"Reference","previous_headings":"","what":"Hierarchical tree printing — .print_leaf","title":"Hierarchical tree printing — .print_leaf","text":"Hierarchical tree printing","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hierarchical tree printing — .print_leaf","text":"","code":".print_leaf(level_index, availableDT, inherit_last = TRUE, indent)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hierarchical tree printing — .print_leaf","text":"level_index col availability matrix start print availableDT availability matrix given data.table inherit_last (boolean) determine behavior previous level last level (intended values print) TRUE behavior defined. #TODO indent indent characters print level (top level ”)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hierarchical tree printing — .print_leaf","text":"Hierarchical tree","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Hierarchical tree printing — .print_leaf","text":"Much inspiration taken https://rdrr.io/cran/fs/src/R/tree.R","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-prov_match.html","id":null,"dir":"Reference","previous_headings":"","what":"Check provenance info matches across list of S4 subobjects — .prov_match","title":"Check provenance info matches across list of S4 subobjects — .prov_match","text":"Check provenance info matches across list S4 subobjects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-prov_match.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check provenance info matches across list of S4 subobjects — .prov_match","text":"","code":".prov_match(..., verbose = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-prov_match.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check provenance info matches across list of S4 subobjects — .prov_match","text":"... list s4 subobjects match provenance verbose print discovered provenance info","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-prov_match.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check provenance info matches across list of S4 subobjects — .prov_match","text":"logical NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-py_install_prompt.html","id":null,"dir":"Reference","previous_headings":"","what":"Prompt User for Python Install — .py_install_prompt","title":"Prompt User for Python Install — .py_install_prompt","text":"prompts user install package","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-py_install_prompt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prompt User for Python Install — .py_install_prompt","text":"","code":".py_install_prompt(package = NULL, env = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-py_install_prompt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prompt User for Python Install — .py_install_prompt","text":"package python package/github url env environment package installed","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-py_install_prompt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prompt User for Python Install — .py_install_prompt","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-read_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read cell metadata — .read_cell_metadata","title":"Read cell metadata — .read_cell_metadata","text":"read cell metadata list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-read_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read cell metadata — .read_cell_metadata","text":"","code":".read_cell_metadata(   metadata,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-read_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read cell metadata — .read_cell_metadata","text":"metadata nested list cell metadata information provenance provenance information (optional) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-read_cell_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read cell metadata — .read_cell_metadata","text":"cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rescale_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Rescale polygons — .rescale_polygons","title":"Rescale polygons — .rescale_polygons","text":"rescale individual polygons factor x y","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rescale_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rescale polygons — .rescale_polygons","text":"","code":".rescale_polygons(spatVector, spatVectorCentroids, fx = 0.5, fy = 0.5)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rescale_polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rescale polygons — .rescale_polygons","text":"polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Rotate spatial locations — .rotate_spatial_locations","title":"Rotate spatial locations — .rotate_spatial_locations","text":"Rotate given spatlocs given radians","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rotate spatial locations — .rotate_spatial_locations","text":"","code":".rotate_spatial_locations(   spatlocs,   rotateradians = c(xy = 0, zy = 0, xz = 0),   rcenter = c(0, 0, 0),   geom = c(\"sdimx\", \"sdimy\", \"sdimz\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rotate spatial locations — .rotate_spatial_locations","text":"spatlocs spatial locations use rotateradians Named vector radians rotation along 3 coordinate axes. single value provided, treated xy rotation. rcenter center rotation given vector xy(z) coordinates (defaults coordinate center) geom character. Named vector colames x, y, z coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rotate spatial locations — .rotate_spatial_locations","text":"spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Rotate spatial locations — .rotate_spatial_locations","text":"Radians provided rotateradians param named vector values xy (yaw), zy (pitch), xz (roll)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Scale spatial locations — .scale_spatial_locations","title":"Scale spatial locations — .scale_spatial_locations","text":"Simple scaling spatial locations given scale_factor. Values scaled coordinate origin coordinates provided scenter param. Default values supply values z axis, values applied input data.table z information detected third item geom param.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scale spatial locations — .scale_spatial_locations","text":"","code":".scale_spatial_locations(   spatlocs,   scale_factor = c(1, 1, 1),   scenter = c(0, 0, 0),   geom = c(\"sdimx\", \"sdimy\", \"sdimz\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scale spatial locations — .scale_spatial_locations","text":"spatlocs data.table. spatial locations information scale scale_factor scaling factor apply coordinates. Default c(1, 1, 1) scenter center scale spatial coordinates. Given vector xy(z) coordinates. Default c(0, 0, 0) geom character. Named vector colnames x, y, (z) coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Scale spatial locations — .scale_spatial_locations","text":"spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Scale spatial locations — .scale_spatial_locations","text":"scale_factor either given single value applied x, y, z (available) dimensions vector named values 'x', y', ('z').","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Shift spatial locations — .shift_spatial_locations","title":"Shift spatial locations — .shift_spatial_locations","text":"Shift given coordinates given translation values","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shift spatial locations — .shift_spatial_locations","text":"","code":".shift_spatial_locations(   spatlocs,   dx = 0,   dy = 0,   dz = 0,   geom = c(\"sdimx\", \"sdimy\", \"sdimz\"),   copy_obj = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shift spatial locations — .shift_spatial_locations","text":"spatlocs spatial locations use dx value shift coordinates positive x direction dy value shift coordinates positive y direction dz value shift coordinates positive z direction geom character vector. Expected colnames x, y, z coords copy_obj logical. copy/duplicate object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shift spatial locations — .shift_spatial_locations","text":"spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Shift spatial network — .shift_spatial_network","title":"Shift spatial network — .shift_spatial_network","text":"Shift spatial network coordinates","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shift spatial network — .shift_spatial_network","text":"","code":".shift_spatial_network(spatnet, dx = 0, dy = 0, dz = 0, copy_obj = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shift spatial network — .shift_spatial_network","text":"spatnet spatial network data.table dx distance shift x axis dy distance shift y axis dz distance shift z axis copy_obj copy/duplicate object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shift spatial network — .shift_spatial_network","text":"spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatraster_sample_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample values from SpatRaster — .spatraster_sample_values","title":"Sample values from SpatRaster — .spatraster_sample_values","text":"Sample numerical values SpatRaster. output format depends value output param.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatraster_sample_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample values from SpatRaster — .spatraster_sample_values","text":"","code":".spatraster_sample_values(   raster_object,   size = 5000,   output = c(\"data.frame\", \"array\", \"magick\", \"EBImage\"),   verbose = NULL,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatraster_sample_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample values from SpatRaster — .spatraster_sample_values","text":"raster_object terra SpatRaster sample size rough maximum pixels allowed resampling output output return . Defaults \"data.frame\" verbose verbose ... additional params pass terra::spatSample","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatraster_sample_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample values from SpatRaster — .spatraster_sample_values","text":"magick EBImage image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatvector_to_dt.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert spatVector to data.table — .spatvector_to_dt","title":"Convert spatVector to data.table — .spatvector_to_dt","text":"convert spatVector data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatvector_to_dt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert spatVector to data.table — .spatvector_to_dt","text":"","code":".spatvector_to_dt(spatvector, include_values = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatvector_to_dt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert spatVector to data.table — .spatvector_to_dt","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spline_poly.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert spline to polygon — .spline_poly","title":"Convert spline to polygon — .spline_poly","text":"spline polynomial smooth polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spline_poly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert spline to polygon — .spline_poly","text":"","code":".spline_poly(xy, vertices = 20, k = 3, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spline_poly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert spline to polygon — .spline_poly","text":"xy xy vertices vertices k k ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spline_poly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert spline to polygon — .spline_poly","text":"polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-subset_giotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset Giotto — .subset_giotto","title":"Subset Giotto — .subset_giotto","text":"Internal subset Giotto object including previous analyses specific spatial unit feature type. master workflow aggregate data subsetting. subsetGiotto, subsetGiottoLocs, subsetGiottoLocsMulti provide params pass function. function also hides confusing needed internal params exported functions. x_max, x_min, y_max, y_min params provided subsetting feature info downstream subsetGiottoLocs. polygon subsetting: Polygons subset subset using poly_ID values MUST match cell_ids, otherwise incorrect empty polygons can returned. subsetting subcellular information without editing aggregate information, use subsetGiottoLocsSubcellular","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-subset_giotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset Giotto — .subset_giotto","text":"","code":".subset_giotto(   gobject,   spat_unit = \":all:\",   feat_type = \"rna\",   spat_unit_fsub = \":all:\",   feat_type_ssub = \":all:\",   cell_ids = NULL,   feat_ids = NULL,   poly_info = spat_unit,   x_max = NULL,   x_min = NULL,   y_max = NULL,   y_min = NULL,   verbose = FALSE,   toplevel_params = 2 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-subset_giotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset Giotto — .subset_giotto","text":"gobject giotto object spat_unit, feat_type character vector. (default = '::') One spatial units feature types subset. Accepts '::' token subset across available. spat_unit_fsub character vector. (default = '::') limit feat_id subsets spat_units feat_type_ssub character vector. (default = '::') limit cell_id subsets feat_types cell_ids character. cell IDs keep feat_ids character. feature IDs keep poly_info character. polygon info(s) subset present. (defaults spat_unit) x_max, x_min, y_max, y_min feature info . minimum maximum x y coordinates keep verbose verbose toplevel_params expected stackframe parameters extracted","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-subset_giotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset Giotto — .subset_giotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-terra_writeraster_datatype.html","id":null,"dir":"Reference","previous_headings":"","what":".terra_writeraster_datatype — .terra_writeraster_datatype","title":".terra_writeraster_datatype — .terra_writeraster_datatype","text":"find likely compatible datatype given image characteristics. Values given arguments take priority found giottoLargeImage metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-terra_writeraster_datatype.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".terra_writeraster_datatype — .terra_writeraster_datatype","text":"","code":".terra_writeraster_datatype(   giottoLargeImage = NULL,   quick_INTS_maxval = NULL,   max_intensity = NULL,   min_intensity = NULL,   is_int = NULL,   signed = NULL,   bitDepth = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-terra_writeraster_datatype.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":".terra_writeraster_datatype — .terra_writeraster_datatype","text":"giottoLargeImage giottoLargeImage object determine max_intensity, min_intensity, is_int settings quick_INTS_maxval Treat maximum intensity find compatible unsigned integer settings max_intensity, min_intensity value given image maximum/minimum intensity is_int image integer (TRUE) floating point (FALSE) signed image signed (TRUE) unsigned (TRUE) bitDepth image bitDepth verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-terra_writeraster_datatype.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".terra_writeraster_datatype — .terra_writeraster_datatype","text":"datatype terra writeRaster function","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate network edge euclidean distances — edge_distances","title":"Calculate network edge euclidean distances — edge_distances","text":"Calculate network edge euclidean distances","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate network edge euclidean distances — edge_distances","text":"","code":"edge_distances(x, y, x_node_ids = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate network edge euclidean distances — edge_distances","text":"x matrix nodes info coords. Rows samples, Cols variables y network data.table cols. Usually integer indices matching rows x. x_node_ids y indexed character cols, node IDs apply coords x must supplied character vector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate network edge euclidean distances — edge_distances","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate network edge euclidean distances — edge_distances","text":"","code":"m <- matrix(c(0, 0, 0, 1, 1, 1, 3, 2, 4), byrow = TRUE, nrow = 3) edges <- data.table::data.table(     from = c(1, 1),     to = c(2, 3) )  edge_distances(m, edges) #> [1] 1.732051 5.385165"},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":null,"dir":"Reference","previous_headings":"","what":"estimateImageBg — estimateImageBg","title":"estimateImageBg — estimateImageBg","text":"helps estimate color background color plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"estimateImageBg — estimateImageBg","text":"","code":"estimateImageBg(mg_object, top_color_range = seq_len(50))"},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"estimateImageBg — estimateImageBg","text":"mg_object magick image Giotto image object top_color_range top possible background colors return","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"estimateImageBg — estimateImageBg","text":"vector pixel color frequencies associated barplot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"estimateImageBg — estimateImageBg","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, name = \"image\") mgimg <- as(g_image, \"giottoImage\")  estimateImageBg(mgimg)  #> Most abundant pixel colors: #> 276 261 159 155 132 103 100 79 73 69 67 66 64 55 48 43 43 43 43 39 39 39 36 36 #>  36 35 35 34 34 33 33 33 33 32 32 31 31 31 31 31 31 30 30 30 30 30 30 30 30 30"},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate raw inputs to Giotto formatting — evaluate_input","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"Experimental. Evaluate raw inputs formats directly compatible Giotto's functionality. Note function formats data. output function still needs put Giotto subobject. wrapper function individual GiottoClass evaluation functions.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"","code":"evaluate_input(type, x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"type character. Type giotto data evaluate . x data evaluate ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"character class x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"","code":"x <- GiottoData::loadSubObjectMini(\"exprObj\", 1)  evaluate_input(type = \"expression\", x) #> An object of class exprObj : \"normalized\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                                                                           #> Mlc1    .       .        .        .        . .  5.291601 . .        5.821597 . .        . #> Gprc5b  .       6.398031 .        7.454658 . .  6.273066 . 7.680054 6.808785 . 5.082989 . #> Gfap   10.48137 .        7.901442 5.886051 . . 10.746982 . 5.701006 5.821597 . .        . #>               #> Mlc1   ...... #> Gprc5b ...... #> Gfap   ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/exprObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 exprObj — exprObj-class","title":"S4 exprObj — exprObj-class","text":"Framework store aggregated expression information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/exprObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 exprObj — exprObj-class","text":"exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/exprObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 exprObj — exprObj-class","text":"name name exprObj exprMat matrix expression information spat_unit spatial unit expression (e.g. 'cell') feat_type feature type expression (e.g. 'rna', 'protein') provenance origin data expression information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/exprObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 exprObj — exprObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"exprObj\") #> An object of class exprObj : \"normalized\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                                                                           #> Mlc1    .       .        .        .        . .  5.291601 . .        5.821597 . .        . #> Gprc5b  .       6.398031 .        7.454658 . .  6.273066 . 7.680054 6.808785 . 5.082989 . #> Gfap   10.48137 .        7.901442 5.886051 . . 10.746982 . 5.701006 5.821597 . .        . #>               #> Mlc1   ...... #> Gprc5b ...... #> Gfap   ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a SpatExtent — ext","title":"Get a SpatExtent — ext","text":"Get SpatExtent object. spatial minmax x y object mapped .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a SpatExtent — ext","text":"","code":"# S4 method for class 'spatLocsObj' ext(x, ...)  # S4 method for class 'giottoPolygon' ext(x, ...)  # S4 method for class 'giottoPoints' ext(x, ...)  # S4 method for class 'spatialNetworkObj' ext(x, ...)  # S4 method for class 'giottoLargeImage' ext(x, ...)  # S4 method for class 'giottoImage' ext(x, ...)  # S4 method for class 'giotto' ext(   x,   spat_unit = \":all:\",   feat_type = \":all:\",   all_data = TRUE,   prefer = c(\"polygon\", \"spatlocs\", \"points\", \"images\"),   name = list(spatlocs = \":all:\"),   verbose = NULL,   ... )  # S4 method for class 'giottoAffineImage' ext(x, ...)  # S4 method for class 'affine2d' ext(x, ...)  # S4 method for class 'giottoPoints,SpatExtent' ext(x) <- value  # S4 method for class 'giottoPolygon,SpatExtent' ext(x) <- value  # S4 method for class 'giottoLargeImage,SpatExtent' ext(x) <- value  # S4 method for class 'ANY,ANY' ext(x) <- value  # S4 method for class 'giottoImage,SpatExtent' ext(x) <- value  # S4 method for class 'affine2d,ANY' ext(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a SpatExtent — ext","text":"x spatial object ... additional params pass spat_unit character. Spatial unit limit search . provided, default set. feat_type character. Feature type limit search \"points\" information. provided, default set. all_data logical. TRUE (default), spatial information designated prefer searched combined SpatExtent returned. FALSE, SpatExtent first existing data ordered prefer returned. prefer character vector. Order preferred data get extent . allowed terms \"polygon\", \"spatlocs\", \"points\", \"images\". also default ordering. Omitting terms removes search. name named list. Specific object names check. List names correspond allowed terms prefer. one name allowed \"images\" moment, produces combined SpatExtent verbose verbose value value set. Accepts object ext() work ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a SpatExtent — ext","text":"SpatExtent","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a SpatExtent — ext","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" # giotto %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ext(g) # defaults to checking first giottoPolygon extent #> SpatExtent : 6391.46568586489, 6903.57332779812, -5153.89721175534, -4694.86823300896 (xmin, xmax, ymin, ymax) ext(g, prefer = \"spatlocs\") # check first spatLocsObj extent #> SpatExtent : 6401.14818002375, 6899.3228463116, -5147.19306531348, -4700.15708342436 (xmin, xmax, ymin, ymax) # first spatLocsObj from a different spat_unit ext(g, spat_unit = \"aggregate\", prefer = \"spatlocs\") #> SpatExtent : 6401.41164725267, 6899.10802819571, -5146.74746408943, -4700.32590047134 (xmin, xmax, ymin, ymax)  # from first image object ext(g, prefer = \"image\") #> SpatExtent : 6400.029, 6900.037, -5150.007, -4699.967 (xmin, xmax, ymin, ymax)  # add a dummy image with different spatial extent r <- terra::rast(array(seq(25), dim = c(5, 5))) test <- createGiottoLargeImage(r) ext(test) <- c(1e5, 1.1e5, 0, 10) g <- setGiotto(g, test) # add image  # combined from all image objects ext(g, prefer = \"image\", name = list(images = list_images_names(g))) #> SpatExtent : 6400.029, 110000, -5150.007, 10 (xmin, xmax, ymin, ymax)  # combined from all spatial data types in giotto object ext(g, all_data = TRUE, name = list(images = list_images_names(g))) #> SpatExtent : 6391.46568586489, 110000, -5153.89721175534, 10 (xmin, xmax, ymin, ymax)  # spatLocsObj %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% sl <- getSpatialLocations(g) ext(sl) #> SpatExtent : 6402.43781589887, 6899.20308651186, -5146.72565198022, -4700.15708342436 (xmin, xmax, ymin, ymax)  # giottoPolygon %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # get extent gpoly <- getPolygonInfo(g, return_giottoPolygon = TRUE) ext(gpoly) #> SpatExtent : 6399.24384990901, 6903.24298517207, -5152.38959073896, -4694.86823300896 (xmin, xmax, ymin, ymax)  # set extent plot(gpoly) # before  ext(gpoly) <- ext(0, 20, 30, 60) plot(gpoly) # after   # giottoPoints %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # get extent gpoints <- getFeatureInfo(g, return_giottoPoints = TRUE) ext(gpoints) #> SpatExtent : 6400.037, 6900.0317, -5149.9834, -4699.9785 (xmin, xmax, ymin, ymax)  # set extent plot(gpoints) # before  ext(gpoints) <- ext(0, 2000, 3000, 6000) plot(gpoints) # after"},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":null,"dir":"Reference","previous_headings":"","what":"fDataDT — fDataDT","title":"fDataDT — fDataDT","text":"show feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"fDataDT — fDataDT","text":"","code":"fDataDT(gobject, spat_unit = NULL, feat_type = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"fDataDT — fDataDT","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"fDataDT — fDataDT","text":"data.table feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"fDataDT — fDataDT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  fDataDT(g) #>            feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det #>             <char>    <int>      <num>      <num>     <num>         <num> #>   1:         Gna12      502  80.448718  1987.1333 3.1845085      3.958433 #>   2:         Ccnd2      357  57.211538  1254.4730 2.0103734      3.513930 #>   3:        Btbd17      252  40.384615   781.9747 1.2531645      3.103074 #>   4:          Sox9      309  49.519231  1019.7255 1.6341755      3.300083 #>   5:          Sez6      504  80.769231  2177.4740 3.4895416      4.320385 #>  ---                                                                      #> 630:        Lhfpl3      235  37.660256   732.3595 1.1736530      3.116423 #> 631: C030029H02Rik       72  11.538462   203.0811 0.3254506      2.820572 #> 632:       Gm19935       57   9.134615   172.1079 0.2758139      3.019436 #> 633: 9630013A20Rik       52   8.333333   157.2602 0.2520196      3.024235 #> 634: 2900040C04Rik       61   9.775641   179.7015 0.2879831      2.945926 #>         hvf #>      <char> #>   1:     no #>   2:     no #>   3:     no #>   4:     no #>   5:     no #>  ---        #> 630:     no #> 631:     no #> 632:     no #> 633:     no #> 634:     no"},{"path":"https://drieslab.github.io/GiottoClass/reference/featMetaObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 featMetaObj — featMetaObj-class","title":"S4 featMetaObj — featMetaObj-class","text":"Framework store feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featMetaObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 featMetaObj — featMetaObj-class","text":"featMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featMetaObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 featMetaObj — featMetaObj-class","text":"metaDT metadata info col_desc (optional) character vector describing columns metadata spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') provenance origin data aggregated expression information (applicable)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featMetaObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 featMetaObj — featMetaObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"featMetaObj\") #> An object of class featMetaObj  #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #>    feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det hvg_orig #>     <char>    <int>      <num>      <num>     <num>         <num>   <char> #> 1:    Mlc1       80   17.31602   526.5915  1.139808      6.582394       no #> 2:  Gprc5b      138   29.87013   944.0153  2.043323      6.840690       no #> 3:    Gfap      151   32.68398  1229.1943  2.660594      8.140359      yes #>          var    hvf #>        <num> <char> #> 1:  1.815718    yes #> 2:  2.388911    yes #> 3: 12.899599    yes"},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Feature type information — featType-generic","title":"Feature type information — featType-generic","text":"access set feat_type slot S4 subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Feature type information — featType-generic","text":"","code":"# S4 method for class 'ANY' featType(x)  # S4 method for class 'list' featType(x)  # S4 method for class 'featData' featType(x)  # S4 method for class 'featData' featType(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Feature type information — featType-generic","text":"x Giotto S4 class subobject feature type value value set feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Feature type information — featType-generic","text":"feat_type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Feature type information — featType-generic","text":"featType(): Get feature type information featType(featData): Get feature type information featType(featData) <- value: Set feature type information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Feature type information — featType-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"featMetaObj\")  featType(g) #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giotto feature network Class — featureNetwork-class","title":"S4 giotto feature network Class — featureNetwork-class","text":"Giotto class store operate feature network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giotto feature network Class — featureNetwork-class","text":"featureNetwork","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giotto feature network Class — featureNetwork-class","text":"contains feature network information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giotto feature network Class — featureNetwork-class","text":"name name feature network network_datatable feature network data.table format network_lookup_id table mapping numeric network ID unique feature numerical IDs full fully connected network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giotto feature network Class — featureNetwork-class","text":"","code":"featureNetwork() #> An object of class \"featureNetwork\" #> Slot \"network_datatable\": #> NULL #>  #> Slot \"network_lookup_id\": #> NULL #>  #> Slot \"full\": #> NULL #>  #> Slot \"name\": #> [1] NA #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":null,"dir":"Reference","previous_headings":"","what":"Flip an object — flip","title":"Flip an object — flip","text":"Flip object designated x y value depending direction param input. Note behavior may different terra's","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flip an object — flip","text":"","code":"# S4 method for class 'giotto' flip(   x,   direction = \"vertical\",   x0 = 0,   y0 = 0,   spat_unit = \":all:\",   feat_type = \":all:\",   ... )  # S4 method for class 'giottoPolygon' flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for class 'giottoPoints' flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for class 'spatLocsObj' flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for class 'spatialNetworkObj' flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for class 'giottoLargeImage' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)  # S4 method for class 'SpatExtent' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)  # S4 method for class 'giottoLargeImage' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)  # S4 method for class 'giottoAffineImage' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)  # S4 method for class 'affine2d' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)"},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flip an object — flip","text":"x object direction character. Direction flip. either partial match 'vertical' 'horizontal' x0 x value flip horizontally (ignored vertical). Pass NULL flip extent y0 y value flip vertically (ignored horizontal). Pass NULL flip extent spat_unit character vector. spatial units affect feat_type character vector. feature types affect ... additional args pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Flip an object — flip","text":"flipped object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Flip an object — flip","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  flip(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx    sdimy                                 cell_ID #>       <num>    <num>                                  <char> #> 1: 6637.881 5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx    sdimy #> [1,] 6401.412 4700.326 #> [2,] 6899.108 5146.747 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert gef to Giotto — gefToGiotto","title":"Convert gef to Giotto — gefToGiotto","text":"Converts .gef file (output stereo-seq pipeline) giotto subcellular object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert gef to Giotto — gefToGiotto","text":"","code":"gefToGiotto(gef_file, bin_size = \"bin100\", verbose = FALSE, h5_file = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert gef to Giotto — gefToGiotto","text":"gef_file path .gef file bin_size bin size select .gef file verbose verbose h5_file name create -disk HDF5 file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert gef to Giotto — gefToGiotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert gef to Giotto — gefToGiotto","text":"Function beta. Converts .gef object Giotto object. six possible choices bin_size: bin1, bin10, bin20, bin50, bin100, bin200. See SAW pipeline additional information gef file.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial grids — generate_grid","title":"Spatial grids — generate_grid","text":"Generate spatial grid spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial grids — generate_grid","text":"","code":"triGrid(extent, ccd, id_prefix = \"ID_\")  orthoGrid(extent, ccd, id_prefix = \"ID_\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial grids — generate_grid","text":"extent SpatExtent anything else SpatExtent can extracted created ccd center center distance id_prefix character. prefix add ID names generated","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial grids — generate_grid","text":"spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial grids — generate_grid","text":"","code":"e <- ext(0, 100, 0, 100) x <- triGrid(extent = e, ccd = 10) plot(x$sdimx, x$sdimy, asp = 1L)   x <- orthoGrid(extent = e, ccd = 10) plot(x$sdimx, x$sdimy, asp = 1L)"},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"getCellMetadata — getCellMetadata","title":"getCellMetadata — getCellMetadata","text":"Get cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getCellMetadata — getCellMetadata","text":"","code":"getCellMetadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   output = c(\"cellMetaObj\", \"data.table\"),   copy_obj = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getCellMetadata — getCellMetadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") output return either 'data.table' 'cellMetaObj' copy_obj whether deep copy/duplicate getting object (default = TRUE) set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getCellMetadata — getCellMetadata","text":"data.table cellMetaObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getCellMetadata — getCellMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getCellMetadata(g) #> An object of class cellMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #> dimensions: 624 7  #>  #>               cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                <char>     <int>    <int>      <num>      <num>       <num> #> 1: AACTCGATGGCGCAGT-1         1      265   41.79811  1057.9308           2 #> 2: GGCTGGCTAGCTTAAA-1         1      279   44.00631  1064.7493           5 #> 3: GACGCCTGTTGCAGGG-1         1      219   34.54259   964.9294           2 #>    custom_leiden #>            <num> #> 1:             4 #> 2:             3 #> 3:             3"},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dimension reduction — getDimReduction","title":"Get dimension reduction — getDimReduction","text":"Function get dimension reduction object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dimension reduction — getDimReduction","text":"","code":"getDimReduction(   gobject,   spat_unit = NULL,   feat_type = NULL,   reduction = c(\"cells\", \"feats\"),   reduction_method = NULL,   name = NULL,   output = c(\"dimObj\", \"matrix\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dimension reduction — getDimReduction","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") reduction reduction cells features (e.g. \"cells\", \"feats\") reduction_method reduction method (e.g. \"pca\", \"umap\", \"tsne\") name name reduction results output object type return . Either 'dimObj' (default) 'matrix' embedding coordinates. set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dimension reduction — getDimReduction","text":"dim reduction object (default) dim reduction coordinates","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dimension reduction — getDimReduction","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getDimReduction(g) #> An object of class dimObj : \"pca\" #> --| Contains dimension reduction generated with: pca  #> ----| for feat_type: rna  #> ----|     spat_unit: cell  #>  #>    100 dimensions for 624 data points #>  #> Additional included info: #> [1] \"eigenvalues\" \"loadings\"    #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get expression values — getExpression","title":"Get expression values — getExpression","text":"Function get expression values giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get expression values — getExpression","text":"","code":"getExpression(   gobject,   values = NULL,   spat_unit = NULL,   feat_type = NULL,   output = c(\"exprObj\", \"matrix\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get expression values — getExpression","text":"gobject giotto object values expression values extract (e.g. \"raw\", \"normalized\", \"scaled\") spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") output object type retrieve expression . Currently either matrix' matrix object contained exprObj 'exprObj' (default) exprObj allowed. set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get expression values — getExpression","text":"exprObj matrix depending output param","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get expression values — getExpression","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getExpression(g) #> An object of class exprObj : \"raw\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #>  #> contains: #> 634 x 624 sparse Matrix of class \"dgCMatrix\" #>                                          #> Gna12  1 2 1 1 9 1 3 5 3 . . 10 7 ...... #> Ccnd2  . 1 1 . . 1 . 1 1 . .  . 3 ...... #> Btbd17 . 1 1 1 . . 2 . . . .  . . ...... #>  #>  ........suppressing 611 columns and 628 rows in show(); maybe adjust options(max.print=, width=) #>                                                #> Gm19935       . 1 . . . . . . . . 1 . . ...... #> 9630013A20Rik . . . . . . . . . . 1 . . ...... #> 2900040C04Rik 1 . . . . . . . . 1 . . . ...... #>  #>  First four colnames: #>  AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 #>  AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1"},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"Get feature info — getFeatureInfo","title":"Get feature info — getFeatureInfo","text":"Get giotto points spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get feature info — getFeatureInfo","text":"","code":"getFeatureInfo(   gobject = gobject,   feat_type = NULL,   return_giottoPoints = FALSE,   set_defaults = TRUE,   simplify = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get feature info — getFeatureInfo","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_giottoPoints return giottoPoints object set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. simplify logical. Whether take object list length 1.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get feature info — getFeatureInfo","text":"giotto points spatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get feature info — getFeatureInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getFeatureInfo(g) #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  source      : rna_feature_spatVector.shp #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3"},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"getFeatureMetadata — getFeatureMetadata","title":"getFeatureMetadata — getFeatureMetadata","text":"Get feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getFeatureMetadata — getFeatureMetadata","text":"","code":"getFeatureMetadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   output = c(\"featMetaObj\", \"data.table\"),   copy_obj = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getFeatureMetadata — getFeatureMetadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") output return either 'data.table' 'featMetaObj' copy_obj whether perform deepcopy data.table information set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getFeatureMetadata — getFeatureMetadata","text":"data.table featMetaObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getFeatureMetadata — getFeatureMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getFeatureMetadata(g) #> An object of class featMetaObj  #> spat_unit : \"z0\" #> feat_type : \"rna\" #> provenance: z0  #>  #>    feat_ID #>     <char> #> 1:    Mlc1 #> 2:  Gprc5b #> 3:    Gfap"},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get giotto image object — getGiottoImage","title":"Get giotto image object — getGiottoImage","text":"Get giotto one image objects gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get giotto image object — getGiottoImage","text":"","code":"getGiottoImage(gobject, image_type = NULL, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get giotto image object — getGiottoImage","text":"gobject giotto object image_type deprecated name character vector. Names giotto image object(s) showGiottoImageNames get","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get giotto image object — getGiottoImage","text":"giotto image object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get giotto image object — getGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getGiottoImage(gobject = g) #> An object of class giottoLargeImage : \"dapi_z0\" #> Image extent            : 6400.029, 6900.037, -5150.007, -4699.967 (xmin, xmax, ymin, ymax) #> Original image extent   : 6400.029, 6900.037, -5150.007, -4699.967 (xmin, xmax, ymin, ymax) #> Scale factor            : 0.108626547903541, 0.10862659908279 (x, y) #> Resolution              : 9.2058527063567, 9.20584836903386 (x, y) #> Layers                  : 1  #> Estimated max intensity : 255  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoData/Mini_datasets/Vizgen/VizgenObject/Images/dapi_z0_spatRaster'"},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Get multiomics integration results — getMultiomics","title":"Get multiomics integration results — getMultiomics","text":"Get multiomics integration result Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get multiomics integration results — getMultiomics","text":"","code":"getMultiomics(   gobject = NULL,   spat_unit = NULL,   feat_type = NULL,   integration_method = \"WNN\",   result_name = \"theta_weighted_matrix\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get multiomics integration results — getMultiomics","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') feat_type integrated feature type (e.g. 'rna_protein') integration_method multiomics integration method used. Default = 'WNN' result_name Default = 'theta_weighted_matrix'","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get multiomics integration results — getMultiomics","text":"multiomics integration result (e.g. theta_weighted_matrix WNN)","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get multiomics integration results — getMultiomics","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- setMultiomics(     gobject = g, result = matrix(rnorm(100), nrow = 10),     spat_unit = \"cell\", feat_type = \"rna_protein\" )  getMultiomics(gobject = g, spat_unit = \"cell\", feat_type = \"rna_protein\") #>               [,1]        [,2]       [,3]        [,4]        [,5]       [,6] #>  [1,] -0.701836993  0.90639045  1.6667728 -1.25745550  0.37969672 -0.2013585 #>  [2,]  0.573351259 -0.77007572  1.0805134 -0.27499746  0.81051411 -1.7947501 #>  [3,]  0.653506513 -0.10392922  1.0956876  1.18512009  0.16798153 -1.5936760 #>  [4,]  1.102562583 -0.59883015 -0.8235445  0.03108054 -0.82634150 -0.5880921 #>  [5,] -0.331979510  0.86307592 -0.7896969 -0.20427061  0.48015487 -2.4436502 #>  [6,] -0.006015914  1.53498056 -2.2300375 -1.34758305 -0.22734637  0.8733072 #>  [7,]  0.542548136 -0.07677495  1.2682960  0.32840023 -0.38144334 -1.5700947 #>  [8,]  1.073179083  0.36398407  0.7477098  1.50785612 -0.51130892  1.2064433 #>  [9,]  0.431113801  0.80003990  0.2902944  0.51282324  1.61615062 -0.6020315 #> [10,]  0.899647924 -1.51114608 -0.2336790  0.27261523  0.05862038  0.6160790 #>              [,7]        [,8]        [,9]       [,10] #>  [1,] -0.29940886  0.61040765  0.21277709 -0.43014614 #>  [2,] -0.54314989  0.86164700 -0.36930863 -0.23013339 #>  [3,] -0.11165896  0.88285986 -0.10648446  1.82750672 #>  [4,] -0.59879136  0.25782948 -0.52105633  1.63416402 #>  [5,] -0.64283303 -2.41919619 -0.31239384 -0.30347819 #>  [6,] -2.18494492  0.98255604 -1.73132386  0.05761964 #>  [7,]  0.11409361  0.73347719  1.46947149 -0.50750744 #>  [8,]  0.01148282  0.76860157  0.01044213 -1.61633811 #>  [9,]  0.35329552 -0.01777067  0.40827683  0.89181656 #> [10,]  2.29670311 -1.10088452  1.70418504 -0.03268551"},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Get nearest neighbor network — getNearestNetwork","title":"Get nearest neighbor network — getNearestNetwork","text":"Get NN-network Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get nearest neighbor network — getNearestNetwork","text":"","code":"getNearestNetwork(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_type = NULL,   name = NULL,   output = c(\"nnNetObj\", \"igraph\", \"data.table\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get nearest neighbor network — getNearestNetwork","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_type \"kNN\" \"sNN\" name name NN network used output return giotto nnNetObj, igraph, data.table object. Default 'nnNetObj' set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get nearest neighbor network — getNearestNetwork","text":"Giotto nnNetObj, igraph data.table object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get nearest neighbor network — getNearestNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getNearestNetwork(gobject = g) #> The NN network type was not specified, default to the #>  first: \"sNN\" #> The NN network name was not specified, default to the #>  first: \"sNN.pca\" #> An object of class nnNetObj : \"sNN.pca\" #> --| Contains nearest neighbor network generated with: sNN  #> ----| for feat_type: rna  #> ----|     spat_unit: cell  #> ----|     provenance: cell  #>  #> IGRAPH 999a381 DNW- 624 3748 --  #> + attr: name (v/c), weight (e/n), distance (e/n), shared (e/n), rank #> | (e/n) #> + edges from 999a381 (vertex names): #>  [1] AAAGGGATGTAGCAAG-1->CAGTGTCCGCAGAATG-1 #>  [2] AAAGGGATGTAGCAAG-1->ACGTAGATTGCTGATG-1 #>  [3] AAAGGGATGTAGCAAG-1->CGTACCTGATAGGCCT-1 #>  [4] AAAGGGATGTAGCAAG-1->GATAAATCGGTGGATG-1 #>  [5] AAAGGGATGTAGCAAG-1->AACCCAGAGACGGAGA-1 #>  [6] AAAGGGATGTAGCAAG-1->GCCTTCAGCCCTACCG-1 #>  [7] AAATGGCATGTCTTGT-1->ACCCTTCATCTGCGAA-1 #> + ... omitted several edges #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"Get polygon info — getPolygonInfo","title":"Get polygon info — getPolygonInfo","text":"Get giotto polygon spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get polygon info — getPolygonInfo","text":"","code":"getPolygonInfo(   gobject = NULL,   polygon_name = NULL,   polygon_overlap = NULL,   return_giottoPolygon = FALSE,   verbose = TRUE,   simplify = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get polygon info — getPolygonInfo","text":"gobject giotto object polygon_name name polygons. Default \"cell\" polygon_overlap include polygon overlap information return_giottoPolygon (Defaults FALSE) Return giottoPolygon S4 object verbose verbose simplify logical. Whether take object list length 1.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get polygon info — getPolygonInfo","text":"spatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get polygon info — getPolygonInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getPolygonInfo(g) #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 498, 1  (geometries, attributes) #>  extent      : 6399.244, 6903.243, -5152.39, -4694.868  (xmin, xmax, ymin, ymax) #>  source      : z0_spatInfo_spatVector.shp #>  coord. ref. :   #>  names       :                                 poly_ID #>  type        :                                   <chr> #>  values      :  40951783403982682273285375368232495429 #>                240649020551054330404932383065726870513 #>                274176126496863898679934791272921588227"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial enrichment — getSpatialEnrichment","title":"Get spatial enrichment — getSpatialEnrichment","text":"Function get spatial enrichment data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial enrichment — getSpatialEnrichment","text":"","code":"getSpatialEnrichment(   gobject,   spat_unit = NULL,   feat_type = NULL,   name = \"DWLS\",   output = c(\"spatEnrObj\", \"data.table\"),   copy_obj = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial enrichment — getSpatialEnrichment","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name spatial enrichment results. Default \"DWLS\" output format get information (e.g. \"data.table\") copy_obj whether deep copy/duplicate getting object (default = TRUE) set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial enrichment — getSpatialEnrichment","text":"spatEnrObj data.table fractions","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get spatial enrichment — getSpatialEnrichment","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getSpatialEnrichment(g, spat_unit = \"aggregate\", name = \"cluster_metagene\") #> An object of class spatEnrObj : \"cluster_metagene\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>    ------------------------ #>  #> preview: #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #>  #> ...first 20 remaining colnames: #>  #>    #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial grid — getSpatialGrid","title":"Get spatial grid — getSpatialGrid","text":"Function get spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial grid — getSpatialGrid","text":"","code":"getSpatialGrid(   gobject,   spat_unit = NULL,   feat_type = NULL,   name = NULL,   return_grid_Obj = FALSE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial grid — getSpatialGrid","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name spatial grid return_grid_Obj return grid object (default = FALSE) set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial grid — getSpatialGrid","text":"spatialGridObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get spatial grid — getSpatialGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  getSpatialGrid(g) #> The grid name was not specified, default to the first: \"spatial_grid\" #>         x_start y_start  x_end y_end   gr_name gr_x_name gr_y_name #>           <num>   <num>  <num> <num>    <char>    <char>    <char> #>      1:  3067.5   -5445 3072.5 -5440      gr_1    gr_x_1    gr_y_1 #>      2:  3072.5   -5445 3077.5 -5440      gr_2    gr_x_2    gr_y_1 #>      3:  3077.5   -5445 3082.5 -5440      gr_3    gr_x_3    gr_y_1 #>      4:  3082.5   -5445 3087.5 -5440      gr_4    gr_x_4    gr_y_1 #>      5:  3087.5   -5445 3092.5 -5440      gr_5    gr_x_5    gr_y_1 #>     ---                                                            #> 388796:  6417.5   -2570 6422.5 -2565 gr_388796  gr_x_671  gr_y_576 #> 388797:  6422.5   -2570 6427.5 -2565 gr_388797  gr_x_672  gr_y_576 #> 388798:  6427.5   -2570 6432.5 -2565 gr_388798  gr_x_673  gr_y_576 #> 388799:  6432.5   -2570 6437.5 -2565 gr_388799  gr_x_674  gr_y_576 #> 388800:  6437.5   -2570 6442.5 -2565 gr_388800  gr_x_675  gr_y_576"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial locations — getSpatialLocations","title":"Get spatial locations — getSpatialLocations","text":"Function get spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial locations — getSpatialLocations","text":"","code":"getSpatialLocations(   gobject,   spat_unit = NULL,   name = NULL,   output = c(\"spatLocsObj\", \"data.table\"),   copy_obj = TRUE,   verbose = TRUE,   set_defaults = TRUE,   simplify = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial locations — getSpatialLocations","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") name name spatial locations (defaults first name spatial_locs slot, e.g. \"raw\") output object type get spatial locations . Default 'spatLocsObj'. Returning 'data.table' also possible. copy_obj whether copy/duplicate getting object (default = TRUE) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. simplify logical. Whether take object list length 1.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial locations — getSpatialLocations","text":"data.table coordinates spatLocsObj depending output","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get spatial locations — getSpatialLocations","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getSpatialLocations(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"z0\" #> provenance: z0  #> dimensions: 498 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6405.067 -4780.499  40951783403982682273285375368232495429 #> 2: 6426.020 -4972.519 240649020551054330404932383065726870513 #> 3: 6428.456 -4799.158 274176126496863898679934791272921588227 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6402.438 -5146.726 #> [2,] 6899.203 -4700.157 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial network — getSpatialNetwork","title":"Get spatial network — getSpatialNetwork","text":"Function get spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial network — getSpatialNetwork","text":"","code":"getSpatialNetwork(   gobject,   spat_unit = NULL,   name = NULL,   output = c(\"spatialNetworkObj\", \"networkDT\", \"networkDT_before_filter\", \"outputObj\"),   set_defaults = TRUE,   copy_obj = TRUE,   verbose = TRUE,   simplify = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial network — getSpatialNetwork","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") name name spatial network output object type return . Options: 'spatialNetworkObj' (default), 'networkDT' 'networkDT_before_filter' data.table outputs. set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. copy_obj whether copy/duplicate getting object (default = TRUE) verbose verbose simplify logical. Whether take object list length 1.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial network — getSpatialNetwork","text":"spatialNetworkObj data.table","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get spatial network — getSpatialNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getSpatialNetwork(g) #> An object of class spatialNetworkObj : \"Delaunay_network\" #> Contains spatial network generated with: deldir  #> spat_unit : \"cell\" #> provenance: cell  #>    1770 connections (filtered) #>    1814 connections (before filter) #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_adj_rescale_img.html","id":null,"dir":"Reference","previous_headings":"","what":"get_adj_rescale_img — get_adj_rescale_img","title":"get_adj_rescale_img — get_adj_rescale_img","text":"get_adj_rescale_img","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_adj_rescale_img.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_adj_rescale_img — get_adj_rescale_img","text":"","code":"get_adj_rescale_img(img_minmax, spatial_locs, scale_factor = 1)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_adj_rescale_img.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_adj_rescale_img — get_adj_rescale_img","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_adj_rescale_img.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get_adj_rescale_img — get_adj_rescale_img","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_spatlocs <- getSpatialLocations(g) g_image <- getGiottoImage(g, name = \"image\") mgimg <- as(g_image, \"giottoImage\") minmax <- get_img_minmax(slot(mgimg, \"mg_object\")) #> Warning: `get_img_minmax()` was deprecated in GiottoClass 0.3.1. #> ℹ Please use `ext()` instead.  get_adj_rescale_img(img_minmax = minmax, spatial_locs = g_spatlocs) #> Warning: `get_adj_rescale_img()` was deprecated in GiottoClass 0.3.1. #> ℹ this is too specific to the inner workings of `giottoImage` #> ℹ We can simply use `ext<-` to set a new extent instead of this. #> xmin_adj_orig xmax_adj_orig ymin_adj_orig ymax_adj_orig  #>          3069         -6198         -5270          2568"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":null,"dir":"Reference","previous_headings":"","what":"get_distance — get_distance","title":"get_distance — get_distance","text":"estimate average distance neighboring cells network table input","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_distance — get_distance","text":"","code":"get_distance(networkDT, method = c(\"mean\", \"median\"))"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_distance — get_distance","text":"networkDT networkDT method method","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_distance — get_distance","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get_distance — get_distance","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spat_net <- getSpatialNetwork(g, output = \"networkDT\")  get_distance(spat_net, method = \"mean\") #> [1] 137.93"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":null,"dir":"Reference","previous_headings":"","what":"get_img_minmax — get_img_minmax","title":"get_img_minmax — get_img_minmax","text":"get_img_minmax","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_img_minmax — get_img_minmax","text":"","code":"get_img_minmax(mg_img, negative_y = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_img_minmax — get_img_minmax","text":"mg_img magick object negative_y Map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_img_minmax — get_img_minmax","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get_img_minmax — get_img_minmax","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, name = \"image\") mgimg <- as(g_image, \"giottoImage\")  get_img_minmax(slot(mgimg, \"mg_object\")) #> $img_xmax #> [1] 243 #>  #> $img_xmin #> [1] 0 #>  #> $img_ymax #> [1] 0 #>  #> $img_ymin #> [1] -172 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Get multiomics integration results — get_multiomics","title":"Get multiomics integration results — get_multiomics","text":"Get multiomics integration result Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get multiomics integration results — get_multiomics","text":"","code":"get_multiomics(   gobject,   spat_unit = NULL,   feat_type = NULL,   integration_method = \"WNN\",   result_name = \"theta_weighted_matrix\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get multiomics integration results — get_multiomics","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') feat_type integrated feature type (e.g. 'rna_protein') integration_method multiomics integration method used. Default = 'WNN' result_name Default = 'theta_weighted_matrix'","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get multiomics integration results — get_multiomics","text":"multiomics integration result (e.g. theta_weighted_matrix WNN)","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get multiomics integration results — get_multiomics","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- setMultiomics(     gobject = g, result = matrix(rnorm(100), nrow = 10),     spat_unit = \"cell\", feat_type = \"rna_protein\" )  get_multiomics(gobject = g, spat_unit = \"cell\", feat_type = \"rna_protein\") #>             [,1]        [,2]       [,3]       [,4]       [,5]        [,6] #>  [1,] -0.1698655 -1.24095435 -2.7800737 -1.5206390 -2.5197112  0.47131362 #>  [2,]  1.1884979  1.47605219 -1.9719497  1.7008620 -1.1675388 -0.05642605 #>  [3,] -0.6211862 -0.07589098 -0.4848200 -0.4662269 -0.7923482  1.19142146 #>  [4,] -0.4248148  0.62842700 -1.3848879 -0.3168777 -0.3003550 -0.02745457 #>  [5,] -1.2693983  0.19674511 -0.1762610 -1.2131392  0.1794639  0.88144485 #>  [6,] -0.2533625  0.08158049  0.2596137  0.2466786 -0.9374372 -3.09168198 #>  [7,] -0.1116180 -0.89830298 -0.2510197  0.1118254  1.4479660  1.12917805 #>  [8,] -0.1315426 -0.61990929 -1.0445444 -1.0078516  1.3361280  1.96047642 #>  [9,]  0.8725992 -1.06214909 -2.0920704  1.2416995  0.4995538  0.24592419 #> [10,] -0.1657629  0.78311754 -0.5391583  1.3815616 -2.7557557 -0.43052706 #>              [,7]       [,8]        [,9]       [,10] #>  [1,] -0.28259708 -0.9525677 -0.61461492  0.01302273 #>  [2,] -0.37221254 -0.4087357 -0.87151065  1.04067074 #>  [3,]  0.18263134 -2.2371918 -0.50174591  0.48370651 #>  [4,]  0.06055847  1.6845247  0.61345388 -1.38514216 #>  [5,] -0.28844587  0.8478142 -2.27293071 -0.98822934 #>  [6,]  1.40416927 -1.4393261 -0.02903636 -0.81254630 #>  [7,]  1.96437541  0.7074581 -1.31878087 -0.03695966 #>  [8,] -1.76916228  2.4144420 -1.59245568  0.12226510 #>  [9,]  0.11502054 -0.9043406 -0.15879473 -0.74855108 #> [10,] -0.47298787  0.4745312  0.39397965  0.09353390"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giotto Class — giotto-class","title":"S4 giotto Class — giotto-class","text":"Giotto's core object encapsulates components spatial-omic project facilitates analyses.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giotto Class — giotto-class","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giotto Class — giotto-class","text":"[initialize] giotto class robust initialize() method automatically called upon setting data object, updates giottoInstructions, loading saved objects. performs following steps: Update object subobjects class definition changes needed Ensure set giottoInstructions available, otherwise generate defaults Ensure giotto python environment accessible options giotto.has_conda giotto.use_conda TRUE Check active spat_unit feat_type Ensure spatial/cell ID consistency initialize cell_ID feat_ID slots active spat_unit feat_type, well cell feature metadata exist. Values IDs metadata pulled existing data spatial_info/feat_info expression slots, preference latter. Perform slot-specific hierarchical checks ensure dependent pieces information added data depend existing information consistent across slots. Object validity checking","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giotto Class — giotto-class","text":"expression expression information expression_feat different features modalities rna, protein, metabolites, ... provided expression slot. spatial_locs spatial location coordinates cells/spots/grids spatial_info information spatial units (Giotto spatVector) cell_metadata metadata cells feat_metadata metadata available features feat_info information features (Giotto spatVector) cell_ID unique cell IDs feat_ID unique feature IDs features modalities spatial_network spatial network data.table/data.frame format spatial_grid spatial grid data.table/data.frame format spatial_enrichment slot save spatial enrichment-like results dimension_reduction slot save dimension reduction coordinates nn_network nearest neighbor network igraph format images slot store giotto image objects parameters slot save parameters used instructions slot global function instructions offset_file offset file used stitch together image fields versions giotto object metadata versioning info join_info information joined Giotto objects multiomics multiomics integration results h5_file path h5 file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giotto Class — giotto-class","text":"","code":"giotto() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> An object of class giotto  #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoAffineImage-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giottoAffineImage Class — giottoAffineImage-class","title":"S4 giottoAffineImage Class — giottoAffineImage-class","text":"Class extending giottoLargeImage. shear() spin() operations performed giottoLargeImage, class instantiated. provides way storing affine transformation also lazily performing required plotting preview. possible force deferred affine transform using doDeferred() return processed giottoLargeImage.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoAffineImage-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giottoAffineImage Class — giottoAffineImage-class","text":"giottoAffineImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoAffineImage-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giottoAffineImage Class — giottoAffineImage-class","text":"affine contains affine2d object allowing lazily performed spatial transforms funs list functions associated object. Primarily perform delayed/lazy operation","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giottoImage Class — giottoImage-class","title":"S4 giottoImage Class — giottoImage-class","text":"Framework giotto object store work spatial expression data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giottoImage Class — giottoImage-class","text":"giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giottoImage Class — giottoImage-class","text":"[mg_object] Core object image can read magick package [boundaries] Boundary adjustments can used manually automatically script adjust image spatial data.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giottoImage Class — giottoImage-class","text":"name name Giotto image mg_object magick image object minmax minimum maximum associated spatial location coordinates boundaries x y coordinate adjustments (default 0) scale_factor image scaling relative spatial locations resolution spatial location units covered per pixel file_path file path image given OS_platform Operating System run Giotto analysis ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giottoImage Class — giottoImage-class","text":"","code":"giottoImage() #> An object of class ' giottoImage ' with name  test  #>   #> Min and max values are:  #>  Max on x-axis:   #>  Min on x-axis:   #>  Max on y-axis:   #>  Min on y-axis:   #>   #> Boundary adjustment are:  #>  Max adjustment on x-axis:   #>  Min adjustment on x-axis:   #>  Max adjustment on y-axis:   #>  Min adjustment on y-axis:   #>   #> Boundaries are:  #>  Image x-axis max boundary:    #>  Image x-axis min boundary:    #>  Image y-axis max boundary:    #>  Image y-axis min boundary:    #>   #> Scale factor:  #> NULL #>  #>  Resolution:  #> NULL #>  #>  File Path:  #> NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoLargeImage-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giottoLargeImage Class — giottoLargeImage-class","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"Image class Giotto uses terra SpatRaster backend. images loaded file disk worked lazily, values needed moment loaded/sampled memory. Since SpatRaster objects C pointers, giottoLargeImage inheriting classes need run reconnect() loading saved object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoLargeImage-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"giottoLargeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoLargeImage-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"name name large Giotto image raster_object terra SpatRaster object extent tracks extent raster object. Note processes rely extent raster object instead . overall_extent terra extent object covering original extent image scale_factor image scaling relative spatial locations resolution spatial location units covered per pixel max_intensity approximate maximum value min_intensity approximate minimum value max_window value set maximum intensity color scaling colors color mappings hex codes is_int values integers file_path file path image given OS_platform Operating System run Giotto analysis ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoLargeImage-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"","code":"giottoLargeImage() #> NULL giottoLargeImage"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoMasterToSuite.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a master Giotto object to suite — giottoMasterToSuite","title":"Convert a master Giotto object to suite — giottoMasterToSuite","text":"Convert master Giotto object suite","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoMasterToSuite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a master Giotto object to suite — giottoMasterToSuite","text":"","code":"giottoMasterToSuite(gobject, expression_feat = \"rna\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoMasterToSuite.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a master Giotto object to suite — giottoMasterToSuite","text":"gobject Giotto object created master version expression_feat available features (e.g. rna, protein, ...)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoMasterToSuite.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a master Giotto object to suite — giottoMasterToSuite","text":"Giotto object compatible suite version","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giotto points Class — giottoPoints-class","title":"S4 giotto points Class — giottoPoints-class","text":"Giotto class store operate points data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giotto points Class — giottoPoints-class","text":"giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giotto points Class — giottoPoints-class","text":"Contains vector-type feature data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giotto points Class — giottoPoints-class","text":"feat_type name feature type spatVector terra spatVector store point shapes networks feature networks unique_ID_cache cached unique feature IDs match spatVector slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giotto points Class — giottoPoints-class","text":"","code":"giottoPoints() #> An object of class giottoPoints #> feat_type : \"NA\" #> Feature Information: #> NULL #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giotto polygon Class — giottoPolygon-class","title":"S4 giotto polygon Class — giottoPolygon-class","text":"Giotto class store operate polygon-like data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giotto polygon Class — giottoPolygon-class","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giotto polygon Class — giottoPolygon-class","text":"holds polygon data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giotto polygon Class — giottoPolygon-class","text":"name name polygon shapes spatVector terra spatVector store polygon shapes spatVectorCentroids centroids polygon shapes overlaps information overlapping points polygons unique_ID_cache cached unique spatial IDs match spatVector slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giotto polygon Class — giottoPolygon-class","text":"","code":"giottoPolygon() #> An object of class giottoPolygon #> spat_unit : \"NA\" #> Spatial Information: #> NULL #>  centroids   : NULL #>  overlaps    : NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Giotto to anndata — giottoToAnnData","title":"Convert Giotto to anndata — giottoToAnnData","text":"Converts Giotto object spatial anndata (e.g. scanpy) .h5ad file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Giotto to anndata — giottoToAnnData","text":"","code":"giottoToAnnData(   gobject = NULL,   spat_unit = NULL,   feat_type = NULL,   python_path = NULL,   env_name = \"giotto_env\",   save_directory = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Giotto to anndata — giottoToAnnData","text":"gobject giotto object converted spat_unit spatial unit used conversion. feat_type feature type used conversion. python_path path python executable within conda/miniconda environment env_name name environment containing python_path executable save_directory directory file saved.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Giotto to anndata — giottoToAnnData","text":"vector containing .h5ad file path(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert Giotto to anndata — giottoToAnnData","text":"Function beta. Converts Giotto object .h5ad file(s). multiple spatial units /feature types, one spatial unit /feature type specified, specified spatial unit /feature type used. NULL, default, spatial units used conversion. multiple spatial units feature types specified, multiple AnnData object created returned. function create .txt files record key_added parameters networks. named corresponding spatial unit feature type pair. save_directory created already exist. default save_directory working directory.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeurat.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated — giottoToSeurat","title":"Deprecated — giottoToSeurat","text":"Deprecated. Please use either giottoToSeuratV4 giottoToSeuratV5","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeurat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated — giottoToSeurat","text":"","code":"giottoToSeurat(gobject, spat_unit = NULL, obj_use = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeurat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deprecated — giottoToSeurat","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') obj_use Giotto object (deprecated, use gobject) ... additional params pass get_spatial_locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeurat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deprecated — giottoToSeurat","text":"Seurat object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV4.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Giotto to Seurat V4 — giottoToSeuratV4","title":"Convert Giotto to Seurat V4 — giottoToSeuratV4","text":"Converts Giotto object Seurat object. functions extracts specific sets data belonging specified spatial unit. default values 'cell' 'rna' respectively.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV4.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Giotto to Seurat V4 — giottoToSeuratV4","text":"","code":"giottoToSeuratV4(gobject, spat_unit = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV4.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Giotto to Seurat V4 — giottoToSeuratV4","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') ... additional params pass get_spatial_locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV4.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Giotto to Seurat V4 — giottoToSeuratV4","text":"Seurat object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV5.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Giotto to Seurat V5 — giottoToSeuratV5","title":"Convert Giotto to Seurat V5 — giottoToSeuratV5","text":"Converts Giotto object Seurat object. functions extracts specific sets data belonging specified spatial unit. default values 'cell' 'rna' respectively.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV5.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Giotto to Seurat V5 — giottoToSeuratV5","text":"","code":"giottoToSeuratV5(   gobject,   spat_unit = NULL,   res_type = c(\"hires\", \"lowres\", \"fullres\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV5.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Giotto to Seurat V5 — giottoToSeuratV5","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') res_type type 10x image output resolution ... additional params pass get_spatial_locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV5.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Giotto to Seurat V5 — giottoToSeuratV5","text":"Seurat object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Giotto to SpatialData — giottoToSpatialData","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"Converts Giotto object SpatialData object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"","code":"giottoToSpatialData(   gobject = NULL,   spat_unit = NULL,   feat_type = NULL,   spot_radius = NULL,   python_path = NULL,   env_name = NULL,   save_directory = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"gobject giotto object converted spat_unit spatial unit used conversion feat_type feature type used conversion spot_radius radius spots python_path path python executable within conda/miniconda environment env_name name environment containing python_path executable save_directory directory SpatialData object saved","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"SpatialData object saved disk.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"Function beta. Converts saves Giotto object SpatialData format disk.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"Utility function convert Giotto object SpatialExperiment object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"","code":"giottoToSpatialExperiment(giottoObj, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"giottoObj Input Giotto object convert SpatialExperiment object verbose boolean value specifying progress messages displayed . Default TRUE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"SpatialExperiment object contains data input Giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"","code":"if (FALSE) { # \\dontrun{ mini_gobject <- GiottoData::loadGiottoMini(\"vizgen\") giottoToSpatialExperiment(mini_gobject) } # }"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto instructions — createGiottoInstructions","title":"Giotto instructions — createGiottoInstructions","text":"Giotto instructions default settings applied giotto object level. added object, affect way object behaves. can create giottoInstructions object using createGiottoInstructions() add giotto object creation using instructions() generic. Specific settings can replaced retrieved using param argument. Additionally, using instructions<-() replacement function, initialize() called giotto object initialize = TRUE. giottoInstructions object provided giotto object creation, default one created giotto object initialization.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto instructions — createGiottoInstructions","text":"","code":"createGiottoInstructions(   python_path = getOption(\"giotto.py_path\"),   show_plot = NULL,   return_plot = NULL,   save_plot = NULL,   save_dir = NULL,   plot_format = NULL,   dpi = NULL,   units = NULL,   height = NULL,   width = NULL,   is_docker = FALSE,   plot_count = 0,   fiji_path = NULL,   no_python_warn = FALSE )  # S4 method for class 'missing,missing' instructions(gobject, param, ...)  # S4 method for class 'giotto,missing' instructions(gobject)  # S4 method for class 'giotto,character' instructions(gobject, param)  # S4 method for class 'giottoInstructions,character' instructions(gobject, param)  # S4 method for class 'giotto,missing,missing' instructions(gobject, initialize) <- value  # S4 method for class 'giotto,missing,logical' instructions(gobject, initialize) <- value  # S4 method for class 'giotto,character,missing' instructions(gobject, param, initialize) <- value  # S4 method for class 'giotto,character,logical' instructions(gobject, param, initialize) <- value  # S4 method for class 'giottoInstructions,character,ANY' instructions(gobject, param) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto instructions — createGiottoInstructions","text":"python_path path python binary use directory one level env directory (similar output reticulate::miniconda_path()) show_plot print plot console, default = TRUE return_plot return plot object, default = TRUE save_plot automatically save plot, dafault = FALSE save_dir path directory save plots plot_format format plots (defaults png) dpi resolution raster images units units format (defaults ) height height plots width width  plots is_docker using docker implementation Giotto (defaults FALSE) plot_count (global option) start count creating automatic unique plots fiji_path path fiji executable no_python_warn turn warning compatible python env detected gobject giotto object param Specific param instructions access modify ... params pass createGiottoInstructions() initialize (boolean, default = TRUE) whether initialize giotto object value value set","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto instructions — createGiottoInstructions","text":"giottoInstructions, instructions settings, giotto objects modified instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto instructions — createGiottoInstructions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  # create instructions ins <- instructions() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  # get instructions instrs <- instructions(g) force(instrs) #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : TRUE #> return_plot      : FALSE #> save_plot        : FALSE #> save_dir         : NA #> plot_format      : png #> dpi              : 300 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna  # get single instructions param instructions(g, \"show_plot\") #> [1] TRUE  # replace an instruction param instructions(g, \"show_plot\") <- FALSE instructions(g, \"show_plot\") #> [1] FALSE  # replace multiple instruction params instructions(g) #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : FALSE #> return_plot      : FALSE #> save_plot        : FALSE #> save_dir         : NA #> plot_format      : png #> dpi              : 300 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna instructions(g, c(\"show_plot\", \"dpi\")) <- list(TRUE, 600) instructions(g) #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : TRUE #> return_plot      : FALSE #> save_plot        : FALSE #> save_dir         : NA #> plot_format      : png #> dpi              : 600 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna  # replace instructions i <- createGiottoInstructions() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" instructions(g) <- i instructions(g) #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : TRUE #> return_plot      : TRUE #> save_plot        : FALSE #> save_dir         : /home/runner/work/GiottoClass/GiottoClass/docs/reference #> plot_format      : png #> dpi              : 300 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto python environment — giotto_python","title":"Giotto python environment — giotto_python","text":"Giotto several functions utilize python packages. facilitate , utilities provided creating, removing, attaching python environments. Python environments currently handled entirely reticulate. Creating environment installGiottoEnvironment() can used create default miniconda environment called giotto_env includes commonly used python packages. See python versions section specific packages version numbers. Custom environments manageable reticulate also compatible can hooked Giotto creation. checkGiottoEnvironment() can used order test envname full python path accessible Giotto. also check \"giotto.py_path\" option. Choosing environments one python environment may initialized used reticulate single R session. order switch another environment, R session must restarted. Whenever following happens first time session: giotto object creation (due creation default giottoInstructions) giottoInstructions creation (createGiottoInstructions()) GiottoClass::set_giotto_python_path() called (direct) , Giotto automatically detects activates python environment based following defaults decreasing priority: User provided (python_path param NULL) provided path envname option \"giotto.py_path\" Default expected giotto environment location based reticulate::miniconda_path() Envname \"giotto_env\" System default python environment behavior mediated set_giotto_python_path() utility function, find environment initialize .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto python environment — giotto_python","text":"","code":"checkGiottoEnvironment(   envname = NULL,   mini_install_path = deprecated(),   verbose = NULL )  installGiottoEnvironment(   packages_to_install = c(\"pandas==1.5.1\", \"networkx==2.8.8\", \"python-igraph==0.10.2\",     \"leidenalg==0.9.0\", \"python-louvain==0.16\", \"python.app==1.4\", \"scikit-learn==1.1.3\",     \"smfishhmrf\", \"session-info\"),   pip_packages = c(\"python-louvain\", \"smfishhmrf\", \"session-info\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   confirm = TRUE,   envname = \"giotto_env\",   conda = \"auto\",   force_miniconda = FALSE,   force_environment = FALSE,   verbose = NULL )  removeGiottoEnvironment(   envname = \"giotto_env\",   mini_path = deprecated(),   conda = \"auto\",   verbose = TRUE )  set_giotto_python_path(python_path = NULL, verbose = NULL, initialize = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto python environment — giotto_python","text":"envname character. (optional) name miniconda conda environment path python executable. using installGiottoEnvironment(), default \"giotto_env\" mini_install_path (optional) desired miniconda installation location. Default chosen reticulate::install_miniconda() verbose verbose packages_to_install python modules (packages) install Giotto. pip_packages python packages mush installed pip, names needed python_version python version use within giotto conda environment. Default v3.10.2 confirm whether pause confirmation conda environment install location (default = TRUE) conda either \"auto\" (default) allow reticulate handle , full filepath conda executable. can also set option \"reticulate.conda_binary\" Sys.setenv() \"RETICULATE_CONDA\" tell reticulate look. force_miniconda force reinstallation miniconda force_environment force reinstallation giotto environment mini_path deprecated python_path character. Name environment full path python executable. initialize force initialization set python path. Default = TRUE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto python environment — giotto_python","text":"installed Giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Giotto python environment — giotto_python","text":"checkGiottoEnvironment(): Based envname, detect conda miniconda environment accessible Giotto. default, envname \"giotto_env\", option \"giotto.py_path\" checked, alternative can provided. Setting envname \":auto:\" let  Giotto autodetect python env use. See section set_giotto_python_path() details autodetection. Returns TRUE env detected accessible Giotto. FALSE . initialize python environment detection. installGiottoEnvironment(): Install giotto python environment using miniconda reticulate. default, envname used \"giotto_env\". another name used, provide envname start session (see Choosing environment ).  includes miniconda installation also set python packages Giotto may often use. See details information setting environment .yml Returns NULL removeGiottoEnvironment(): Remove python environment Returns NULL set_giotto_python_path(): Detect activate python path. python_path param accepts full filepaths python executable envnames. final path use determined follows decreasing priority: User provided (python_path NULL) provided path envname option \"giotto.py_path\" Default expected giotto environment location based reticulate::miniconda_path() Envname \"giotto_env\" System default python environment function exits without anything option \"giotto.use_conda\" FALSE. default function force initialization python environment set, locking session environment. can skipped initialize = FALSE, however case, actual python path set downstream may differ expected reported function. Returns detected path python binary NULL none found.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"python-versions","dir":"Reference","previous_headings":"","what":"python versions","title":"Giotto python environment — giotto_python","text":"default, Python v3.10.2 used following python modules giotto environment installation: giotto environment can custom installed changing python_version parameter module versions packages_to_install parameter. example, giotto environment works well, default environment status past releases Giotto. Python  v3.6","code":"- pandas==1.5.1    - networkx==2.8.8    - python-igraph==0.10.2    - leidenalg==0.9.0    - python-louvain==0.16    - python.app==1.4    - scikit-learn==1.1.3 - pandas==1.1.5   - networkx==2.6.3   - python-igraph==0.9.6   - leidenalg==0.8.7   - python-louvain==0.15   - python.app==2 # macOS only   - scikit-learn==0.24.2"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"-yml-installs","dir":"Reference","previous_headings":"","what":".yml installs","title":"Giotto python environment — giotto_python","text":"Please note multiple .yml files provided repository advanced installation convenience. install --date Giotto environment using .yml file, open shell compatible conda/miniconda navigate directory specified system.file(package = \"Giotto\", \"python/configuration\"). directory, run following create environment one step:","code":"conda env create -n giotto_env -f ./genv.yml"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto python environment — giotto_python","text":"","code":"# detect without initialization # check default env location checkGiottoEnvironment() #> Giotto can access environment found at: #>  '/usr/share/miniconda/envs/giotto_env/bin/python' #>  If this is the wrong environment, try specifying `envname` param #>  or set option \"giotto.py_path\" with the desired envname or path #> [1] TRUE  # use environment name checkGiottoEnvironment(\"giotto_env\") #> Giotto can access environment found at: #>  '/usr/share/miniconda/envs/giotto_env/bin/python' #>  If this is the wrong environment, try specifying `envname` param #>  or set option \"giotto.py_path\" with the desired envname or path #> [1] TRUE  # full path # (use this if a different install location specified with .condarc) if (FALSE) {     checkGiottoEnvironment(         \"/Users/example/Library/r-miniconda-arm64/envs/giotto_env/bin/pythonw\"     ) } if (FALSE) {     # default environment installation     installGiottoEnvironment()      # install to alternate location     temp_env <- tempdir()     installGiottoEnvironment(mini_install_path = temp_env) } # detect AND initialize a python environment if (FALSE) {     set_giotto_python_path() }"},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate regular hexagon vertices — hexVertices","title":"Generate regular hexagon vertices — hexVertices","text":"Generates vertex coordinates regular hexagon.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate regular hexagon vertices — hexVertices","text":"","code":"hexVertices(radius, major_axis = c(\"v\", \"h\"))"},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate regular hexagon vertices — hexVertices","text":"radius radius hexagon major_axis orientation major axis 'v' vertical (default) 'h' horizontal","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate regular hexagon vertices — hexVertices","text":"data.table regular hexagon vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate regular hexagon vertices — hexVertices","text":"","code":"hexVertices(radius = 10) #>            x     y #>        <num> <num> #> 1:  0.000000    10 #> 2:  8.660254     5 #> 3:  8.660254    -5 #> 4:  0.000000   -10 #> 5: -8.660254    -5 #> 6: -8.660254     5"},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":null,"dir":"Reference","previous_headings":"","what":"Histogram — hist","title":"Histogram — hist","text":"Create histogram pixel values giottoLargeImage. Wrapper around terra::hist()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Histogram — hist","text":"","code":"# S4 method for class 'giottoLargeImage' hist(x, show_max = TRUE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Histogram — hist","text":"x giottoLargeImage show_max logical. Plot set max intensity vertical red line ... Arguments passed terra::hist","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Histogram — hist","text":"histogram","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Histogram — hist","text":"","code":"f <- system.file(package = \"GiottoClass\", \"extdata/toy_intensity.tif\") gimg <- createGiottoLargeImage(f, use_rast_ext = TRUE, verbose = FALSE)  hist(gimg) #> Warning: [hist] a sample of 83% of the cells was used"},{"path":"https://drieslab.github.io/GiottoClass/reference/init_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize cell metadata slot — init_cell_metadata","title":"Initialize cell metadata slot — init_cell_metadata","text":"Generate cellMetaObjs hold cell metadata spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize cell metadata slot — init_cell_metadata","text":"","code":"init_cell_metadata(gobject, provenance = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/init_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize cell metadata slot — init_cell_metadata","text":"gobject giotto object provenance provenance information (optional) feature type giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_cell_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize cell metadata slot — init_cell_metadata","text":"cellMetaObjs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_feat_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize feature metadata slot — init_feat_metadata","title":"Initialize feature metadata slot — init_feat_metadata","text":"Generate featMetaObjs hold feature metadata spatial unit feature type giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_feat_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize feature metadata slot — init_feat_metadata","text":"","code":"init_feat_metadata(gobject, provenance = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/init_feat_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize feature metadata slot — init_feat_metadata","text":"gobject giotto object provenance provenance information (optional)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_feat_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize feature metadata slot — init_feat_metadata","text":"featMetaObjs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":null,"dir":"Reference","previous_headings":"","what":"Join giotto objects — joinGiottoObjects","title":"Join giotto objects — joinGiottoObjects","text":"Function join multiple giotto objects together","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Join giotto objects — joinGiottoObjects","text":"","code":"joinGiottoObjects(   gobject_list,   gobject_names = NULL,   join_method = c(\"shift\", \"z_stack\", \"no_change\"),   z_vals = 1000,   x_shift = NULL,   y_shift = NULL,   x_padding = NULL,   y_padding = NULL,   dry_run = FALSE,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Join giotto objects — joinGiottoObjects","text":"gobject_list list giotto objects gobject_names unique giotto names giotto object join_method method join giotto objects, see details z_vals distance(s) along z-axis method z-stack (default step 1000) x_shift numeric vector values shift along x-axis method \"shift\" y_shift numeric vector values shift along y-axis method \"shift\" x_padding x padding datasets method shift y_padding y padding datasets method shift. applied y shifts given. dry_run logical. Plot expected object locations join, actually perform . verbose verbose Preview gobject space bounding polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Join giotto objects — joinGiottoObjects","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Join giotto objects — joinGiottoObjects","text":"function joins expression spatial information multiple giotto objects single one. Giotto supports multiple ways joining spatial information selected param join_method: \"shift\" (default) Spatial locations different datasets shifted numeric vectors values supplied x_shift, y_shift, x_padding, y_padding. particularly useful data provided tiles ROIs analyzing multiple spatial datasets together keeping spatial data separate. shift values given value needed giotto object joined gobject_list. Order matters. regular step value desired instead specific list values, use x_padding y_padding. shift padding values can used time. x_shift NULL, defaults x range gobjects list datasets xshifted exactly next overlaps. additional default x_padding = 1000 applied x_shift, x_padding, y_shift, y_padding NULL. \"z_stack\" Datasets spatially combined change x y spatial locations, z value incorporated dataset based input supplied param z_vals. specify z value dataset join, numeric vector must given value element gobject_list. Order matters. Alternatively, single numeric value can supplied z_vals case input treated z step value. \"no_change\" changes applied spatial locations datasets joining.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Join giotto objects — joinGiottoObjects","text":"","code":"# joining objects with no spatial information m1 <- matrix(rnorm(100), nrow = 10) m2 <- matrix(rnorm(100), nrow = 10) colnames(m1) <- paste0(\"cell_\", seq_len(10)) colnames(m2) <- paste0(\"cell_\", seq_len(10)) rownames(m1) <- rownames(m2) <- paste0(\"feat_\", seq_len(10))  g1 <- createGiottoObject(expression = m1) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed g2 <- createGiottoObject(expression = m2) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed  joinGiottoObjects(     gobject_list = list(g1, g2),     gobject_names = c(\"g1\", \"g2\") ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 10, 20 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw #> spatial locations ---------------- #>   [cell] raw #>  #>  #> Use objHistory() to see steps and params used  # dry run joining objects with spatial information # a default x_padding of 1000 is applied viz <- GiottoData::loadGiottoMini(\"viz\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" joinGiottoObjects(     list(viz, viz),     gobject_names = c(\"v1\", \"v2\"),     dry_run = TRUE )   # place them right next to each other # note that this means generated spatial networks will be more likely to # link across the datasets joinGiottoObjects(     list(viz, viz),     gobject_names = c(\"v1\", \"v2\"),     dry_run = TRUE,     x_padding = 0 )   # join the spatial objects joined_viz <- joinGiottoObjects(     list(viz, viz),     gobject_names = c(\"v1\", \"v2\") ) #> Warning: spatial locations have been modified. #>  Relevant spatial networks may need to be #>  regenerated #> Warning: spatial locations have been modified. #>  Relevant spatial networks may need to be #>  regenerated #> Warning: spat_unit: z1 spatloc name: raw #>  cell IDs in spatial locations are missing from spatial #>  polygon info #> Warning: spat_unit: aggregate spatloc name: raw #>  cell IDs in spatial locations are missing from spatial #>  polygon info"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":null,"dir":"Reference","previous_headings":"","what":"List cell ID names — list_cell_id_names","title":"List cell ID names — list_cell_id_names","text":"lists available cell id names. effect, names spat_units poly info gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List cell ID names — list_cell_id_names","text":"","code":"list_cell_id_names(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List cell ID names — list_cell_id_names","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List cell ID names — list_cell_id_names","text":"vector names available sets cell_IDs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List cell ID names — list_cell_id_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_cell_id_names(g) #> [1] \"cell\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"list_cell_metadata — list_cell_metadata","title":"list_cell_metadata — list_cell_metadata","text":"lists available cell metadata.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_cell_metadata — list_cell_metadata","text":"","code":"list_cell_metadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_cell_metadata — list_cell_metadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_cell_metadata — list_cell_metadata","text":"names locations available cell metadata data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_cell_metadata — list_cell_metadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_cell_metadata(g) #>    spat_unit feat_type #>       <char>    <char> #> 1:      cell       rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":null,"dir":"Reference","previous_headings":"","what":"list_dim_reductions — list_dim_reductions","title":"list_dim_reductions — list_dim_reductions","text":"return available dimension reductions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_dim_reductions — list_dim_reductions","text":"","code":"list_dim_reductions(   gobject,   data_type = NULL,   spat_unit = NULL,   feat_type = NULL,   dim_type = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_dim_reductions — list_dim_reductions","text":"gobject giotto object data_type \"cells\" \"feats\" data used dim reduction spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") dim_type dimensional reduction method (e.g. \"pca\", \"umap\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_dim_reductions — list_dim_reductions","text":"names locations dimension reduction data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_dim_reductions — list_dim_reductions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_dim_reductions(g) #>    data_type spat_unit feat_type dim_type        name #>       <char>    <char>    <char>   <char>      <char> #> 1:     cells      cell       rna      pca         pca #> 2:     cells      cell       rna      pca  custom_pca #> 3:     cells      cell       rna     umap        umap #> 4:     cells      cell       rna     umap custom_umap #> 5:     cells      cell       rna     tsne        tsne"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_dim_reductions_names — list_dim_reductions_names","title":"list_dim_reductions_names — list_dim_reductions_names","text":"return available dimension reductions object names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_dim_reductions_names — list_dim_reductions_names","text":"","code":"list_dim_reductions_names(   gobject,   data_type = \"cells\",   spat_unit = NULL,   feat_type = NULL,   dim_type = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_dim_reductions_names — list_dim_reductions_names","text":"gobject giotto object data_type cells feats dim reduction spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") dim_type dimensional reduction type (method)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_dim_reductions_names — list_dim_reductions_names","text":"names dimension reduction object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"list_dim_reductions_names — list_dim_reductions_names","text":"function can used find names used","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_dim_reductions_names — list_dim_reductions_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_dim_reductions_names(g,     spat_unit = \"cell\", feat_type = \"rna\",     dim_type = \"pca\" ) #> [1] \"pca\"        \"custom_pca\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"list_expression — list_expression","title":"list_expression — list_expression","text":"lists available matrices","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_expression — list_expression","text":"","code":"list_expression(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_expression — list_expression","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_expression — list_expression","text":"names locations available matrices data.table. col order matters.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_expression — list_expression","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_expression(g) #>    spat_unit feat_type       name #>       <char>    <char>     <char> #> 1:      cell       rna        raw #> 2:      cell       rna normalized #> 3:      cell       rna     scaled"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_expression_names — list_expression_names","title":"list_expression_names — list_expression_names","text":"lists available matrices names given spatial unit feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_expression_names — list_expression_names","text":"","code":"list_expression_names(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_expression_names — list_expression_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_expression_names — list_expression_names","text":"vector names available matrices","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_expression_names — list_expression_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_expression_names(g, spat_unit = \"cell\", feat_type = \"rna\") #> [1] \"raw\"        \"normalized\" \"scaled\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":null,"dir":"Reference","previous_headings":"","what":"List feat ID names — list_feat_id_names","title":"List feat ID names — list_feat_id_names","text":"lists available feat id names effect, names feat_types feature info gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List feat ID names — list_feat_id_names","text":"","code":"list_feat_id_names(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List feat ID names — list_feat_id_names","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List feat ID names — list_feat_id_names","text":"vector names available sets feat_IDs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List feat ID names — list_feat_id_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_feat_id_names(g) #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"list_feat_metadata — list_feat_metadata","title":"list_feat_metadata — list_feat_metadata","text":"lists available feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_feat_metadata — list_feat_metadata","text":"","code":"list_feat_metadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_feat_metadata — list_feat_metadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_feat_metadata — list_feat_metadata","text":"names locations available feature metadata data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_feat_metadata — list_feat_metadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_feat_metadata(g) #>    spat_unit feat_type #>       <char>    <char> #> 1:      cell       rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":null,"dir":"Reference","previous_headings":"","what":"list_feature_info — list_feature_info","title":"list_feature_info — list_feature_info","text":"return available giotto spatial feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_feature_info — list_feature_info","text":"","code":"list_feature_info(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_feature_info — list_feature_info","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_feature_info — list_feature_info","text":"names available feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_feature_info — list_feature_info","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_feature_info(g) #>    feat_info #>       <char> #> 1:       rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_feature_info_names — list_feature_info_names","title":"list_feature_info_names — list_feature_info_names","text":"return available names giotto feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_feature_info_names — list_feature_info_names","text":"","code":"list_feature_info_names(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_feature_info_names — list_feature_info_names","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_feature_info_names — list_feature_info_names","text":"vector names available feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_feature_info_names — list_feature_info_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_feature_info_names(g) #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":null,"dir":"Reference","previous_headings":"","what":"list_giotto_data — list_giotto_data","title":"list_giotto_data — list_giotto_data","text":"list available data within specified giotto object slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_giotto_data — list_giotto_data","text":"","code":"list_giotto_data(gobject = NULL, slot = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_giotto_data — list_giotto_data","text":"gobject giotto object slot giotto object slot interest (e.g. \"expression\", \"spatial_locs\", etc.) ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_giotto_data — list_giotto_data","text":"names locations data within giotto object slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_giotto_data — list_giotto_data","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_giotto_data(gobject = g, slot = \"expression\") #>    spat_unit feat_type       name #>       <char>    <char>     <char> #> 1:      cell       rna        raw #> 2:      cell       rna normalized #> 3:      cell       rna     scaled"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":null,"dir":"Reference","previous_headings":"","what":"list_images — list_images","title":"list_images — list_images","text":"Prints available giotto images attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_images — list_images","text":"","code":"list_images(gobject, img_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_images — list_images","text":"gobject giotto object img_type \"image\" \"largeImage\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_images — list_images","text":"data.table giotto image names attached giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_images — list_images","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" list_images(g) #> Index: <img_type> #>        name   img_type #>      <char>     <char> #> 1:  dapi_z0 largeImage #> 2:  dapi_z1 largeImage #> 3: polyT_z0 largeImage #> 4: polyT_z1 largeImage list_images(g, img_type = \"largeImage\") #>        name   img_type #>      <char>     <char> #> 1:  dapi_z0 largeImage #> 2:  dapi_z1 largeImage #> 3: polyT_z0 largeImage #> 4: polyT_z1 largeImage"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_images_names — list_images_names","title":"list_images_names — list_images_names","text":"return available image names given image type attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_images_names — list_images_names","text":"","code":"list_images_names(gobject, img_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_images_names — list_images_names","text":"gobject giotto object img_type passing NULL (default) gets image names. Can specify \"image\" \"largeImage\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_images_names — list_images_names","text":"vector names available image names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_images_names — list_images_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" list_images_names(g) #> [1] \"dapi_z0\"  \"dapi_z1\"  \"polyT_z0\" \"polyT_z1\" list_images_names(g, img_type = \"largeImage\") #> [1] \"dapi_z0\"  \"dapi_z1\"  \"polyT_z0\" \"polyT_z1\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":null,"dir":"Reference","previous_headings":"","what":"list_nearest_networks — list_nearest_networks","title":"list_nearest_networks — list_nearest_networks","text":"return available nearest neighbor network information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_nearest_networks — list_nearest_networks","text":"","code":"list_nearest_networks(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_nearest_networks — list_nearest_networks","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_type nearest neighbor method (e.g. \"sNN\", \"kNN\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_nearest_networks — list_nearest_networks","text":"names locations nearest neighbor networks data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_nearest_networks — list_nearest_networks","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_nearest_networks(g) #>    spat_unit feat_type nn_type      name #>       <char>    <char>  <char>    <char> #> 1:      cell       rna     sNN   sNN.pca #> 2:      cell       rna     sNN custom_NN"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_nearest_networks_names — list_nearest_networks_names","title":"list_nearest_networks_names — list_nearest_networks_names","text":"return available nearest neighbor network object names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_nearest_networks_names — list_nearest_networks_names","text":"","code":"list_nearest_networks_names(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_type = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_nearest_networks_names — list_nearest_networks_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_type nearest neighbor method (e.g. \"sNN\", \"kNN\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_nearest_networks_names — list_nearest_networks_names","text":"names nearest neighbor network object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"list_nearest_networks_names — list_nearest_networks_names","text":"function can used find names used","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_nearest_networks_names — list_nearest_networks_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_nearest_networks_names(g,     spat_unit = \"cell\", feat_type = \"rna\",     nn_type = \"sNN\" ) #> [1] \"sNN.pca\"   \"custom_NN\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_enrichments — list_spatial_enrichments","title":"list_spatial_enrichments — list_spatial_enrichments","text":"return available spatial enrichment results","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_enrichments — list_spatial_enrichments","text":"","code":"list_spatial_enrichments(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_enrichments — list_spatial_enrichments","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_enrichments — list_spatial_enrichments","text":"names locations available data data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_enrichments — list_spatial_enrichments","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_enrichments(g) #>    spat_unit feat_type             name #>       <char>    <char>           <char> #> 1: aggregate       rna cluster_metagene"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_enrichments_names — list_spatial_enrichments_names","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"returns available spatial enrichment names given spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"","code":"list_spatial_enrichments_names(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"vector names available spatial enrichments","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_enrichments_names(g, spat_unit = \"aggregate\", feat_type = \"rna\") #> [1] \"cluster_metagene\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_grids — list_spatial_grids","title":"list_spatial_grids — list_spatial_grids","text":"return available spatial grids attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_grids — list_spatial_grids","text":"","code":"list_spatial_grids(   gobject,   spat_unit = NULL,   feat_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_grids — list_spatial_grids","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_grids — list_spatial_grids","text":"data.table names locations available spatial grids. col order matters","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_grids — list_spatial_grids","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  list_spatial_grids(g) #>    spat_unit feat_type         name #>       <char>    <char>       <char> #> 1:      cell       rna spatial_grid"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_grids_names — list_spatial_grids_names","title":"list_spatial_grids_names — list_spatial_grids_names","text":"return available spatial grids name given spatial unit attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_grids_names — list_spatial_grids_names","text":"","code":"list_spatial_grids_names(   gobject,   spat_unit = NULL,   feat_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_grids_names — list_spatial_grids_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_grids_names — list_spatial_grids_names","text":"vector names available spatial grids names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_grids_names — list_spatial_grids_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  list_spatial_grids_names(g, spat_unit = \"cell\", feat_type = \"rna\") #> [1] \"spatial_grid\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_info — list_spatial_info","title":"list_spatial_info — list_spatial_info","text":"return available giotto spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_info — list_spatial_info","text":"","code":"list_spatial_info(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_info — list_spatial_info","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_info — list_spatial_info","text":"names available spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_info — list_spatial_info","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_info(g) #>    spat_info #>       <char> #> 1:        z0 #> 2:        z1 #> 3: aggregate"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_info_names — list_spatial_info_names","title":"list_spatial_info_names — list_spatial_info_names","text":"return available names giotto spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_info_names — list_spatial_info_names","text":"","code":"list_spatial_info_names(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_info_names — list_spatial_info_names","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_info_names — list_spatial_info_names","text":"vector names available spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_info_names — list_spatial_info_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_info_names(g) #> [1] \"z0\"        \"z1\"        \"aggregate\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_locations — list_spatial_locations","title":"list_spatial_locations — list_spatial_locations","text":"shows available spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_locations — list_spatial_locations","text":"","code":"list_spatial_locations(gobject, spat_unit = NULL, return_uniques = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_locations — list_spatial_locations","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_locations — list_spatial_locations","text":"names locations available data.table data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_locations — list_spatial_locations","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_locations(g) #>    spat_unit   name #>       <char> <char> #> 1:      cell    raw"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_locations_names — list_spatial_locations_names","title":"list_spatial_locations_names — list_spatial_locations_names","text":"lists available spatial location names given spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_locations_names — list_spatial_locations_names","text":"","code":"list_spatial_locations_names(gobject, spat_unit = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_locations_names — list_spatial_locations_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_locations_names — list_spatial_locations_names","text":"vector names available spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_locations_names — list_spatial_locations_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_locations_names(g, spat_unit = \"cell\") #> [1] \"raw\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_networks — list_spatial_networks","title":"list_spatial_networks — list_spatial_networks","text":"return available spatial networks attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_networks — list_spatial_networks","text":"","code":"list_spatial_networks(gobject, spat_unit = NULL, return_uniques = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_networks — list_spatial_networks","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_networks — list_spatial_networks","text":"data.table names locations available spatial networks, col order matters list unique nestings","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_networks — list_spatial_networks","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_networks(g) #>    spat_unit             name #>       <char>           <char> #> 1: aggregate Delaunay_network #> 2: aggregate      kNN_network"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_networks_names — list_spatial_networks_names","title":"list_spatial_networks_names — list_spatial_networks_names","text":"return available names giotto feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_networks_names — list_spatial_networks_names","text":"","code":"list_spatial_networks_names(gobject, spat_unit = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_networks_names — list_spatial_networks_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_networks_names — list_spatial_networks_names","text":"vector names available feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_networks_names — list_spatial_networks_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_networks_names(g, spat_unit = \"cell\") #> [1] \"Delaunay_network\" \"spatial_network\""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"loadGiotto — loadGiotto","title":"loadGiotto — loadGiotto","text":"Saves Giotto object specific folder structure","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"loadGiotto — loadGiotto","text":"","code":"loadGiotto(   path_to_folder,   load_params = list(),   reconnect_giottoImage = TRUE,   python_path = NULL,   init_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"loadGiotto — loadGiotto","text":"path_to_folder path folder Giotto object stored saveGiotto load_params additional parameters loading reading giotto object reconnect_giottoImage (default = TRUE) whether attempt reconnection magick based image objects python_path (optional) manually set python path init_gobject logical. Whether initialize giotto object loading. (default = TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"loadGiotto — loadGiotto","text":"Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"loadGiotto — loadGiotto","text":"Works together saveGiotto save re-load Giotto objects. Additional load_params need provided list go readRDS qread can set python path, alternatively look existing Giotto python environment.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"loadGiotto — loadGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" td <- tempdir() saveGiotto(gobject = g, dir = td) #> 1. Start writing feature information #> 2. Start writing spatial information #> For spatial information: cell #> 3. Start writing image information #> For image information: alignment #> For image information: image  loadGiotto(path_to_folder = paste0(td, \"/saveGiottoDir\")) #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":null,"dir":"Reference","previous_headings":"","what":"makePseudoVisium — makePseudoVisium","title":"makePseudoVisium — makePseudoVisium","text":"Generates pseudo-visium grid spots across provided spatial extent","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"makePseudoVisium — makePseudoVisium","text":"","code":"makePseudoVisium(extent = NULL, micron_size = 1, name = \"pseudo_visium\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"makePseudoVisium — makePseudoVisium","text":"extent SpatExtent anything else SpatExtent can extracted created micron_size size micrometer relative spatial coordinates name character. (default 'pseudo_visium') Name giottoPolygon object create","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"makePseudoVisium — makePseudoVisium","text":"giottoPolygon pseudo-visium spots.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"makePseudoVisium — makePseudoVisium","text":"function generates pseudo-Visium grid spots based input spatial locations. micron_size param used determine size spots","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"makePseudoVisium — makePseudoVisium","text":"","code":"e <- ext(0, 2000, 0, 2000) x <- makePseudoVisium(extent = e, micron_size = 1) #> 390 polygons generated plot(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"mean_flex — mean_flex","title":"mean_flex — mean_flex","text":"mean_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mean_flex — mean_flex","text":"","code":"mean_flex(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mean_flex — mean_flex","text":"x data use ... arguments pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mean_flex — mean_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"mean_flex — mean_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  mean_flex(m) #> [1] 0.06142303"},{"path":"https://drieslab.github.io/GiottoClass/reference/miscData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic class for additional miscellaneous information — miscData-class","title":"Basic class for additional miscellaneous information — miscData-class","text":"Classes (dimObj) can hold information multiple types methods use misc slot hold additional information specific method. Information may stored within S3 structures.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/miscData-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basic class for additional miscellaneous information — miscData-class","text":"slot miscellaneous information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/miscData-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Basic class for additional miscellaneous information — miscData-class","text":"","code":"g <- GiottoData::loadSubObjectMini(\"dimObj\")  slot(g, \"misc\") #> $eigenvalues #>   [1] 33.2534135 32.0046063 30.0502213 23.4352729 14.9873873 14.4036736 #>   [7] 11.8499793 10.6893086  9.3040152  6.9800585  6.8538084  6.0485295 #>  [13]  5.7915560  5.1138968  4.9417237  4.7024725  4.3698509  4.1615473 #>  [19]  3.9581798  3.5429980  3.4268141  3.3099700  3.2350908  3.1648805 #>  [25]  3.0439582  2.9064535  2.8524063  2.7202686  2.6799304  2.5689859 #>  [31]  2.5279120  2.4568203  2.4413820  2.4043215  2.2542061  2.2058793 #>  [37]  2.1896105  2.1608223  2.1332721  2.0909430  2.0288850  1.9923129 #>  [43]  1.9176801  1.8699125  1.8353129  1.7768831  1.7700422  1.7509328 #>  [49]  1.7226019  1.6894990  1.6530223  1.6411241  1.5851496  1.5687056 #>  [55]  1.5454645  1.5241935  1.4727217  1.4685526  1.4528981  1.4055974 #>  [61]  1.3715253  1.3659691  1.3286971  1.2883263  1.2804195  1.2507976 #>  [67]  1.2475448  1.2363812  1.1837924  1.1801315  1.1659735  1.1448418 #>  [73]  1.1201655  1.0999292  1.0838246  1.0546067  1.0483329  1.0319266 #>  [79]  0.9870703  0.9835202  0.9510675  0.9296043  0.9225639  0.9045214 #>  [85]  0.8797710  0.8550994  0.8356013  0.8292998  0.8066431  0.8016031 #>  [91]  0.7671520  0.7594730  0.7402408  0.7279798  0.7131876  0.6834403 #>  [97]  0.6823937  0.6489129  0.6446519  0.6206416 #>  #> $loadings #>                  Dim.1         Dim.2         Dim.3         Dim.4         Dim.5 #> Mlc1      0.0497209920  0.0516028482 -0.0788876048  0.0032493081  6.602336e-02 #> Gprc5b    0.0776530195  0.0767287111 -0.1003795798 -0.0429921843 -6.838634e-02 #> Gfap      0.2737382490  0.2308157480 -0.2703730778 -0.1253583035 -3.101030e-01 #> Ednrb     0.0840708314  0.0699607215 -0.0933344159 -0.0320003544  3.835691e-02 #> Sox9      0.0701589058  0.0648677354 -0.0882498978 -0.0089310657  8.022850e-02 #> Aqp4      0.1648074467  0.1639844662 -0.2047222491 -0.0886550945  3.217967e-02 #> Gjc3      0.0787488199  0.0902074332 -0.0900546455 -0.0683712434 -3.690813e-01 #> Sox8      0.0239282810  0.0501925669 -0.0283113185 -0.0160920618 -1.362323e-01 #> Ntsr2     0.1704425415  0.1601869753 -0.2146941517 -0.0504471528  2.278867e-01 #> Smo       0.0101445414 -0.0602267061 -0.0080775417 -0.0514860143 -8.651041e-05 #> C1qb      0.3469055234 -0.0556488977  0.2697640508  0.0633723690 -4.540910e-03 #> Olig1     0.0649931574  0.0709296076 -0.0604750868 -0.0437817503 -3.264669e-01 #> C1qa      0.3435753209 -0.0679235461  0.2732874719  0.0596583452 -1.168577e-02 #> Pth1r     0.0269966628 -0.0234988709 -0.0578083113  0.0128749364 -5.972937e-02 #> Gabbr2   -0.0968959099  0.0393425389  0.0697732292  0.0299199523 -9.626442e-04 #> Timp4     0.0536090931  0.0280895417 -0.0753163592  0.0158564413  4.382947e-02 #> Abcc9     0.0165480319 -0.0466802006 -0.0509001991  0.0153604110 -1.197030e-01 #> Csf1r     0.2636662717 -0.0386831102  0.2243084956  0.0669753056  9.956118e-03 #> Ntrk2     0.0881426645  0.1012229752 -0.1330898636 -0.0116179071  1.422470e-01 #> Adgrg1    0.0956322507  0.0336898984 -0.0983375842  0.0360269420  8.868170e-02 #> Ntrk3    -0.1084430931  0.0220051827  0.0772323289  0.0089486275 -1.086369e-02 #> Erbb4    -0.0061492024  0.0287309846 -0.0052711701 -0.0106869915 -2.363755e-02 #> Selplg    0.2163849803 -0.0146272024  0.1797440166  0.0711729672 -3.951132e-05 #> Cspg5     0.0508038447  0.1051590276 -0.1171638694 -0.0073861327  1.627924e-01 #> Dlk1      0.0319763185  0.0403762064 -0.0285589767 -0.0211066951 -7.607112e-02 #> Gpr37l1   0.1435865057  0.1348871702 -0.1928914087 -0.0302268679  2.051102e-01 #> Fgfr3     0.0996140210  0.0850286103 -0.1355375615 -0.0118240087  1.574511e-01 #> Slc25a18  0.0698809750  0.0686974956 -0.0947152143 -0.0096511715  1.026733e-01 #> Igf1r    -0.0014116337 -0.0596930778 -0.0528646487  0.0773945525  1.281184e-02 #> S1pr1     0.0822799744  0.0362846623 -0.1354970039  0.0181807874  1.784681e-01 #> Grm5     -0.1118001691  0.0475255721  0.0861476556  0.0347360399 -1.072351e-02 #> Axl       0.0858668222 -0.0487149935 -0.0215858560 -0.0347855205  5.258418e-03 #> Efemp1    0.0261969437 -0.1986612549 -0.0252210424 -0.2406020556  5.172519e-02 #> Adgrb3   -0.0544048314  0.0550664169  0.0217421136  0.0173602267  4.369901e-02 #> Fn1       0.0197391341 -0.3432218159 -0.0678838022 -0.2440058578  5.826913e-02 #> Mertk     0.1227479861  0.0330014625 -0.0359677503  0.0058191331  1.050344e-01 #> Adgrl2    0.0181563638 -0.0994313729 -0.0215071929 -0.0455756732  1.688788e-02 #> Fzd2      0.0166298244 -0.1219469652 -0.0205442251 -0.1621939124  3.165561e-02 #> Aldh1l1   0.0621044803  0.0450324509 -0.0755769710 -0.0463455168  4.455743e-02 #> Adgrg6    0.0049233608 -0.0962329171 -0.0395936687  0.0275253785  1.009561e-02 #> Egfr      0.0095100368 -0.0457057148 -0.0148372962 -0.1032193882  7.474851e-02 #> Kit      -0.0111042732 -0.0886068185  0.0082155796 -0.1106598956 -7.255914e-02 #> Ptgdr     0.0045409154 -0.0885371528  0.0038310671 -0.1341326756  7.176816e-02 #> Gad1     -0.0860206201  0.0439393653  0.0519458282  0.0080321157 -8.142480e-03 #> Tyro3     0.0171943705  0.0416572563 -0.0222654682 -0.0109172887 -1.119973e-01 #> Atp13a5   0.0206112315 -0.1426519762 -0.0496623163 -0.1027289390 -2.015837e-01 #> Ddr2      0.0197099222 -0.1317915730 -0.0023189303 -0.1419593244 -9.013596e-03 #> Rspo3    -0.0315132700 -0.0820764063  0.0224241276 -0.0986280620  4.999107e-02 #> Arhgap29  0.0170582653 -0.1760750472 -0.0446192339 -0.0791462003 -8.717547e-02 #> Fzd7      0.0013466497 -0.0541730858  0.0065291313 -0.0491961687 -3.135484e-02 #> Slc47a1   0.0070042606 -0.2605398556  0.0078046531 -0.4140449341  2.305858e-01 #> Ptger3    0.0028027777 -0.0436933914  0.0017106060 -0.0496212778 -4.140198e-02 #> Bdkrb1    0.0071407966 -0.0148844898 -0.0111734972 -0.0343489894  1.922939e-02 #> Traf4     0.0127022727 -0.0131715780 -0.0050164887 -0.0471016364 -8.346302e-02 #> Cx3cr1    0.2910208672 -0.0295179146  0.2327469236  0.0753681382  2.887251e-02 #> Anxa11   -0.0350383434 -0.0444961512  0.0227879282 -0.0003838839 -8.668919e-03 #> Adgrb1   -0.0912517077  0.0522565195  0.0642316823  0.0288516773 -2.134981e-02 #> Lpar1     0.0309961553 -0.0892477881 -0.0138536553 -0.1042763602 -9.845681e-02 #> Gpr17     0.0210630145  0.0267569595 -0.0347693627 -0.0180771947 -2.030246e-01 #> Cxcl12   -0.0205191339 -0.1197577846 -0.0109975056 -0.0464815062 -3.201204e-02 #> Epha4    -0.0933744058  0.0227970528  0.0629049097  0.0199398111  1.216961e-02 #> Gpr182    0.0217907242 -0.1307174869 -0.0290431428 -0.0359762880 -7.534909e-02 #> P2ry14    0.0061803999 -0.0464150639 -0.0177050305 -0.0297627807 -5.987862e-02 #> Hcar1     0.0112922586 -0.1115686468 -0.0095453473 -0.1018621177 -2.872211e-02 #> Ephb1     0.0142380691  0.0436005945 -0.0301308696 -0.0124731567 -3.450293e-02 #> Grm3      0.0503104535  0.0462853583 -0.0795484416 -0.0249577215 -5.127534e-02 #> P2ry1     0.0082016818 -0.0596404982 -0.0106745751 -0.0548097432 -1.740224e-02 #> Ptk7     -0.0066957877 -0.0125314706  0.0086372160 -0.0162025281 -1.046542e-02 #> Slco1a4   0.0223657930 -0.1657536092 -0.1369393395  0.2191105340 -5.040751e-03 #> Insrr     0.0104466450 -0.0690139103  0.0026752471 -0.0726142014 -8.709213e-02 #> Cmklr1    0.0763628647 -0.0475073233  0.0501998735  0.0350138248 -4.970904e-03 #> Fzd6      0.0192202128 -0.0748877500 -0.0529204409  0.0429010577  7.222569e-03 #> S1pr5     0.0284583918  0.0327079131 -0.0317267539 -0.0271689854 -1.673905e-01 #> Pdgfrb    0.0231063599 -0.0968995924 -0.0605968579 -0.0255074465 -1.062949e-01 #> Flt1      0.0246441573 -0.2259779787 -0.1861946652  0.2724661325 -1.032480e-02 #> Adgrl4    0.0280961325 -0.1382446041 -0.1168323871  0.1888979843  1.109663e-02 #> Lpar6     0.0625796806 -0.0137831249  0.0367979155  0.0174625835  7.205206e-03 #> Epha6    -0.0883902219  0.0310861900  0.0643222427  0.0286811098 -9.171165e-03 #> Emcn      0.0083437378 -0.0598648781 -0.0522568392  0.0706115352 -2.681291e-02 #> Cldn5     0.0311045271 -0.2946074660 -0.2310564448  0.3717678593  1.299561e-02 #> P2ry12    0.2344889997 -0.0116937160  0.1840545925  0.0754388728  2.322359e-02 #> Adgrf5    0.0266564647 -0.1775220011 -0.1348469482  0.2125852103 -9.071991e-03 #> P2yr13    0.1070261760 -0.0040461073  0.0854383239  0.0344185804  7.275986e-03 #> Adgre1    0.1063901755 -0.0230391639  0.0925878260  0.0249118824 -1.363161e-03 #> Cx3cl1   -0.1207742925  0.0391257213  0.0897826344  0.0332051052 -7.772283e-03 #> Plxnb3    0.0465977442  0.0271233361 -0.0068886248 -0.0066219585 -3.097681e-02 #> Flt4      0.0062416946 -0.0660399618 -0.0507326584  0.0868945900  8.260962e-03 #> Slc17a7  -0.1921862304  0.0788625906  0.1402943023  0.0679087015  9.239846e-03 #> Cd300c2   0.1054073418 -0.0143207295  0.0880892016  0.0232454239 -1.552302e-03 #> Tek       0.0133424704 -0.1214264457 -0.0950472703  0.1538389566 -5.129120e-03 #> Kdr       0.0022649406 -0.1017476134 -0.0655678924  0.0854487303 -8.440583e-03 #> Kcnj8     0.0057131652 -0.0600056637 -0.0504989633  0.0313678625 -1.127657e-01 #> S1pr3     0.0090193031 -0.0304064386 -0.0348778543  0.0102899655 -7.646302e-02 #> Tie1      0.0121630145 -0.0911768640 -0.0585413651  0.1039348344 -6.046745e-04 #> Pdgfra    0.0232382302 -0.0434901119 -0.0259810889 -0.0291148512 -1.264767e-01 #> Baiap2   -0.1134937277  0.0312269711  0.0847938141  0.0446083687 -2.995924e-04 #> Calcrl    0.0172670916 -0.0648868288 -0.0450806533  0.0565117118  2.899586e-03 #> Adrb2     0.0565699931 -0.0791478593  0.0446794048 -0.0935164553  3.025000e-02 #> Ccr2      0.0799214988 -0.0207712131  0.0667926120  0.0112386552 -1.135570e-02 #> Alk      -0.0010488678 -0.0386206408 -0.0004323964 -0.0506666242 -7.061478e-02 #> Tacr3    -0.0106678914  0.0043610542  0.0246442035  0.0067405818  9.965484e-04 #> Erbb3     0.0362406240  0.0303559518 -0.0228320219 -0.0204566277 -1.253986e-01 #> Pcdh15    0.0080932950  0.0218323904 -0.0177765291 -0.0113617353 -1.402757e-01 #> Grm7     -0.0892227313  0.0383326484  0.0626967229  0.0281851690 -2.794878e-02 #> F2r       0.0085739763 -0.0195181421 -0.0178674193  0.0234289168 -2.745732e-02 #> Bdkrb2    0.0084295968 -0.0521024891  0.0011408388 -0.0498454028 -5.117463e-02 #> Adgrv1    0.0052015216 -0.0634093489 -0.0061167662 -0.1132172762  7.952108e-02 #> Gprc5c    0.0218727090 -0.0799980468 -0.0023058938 -0.0650826276 -7.341098e-02 #> Tbxa2r    0.0115847334 -0.0363309895 -0.0153433217 -0.0168574532 -7.206869e-02 #> Ackr1    -0.0370746086 -0.0755354129 -0.0157640192  0.1054937156 -6.277259e-03 #> Lpar2     0.0096101481 -0.0183460648  0.0146876147 -0.0096323289 -1.428391e-02 #> Myh11     0.0002481764 -0.0253004153 -0.0093169064  0.0047274734 -1.017785e-02 #> Musk     -0.0062468259 -0.0002631417  0.0015877339 -0.0097866189 -3.799166e-04 #> Cnr1     -0.0381544081  0.0136333966  0.0235657726  0.0089730684  8.090727e-03 #> C3ar1     0.0938388877 -0.0167860039  0.0829960890  0.0252519568 -9.482789e-04 #> S1pr4     0.0084920039 -0.0293263522 -0.0121548940  0.0406779781 -5.382158e-04 #> C5ar1     0.0407262608 -0.0242408168  0.0197387038  0.0060726039  2.093155e-04 #> Fpr1      0.0102649869 -0.0089007948  0.0016960977 -0.0065596254 -6.134903e-03 #> Sctr      0.0120875632  0.0147438127 -0.0194051222 -0.0085722504  2.082209e-02 #> Gpr158   -0.0719496806  0.0266717042  0.0513712092  0.0216498668  2.935536e-03 #> Cxcr4     0.0211939611  0.0230622688 -0.0245363058 -0.0109080198  9.472430e-03 #> Hrh2     -0.0157438030  0.0061802567  0.0113053430  0.0029460645 -1.708804e-03 #> Slc17a6   0.0075493320  0.0126347130 -0.0160556510 -0.0084332711  1.170607e-02 #> Ppp1r3g   0.0149426987  0.0057072636 -0.0289783198  0.0056083236  2.498537e-02 #> Pln       0.0014566290 -0.0267677730 -0.0169765597  0.0225011657  1.028331e-03 #> Grin2b   -0.1116344588  0.0446090148  0.0803789620  0.0382154030  3.556127e-03 #> Taar7e   -0.0084726099  0.0011463210  0.0061755177 -0.0003439554 -1.293362e-03 #> Ptger2   -0.0141897939  0.0058535637  0.0102115853  0.0044346091  2.976632e-03 #> Mc4r     -0.0127097543  0.0043602053  0.0225416940  0.0110976884  3.705846e-03 #> Ghsr     -0.0154668954  0.0060562428  0.0124322219  0.0057590823  3.963661e-03 #> Nmbr     -0.0074165903  0.0065195240  0.0020395102 -0.0012619081  2.023811e-03 #>                  Dim.6         Dim.7         Dim.8         Dim.9        Dim.10 #> Mlc1      0.0182761915  0.0523347399 -0.0032111655  0.0230235230 -0.0565248194 #> Gprc5b   -0.0262843505 -0.0142032221 -0.0142765047 -0.0192770183 -0.1838368268 #> Gfap     -0.1432109312 -0.4711696419  0.1988483486 -0.0869773334  0.2599315051 #> Ednrb     0.0253695787  0.0240351780 -0.0244233651 -0.0168323839  0.0570961610 #> Sox9      0.0194617958  0.0161285816  0.0068747388  0.0009833111 -0.0370000232 #> Aqp4      0.0168151610 -0.2000194904  0.0644950601 -0.1064427544  0.1678385426 #> Gjc3     -0.2249668222  0.0187125465  0.0092513338  0.0300164662 -0.3656457906 #> Sox8     -0.1029165155  0.1565858604 -0.0842068247  0.0378807824  0.0503488863 #> Ntsr2     0.0884161928  0.0601591399 -0.0371910160 -0.0121313690 -0.0967083510 #> Smo       0.0204032629 -0.0058044858 -0.0164654277 -0.0517538708 -0.0178307007 #> C1qb     -0.0045146343  0.0134397160 -0.0040260989 -0.0055953051  0.0022908235 #> Olig1    -0.2183227094  0.2992207978 -0.1164606632  0.0861061922 -0.0153730282 #> C1qa      0.0265435115  0.0352839876 -0.0058782320 -0.0609901020  0.0776634792 #> Pth1r     0.1192601525 -0.0822562649 -0.0551762874  0.1662151256  0.0796146349 #> Gabbr2   -0.0060420466 -0.0368598736  0.0037237541 -0.0011252517  0.0028840412 #> Timp4     0.0221961075  0.0189454104 -0.0167912932  0.0384199346 -0.0328686964 #> Abcc9     0.2182095325 -0.1094258097 -0.1166292107  0.3197324458  0.1021869060 #> Csf1r    -0.0039872866  0.0069499252 -0.0041173345  0.0380562065 -0.0336859045 #> Ntrk2     0.0511733493  0.0717327091 -0.0538904965 -0.0099616986  0.0022584798 #> Adgrg1    0.0025298039  0.0678773694 -0.0206161289  0.0118832364 -0.0138546410 #> Ntrk3    -0.0182734701 -0.0303329643 -0.0569219300 -0.0239051225  0.0257590069 #> Erbb4     0.0337810072  0.1114888125  0.3676286293  0.1321977194  0.0391943206 #> Selplg   -0.0166492391 -0.0325701147  0.0124583651  0.0443160605 -0.0694815595 #> Cspg5     0.0588053237  0.2497969941 -0.0838835292  0.0292717363 -0.0184636223 #> Dlk1     -0.0370457788 -0.1189503512  0.0509739104 -0.0419006607  0.0493256471 #> Gpr37l1   0.0734524486  0.1365465240 -0.0665429465  0.0053271636 -0.0120350632 #> Fgfr3     0.0614918237  0.0683553459 -0.0434531749  0.0043267879 -0.0333005827 #> Slc25a18  0.0460450575  0.0471420472 -0.0256322576  0.0074784083 -0.0294715381 #> Igf1r    -0.0263860700 -0.0048914895  0.0237747562  0.0040855296 -0.0238764256 #> S1pr1     0.0426441384  0.0926183601 -0.0370001534  0.0361212152 -0.0885373515 #> Grm5     -0.0136265137 -0.0253368634 -0.0126006461  0.0083492739  0.0137399997 #> Axl       0.0615630618  0.0589631247 -0.0269283237 -0.1510596057  0.0873346031 #> Efemp1   -0.0977795336 -0.0093346860 -0.0148519474 -0.0732247206  0.0319738411 #> Adgrb3    0.0145943190  0.0249535626 -0.0514289160  0.0065675597 -0.0325743291 #> Fn1      -0.1096320687 -0.0409607248  0.0152232255  0.0225005722 -0.1048090707 #> Mertk     0.0538613613  0.0560714056 -0.0498987058  0.0259874221 -0.0544846829 #> Adgrl2   -0.0366391336  0.0140412802  0.0017077132  0.0088470687  0.0197063658 #> Fzd2      0.0216025019  0.0307080767  0.0038099869 -0.0627489303 -0.0376647634 #> Aldh1l1   0.0394606780 -0.0008650916 -0.0000883376 -0.0235530985 -0.0243189179 #> Adgrg6   -0.0455938014 -0.0190336401  0.0132880950 -0.0100387100  0.0025972170 #> Egfr     -0.0401506692  0.0092118002  0.0368625802  0.0997577331 -0.0045246001 #> Kit       0.1643328179  0.1499310890  0.3135276581 -0.1312016816 -0.0493314123 #> Ptgdr    -0.1020698484 -0.0355963141 -0.0090650888  0.0866547249  0.0186403635 #> Gad1      0.0848189702  0.1838049694  0.6135398399  0.2338461742  0.0557006851 #> Tyro3    -0.0738582593  0.0109487326 -0.0099308167  0.0201310895 -0.1868869758 #> Atp13a5   0.4156398041 -0.0355734050 -0.1188530829  0.1366726192 -0.0923436606 #> Ddr2      0.0040989042  0.0267001405  0.0209132411 -0.0491070756 -0.0262668026 #> Rspo3    -0.0756654554 -0.0391532961 -0.0063675757  0.0419050952 -0.0126148277 #> Arhgap29  0.1372343146  0.0027473224  0.0019229703 -0.0976372311 -0.0599879224 #> Fzd7      0.0661308956  0.0011388257  0.0005691529 -0.0592336654 -0.0302951848 #> Slc47a1  -0.3312521538 -0.0982370651 -0.0191476757  0.3045847111  0.0636210042 #> Ptger3    0.0823116370  0.0008631737 -0.0126837316 -0.0556000006 -0.0561456432 #> Bdkrb1   -0.0110628329  0.0038829796 -0.0126303100 -0.0015596184  0.0385526580 #> Traf4    -0.0808205267  0.2112513817 -0.0882192494  0.0448418656  0.1575704037 #> Cx3cr1   -0.0129814026 -0.0068088011  0.0008859339  0.0592343574 -0.0152954051 #> Anxa11    0.0021707801 -0.0237110949 -0.0335613289 -0.0294535031  0.0110179284 #> Adgrb1   -0.0219547105 -0.0172104134 -0.0214982229 -0.0009003600  0.0378630598 #> Lpar1     0.0783012522  0.0226794982  0.0067210488 -0.1607157529 -0.1337221635 #> Gpr17    -0.1526390784  0.3688384783 -0.1294798463  0.0839906271  0.3339011675 #> Cxcl12    0.0526751453  0.0134351442 -0.0094111965 -0.2086585188  0.0699296202 #> Epha4    -0.0200133275 -0.0480430223 -0.0678625229 -0.0189400851 -0.0229643168 #> Gpr182    0.1079706752  0.0638529181 -0.0076090173 -0.2943283561  0.0600448604 #> P2ry14    0.1220119244 -0.0366363062 -0.0565692745  0.0900498243 -0.0062950824 #> Hcar1     0.0576000275  0.0198625904  0.0091702233 -0.1221614800 -0.0310066152 #> Ephb1    -0.0292070142  0.0004742995 -0.0236911493  0.0113924043 -0.1542648150 #> Grm3      0.0351743531  0.0571313420 -0.0725842424  0.1151556875 -0.1887728158 #> P2ry1     0.0358421937  0.0111424937  0.0177445814 -0.1054133335  0.0425056551 #> Ptk7      0.0260353345 -0.0136236204 -0.0294950704 -0.0679230151  0.0395012941 #> Slco1a4  -0.0961948275  0.0102387245  0.0287978466  0.0077820664  0.0249941964 #> Insrr     0.1781679883  0.0548541029  0.0222958755 -0.1361325513 -0.1062319262 #> Cmklr1    0.0099328492  0.0193009821 -0.0099965038 -0.0915459348  0.0360559183 #> Fzd6      0.0049384870  0.0037551518  0.0119213403 -0.0466852506 -0.0302180426 #> S1pr5    -0.0963220515 -0.0200308654  0.0157231644  0.0152259591 -0.2850641058 #> Pdgfrb    0.2444966016 -0.0199654261 -0.1009689639  0.1049792714  0.0321909308 #> Flt1     -0.0480002049 -0.0339990747  0.0201293447  0.0775369960 -0.0335155759 #> Adgrl4   -0.0540856447 -0.0192198062  0.0214288318  0.0394870638 -0.0123241612 #> Lpar6     0.0152195164 -0.0119031659 -0.0097962263 -0.0018392043 -0.0208473398 #> Epha6     0.0008702446 -0.0431423394 -0.0342848963  0.0084888638 -0.0062207879 #> Emcn      0.0362734114 -0.0132948332 -0.0258691475  0.0708762937  0.0047825581 #> Cldn5    -0.1392357468 -0.0097382495  0.0652331858 -0.0444962737 -0.0120198376 #> P2ry12   -0.0177365118 -0.0370678484  0.0276946109  0.0997067491 -0.0721659528 #> Adgrf5   -0.0413667325 -0.0329967612  0.0198819317  0.0161114927  0.0033448417 #> P2yr13   -0.0082818847 -0.0144377919  0.0084739744  0.0408468585 -0.0348846960 #> Adgre1   -0.0011878222 -0.0045784911  0.0032807719  0.0095419015  0.0322537272 #> Cx3cl1   -0.0107519255 -0.0421281655 -0.0584679024 -0.0313878944  0.0043828950 #> Plxnb3   -0.0229208157 -0.0145414992  0.0206280347  0.0098718099 -0.0151000542 #> Flt4     -0.0407707809 -0.0005811435  0.0145972334 -0.0212555132 -0.0004953907 #> Slc17a7  -0.0242712193 -0.0979783263 -0.1285110480 -0.0386990784 -0.0099813102 #> Cd300c2  -0.0073314833 -0.0059082275 -0.0032696116 -0.0103259388 -0.0118695369 #> Tek      -0.0573345418 -0.0022282707  0.0165178813  0.0087699128  0.0262024416 #> Kdr      -0.0107854074 -0.0025793169  0.0115552863 -0.0180621328 -0.0250915484 #> Kcnj8     0.2045155436 -0.0946506905 -0.1068115750  0.3042285899  0.0935257937 #> S1pr3     0.1386004900 -0.0674970925 -0.0666056885  0.2159729786  0.0750633031 #> Tie1     -0.0548695049 -0.0166445194  0.0189586577  0.0192321890  0.0162260876 #> Pdgfra   -0.0297257338  0.2386784657 -0.0848398924 -0.0967451134  0.2110233808 #> Baiap2   -0.0115012871 -0.0583945948 -0.0714922429 -0.0309682971 -0.0044146994 #> Calcrl   -0.0071179870  0.0524515412 -0.0178244031 -0.0861124287  0.0411015504 #> Adrb2    -0.0332014648 -0.0070854688 -0.0264526840  0.0668783186  0.0975938139 #> Ccr2     -0.0132483753 -0.0013696773 -0.0088841233 -0.0388934439  0.0405884747 #> Alk       0.1114862567  0.1088347245  0.1240958399 -0.0336476065 -0.0480216416 #> Tacr3    -0.0032662136 -0.0164904025 -0.0212280263 -0.0152076821  0.0093712519 #> Erbb3    -0.0755090443 -0.0476671923  0.0253089240  0.0038305963 -0.1736720944 #> Pcdh15   -0.0986505507  0.2108748802 -0.0616036616  0.0582094530  0.0995608816 #> Grm7     -0.0117355616 -0.0472979114 -0.0517445020  0.0052776521 -0.0303220363 #> F2r       0.0025829869  0.0448033026 -0.0441688051  0.0343268188  0.0459188791 #> Bdkrb2    0.0965724175  0.0225397516 -0.0149999178 -0.0513786240  0.0381847660 #> Adgrv1   -0.0956791788 -0.0140641034 -0.0192251505  0.0832828316  0.0196034708 #> Gprc5c    0.1159648986  0.0361277804 -0.0085545908 -0.0805841731  0.0241521925 #> Tbxa2r    0.1332069647 -0.0487187735 -0.0578621117  0.1351736582  0.0983806334 #> Ackr1    -0.0402437814 -0.0218632455 -0.0083402505 -0.0896553691  0.0483979616 #> Lpar2     0.0287285454  0.0132225173  0.0077164653 -0.0818933444 -0.0038463804 #> Myh11    -0.0036734615 -0.0055023409  0.0014547530 -0.0327252066  0.0157818985 #> Musk      0.0231233802  0.0116212710 -0.0012895142 -0.0483731970  0.0115294539 #> Cnr1      0.0505729503  0.0964790514  0.3168813572  0.1196215675  0.0073378777 #> C3ar1     0.0007318926  0.0010301581 -0.0061584228 -0.0135860793  0.0483668571 #> S1pr4    -0.0180446600 -0.0102688902  0.0149532714 -0.0170945729 -0.0196138485 #> C5ar1     0.0186444390  0.0018633778 -0.0030160165 -0.0258686179 -0.0023665300 #> Fpr1      0.0157190855 -0.0105032449  0.0088762163 -0.0436370035  0.0104033105 #> Sctr      0.0105464895 -0.0154293556  0.0079620554 -0.0492531151  0.1157915984 #> Gpr158   -0.0013906665 -0.0285510908  0.0066147622 -0.0063789614  0.0156349912 #> Cxcr4     0.0079715926 -0.0270573006  0.0392406051 -0.0736354782  0.2009611041 #> Hrh2      0.0037567682  0.0042090412  0.0363706629  0.0104729169 -0.0027312019 #> Slc17a6   0.0094554493 -0.0371135225  0.0294658628 -0.0940261543  0.2309738144 #> Ppp1r3g   0.0064060794 -0.0023706537 -0.0041348103 -0.0038533715 -0.0182513720 #> Pln      -0.0079839216  0.0027920698 -0.0001577965 -0.0259833660 -0.0028082592 #> Grin2b   -0.0098278028 -0.0376438960 -0.0441121734  0.0020787405 -0.0057836993 #> Taar7e    0.0018212011 -0.0050037885 -0.0027950221 -0.0293574790  0.0418934633 #> Ptger2   -0.0004158681 -0.0088473544 -0.0103205013 -0.0023845578 -0.0041437677 #> Mc4r     -0.0049557329 -0.0168116324 -0.0257267649 -0.0072906204  0.0015155054 #> Ghsr     -0.0014022151 -0.0115142582 -0.0161237546 -0.0047397372 -0.0017167726 #> Nmbr      0.0155946934  0.0311940862  0.0926225820  0.0275221170  0.0021430226 #>                Dim.11        Dim.12       Dim.13        Dim.14        Dim.15 #> Mlc1     -0.020038499  4.368805e-02  0.017658374  0.0237889875 -0.0014887323 #> Gprc5b   -0.068977469  4.674161e-02 -0.002836844  0.0284616446  0.0248883319 #> Gfap      0.048051535 -2.123727e-01 -0.044360958  0.0176188656 -0.0349386185 #> Ednrb    -0.015601154 -1.024983e-01 -0.015521455 -0.0016168062 -0.0242628718 #> Sox9     -0.022351154 -1.628976e-02  0.022344373  0.0160212396 -0.0068392065 #> Aqp4      0.059265354 -8.562509e-02  0.009188955  0.0018077803 -0.0133083070 #> Gjc3     -0.114414832  1.943950e-01  0.014800378  0.0434896008  0.0195239198 #> Sox8      0.053299106 -4.882687e-02  0.011487680 -0.0189883241 -0.0213036740 #> Ntsr2    -0.001226814 -7.304461e-02 -0.046950518  0.0078976770  0.0190433563 #> Smo       0.054121946 -3.341464e-02 -0.007959094  0.0061000344  0.0509233702 #> C1qb     -0.101234587 -2.376866e-02  0.037292350 -0.0698355400  0.0100176748 #> Olig1     0.019274275  2.066780e-02  0.046628180 -0.0067943529 -0.0130086862 #> C1qa     -0.327690347 -8.079755e-02  0.187035639 -0.0143639919 -0.0764908759 #> Pth1r    -0.033888270  2.302678e-02 -0.067313192  0.0058266081 -0.0035007286 #> Gabbr2    0.002082942 -1.281311e-02  0.004470428  0.0213185548 -0.0088500700 #> Timp4    -0.011867477  3.201045e-02  0.013056866 -0.0017636056  0.0318700042 #> Abcc9    -0.055676500  7.322120e-02 -0.048006826 -0.0971730542 -0.0148455220 #> Csf1r     0.090485252  1.870855e-02 -0.039799256  0.1299624621  0.1228744218 #> Ntrk2    -0.002305177  8.433210e-02  0.077825345 -0.0130551067 -0.0231232906 #> Adgrg1    0.037618933 -8.115803e-03 -0.004499510  0.0239912380 -0.0160994961 #> Ntrk3     0.001613438 -5.524433e-02 -0.026061707  0.0141709575  0.0365869334 #> Erbb4    -0.031161339  3.359559e-03 -0.041391658 -0.0245055347  0.0150867771 #> Selplg    0.360991432  1.350267e-01 -0.225287845 -0.1795895858 -0.2757356520 #> Cspg5     0.008299183  3.079263e-02  0.011680749 -0.0200124690 -0.0131399212 #> Dlk1      0.059565965  6.223031e-03  0.001409311  0.0231149143  0.0268276298 #> Gpr37l1   0.024192425  9.223149e-03  0.015303567 -0.0185641211 -0.0086416711 #> Fgfr3    -0.003980442 -5.142991e-03 -0.021400008  0.0046432699  0.0009511007 #> Slc25a18 -0.035707907  1.989756e-02  0.010314425 -0.0021704947 -0.0054221087 #> Igf1r     0.032290062  6.592975e-02  0.030046617  0.0029889587  0.0690760677 #> S1pr1    -0.025646773  8.776936e-03 -0.016551446 -0.0107987934 -0.0082841000 #> Grm5      0.001272481 -2.842221e-02 -0.019232234  0.0199228111 -0.0132919475 #> Axl      -0.224627641  4.057458e-02 -0.140459983 -0.0431340380 -0.0972244586 #> Efemp1   -0.063983319  1.050285e-01 -0.214728944 -0.0561439709  0.0317470021 #> Adgrb3   -0.007785840 -1.453906e-02 -0.015905161  0.0054159650 -0.0058714403 #> Fn1       0.138224315 -1.450282e-01  0.131583990 -0.3005558461  0.1004061129 #> Mertk     0.057607747  1.264080e-02 -0.011221515  0.0791285694  0.0045157935 #> Adgrl2    0.005448365 -4.522455e-02  0.016707469  0.1167408842  0.0349196891 #> Fzd2      0.021456793 -4.520484e-03 -0.031130641  0.0229075191  0.0411838705 #> Aldh1l1  -0.023774029 -3.310673e-02 -0.008989503 -0.0305344894  0.0121229100 #> Adgrg6   -0.002028408  1.417053e-02 -0.068536134 -0.0802461509 -0.0976092037 #> Egfr     -0.032643563  4.620965e-03  0.012019488  0.0680026874 -0.0385026926 #> Kit       0.062544512 -2.977408e-05  0.041694999  0.1179445218 -0.0477153865 #> Ptgdr    -0.018796432  3.768817e-02 -0.028867877 -0.0162704191 -0.0358041253 #> Gad1     -0.081662277  2.961620e-02 -0.074720040 -0.0425537856  0.0122241666 #> Tyro3    -0.060221733  9.530014e-02  0.017485340  0.0082586590  0.0116224161 #> Atp13a5   0.112565194 -7.938054e-02  0.189537016 -0.0156263922 -0.0443578053 #> Ddr2      0.030475355 -8.566765e-02  0.064196123 -0.0702987777  0.0288278930 #> Rspo3     0.013146570 -2.064306e-02  0.020612609 -0.0389510848 -0.0097748976 #> Arhgap29  0.086391089 -8.757781e-02  0.054522767  0.0140487132 -0.0008055760 #> Fzd7      0.067595298 -1.422837e-02 -0.013572216 -0.0669776365 -0.0656715065 #> Slc47a1  -0.050996249  5.620700e-02  0.012737699  0.1145287300 -0.0825635458 #> Ptger3    0.060555965 -6.480637e-02  0.091237575  0.0322293786 -0.0394575438 #> Bdkrb1   -0.023814487  9.738136e-03 -0.063245451  0.0795604817 -0.0031514369 #> Traf4     0.083523840 -6.639744e-02  0.003518718  0.0001757780 -0.0212051429 #> Cx3cr1    0.053597388 -2.543381e-02  0.040688981  0.0683239127  0.0999276030 #> Anxa11   -0.003010427  2.152018e-02 -0.071228730  0.0077393588 -0.0219749559 #> Adgrb1    0.015425028 -4.084913e-02 -0.003809899  0.0194410205 -0.0032592180 #> Lpar1     0.014754245 -2.576004e-02  0.061073459 -0.0013049857  0.0621189330 #> Gpr17     0.138087162 -1.506092e-01  0.033908953 -0.0329730922 -0.0349453212 #> Cxcl12    0.010472411  1.618876e-01 -0.039533546  0.0813602459  0.0562750941 #> Epha4     0.010078760 -3.572675e-02  0.006354623  0.0003399448  0.0215361453 #> Gpr182   -0.109821109  9.717282e-02 -0.342385852  0.0263718387  0.0780167142 #> P2ry14    0.025744756 -3.130308e-02  0.064018359 -0.0698339489  0.0004043104 #> Hcar1     0.023663773 -1.996512e-02 -0.020023651  0.0115497981 -0.0252107528 #> Ephb1    -0.041200461  8.964523e-02  0.006980214  0.0055263742  0.0093595685 #> Grm3     -0.081837046  1.407191e-01 -0.039754260 -0.0130252228  0.0270471365 #> P2ry1     0.019465520  1.159565e-01 -0.035449554  0.0327524591  0.0232735723 #> Ptk7     -0.054204872  4.565399e-02 -0.093852867  0.0296128220  0.0292700301 #> Slco1a4   0.026249502 -3.491470e-02  0.042919890  0.0730236054 -0.1022275730 #> Insrr     0.095621861 -1.533824e-01  0.204867785  0.1376381615 -0.0902709094 #> Cmklr1   -0.139354247  2.837330e-02 -0.097973780 -0.1828790083  0.1532248356 #> Fzd6      0.019700882 -3.153353e-02  0.060359651  0.0336855298 -0.0473389691 #> S1pr5    -0.099641429  1.650677e-01  0.012417042  0.0160684983  0.0138651449 #> Pdgfrb   -0.038634441  4.812030e-02 -0.085069028  0.0498834091  0.0042292514 #> Flt1      0.032912792 -2.501097e-02  0.104390299  0.0463256622 -0.0241453908 #> Adgrl4    0.006514742 -1.111846e-02  0.037774748  0.1104409943 -0.0438263950 #> Lpar6     0.027827744 -2.145519e-02  0.035808458 -0.0112963829  0.0082153393 #> Epha6    -0.003052361 -3.446541e-02  0.010886529  0.0035294614 -0.0218302935 #> Emcn     -0.016019154  1.716235e-02  0.012921194  0.0353054068  0.0213335308 #> Cldn5    -0.021538240 -2.382138e-02 -0.013384328  0.0471020173  0.0442081829 #> P2ry12    0.386611849  3.758621e-02 -0.150877086  0.1362033992  0.2274988614 #> Adgrf5   -0.028749322 -1.470955e-04  0.021316722  0.0678092908 -0.0358465017 #> P2yr13    0.207066615  2.565520e-02 -0.089833735  0.0422417903  0.0750839493 #> Adgre1   -0.095656927 -1.756532e-02  0.107954947 -0.0227176085 -0.0383590848 #> Cx3cl1    0.021479037 -4.089392e-02  0.013394243  0.0319552624 -0.0267426785 #> Plxnb3    0.065918965 -9.441912e-03 -0.048090419  0.0222511744  0.0355124826 #> Flt4      0.001237470 -2.865386e-03 -0.026920011  0.0194351234 -0.0670762547 #> Slc17a7   0.009820295 -5.657356e-02  0.022882705  0.0289331122 -0.0288857867 #> Cd300c2  -0.124936281  9.072016e-03  0.043270492 -0.1179520783 -0.1136348081 #> Tek      -0.026549529 -6.871399e-03 -0.033318674 -0.0250430705  0.0945011680 #> Kdr       0.052464221 -1.417103e-02  0.073185734 -0.0580878424 -0.0499141067 #> Kcnj8    -0.065786997  9.127713e-02 -0.084275580 -0.0697282946 -0.0022770086 #> S1pr3    -0.051759416  5.563742e-02 -0.059414484 -0.0998813301  0.1009654089 #> Tie1     -0.002356740 -3.315768e-02  0.038728151 -0.0028230776  0.0074174825 #> Pdgfra    0.010513231 -5.051568e-03 -0.138495694  0.0242937847  0.0676010310 #> Baiap2    0.007200391 -2.414732e-02  0.034097473  0.0250554738 -0.0192283730 #> Calcrl   -0.060814149  5.472863e-02 -0.132005341 -0.0018959508 -0.0293391108 #> Adrb2    -0.123244758  2.106492e-02  0.020081861  0.4879664947 -0.0445119354 #> Ccr2     -0.283568784 -1.601459e-02  0.085028130 -0.1841681385 -0.1812689180 #> Alk       0.076684898 -1.207731e-01  0.148315607  0.0466881448 -0.0547710748 #> Tacr3     0.049412737  4.400015e-02  0.009896008  0.0921289200  0.0396572347 #> Erbb3    -0.044241686  9.601851e-02 -0.002442638  0.0032250763 -0.0051474845 #> Pcdh15    0.053854483 -3.008760e-02  0.023461279 -0.0073391578 -0.0196114268 #> Grm7     -0.007287395 -1.344405e-02  0.005035987  0.0023805202 -0.0154317516 #> F2r       0.001451940 -2.096208e-02 -0.010549611 -0.0738825588  0.0958259817 #> Bdkrb2   -0.029166120  9.077230e-02 -0.120356979  0.2531860520 -0.0304536349 #> Adgrv1   -0.009712447  5.085587e-02  0.023711517 -0.0108005355 -0.0247119858 #> Gprc5c   -0.035661611 -3.970576e-03 -0.039994591 -0.0012071195  0.0548320266 #> Tbxa2r   -0.097691236  1.003580e-01 -0.139867799  0.1638783163 -0.0169647743 #> Ackr1    -0.046878595  7.685558e-02 -0.109219154 -0.0541586716 -0.0375944823 #> Lpar2     0.099609394  1.351002e-01 -0.157220735 -0.0437225369 -0.2436105833 #> Myh11    -0.009800230 -2.402366e-02 -0.046643726 -0.2708892012  0.3534617551 #> Musk      0.023765552  6.188543e-02 -0.020671571  0.0881352148  0.0108528417 #> Cnr1     -0.044705047  2.661707e-02 -0.032900404 -0.0432178116  0.0170531212 #> C3ar1    -0.217256238 -6.165339e-02  0.148903746  0.0115011540 -0.0015004071 #> S1pr4     0.122986307  8.022143e-02 -0.082475141 -0.1293823329 -0.3283005053 #> C5ar1    -0.023902383  1.758769e-02  0.043925717 -0.1656464882 -0.3114631520 #> Fpr1      0.124247047  1.377279e-01 -0.062998951 -0.1326442696 -0.2698508684 #> Sctr      0.058895464  2.507629e-01  0.187262382 -0.0276457442  0.0464031290 #> Gpr158    0.010388267  2.916726e-02  0.027324178  0.0135457379 -0.0009297620 #> Cxcr4     0.078613675  3.731709e-01  0.294305974 -0.0264462299  0.0683632093 #> Hrh2     -0.007431172 -2.976020e-03 -0.003014343  0.0056026710  0.0005081364 #> Slc17a6   0.108970045  4.884665e-01  0.363774343 -0.0446393170  0.0800956523 #> Ppp1r3g  -0.009724545 -1.351029e-02 -0.004009719  0.0350344285  0.0006084764 #> Pln      -0.018882124 -2.320328e-02 -0.027951321 -0.2258460285  0.3369657983 #> Grin2b    0.002923810 -2.836359e-02  0.008477210  0.0141848516 -0.0053046041 #> Taar7e    0.032187101  1.041645e-01  0.051049250  0.0559371230  0.0346327649 #> Ptger2   -0.002746009 -7.342839e-03  0.003745769  0.0042079710  0.0007848482 #> Mc4r     -0.012113758 -1.633702e-02  0.029642096  0.0401400378  0.0136978701 #> Ghsr      0.005407458 -1.780903e-02 -0.003365696  0.0051626510 -0.0045798759 #> Nmbr     -0.006712408 -4.749770e-03 -0.006284959  0.0077549790 -0.0082885593 #>                 Dim.16        Dim.17        Dim.18        Dim.19        Dim.20 #> Mlc1     -0.0085195737  0.0454076670  0.1141469728  0.1513094573 -0.0766586895 #> Gprc5b   -0.0500574777 -0.0298408946 -0.0207443142 -0.0103294732  0.0051805356 #> Gfap      0.0216685881 -0.0083902605  0.1127647026  0.0847494263 -0.1004269992 #> Ednrb    -0.0104222666 -0.0317058324 -0.0683060104 -0.0132046955 -0.0030006882 #> Sox9      0.0210271532 -0.0028138266  0.1016544006  0.1087184388 -0.0800062370 #> Aqp4     -0.0170123248  0.0008515506 -0.0907580762 -0.1102144520  0.0660046002 #> Gjc3     -0.0122032831  0.0037671917 -0.0596671988 -0.0384069600  0.0132272069 #> Sox8     -0.0066824876  0.0004354844 -0.0098163567 -0.0109910258  0.0209243325 #> Ntsr2    -0.0112551622 -0.0153751094 -0.1713090778 -0.1075917045  0.1482549542 #> Smo       0.0306897168  0.0219460791  0.0233310357 -0.0136375939  0.0884135721 #> C1qb     -0.0409410741 -0.0511507092  0.0487433495 -0.0211217942  0.0098252555 #> Olig1    -0.0119025347 -0.0019798549 -0.0099140478  0.0033068686  0.0017079799 #> C1qa     -0.0209453769 -0.0218387278 -0.0107061349  0.0245603448 -0.0424701592 #> Pth1r    -0.0347251586 -0.0085555092 -0.0610277157  0.0208458915 -0.0262114002 #> Gabbr2   -0.0154657559  0.0071990985  0.0104283824 -0.0101539791 -0.0209078076 #> Timp4     0.0324223011 -0.0283840251  0.0942773611  0.0487786526 -0.0750493254 #> Abcc9    -0.0389316092 -0.0625035564  0.0385656652  0.0335835478 -0.0523465666 #> Csf1r    -0.0248393156  0.0476564696 -0.0203139565  0.0009389249 -0.0019761272 #> Ntrk2    -0.0159508375  0.0113695354  0.0865325152  0.0968588564 -0.0755840856 #> Adgrg1   -0.0307271364 -0.0147501566 -0.0001438173  0.0147913832 -0.0750199213 #> Ntrk3     0.0384152848  0.0360930244 -0.0191884919 -0.0445150077 -0.0183318294 #> Erbb4    -0.0333265208 -0.0106397540 -0.0338524500 -0.0190270225  0.1184402252 #> Selplg    0.1489658753  0.0036772270  0.0463846756 -0.0732508326  0.0116206437 #> Cspg5    -0.0071345916  0.0596091816  0.1057696857  0.0874017671 -0.0322829174 #> Dlk1     -0.0064684238  0.0330054653 -0.0452406001 -0.0958555918  0.1600062159 #> Gpr37l1  -0.0048062606 -0.0242112009  0.0231265309 -0.0142099244 -0.0106654361 #> Fgfr3    -0.0315245960 -0.0002881528 -0.1252693313 -0.0772715734  0.0847207016 #> Slc25a18 -0.0087766563 -0.0122841616  0.0686878388  0.1072909913 -0.0958635702 #> Igf1r     0.0670524753  0.0349615396  0.1066345624  0.0793229270 -0.0239854144 #> S1pr1     0.0087940692 -0.0021814639 -0.0241949414  0.0217024555 -0.0867462026 #> Grm5      0.0058530966 -0.0588878975 -0.0260135281  0.0112729399  0.0045433718 #> Axl       0.0144491795 -0.0533305361  0.1180891246 -0.0866044244  0.0060023412 #> Efemp1   -0.1698305577 -0.0640437451  0.1243797084  0.0533954899  0.0463348934 #> Adgrb3   -0.0006359178  0.0336053743  0.0031116729 -0.0125861508  0.0634926068 #> Fn1      -0.0765182478  0.0321032722 -0.1279909228  0.2748594327  0.1051273413 #> Mertk     0.0612397009  0.0869306803 -0.0775929957 -0.0607464315  0.1358840897 #> Adgrl2    0.0648811954  0.0754398659 -0.1147039779  0.0723471751 -0.1100928177 #> Fzd2      0.0535511337 -0.0646638993 -0.0060897911  0.0581720171 -0.0296291388 #> Aldh1l1  -0.0103812490 -0.0096530135  0.0042989221 -0.0053076862  0.0380473153 #> Adgrg6   -0.1681465359  0.0804366158 -0.3559356963  0.1330779361 -0.1290750023 #> Egfr      0.0464905737 -0.0305696569 -0.0154221700 -0.1066828423 -0.0808547713 #> Kit       0.0624612115 -0.0486648677  0.0096271870  0.0102961991 -0.3893420909 #> Ptgdr    -0.0369411258 -0.0209260964  0.0177430452 -0.0347500635 -0.0504868547 #> Gad1     -0.0413188454  0.0368202075  0.0369085803  0.0404838547  0.1797804460 #> Tyro3    -0.0128712224  0.0178923762 -0.0158121756 -0.0089876886 -0.0381978325 #> Atp13a5  -0.0794982137 -0.0900595277  0.0579663552 -0.3027185909  0.0691629020 #> Ddr2     -0.0192656947  0.0322949084 -0.0301332691  0.1766780402  0.0829158321 #> Rspo3    -0.0646678479 -0.0416882439 -0.0073931027  0.0109789258  0.0182446502 #> Arhgap29 -0.0217738556  0.0966237051 -0.0282157908  0.1917526928  0.0515756960 #> Fzd7     -0.0060437078  0.0428452705  0.0023495968  0.0354589147  0.0796198080 #> Slc47a1   0.0390428076 -0.0591409839  0.0819137807 -0.2825177989 -0.1198303360 #> Ptger3    0.0081953097  0.0740305784  0.0113457560 -0.0730162432  0.1859162379 #> Bdkrb1   -0.0035743200 -0.0133019427  0.0088635229 -0.0895456974 -0.0239729396 #> Traf4     0.0153475651 -0.0538373869 -0.0102294346  0.0182948930 -0.0006881794 #> Cx3cr1   -0.1152625193 -0.0196091336 -0.0274092428  0.1009393315 -0.0656781984 #> Anxa11    0.0306192051  0.0870956520  0.0036225158  0.0812796929  0.0263027989 #> Adgrb1   -0.0030309554  0.0031840676 -0.0374522760 -0.0153275825  0.0119889861 #> Lpar1     0.0476278263  0.0435928617  0.0020280490  0.0746232367  0.1298102224 #> Gpr17     0.0025401731  0.0005662896 -0.0009479047  0.0123481736  0.0224614597 #> Cxcl12    0.0259587751 -0.0803145670  0.2205790155 -0.0035209260  0.0561066541 #> Epha4     0.0184253750  0.0499462286  0.0336221642 -0.0186218203 -0.0147029244 #> Gpr182   -0.2534755411  0.0179822335  0.0373355099 -0.0495708868  0.0298790012 #> P2ry14   -0.0310073220  0.0288208597 -0.0417865789  0.0630527757  0.1301326691 #> Hcar1    -0.0470973355  0.0150505934  0.0450643238 -0.0254178679  0.0516577090 #> Ephb1     0.0127975795  0.0281064229  0.0253179143  0.0118765408 -0.0003328962 #> Grm3      0.0022015552  0.0155877839 -0.0300991692  0.0250237786  0.0006109857 #> P2ry1     0.0390721615 -0.0938427445  0.0562992587 -0.1027277123 -0.1332649744 #> Ptk7     -0.0409135357  0.0276891219  0.0199729404  0.1202901991  0.0149972077 #> Slco1a4  -0.0094815222 -0.0289233363 -0.1179435583 -0.0949682511 -0.1655249618 #> Insrr     0.0597817209  0.0218277702 -0.0786127688 -0.1992064243 -0.1614080209 #> Cmklr1    0.1632097386  0.0013436902  0.0207133275 -0.1653705027  0.0446512577 #> Fzd6      0.0265825012 -0.0466494382  0.1776002862 -0.0321665848  0.1161788872 #> S1pr5     0.0105981644  0.0057982787 -0.0104436839 -0.0055524275  0.0047167544 #> Pdgfrb   -0.0462453982  0.0160977721 -0.0875000320 -0.0833225399 -0.0444915005 #> Flt1      0.0976784033 -0.0651955465  0.2884047257  0.0587774703  0.1567360944 #> Adgrl4   -0.0719041934  0.0320504003 -0.0174235225  0.1958715886 -0.2212886929 #> Lpar6     0.0369442430  0.0307401746 -0.0111028141 -0.0539153396  0.1667735958 #> Epha6    -0.0328633984  0.0311962798  0.0146187070 -0.0304263515 -0.0399829420 #> Emcn      0.0112364215 -0.0608089652  0.1615072665 -0.0737648102 -0.0399875691 #> Cldn5     0.0204149877 -0.0300858866  0.0162360296 -0.2158661076  0.1110039257 #> P2ry12   -0.1206395661  0.0276429798  0.0376810063 -0.0170559281 -0.0297718489 #> Adgrf5   -0.0179361477 -0.0073426246  0.0599171739  0.0743399481  0.0156419340 #> P2yr13   -0.0498691742 -0.0053933251  0.0438090301 -0.0175744212 -0.0301115745 #> Adgre1   -0.0332917794  0.0027781318 -0.0273154560  0.0623990231 -0.0154906832 #> Cx3cl1   -0.0236891008 -0.0262808304  0.0387385874 -0.0014288352 -0.0200261274 #> Plxnb3    0.0162310820 -0.0063965561 -0.0740935139 -0.0770408568  0.1636894913 #> Flt4     -0.0689538869  0.0311083982 -0.1938909684 -0.0555589375 -0.0894329071 #> Slc17a7  -0.0289146155  0.0425722458  0.0701126970  0.0232735648 -0.0463168975 #> Cd300c2   0.0653548268 -0.0371744124  0.0205018905 -0.0473471820  0.0431594013 #> Tek       0.0428807066  0.0024981139 -0.0606809148 -0.1052841202 -0.0446033273 #> Kdr       0.0369765551  0.0102038582  0.0713548718  0.1320978867  0.1259427385 #> Kcnj8    -0.0791242779 -0.0248090798 -0.0486500116  0.0439075929 -0.0420799390 #> S1pr3     0.0856575460 -0.0040410964  0.0185821025  0.0508504153 -0.0878121111 #> Tie1      0.0573452707  0.0503492062 -0.1206172574  0.0162465182 -0.0191447684 #> Pdgfra   -0.0280317502  0.0103961741  0.0600223309 -0.0192693379  0.0591812252 #> Baiap2   -0.0210210933 -0.0056419399  0.0184234513  0.0248601112  0.0017755543 #> Calcrl   -0.0825650995 -0.0144141564 -0.0286974805 -0.0241529166 -0.0201910941 #> Adrb2     0.3360382142  0.2811331130 -0.1525094350  0.0074651216  0.2421735712 #> Ccr2      0.0584271039 -0.0631775439  0.0210749182 -0.0907168211  0.0473333600 #> Alk      -0.0043677754 -0.0080033500 -0.0526441239 -0.1444832842 -0.1703122653 #> Tacr3     0.1156308656 -0.5966789297 -0.2220151403  0.1309515316  0.1393855384 #> Erbb3     0.0123460118  0.0045883768  0.0145706220 -0.0080291113 -0.0093357840 #> Pcdh15   -0.0091755464 -0.0015889595 -0.0061804856 -0.0125474929  0.0124053132 #> Grm7     -0.0096265761  0.0150826953 -0.0066848793 -0.0249972776 -0.0299233315 #> F2r       0.0719919275 -0.0046989509  0.0245342557 -0.0381912211 -0.0784106718 #> Bdkrb2    0.2010754130  0.0474197417 -0.0581638144  0.1524579982 -0.0697287089 #> Adgrv1   -0.0160691881  0.0132584677  0.0307908039 -0.0093861950 -0.0214274700 #> Gprc5c    0.0740692169  0.0287902200 -0.0017672519  0.0517832804 -0.1127999995 #> Tbxa2r    0.1305016941  0.1503861452 -0.0737853764  0.1974737247  0.0954673505 #> Ackr1    -0.2657185417  0.0858147840 -0.3763377642 -0.1389111711  0.0075835804 #> Lpar2     0.1990541333 -0.0250342554  0.0278117992  0.0038384971 -0.0739159649 #> Myh11     0.3649418131  0.0889725133 -0.1321931539 -0.0430186219 -0.1498945525 #> Musk      0.1214191217 -0.4011116559 -0.1282297031  0.0941054269  0.0118160945 #> Cnr1     -0.0047298496 -0.0408812466 -0.0349508124 -0.0361086685  0.0486008767 #> C3ar1    -0.0117289562  0.0058619154 -0.0525103081  0.1120648053 -0.0385012289 #> S1pr4     0.1511210992  0.0484036098 -0.0919908814  0.0087802323 -0.0217401247 #> C5ar1     0.1443211662  0.0300653021 -0.0607538893  0.0750615740  0.0418080878 #> Fpr1      0.1421456315  0.0744722958 -0.0184353173  0.0521160088  0.0255547151 #> Sctr     -0.0330887728  0.0666106592 -0.0063804028 -0.0209689294  0.0298516721 #> Gpr158   -0.0023256167 -0.0625109056 -0.0336775163  0.0016981989  0.0051665279 #> Cxcr4    -0.0575271503  0.0787331352 -0.0303409285 -0.0114721046  0.0176789925 #> Hrh2      0.0005356513 -0.0148151194 -0.0057769739 -0.0029742509 -0.0092350390 #> Slc17a6  -0.0637812076  0.0811486979 -0.0520220567 -0.0420846588 -0.0016604208 #> Ppp1r3g   0.0174926413 -0.0332248554  0.0471978865  0.0042481764 -0.0125994109 #> Pln       0.3576715486  0.0543837430 -0.0668504524 -0.0935214247 -0.0945407711 #> Grin2b   -0.0037063454 -0.0072530994  0.0167725707  0.0079731903 -0.0081018447 #> Taar7e    0.0737504560 -0.3898461040 -0.1448294465  0.0772201013  0.0581309367 #> Ptger2   -0.0021096567 -0.0010385808 -0.0005894454  0.0127397014 -0.0048440244 #> Mc4r      0.0076238585 -0.1138043516 -0.0467649405  0.0685592598  0.0376308817 #> Ghsr     -0.0106874954  0.0422288348 -0.0115748420 -0.0062335690  0.0068787700 #> Nmbr      0.0034666140  0.0063363502  0.0274438556  0.0325759907 -0.0578854141 #>                 Dim.21        Dim.22        Dim.23        Dim.24       Dim.25 #> Mlc1      0.1915296127 -0.0775793281  1.188980e-01 -0.1047555231  0.039556093 #> Gprc5b   -0.0549817793  0.1054921539  7.393436e-02  0.0955792131 -0.013942117 #> Gfap      0.1922578511 -0.0645327114 -2.621349e-02 -0.0186868143  0.009780146 #> Ednrb    -0.0857139129  0.0753131208  6.767365e-02  0.1590247489 -0.027178242 #> Sox9      0.1795569333 -0.0475052367  4.654244e-02  0.0929118497  0.120863030 #> Aqp4     -0.1309970473  0.0693509209 -2.816152e-02 -0.0218622199 -0.068119575 #> Gjc3     -0.0646711374  0.0237506169  1.489202e-02  0.0248995659 -0.032100665 #> Sox8     -0.0693108081  0.0380768110  1.209124e-02  0.0080231226  0.004328523 #> Ntsr2    -0.3150781218  0.1608868117  2.892064e-02  0.0202361416 -0.074566497 #> Smo       0.0008163573  0.0220998235 -6.797454e-02 -0.0275337637 -0.006732909 #> C1qb     -0.0378975712  0.0022957083 -4.423654e-02 -0.0714302646 -0.035476834 #> Olig1    -0.0067851126  0.0669816723  3.649786e-02  0.0696325488 -0.032918211 #> C1qa     -0.0451707731  0.0255322639  7.364687e-03  0.1398990887  0.142937254 #> Pth1r    -0.1351896289 -0.0296428715 -4.989838e-03 -0.0501482100 -0.032546374 #> Gabbr2   -0.0269917135  0.0391783687 -3.499100e-03 -0.0081500785  0.002617412 #> Timp4    -0.0070541938 -0.0156677502  1.124549e-01  0.0377080530  0.042622457 #> Abcc9    -0.0196602900 -0.0014578050 -8.203687e-02  0.0599900089 -0.057177330 #> Csf1r     0.0310847863  0.0028615381 -5.470127e-03 -0.0234037359 -0.024221078 #> Ntrk2     0.1637291832 -0.0524484108 -3.886686e-02  0.0269026249  0.036738491 #> Adgrg1   -0.0071002039  0.0661790729  5.533680e-02 -0.0285386371  0.064969723 #> Ntrk3    -0.0894624038 -0.0293185716  6.636749e-02  0.0478123480  0.028125640 #> Erbb4    -0.0438301823  0.0505355260  6.982946e-02 -0.0051399622  0.011977923 #> Selplg   -0.0237587787 -0.1423122359  5.340832e-03  0.0240740011  0.053734175 #> Cspg5     0.2482102708 -0.1022354809 -1.241259e-01 -0.0929838030 -0.039540781 #> Dlk1     -0.1502080544 -0.0853319880 -8.517056e-02 -0.2127173934  0.041595810 #> Gpr37l1   0.0135719057  0.0291321546 -3.525957e-02  0.0001086977 -0.013996373 #> Fgfr3    -0.1721850307  0.0678645918 -1.516023e-02  0.0394986280 -0.059449655 #> Slc25a18  0.1097588989  0.0139540116  4.739821e-02  0.1313221098  0.071763583 #> Igf1r    -0.1319286762 -0.0155879648  1.086816e-01 -0.0845456483  0.049837506 #> S1pr1     0.0775983241 -0.0212825731 -1.812987e-02 -0.0295971476 -0.072389663 #> Grm5     -0.0578682216  0.0065440157  4.607397e-02 -0.0570421491  0.050593352 #> Axl      -0.0421322918 -0.2090089904 -1.189651e-02 -0.2001379200  0.101831406 #> Efemp1   -0.0308067445  0.0907488932 -2.116584e-03 -0.0754105592  0.021921933 #> Adgrb3   -0.0361829194 -0.0403740166 -2.195078e-02 -0.1325377403  0.076290144 #> Fn1      -0.0130333973  0.0418717859 -1.778008e-01 -0.0778997286  0.182133989 #> Mertk    -0.0065795361 -0.1505777324 -7.066423e-02 -0.2346000054  0.059578124 #> Adgrl2   -0.2394445015 -0.3259797433  6.379235e-02 -0.0258658395 -0.034654336 #> Fzd2     -0.0599796230 -0.0275748427 -2.405904e-02  0.0472897658  0.023335048 #> Aldh1l1   0.0292838084  0.0370187498  2.924074e-02  0.0246408159  0.019462586 #> Adgrg6    0.0655004840 -0.0256342471  2.808014e-02 -0.0639609223  0.006761307 #> Egfr     -0.0245010706 -0.0394974471  1.304427e-02  0.0507365135 -0.052561221 #> Kit      -0.1302903743  0.0561945445 -3.042602e-01 -0.1074716049 -0.116328470 #> Ptgdr     0.0475336332  0.0729000814  1.396272e-02 -0.0096917636 -0.017308596 #> Gad1      0.0351630056  0.0631986508  1.529795e-01 -0.0705984997  0.083019020 #> Tyro3    -0.0082839583  0.0191431291  4.284894e-03  0.0744030060 -0.019025913 #> Atp13a5   0.1680743403  0.1364207264  8.035783e-02 -0.0519511047  0.096049593 #> Ddr2     -0.0890726112 -0.0377890556 -5.113698e-02 -0.0178983854  0.012928557 #> Rspo3     0.0427108983  0.0620073040 -8.238892e-02 -0.0207517572 -0.005663147 #> Arhgap29 -0.0759247189 -0.1634788782  1.487002e-01  0.0215307366 -0.077727202 #> Fzd7     -0.0049434314  0.0478681321  3.197551e-02  0.0300620233  0.040444167 #> Slc47a1   0.0278350596 -0.0189630903  1.203786e-01  0.0805415257 -0.100325586 #> Ptger3    0.1821198247  0.0940800936  3.031294e-01 -0.0568593610 -0.171691783 #> Bdkrb1   -0.1705963809 -0.1837312611  1.690605e-01  0.1422144193 -0.029735535 #> Traf4    -0.0652595237 -0.1566988300  7.713567e-03  0.0098088611  0.003184511 #> Cx3cr1   -0.0523244863  0.1614972308  3.348895e-02  0.1108636180 -0.038719249 #> Anxa11    0.0235100249  0.1610749464  7.062493e-02 -0.1370160976 -0.152779570 #> Adgrb1   -0.1035804454  0.0239864016  2.194852e-02 -0.0111045282  0.010375879 #> Lpar1     0.0148901669  0.0871035222  5.238635e-02  0.0210393210  0.047568830 #> Gpr17     0.0142770197  0.0502802828 -1.561353e-02 -0.0838472507  0.025720278 #> Cxcl12   -0.0447495610  0.1839532946  4.570104e-02 -0.0229134805 -0.190689409 #> Epha4     0.0029347634  0.0520147048 -1.720780e-02 -0.0361172921  0.006550585 #> Gpr182    0.0330825785 -0.1028483534  1.811424e-01  0.1358389851  0.100979884 #> P2ry14    0.0274296820  0.0409666039  6.252702e-02 -0.0204289854 -0.126415668 #> Hcar1     0.0915852497 -0.0061217078  4.702383e-02  0.0388286949  0.007418826 #> Ephb1     0.0760060150 -0.0925606793 -3.482857e-02 -0.0854802709  0.068879785 #> Grm3     -0.0294356800 -0.0161372792 -1.016288e-01 -0.0571748475 -0.019593065 #> P2ry1     0.0658796707  0.2103749965 -5.493685e-02 -0.0613315566 -0.134045773 #> Ptk7     -0.1271409629  0.0022200278  6.260802e-02  0.0514920068  0.067134756 #> Slco1a4  -0.0581462781  0.2473115570  4.038462e-02 -0.1752912882  0.326081914 #> Insrr     0.0722906354 -0.1653379254  4.408181e-02  0.0576055048  0.053452613 #> Cmklr1    0.0816103928 -0.0748592653  7.695998e-03 -0.0870568740 -0.019758231 #> Fzd6      0.0061848117  0.0564681906 -8.512828e-02  0.0921004446  0.264314420 #> S1pr5    -0.0055743413 -0.0384014178 -1.825326e-02 -0.0331679302  0.009633422 #> Pdgfrb   -0.0473592278 -0.1456486559  1.494873e-02  0.0356618717 -0.027092292 #> Flt1     -0.1026684893 -0.0714492371 -1.135830e-01  0.1238304260 -0.196860521 #> Adgrl4   -0.0177759841 -0.0347506282  4.085207e-01 -0.2671020435 -0.164510243 #> Lpar6     0.1151728438  0.0633872370  9.056173e-02 -0.2518560138 -0.224137363 #> Epha6    -0.0517991009  0.0363953001 -1.383327e-02  0.0205771055 -0.014042106 #> Emcn     -0.0723361689  0.0307737319  1.605557e-01 -0.0804214354  0.112265716 #> Cldn5     0.0643915183  0.0570685391 -1.963390e-01  0.1222492732  0.093313284 #> P2ry12    0.0718742339 -0.0080271530 -1.016152e-02 -0.0225860937 -0.051489517 #> Adgrf5   -0.0604241979 -0.0071129981  4.124845e-02  0.0288662522  0.080089978 #> P2yr13    0.0103589697 -0.0666281028 -3.599000e-02  0.0737256473  0.074483339 #> Adgre1    0.0169277476  0.0940930525 -5.044943e-03  0.0160999981 -0.056368849 #> Cx3cl1    0.0282788378  0.0380254676 -2.730562e-02 -0.0428136299 -0.049911542 #> Plxnb3   -0.1039976175 -0.0452809544 -3.335290e-02 -0.1533483006  0.007199098 #> Flt4      0.0842881314  0.0794349639  5.076787e-02 -0.0713730767  0.022184847 #> Slc17a7   0.0529870744  0.0309162783 -8.536686e-02  0.0009543436 -0.054296954 #> Cd300c2  -0.0022153209 -0.0652456431 -4.496447e-02 -0.1782036297 -0.026796807 #> Tek       0.0349380048 -0.1041160462  9.621805e-03 -0.0632201723 -0.187130120 #> Kdr      -0.0001065728 -0.1522020960 -5.818851e-02  0.1216971770 -0.238345695 #> Kcnj8    -0.0373977761  0.0007711152 -7.692070e-02  0.0047830671 -0.014409797 #> S1pr3    -0.0179942689  0.0141945645  5.989462e-03 -0.0073935241  0.027838346 #> Tie1      0.0490415738 -0.0221670333 -6.525411e-02  0.0408185329 -0.190912656 #> Pdgfra    0.0568424442  0.0135379883 -2.578229e-02  0.0953814973 -0.094924247 #> Baiap2   -0.0229886967 -0.0334974481  8.064383e-05  0.0166931309  0.023302140 #> Calcrl    0.0146759878 -0.0506724135  1.157563e-02 -0.0664675326  0.015409180 #> Adrb2     0.1702886789 -0.0187340267  1.710123e-02  0.0419787429  0.106784215 #> Ccr2     -0.0163637115 -0.0921578924 -5.424001e-02 -0.1957791164 -0.059604232 #> Alk      -0.0091945410 -0.1207342981 -1.613326e-02  0.0259093232  0.015274026 #> Tacr3     0.1166453990 -0.1094358701  9.404744e-02 -0.0297390133  0.065286282 #> Erbb3     0.0504126446 -0.0813916892 -2.597030e-02 -0.0519744464  0.029246012 #> Pcdh15   -0.0137964915  0.0069633706  5.482266e-03 -0.0390587648  0.005226138 #> Grm7     -0.0789824401 -0.0387842261  3.279386e-02 -0.0034453666  0.054725745 #> F2r       0.0002731697  0.0850207656  6.741221e-02 -0.0681855080  0.122440116 #> Bdkrb2   -0.0293343803  0.1707003683 -2.598696e-01 -0.0629872847 -0.057508695 #> Adgrv1    0.0776992061 -0.0166361826 -3.535026e-02 -0.0723248882  0.068710615 #> Gprc5c   -0.0603997950 -0.0022632305 -5.038082e-02  0.0151884955 -0.014245735 #> Tbxa2r    0.0441911551  0.0700651325 -8.228275e-02  0.0202017055  0.154505812 #> Ackr1     0.2846627471 -0.0262780963 -1.053864e-01  0.1223092467 -0.094425835 #> Lpar2    -0.0299119081  0.1651707475  2.160898e-03 -0.0478955122 -0.083232676 #> Myh11     0.0548558494  0.0488557813  1.186295e-01  0.0534110707  0.027524435 #> Musk      0.0487086457  0.0284900644 -2.977132e-03 -0.0276613413 -0.027360978 #> Cnr1      0.0812875540 -0.1086635698 -8.253053e-02  0.2155287355 -0.120389805 #> C3ar1     0.0014665066  0.1555176354  7.966131e-02  0.0598280122 -0.130643545 #> S1pr4     0.0074997616  0.1078870436  8.636952e-02  0.0984612487  0.100035616 #> C5ar1    -0.0107388057 -0.0243464893  2.381740e-02  0.1464612196 -0.122396115 #> Fpr1     -0.0194940999  0.0407137532  1.569073e-01  0.1197729073  0.046365118 #> Sctr     -0.0498048556 -0.0484184472  6.695343e-03 -0.0508495242  0.055967438 #> Gpr158   -0.0306629755 -0.0284880958  3.781557e-03  0.0290347186  0.025185048 #> Cxcr4    -0.0208451388 -0.0238596036  1.731148e-02  0.0177518523  0.043120715 #> Hrh2     -0.0392549625  0.0034152926  9.768157e-03  0.0272326808  0.006284775 #> Slc17a6  -0.0685068391 -0.0232995367  7.812815e-03  0.0252356233  0.019338479 #> Ppp1r3g  -0.1146618589  0.0481419552  9.165347e-02  0.1199346583  0.067176668 #> Pln       0.0377710810  0.0214811455  9.177542e-02  0.0642456846  0.015404950 #> Grin2b   -0.0189247989 -0.0240678424  3.032638e-02 -0.0284279563  0.028220773 #> Taar7e    0.0746391677 -0.0467185618  4.526955e-02 -0.0025209992 -0.011327564 #> Ptger2   -0.0513065600 -0.0282519419 -2.183082e-03  0.0283308709  0.054729800 #> Mc4r      0.0040838607  0.0148713775  2.407896e-02  0.0473205192  0.062254269 #> Ghsr     -0.0429698126  0.0905348676 -7.673134e-03 -0.0353486070 -0.084151681 #> Nmbr      0.0007378491  0.0167915444  4.181913e-02 -0.1192725539  0.039587431 #>                 Dim.26       Dim.27       Dim.28        Dim.29        Dim.30 #> Mlc1      0.0878326009 -0.031554386 -0.052232152  0.0609383219 -4.327478e-02 #> Gprc5b    0.0266762043 -0.039531707 -0.049043569  0.1104838027 -6.467555e-02 #> Gfap     -0.0494719092 -0.017458645 -0.043128027  0.0081429937 -8.251075e-05 #> Ednrb    -0.0530457336 -0.148733210  0.065974757  0.0499350757  3.389917e-02 #> Sox9     -0.0672063613 -0.162932025  0.051151747 -0.1020523191  3.874905e-01 #> Aqp4      0.0592358591  0.030184146 -0.028689560  0.0506476477 -2.481883e-01 #> Gjc3      0.0357945574  0.003202220 -0.006444576  0.0485987561 -8.312943e-02 #> Sox8     -0.0188897330 -0.078855629  0.092491484 -0.0559746829  9.558878e-02 #> Ntsr2     0.0504637656 -0.176450341  0.055451770  0.0134966856  3.486750e-02 #> Smo       0.0453936042  0.023671510 -0.065132998 -0.2113907017 -4.484915e-02 #> C1qb     -0.0215946649 -0.101322647  0.085774897 -0.0819027638 -8.131109e-02 #> Olig1     0.0247423562 -0.085746692  0.076348594  0.0527235675 -3.159326e-02 #> C1qa      0.0590101044  0.032300526  0.020531352  0.0658019746  6.004304e-02 #> Pth1r     0.0793276583 -0.005238304  0.001428507  0.0212095978 -3.044433e-02 #> Gabbr2   -0.0305160056 -0.118445617 -0.067985257  0.0499118246  3.474506e-02 #> Timp4    -0.0493329144 -0.041776903  0.153002613 -0.0330770783  1.500863e-01 #> Abcc9    -0.0757869797  0.037515666 -0.055190640  0.0064512197  5.241319e-02 #> Csf1r    -0.0131894640  0.000217194 -0.077239650  0.1476638797 -4.309852e-02 #> Ntrk2     0.0163004913  0.055111531 -0.074643734 -0.0237210294 -7.040035e-02 #> Adgrg1   -0.0058308493  0.016603641  0.026238851 -0.0101407289 -2.807227e-02 #> Ntrk3     0.0943404860 -0.019256972  0.042941248 -0.0488731366  7.731345e-04 #> Erbb4    -0.0064517986 -0.010028324 -0.008534764  0.0249517081  4.463517e-02 #> Selplg   -0.0062924933 -0.075122971  0.056811882  0.0051738475 -2.786504e-02 #> Cspg5     0.0857373544  0.138007454 -0.148216221 -0.0310079249 -1.113713e-01 #> Dlk1      0.1781898410  0.314953528 -0.054369871 -0.0981283513  2.856689e-01 #> Gpr37l1  -0.0360816617  0.105188454  0.041953590  0.0340459382 -1.103544e-01 #> Fgfr3     0.0168849115 -0.054696630  0.010630278 -0.0264946717  5.159248e-02 #> Slc25a18 -0.0407008927 -0.066576135  0.063476504 -0.0941031416  1.169619e-01 #> Igf1r     0.0989874486  0.031592682  0.034262069 -0.0011935919 -6.570448e-02 #> S1pr1    -0.0067576752 -0.035319043  0.003840092  0.0147899280  1.971587e-02 #> Grm5      0.0668234244 -0.136042051 -0.100133227  0.0216725130  1.294152e-03 #> Axl      -0.1348052408 -0.124081403  0.168227653  0.0894831268 -6.117716e-02 #> Efemp1   -0.0152696437  0.045425742  0.004004264  0.2139556479  2.870743e-02 #> Adgrb3    0.0388614971  0.051592324 -0.149109419 -0.0429966570  3.560675e-03 #> Fn1       0.0335436994 -0.082264286  0.039691909  0.1343236923 -7.331423e-02 #> Mertk    -0.0369605346  0.115825408 -0.079525691  0.0823553238  1.518291e-01 #> Adgrl2   -0.3031091437  0.028781274 -0.207955907  0.0745953458 -6.911698e-02 #> Fzd2     -0.0196474015  0.018704715 -0.023720686 -0.0322295596 -3.000988e-02 #> Aldh1l1  -0.0263065087 -0.060703639 -0.018103907 -0.0417042691  1.716239e-01 #> Adgrg6    0.0361455668  0.003214755  0.047600691  0.0045602572  1.369179e-01 #> Egfr      0.0280105881 -0.011982193  0.016522429  0.0212010703  7.916745e-02 #> Kit       0.0972844998 -0.092067037 -0.034762412 -0.1832517095 -4.940600e-03 #> Ptgdr     0.1345251674 -0.000972766  0.051564822 -0.1181973448  7.937212e-03 #> Gad1      0.0024803734 -0.194092523 -0.192166030  0.0670521660  1.304732e-02 #> Tyro3    -0.0493684085 -0.050504987  0.023277967  0.0372930755 -1.383876e-01 #> Atp13a5   0.1102318274  0.024697697  0.009097302  0.2381686049  3.128646e-02 #> Ddr2     -0.1446549432 -0.027029968  0.068535023  0.1285995983  5.105404e-02 #> Rspo3     0.0383895382 -0.035471854  0.031994932 -0.0143180908  3.120201e-02 #> Arhgap29 -0.1331337804  0.019387670 -0.037186917 -0.0970775070 -1.215439e-02 #> Fzd7     -0.0528645423 -0.011210582 -0.099259268 -0.1107655688 -5.502641e-02 #> Slc47a1   0.0685560012  0.004504328 -0.049894809 -0.1428134117  1.662631e-02 #> Ptger3   -0.1149578447 -0.042873330  0.106208116 -0.3370559455 -9.293049e-02 #> Bdkrb1   -0.1680616312 -0.011605796 -0.161110710 -0.0197742199 -1.050297e-01 #> Traf4    -0.0630089584 -0.027047711 -0.017562959 -0.0463541917 -9.093199e-03 #> Cx3cr1    0.0366827055  0.108030351 -0.128763735 -0.0418743908  2.729474e-02 #> Anxa11   -0.0863467963 -0.041412179  0.061795794 -0.0759335373  4.787142e-02 #> Adgrb1    0.0549825835 -0.008844257  0.051408140 -0.0631193365  4.643709e-02 #> Lpar1     0.0137152954  0.055999299  0.061006148  0.0858385591  2.524876e-04 #> Gpr17    -0.0223114865  0.018027367  0.030622844 -0.0183894958  6.041809e-02 #> Cxcl12   -0.2963198493  0.043134523 -0.119446216  0.0622156948  1.554433e-01 #> Epha4     0.0111556311  0.027688422  0.003784837  0.0138894000 -6.321837e-03 #> Gpr182    0.2007643471  0.035824747 -0.036956261 -0.0773790951 -7.640493e-02 #> P2ry14   -0.2364683506 -0.019830170  0.038821070 -0.1339712090 -5.014946e-02 #> Hcar1     0.1225357064 -0.041110950  0.050346020 -0.1285632251 -4.310207e-02 #> Ephb1    -0.0236999760  0.021289044 -0.054030447 -0.0610688352  5.894711e-02 #> Grm3     -0.0782805813  0.086986043 -0.129667389 -0.0813163748 -6.732860e-02 #> P2ry1    -0.0511806935  0.045476010 -0.002367790  0.1490886369  1.694638e-01 #> Ptk7      0.0798616091  0.070500912  0.026882353 -0.1466074254  9.984724e-02 #> Slco1a4  -0.2864905757  0.101842785 -0.010535223 -0.0650067902 -6.822307e-02 #> Insrr     0.0601051358 -0.035821179  0.025679008  0.0488050424  5.633710e-02 #> Cmklr1    0.0107302382 -0.085659926  0.006279165 -0.0012097785 -1.436438e-02 #> Fzd6     -0.1425180046  0.061246515 -0.147816959 -0.1041921465 -2.410132e-02 #> S1pr5    -0.0506516216  0.017536520 -0.044307381 -0.0790472463  9.719188e-02 #> Pdgfrb    0.0125975243 -0.051232736 -0.086742556 -0.0484353510 -2.149450e-03 #> Flt1      0.1653240781 -0.075068582 -0.050347023  0.0651332978  1.794405e-02 #> Adgrl4    0.1435699479  0.078051246  0.158031934  0.0742145348 -1.074896e-03 #> Lpar6    -0.0222805323 -0.012269824 -0.008655777 -0.0573717230 -5.333696e-02 #> Epha6     0.0159374398 -0.032846947  0.072974666  0.0203934005 -1.367737e-02 #> Emcn      0.0952552735  0.040602359  0.097512203  0.1253907961  2.392048e-03 #> Cldn5     0.0082470676 -0.060041113 -0.053222653 -0.1486896343 -9.740433e-02 #> P2ry12   -0.0337505895 -0.064679455  0.033735272 -0.0276427592 -2.588625e-02 #> Adgrf5    0.0375343520  0.031342987  0.084864311 -0.0314227372  9.929285e-02 #> P2yr13   -0.0363893658 -0.079012939  0.090692759 -0.0009564144  3.512341e-02 #> Adgre1    0.0201581756  0.114743529 -0.058297038 -0.0811050654  3.813620e-02 #> Cx3cl1   -0.0533999581 -0.045979008 -0.044004851  0.0333713394 -8.758802e-03 #> Plxnb3    0.1341216837  0.171633978 -0.001815338 -0.1323667363  3.091820e-01 #> Flt4     -0.0561713369  0.015003327 -0.030172469 -0.0689513385 -6.067844e-02 #> Slc17a7  -0.1062673986 -0.029563099 -0.042975586  0.0216234961 -1.287816e-02 #> Cd300c2  -0.0379306242 -0.069730519  0.031819664 -0.1032123642  7.221290e-02 #> Tek       0.0483088968 -0.064006036  0.048860425  0.0906851316 -3.534582e-02 #> Kdr       0.0440265375 -0.062007461  0.004704177  0.0951282602  1.219989e-01 #> Kcnj8    -0.0753363763 -0.002278412 -0.070268701 -0.0531139703  3.043310e-02 #> S1pr3    -0.0288632831 -0.006001427 -0.021149635 -0.0336954404 -1.976000e-03 #> Tie1      0.0593750107 -0.066463298 -0.054573535  0.0039347637  1.054054e-02 #> Pdgfra    0.0966501397  0.072571474 -0.127076991  0.0151140353  1.331437e-02 #> Baiap2    0.0430865137 -0.068162152 -0.022952534  0.0028469305  3.222641e-02 #> Calcrl   -0.0183297629  0.032420069 -0.003017751  0.1557521916  6.885191e-02 #> Adrb2    -0.0497672651 -0.022470164  0.013146006  0.1804478675  1.209893e-02 #> Ccr2     -0.0538249124 -0.112410077  0.100603060 -0.0738814919 -8.365261e-02 #> Alk       0.0571780616  0.015428745 -0.001127190  0.0187479256  3.411386e-02 #> Tacr3     0.0581946328 -0.023971821 -0.076696685 -0.0818014747 -6.075309e-02 #> Erbb3    -0.0370666800 -0.006967861 -0.014557870 -0.0804474115  1.351229e-01 #> Pcdh15    0.0355974063 -0.032915103 -0.030134878 -0.0367493327  1.059245e-02 #> Grm7      0.0947724949  0.019858967  0.086543510  0.0362762156 -1.441902e-02 #> F2r      -0.0593552348  0.099757387 -0.041277910  0.0043312184  7.406235e-03 #> Bdkrb2    0.0414940104 -0.075858743  0.147780599 -0.0054418456 -3.582223e-02 #> Adgrv1    0.0349501476  0.018624239  0.002272959 -0.0354309548 -2.592842e-02 #> Gprc5c    0.0410839680  0.016269325 -0.026757826 -0.2465729600 -4.951070e-02 #> Tbxa2r    0.1527418870 -0.124352484  0.194509097 -0.1089740480 -9.541720e-02 #> Ackr1    -0.0717578364 -0.109322320 -0.057032195  0.0508922219  1.486985e-01 #> Lpar2    -0.0280515870  0.059642931 -0.037260877  0.1649670014  4.967281e-02 #> Myh11     0.0063646923  0.048941311 -0.050283091  0.0200373312  3.512964e-02 #> Musk     -0.0045792218  0.008050093  0.069816603  0.0292692270 -1.254557e-02 #> Cnr1     -0.1830336117  0.475317766  0.420329340 -0.0044069128 -8.615662e-02 #> C3ar1     0.0813728777  0.198159289 -0.255695077  0.0009797477 -1.036759e-02 #> S1pr4    -0.0203591492  0.096305901 -0.133002377 -0.0003491943 -2.967056e-02 #> C5ar1     0.1262845220  0.056913353 -0.109911244  0.0759594366  1.227053e-01 #> Fpr1      0.1051174552  0.054466506 -0.034666716 -0.0538367837 -9.876932e-02 #> Sctr      0.0298647435  0.013300436  0.027415609 -0.0095308161 -6.271336e-02 #> Gpr158    0.0027107531  0.011647145  0.087454663  0.0338829917 -7.746748e-03 #> Cxcr4     0.0033865260 -0.083185096  0.013639883  0.0035759456  2.864629e-02 #> Hrh2      0.0103471336  0.026383435  0.075884162  0.0206014597 -2.660904e-02 #> Slc17a6  -0.0008164387 -0.085923213  0.041082598 -0.0233140484 -1.242422e-02 #> Ppp1r3g  -0.1384504309 -0.099999760  0.036140294 -0.0796807691  2.628760e-01 #> Pln       0.0445109637 -0.014511131 -0.002485981  0.0051608577  4.888129e-02 #> Grin2b    0.0144133022 -0.030925128 -0.006750256  0.0361246426 -2.548812e-02 #> Taar7e   -0.0124750682 -0.031609189 -0.009036898 -0.0059682948  3.014806e-04 #> Ptger2    0.0764166989  0.093908008  0.112207441 -0.0096151290 -3.695083e-02 #> Mc4r      0.0472528642  0.072213711 -0.077193292 -0.0270830176  3.346141e-03 #> Ghsr      0.0052447572 -0.051142392  0.053817262 -0.1259749510  4.283643e-04 #> Nmbr      0.1145647537 -0.222794650 -0.228934077 -0.0086525620 -2.723308e-02 #>                Dim.31        Dim.32        Dim.33        Dim.34        Dim.35 #> Mlc1      0.046828468 -0.0598006726  2.728154e-02 -0.0447370101  0.0494032685 #> Gprc5b    0.043139566 -0.0645482478 -4.625959e-02 -0.1079741072 -0.0032662485 #> Gfap     -0.084451969  0.0189433844  7.755266e-02  0.0284905859  0.0887666941 #> Ednrb    -0.039601795  0.0165999322  1.015626e-02  0.0763068193  0.0267904621 #> Sox9     -0.006622427  0.0753248866  5.675914e-03 -0.1282415159 -0.0636306132 #> Aqp4      0.057116490 -0.0190713689 -5.925918e-02 -0.0139270737 -0.0245126799 #> Gjc3      0.013838298 -0.0216097008  2.018414e-02  0.0688803634 -0.0659016395 #> Sox8     -0.039792363  0.1001053422  4.248161e-02  0.0892288804  0.0159415039 #> Ntsr2     0.026916552  0.1789323057  8.604315e-02  0.1125314756 -0.1358046150 #> Smo      -0.019469457  0.0586247767  6.891104e-03 -0.0333074462  0.0279408821 #> C1qb      0.012424437 -0.0150347314 -7.047393e-02 -0.0418619337  0.0062502262 #> Olig1     0.066097899  0.0351040968 -8.447867e-03  0.0233609796  0.0013404769 #> C1qa      0.082729243 -0.1669126528 -7.458389e-03  0.1849357542 -0.0376629693 #> Pth1r     0.121885666  0.0380139862 -2.840862e-02 -0.0002658282 -0.0791146653 #> Gabbr2    0.090371961  0.0372215327 -1.220097e-01  0.0435938288 -0.0009317162 #> Timp4    -0.086464280  0.0933513361  4.923471e-02  0.0253984833  0.1920992832 #> Abcc9    -0.084384393 -0.0610777513  5.785971e-02  0.0807878971 -0.0338071616 #> Csf1r    -0.152633159  0.0473608548  4.269237e-02  0.1128218638 -0.0583104455 #> Ntrk2    -0.063591663 -0.1392178360 -4.827163e-02 -0.1001359086 -0.1637454518 #> Adgrg1    0.049207360 -0.1073650837 -8.895728e-02 -0.0377169187 -0.0318250457 #> Ntrk3    -0.111887148 -0.0711837646  4.267670e-02  0.0082900974 -0.1252205428 #> Erbb4     0.025227279 -0.0178451823 -1.220885e-02 -0.0374746419 -0.0142466855 #> Selplg    0.081529945 -0.0201341489 -1.323207e-02 -0.0154868793  0.0379776326 #> Cspg5     0.089496955 -0.0694036862  3.120273e-02 -0.0360626007  0.0188246325 #> Dlk1      0.149039116 -0.1877217986 -1.643182e-01 -0.0652078950 -0.0561248429 #> Gpr37l1  -0.024429701 -0.1005289171 -8.153428e-02 -0.0329499715  0.0363414821 #> Fgfr3     0.019317224 -0.0497822886  2.938358e-02  0.0011134531  0.0805321248 #> Slc25a18 -0.050743001 -0.0296061196  2.556011e-02 -0.0433518931 -0.2193483209 #> Igf1r    -0.076530319 -0.0062404586 -4.564518e-03 -0.0197511675 -0.0701019182 #> S1pr1    -0.021106526 -0.0134251511 -6.357475e-02 -0.0125899223  0.1420520110 #> Grm5     -0.234083083 -0.0954584451 -3.330167e-02  0.0028860124 -0.1660879724 #> Axl       0.044156482 -0.0599993938  1.419222e-02  0.0309315854 -0.1077802711 #> Efemp1   -0.063266484 -0.0088457345  9.670566e-02  0.0566883551  0.0119269021 #> Adgrb3   -0.153774463 -0.0635340697  9.247846e-03  0.1384534955  0.2085176516 #> Fn1      -0.021249829  0.1305903254  4.301929e-02 -0.1323524685 -0.1096978955 #> Mertk    -0.102921918  0.1281939202  1.623788e-01  0.2094871600  0.0207791043 #> Adgrl2   -0.007860873 -0.0021973300  5.234147e-02 -0.1777774342  0.0409187098 #> Fzd2      0.030239235  0.0124965190 -2.269772e-02 -0.1275234384  0.0133330593 #> Aldh1l1  -0.035923302  0.0644376425  1.734290e-02 -0.0587820633  0.0835981892 #> Adgrg6    0.069634243 -0.0587408715 -5.638447e-02  0.0099802747  0.0025818605 #> Egfr     -0.016326186 -0.0320479785 -6.859912e-05  0.1188884863  0.0085784392 #> Kit      -0.108737744  0.0852250667  9.599120e-02  0.1831727742 -0.1136392621 #> Ptgdr     0.019292896  0.0063555982 -4.826008e-02  0.0236474095  0.0269023481 #> Gad1      0.079657186 -0.0686074025 -4.335263e-02 -0.0771170862  0.0970554815 #> Tyro3     0.007539715 -0.0473039552 -3.568943e-02  0.0048044510  0.0286580500 #> Atp13a5  -0.006673755  0.0406455961  3.314240e-02 -0.2153231253  0.0201205947 #> Ddr2     -0.050036007 -0.0780244812  2.745486e-02  0.0928642216  0.1728063915 #> Rspo3     0.076118504  0.0238444237 -1.971699e-02  0.0677722837  0.0314639576 #> Arhgap29  0.012956082 -0.0694323961 -4.035540e-02  0.0135653452 -0.0120986106 #> Fzd7      0.014305674  0.1149147747  7.358168e-02  0.0346162309  0.0129175265 #> Slc47a1   0.012151578 -0.0831412240 -5.128258e-02  0.0155157148  0.0398152983 #> Ptger3   -0.058215780 -0.1489129512 -1.210736e-01  0.1115972400 -0.0120655440 #> Bdkrb1    0.067141336  0.0172753971 -1.802968e-02 -0.2273791512 -0.0992594890 #> Traf4    -0.011866296  0.0004981121 -4.951589e-03 -0.0912585027 -0.0355982296 #> Cx3cr1    0.024277900  0.0352343790 -1.212546e-03 -0.0963795964  0.0462792154 #> Anxa11   -0.002117323 -0.1968707311  1.251938e-01  0.0670237421 -0.1275454963 #> Adgrb1   -0.173912641 -0.1415132139  1.644371e-01 -0.1000261924 -0.1520951604 #> Lpar1     0.038127523 -0.2163020820 -9.496572e-02  0.0329034433  0.0638695741 #> Gpr17    -0.026323726  0.0388872221 -9.339464e-03 -0.0058489438  0.0379973241 #> Cxcl12    0.069416771  0.0506034263 -9.995949e-02  0.0425253996  0.0201389086 #> Epha4     0.056675874  0.0129259063  3.203585e-03  0.0179203115  0.0701734213 #> Gpr182    0.007513760  0.0845145986  9.137210e-02  0.0456192044  0.0147780005 #> P2ry14   -0.103551340 -0.1744112679 -5.322856e-02  0.1540049073  0.0163092480 #> Hcar1    -0.012512550  0.0870098305  2.631313e-03  0.0591000044 -0.0549805473 #> Ephb1    -0.064536802  0.0954271249  9.844991e-02  0.0572161968 -0.0388351299 #> Grm3     -0.035388021 -0.0259657636  2.541851e-04  0.0579422133  0.1305167588 #> P2ry1    -0.039865513 -0.0867544513 -1.093052e-02 -0.0094270283 -0.1347780920 #> Ptk7     -0.148622402 -0.0032059121 -7.716997e-02 -0.0435938209  0.1875523254 #> Slco1a4  -0.009672401 -0.0766497669 -5.563207e-02  0.0127129950  0.0216604487 #> Insrr     0.041762445 -0.0735588622 -1.072453e-02  0.0344998779  0.0853711705 #> Cmklr1   -0.073411183  0.0729766849  3.692986e-02  0.0334058808  0.0186064318 #> Fzd6      0.048545810  0.0841069983  4.021975e-02 -0.0765074943 -0.3001476592 #> S1pr5     0.003558514  0.0183656052  2.431260e-02 -0.0456651753 -0.0083827503 #> Pdgfrb    0.095926352  0.0462783166 -4.922459e-02 -0.1033001766  0.0362304442 #> Flt1     -0.012908200  0.0201207566  2.591138e-02 -0.0023468483 -0.0997050023 #> Adgrl4    0.109940514  0.1702367828  1.635577e-02 -0.0102367887 -0.1158632033 #> Lpar6    -0.176544128  0.2254068050  3.661908e-02 -0.1176513654 -0.0090381637 #> Epha6    -0.025988125 -0.0540053868  1.431176e-01 -0.1163527588  0.0928768639 #> Emcn      0.065982344  0.1227126807  6.668498e-02 -0.0217861866  0.0412138114 #> Cldn5    -0.069025765 -0.0435180826  2.949371e-02 -0.0016895091  0.1635148788 #> P2ry12   -0.023892123 -0.0160430920  1.215217e-02 -0.0679104842  0.0217107768 #> Adgrf5    0.065615569 -0.1000101407 -3.363524e-03  0.0902798957  0.0492302079 #> P2yr13    0.081844806 -0.1299638028 -5.584187e-02  0.0512208005 -0.0410498812 #> Adgre1    0.022579107 -0.0041167572  6.838308e-02 -0.1287046926  0.0487000771 #> Cx3cl1    0.220527393  0.0780650401 -1.431374e-02  0.0131880459  0.1633746357 #> Plxnb3    0.138582381  0.0010790332 -8.468542e-02 -0.0441258190 -0.0894258803 #> Flt4     -0.022974074  0.0076688861 -2.626752e-02 -0.0505514850 -0.0654974113 #> Slc17a7   0.300845666  0.1582499632  2.062201e-02  0.1066829830  0.0546577076 #> Cd300c2  -0.035958983  0.0981355804  8.655646e-03 -0.1665114222 -0.0190512954 #> Tek      -0.039842924  0.0342239248  1.347741e-03  0.0026123442  0.1472952488 #> Kdr      -0.020023374 -0.0874993765 -4.948848e-02  0.0556506639 -0.0064641496 #> Kcnj8    -0.059145594 -0.0433822437  6.304247e-03  0.0736169850 -0.0416797079 #> S1pr3    -0.008363763  0.0283323618  3.141338e-02  0.1134452541 -0.0397475771 #> Tie1     -0.019658018 -0.0394992963 -3.931671e-02  0.0194922677 -0.0953385382 #> Pdgfra   -0.040746646 -0.0797455783  1.714363e-02 -0.0865522199 -0.0509739034 #> Baiap2   -0.060755466 -0.0232509619  1.864062e-02 -0.0520752461  0.0255375312 #> Calcrl   -0.010114340 -0.1490642491  3.701947e-02  0.0965929504  0.0808241665 #> Adrb2    -0.042443886  0.0457706002  1.095481e-01  0.0394581013 -0.0804562647 #> Ccr2      0.052244168  0.0349708865 -6.291725e-02 -0.1560912744  0.0007372440 #> Alk       0.002457115  0.0193345489  6.111945e-02  0.0954399201  0.0496196240 #> Tacr3     0.063014434  0.0090085198  8.880871e-02  0.1086158422  0.0087241236 #> Erbb3    -0.035547031  0.0156821802  2.053372e-02 -0.1219785893 -0.0152604550 #> Pcdh15    0.015756330  0.0416455279 -3.092840e-02 -0.0184354526  0.0008065560 #> Grm7     -0.363749647 -0.0996376725 -7.967975e-02 -0.1242796748 -0.0816284023 #> F2r      -0.035856448 -0.0233279613  6.984108e-02  0.0959805202  0.0058801195 #> Bdkrb2    0.047983723 -0.0300023848 -1.814729e-01 -0.2887648702  0.1216281904 #> Adgrv1   -0.020518436  0.0127412933  4.092209e-02  0.0724540105  0.0447967700 #> Gprc5c    0.024902804  0.0877821129 -2.039111e-02  0.0615017823  0.0072692591 #> Tbxa2r    0.101752456  0.0637760717 -5.673629e-02  0.0118845179  0.0227262969 #> Ackr1    -0.064746410  0.0695407938 -1.187198e-02 -0.0904984610 -0.0710609276 #> Lpar2    -0.125029267  0.0204099466  3.052365e-02 -0.0438830232  0.0037824978 #> Myh11     0.091560936 -0.0414864920 -1.467731e-02 -0.0157910353 -0.0773840292 #> Musk     -0.014367541 -0.0698388453 -2.087723e-02 -0.1051635181  0.0750837693 #> Cnr1     -0.028825368  0.1360820946  8.153354e-02  0.0042860682 -0.0613969703 #> C3ar1    -0.107270182  0.1829165121  4.049878e-02 -0.0819728312  0.0598627527 #> S1pr4    -0.010424609  0.0573312489  3.275797e-02  0.0039531567 -0.0286053617 #> C5ar1     0.010422077 -0.0961241976  1.629990e-02  0.0317985102  0.0618174150 #> Fpr1     -0.016006759  0.1021449753  4.216517e-02  0.0487268964  0.0491982198 #> Sctr     -0.007395809 -0.0195678116  1.143698e-02  0.0155668037  0.0965021426 #> Gpr158   -0.116567139 -0.0108367875  3.243604e-02 -0.0712450487  0.0089005696 #> Cxcr4     0.013367688 -0.0067748190  2.585866e-02  0.0018319666 -0.0134507343 #> Hrh2     -0.139398040 -0.0291304104 -5.949163e-03 -0.0481852135 -0.0997687187 #> Slc17a6  -0.004612063  0.0630069893  3.650120e-02  0.0082822799  0.0213399951 #> Ppp1r3g  -0.080239074  0.1485934844 -8.515849e-03 -0.0923543880  0.1760423755 #> Pln       0.064400597 -0.0366968064 -2.027069e-02 -0.0219495922  0.0470307311 #> Grin2b   -0.048447452  0.0027897013 -8.976805e-02  0.0577922127 -0.0844752800 #> Taar7e   -0.008864837 -0.0358847537  2.822804e-02  0.0176690791 -0.0261339415 #> Ptger2   -0.254762975 -0.0129889699  8.403887e-03 -0.1382598346  0.3049073902 #> Mc4r      0.003322849  0.1230615140  6.443982e-02  0.1014378478  0.0310941899 #> Ghsr      0.215464544 -0.2932875291  7.425669e-01 -0.1957352497  0.0696802111 #> Nmbr     -0.106036672 -0.1269402661 -1.176558e-02  0.0450735836  0.0620510011 #>                 Dim.36       Dim.37        Dim.38        Dim.39        Dim.40 #> Mlc1     -0.0184651881 -0.030304498 -0.0160638709  0.0416501378  5.361885e-02 #> Gprc5b   -0.0939820092 -0.008529965  0.0350760268 -0.2553544395 -1.522452e-01 #> Gfap      0.0262586593  0.072650046  0.0113510685 -0.0715659259  9.849332e-02 #> Ednrb     0.0982531407 -0.104714980  0.0500510838 -0.1137377850 -1.269958e-01 #> Sox9     -0.0371162158 -0.151044779  0.1472019918 -0.0006830817 -1.397952e-01 #> Aqp4     -0.0390975216 -0.029896340 -0.0782866404  0.1162288178 -1.292995e-01 #> Gjc3      0.0468822349 -0.108358110 -0.1102798835  0.1361553064 -6.362949e-02 #> Sox8     -0.0601223808  0.060710974 -0.0614759031  0.1619193810  1.584736e-01 #> Ntsr2     0.1232741324  0.225969719  0.2488331589  0.0844487918  1.063193e-01 #> Smo      -0.0840642444  0.031353996  0.0023371307 -0.0484884572 -3.846325e-02 #> C1qb      0.0497127529  0.023999045 -0.0125238911 -0.0884486690  1.314621e-02 #> Olig1     0.0020762266 -0.047091326 -0.0503973505  0.0003963190 -6.083122e-02 #> C1qa      0.0754253599 -0.130997264  0.0978677252 -0.0278780722  2.200412e-02 #> Pth1r    -0.0030838041 -0.121727640  0.0059440802  0.0256618653 -3.905047e-02 #> Gabbr2    0.0808922385 -0.002790812  0.0233899836  0.0168918251  1.057552e-02 #> Timp4    -0.1270588590 -0.100894925 -0.1736479716 -0.0504274565  2.340758e-02 #> Abcc9     0.0187054444  0.011617286  0.0263868077 -0.0053857508 -1.218239e-01 #> Csf1r     0.1318275669 -0.163527135 -0.0838633215 -0.0052300633 -5.196351e-02 #> Ntrk2    -0.0398631515  0.085021496  0.0212158985  0.0415714242  4.249104e-02 #> Adgrg1   -0.0976986661 -0.012428502 -0.0988359397  0.1831834716 -4.760026e-02 #> Ntrk3    -0.0639744569  0.060570611  0.0078495448  0.0142525062  3.130265e-02 #> Erbb4    -0.0167264390 -0.016592544  0.0789511757  0.0093986326  7.037000e-02 #> Selplg   -0.0341170962  0.002527291 -0.0067316310  0.0186744185 -1.170480e-02 #> Cspg5     0.0680101482 -0.054979539  0.1151432372 -0.0593981661 -1.510112e-01 #> Dlk1     -0.0353745449 -0.218198801 -0.0375729362 -0.0670524620  3.335269e-02 #> Gpr37l1  -0.1523234693 -0.086291714 -0.2568447779  0.1904020485  5.128738e-02 #> Fgfr3     0.0642415927 -0.006308800 -0.0259544162 -0.1127973279  1.599982e-02 #> Slc25a18 -0.0465369947 -0.043853335  0.1848435107  0.1450936692  8.717011e-03 #> Igf1r     0.0399526150  0.026603673 -0.0788252706 -0.0306618990  7.775312e-02 #> S1pr1    -0.0325449201 -0.177263266 -0.2322677195 -0.1147150551  1.007809e-01 #> Grm5     -0.2516548488  0.018275587 -0.0514854108 -0.1098154125  2.549782e-02 #> Axl       0.0904061274 -0.078917037 -0.0569383991  0.0040041984  3.185887e-02 #> Efemp1   -0.0582386384 -0.020314725  0.0286624622  0.1112548354  6.487451e-02 #> Adgrb3    0.2126002272  0.018012550 -0.0611417626 -0.2114866671  1.160864e-01 #> Fn1       0.0234489932 -0.100600776 -0.0637769322 -0.0800411776  3.423702e-03 #> Mertk    -0.0220847008  0.048399868  0.0012613628 -0.0230931269 -5.811036e-02 #> Adgrl2   -0.1018121809 -0.039244339  0.1214987147  0.0966271918  6.848295e-04 #> Fzd2      0.0630975631  0.066823082 -0.0439847934 -0.0855735417 -6.062035e-05 #> Aldh1l1   0.0253316439 -0.035522819  0.0749115497 -0.0114900494 -6.626741e-02 #> Adgrg6    0.0537950862  0.241274154 -0.2195531775  0.0683674891 -2.408349e-01 #> Egfr     -0.0449813943 -0.010427737 -0.0072195101 -0.0074096746 -3.434149e-02 #> Kit      -0.0455521661 -0.084265229 -0.0346420438 -0.0145615556 -2.873945e-01 #> Ptgdr     0.0240254379  0.016648187 -0.0082421640  0.0044110074  7.595321e-02 #> Gad1      0.0795709522  0.028364256  0.0256205028  0.0613774902  6.682388e-02 #> Tyro3    -0.0722179570 -0.004041765 -0.0364148299 -0.1265511842 -7.153692e-03 #> Atp13a5  -0.0119193160  0.084586335  0.0006471908  0.0268182075 -7.756046e-02 #> Ddr2     -0.1338285901  0.025562956  0.1088641291  0.0549546481  6.355574e-02 #> Rspo3    -0.0044048184  0.011137614 -0.0138205060  0.0446353461 -2.149552e-03 #> Arhgap29 -0.0037139699 -0.011861371  0.0182434276  0.0652955305  4.654955e-02 #> Fzd7     -0.0502677342 -0.154618812  0.0863160473  0.0409111381 -2.471826e-02 #> Slc47a1   0.0224130779  0.003298689  0.0590472108 -0.0082628625 -4.528392e-02 #> Ptger3    0.0384768157 -0.049609578 -0.0071401496  0.0388993023  1.089749e-02 #> Bdkrb1    0.0270953361  0.009568066 -0.0759762411 -0.0072058860 -1.084141e-01 #> Traf4     0.0296824167 -0.016055322  0.0370464471  0.0136527758 -1.314091e-02 #> Cx3cr1   -0.1636810075  0.018512548  0.0386548891  0.1218234193  1.213436e-01 #> Anxa11    0.0508793245  0.023968906 -0.0667699889  0.0577319260  6.406210e-02 #> Adgrb1   -0.1725663835 -0.018179117 -0.0451824695 -0.0668524372  8.222429e-02 #> Lpar1    -0.0367472609 -0.116111132  0.1306757422 -0.1388211577 -1.317296e-01 #> Gpr17    -0.0297323810  0.028825072  0.0105482531 -0.0419610908  8.285689e-02 #> Cxcl12    0.0346060269  0.098685686 -0.1628733629  0.0578450895  4.298889e-02 #> Epha4     0.0135408213 -0.025926931  0.0254810852 -0.0050918601 -6.727591e-02 #> Gpr182   -0.0748048751  0.027327328  0.0835617206 -0.0064135173 -2.937942e-02 #> P2ry14   -0.0265676971 -0.174716836  0.1122414679  0.0567899290 -8.275995e-02 #> Hcar1     0.0165664308  0.050496632 -0.1165294466 -0.0351025722  8.169078e-02 #> Ephb1     0.0590708642  0.135181704  0.1128769853  0.0709783108  9.179299e-02 #> Grm3      0.0118479689  0.115666854  0.0235324871 -0.1569341816  1.927289e-01 #> P2ry1     0.1072456043  0.007266877 -0.0472425354  0.0838375817  1.468678e-01 #> Ptk7      0.0823052562  0.036186688 -0.0676373468 -0.0502177537 -3.600953e-03 #> Slco1a4   0.0077821794  0.032812009  0.0538668681 -0.0335722688  8.466779e-03 #> Insrr     0.0381300985  0.045587348  0.0321365280  0.0260483808  2.870478e-01 #> Cmklr1   -0.0740175255 -0.115472686 -0.0577966977  0.0792883802 -2.944634e-02 #> Fzd6      0.2070182469 -0.016673717 -0.2233819981  0.0178819476  3.697770e-02 #> S1pr5    -0.0033012816  0.061338714  0.0764305623  0.0413469057  2.639493e-02 #> Pdgfrb    0.0158029721  0.011404295 -0.1066469405  0.0148675119  1.414339e-01 #> Flt1      0.1009801665 -0.101288027  0.0191020162 -0.0815439050  6.693099e-02 #> Adgrl4    0.1272835024 -0.069567390  0.0804360659 -0.0866085252  1.376898e-02 #> Lpar6    -0.0586611705  0.080686514 -0.0012916598 -0.0274952559 -2.068817e-01 #> Epha6     0.0401898133 -0.015209634 -0.0283085247  0.1162029646 -9.925700e-02 #> Emcn     -0.1110714310  0.015489320 -0.0541160786 -0.0757955706  1.038678e-02 #> Cldn5    -0.1473402691 -0.003748776  0.1145678035  0.1063738699 -3.154296e-02 #> P2ry12    0.0087181022  0.152456837 -0.0246374030 -0.0501469131 -1.167572e-02 #> Adgrf5   -0.0731615024  0.251256309 -0.0753575003  0.1195170426 -2.033394e-01 #> P2yr13    0.0958447599  0.019205108  0.0086681309 -0.0262129339 -1.625402e-02 #> Adgre1   -0.1236192018  0.143904415  0.0104344192  0.0514115871 -5.733619e-02 #> Cx3cl1   -0.0111607015 -0.057099476  0.0367622389  0.0377961096 -1.014273e-01 #> Plxnb3   -0.0580301919 -0.177218373  0.0272946573  0.0619157127 -3.814762e-02 #> Flt4      0.1564807450 -0.049635448  0.0895078862 -0.1678011944  6.297056e-02 #> Slc17a7  -0.0626166295 -0.044459061  0.0484938798 -0.0097180309 -8.290817e-02 #> Cd300c2  -0.0527411828  0.113588822  0.0684308802  0.0530322867 -6.811482e-02 #> Tek      -0.1075037452 -0.181204847  0.1554732761  0.0277579229  9.678577e-02 #> Kdr      -0.0154287112  0.135188283 -0.1020429449  0.0387922063  5.634872e-02 #> Kcnj8     0.0160907110 -0.068873197  0.0285474299  0.0377063746 -5.337167e-02 #> S1pr3     0.0067908368 -0.025080717  0.0175108476 -0.0284456087  5.661047e-02 #> Tie1      0.1751761731 -0.003997850 -0.0373416228 -0.0754304033  3.054548e-02 #> Pdgfra    0.1216957063  0.063385337  0.1436888751 -0.1584631690 -1.639057e-01 #> Baiap2    0.1290711197 -0.037772225  0.0080747252  0.1325683913  9.908312e-03 #> Calcrl   -0.0783124314  0.087704244  0.0471934587  0.0327874872 -1.070924e-01 #> Adrb2    -0.0357940475  0.018562977 -0.0904828555 -0.0090089510 -1.300637e-01 #> Ccr2      0.0252828342  0.090584788 -0.0833943831 -0.0632729178 -1.630121e-02 #> Alk      -0.0492032970  0.019157148 -0.0264414335  0.0416550702  1.255275e-02 #> Tacr3    -0.0535589138  0.004730896 -0.0425153666 -0.0051265568 -9.853447e-03 #> Erbb3     0.0236258806  0.074459182  0.1138411718  0.0812697470 -1.703117e-02 #> Pcdh15   -0.0004332264 -0.035596986 -0.0727413870  0.1276550097  5.727905e-03 #> Grm7      0.0254595499 -0.032995583  0.0297535758  0.0594028503 -2.223731e-02 #> F2r      -0.0211161929  0.153332854  0.0863454750 -0.1951097109 -3.424781e-03 #> Bdkrb2   -0.0157341585  0.023271118  0.1367030101 -0.0248522751  1.484751e-01 #> Adgrv1   -0.0153838170 -0.003352800  0.0724944583 -0.0152677536  1.010589e-01 #> Gprc5c    0.0102780406  0.033180746 -0.0241477500 -0.0110264477  5.397094e-02 #> Tbxa2r   -0.0558196749  0.020794635 -0.0699801286  0.0518509430  7.055661e-02 #> Ackr1    -0.0213723098 -0.148936468 -0.0978936909 -0.0316796292  1.488596e-01 #> Lpar2    -0.0247879032 -0.122258220  0.0836873154  0.0514119058  3.079012e-02 #> Myh11     0.1154721096  0.085550607 -0.0590846312  0.0143622993 -2.695850e-02 #> Musk      0.0388165365 -0.041598096  0.0968544371 -0.0135082858 -4.084980e-02 #> Cnr1     -0.0214784697  0.016354044 -0.0680501854 -0.0844704614 -3.088668e-03 #> C3ar1    -0.0887895541 -0.056778803 -0.0517207885  0.0808060811  1.147404e-01 #> S1pr4     0.0471935318 -0.111264085  0.0106246804 -0.0247261562  2.333620e-02 #> C5ar1    -0.0122438345  0.267574304 -0.0509031489 -0.0755295187 -4.173971e-02 #> Fpr1     -0.0792090017 -0.123477018  0.0769766045  0.0049321412  2.671077e-02 #> Sctr     -0.0196127403 -0.024961104 -0.0077775181 -0.0198646814 -4.114963e-02 #> Gpr158    0.0503474194 -0.031459724  0.0166471130  0.0404700763  5.551943e-02 #> Cxcr4     0.0219997126  0.009940269  0.0754621830 -0.0315285395 -2.099672e-02 #> Hrh2     -0.1401452112  0.033707427 -0.0028436899 -0.1002431670 -3.916837e-02 #> Slc17a6  -0.0034701078  0.006230451  0.0148829739 -0.0309501901  1.716244e-03 #> Ppp1r3g  -0.0016334887 -0.089571735 -0.2226436240 -0.2746964147 -8.193983e-02 #> Pln      -0.0367428755 -0.002472797 -0.0022713359  0.0981751355 -2.531201e-02 #> Grin2b   -0.0899627373  0.035254581  0.0399758963 -0.0229135939  6.190592e-02 #> Taar7e    0.0301153876  0.028150223  0.0011443092 -0.0257971309  3.282681e-02 #> Ptger2    0.4568251485 -0.040841050  0.0250627486  0.2762322424 -1.432585e-01 #> Mc4r      0.1457895275 -0.080847123 -0.0888988041  0.2005187302 -1.070330e-02 #> Ghsr      0.0439222964 -0.091800363 -0.0993547255 -0.0464195668  7.397257e-02 #> Nmbr     -0.0646141507 -0.048184095 -0.2148970819  0.0432620435 -9.744349e-02 #>                 Dim.41       Dim.42       Dim.43        Dim.44        Dim.45 #> Mlc1      0.0643317341 -0.054764478 -0.174173415 -0.0923818740 -5.516297e-03 #> Gprc5b   -0.1021655180 -0.086213482 -0.105730502 -0.2534479133 -4.052155e-02 #> Gfap      0.0740504391 -0.041887867 -0.051935363 -0.0373155836 -2.432162e-03 #> Ednrb     0.0551232520  0.127999610  0.056461436  0.0579064124  2.568717e-02 #> Sox9     -0.0773481265  0.067782335  0.103099053 -0.0506625942 -7.112397e-02 #> Aqp4     -0.0516671195  0.097115387  0.142334263  0.1297990393 -1.181859e-02 #> Gjc3      0.0327259722  0.099922776  0.025632795 -0.0205891646  1.336047e-01 #> Sox8      0.0985313502 -0.112960344  0.025851437 -0.1551140998 -1.326157e-01 #> Ntsr2     0.0785200532 -0.114059990 -0.166204969  0.0204349901 -7.038725e-02 #> Smo      -0.0250814320 -0.038439680 -0.196627335  0.0452529613  1.820839e-01 #> C1qb      0.0212880572 -0.035488603 -0.015494208 -0.0330613409  6.395891e-02 #> Olig1     0.0253190839  0.017203247 -0.054599251 -0.0255273149  8.029054e-02 #> C1qa     -0.0135661511  0.037661404 -0.022047380  0.1568863111 -6.369763e-02 #> Pth1r    -0.0463781685  0.105152855 -0.007516537  0.0006439744 -3.570192e-02 #> Gabbr2   -0.0316439992  0.033223605  0.007232072  0.0014817700  2.633256e-02 #> Timp4     0.0588784958 -0.091471303  0.031377151  0.0583792125  1.494263e-02 #> Abcc9    -0.1109384449 -0.090681367 -0.073249093  0.0462842256  2.509298e-02 #> Csf1r    -0.0362950700  0.281248936  0.033717027 -0.1279655728 -5.613931e-02 #> Ntrk2    -0.1974515406 -0.034326054 -0.042678658 -0.0587749706  6.616282e-02 #> Adgrg1   -0.0383849797  0.048048074 -0.022739842  0.1498210432  1.316412e-01 #> Ntrk3    -0.0009595687 -0.032379267  0.158116075 -0.0451758739 -1.548037e-02 #> Erbb4    -0.0317971617  0.009962084  0.131608987 -0.1085651614  2.160674e-01 #> Selplg    0.0304610903 -0.117080780  0.020348523  0.0619208915  5.391372e-02 #> Cspg5     0.1009722957  0.016925344  0.037964084  0.0070723766 -4.276894e-03 #> Dlk1     -0.0381672000 -0.109022077 -0.006967999 -0.0488579536 -4.593968e-03 #> Gpr37l1  -0.0275785666 -0.019553809  0.254841214  0.0687479732  6.891691e-02 #> Fgfr3    -0.0005879796 -0.102328219  0.014884693  0.0545803003 -1.367574e-02 #> Slc25a18  0.0125550580  0.013679255 -0.208341235 -0.0364212544  1.823488e-01 #> Igf1r     0.1225668687  0.086411412 -0.063731591  0.1148387934 -1.373221e-02 #> S1pr1    -0.0633881381 -0.034127895  0.118770093  0.0579468371 -2.324412e-02 #> Grm5      0.0233830214 -0.001035762 -0.010456036  0.0124027827 -3.124437e-02 #> Axl       0.0074748291 -0.104766730 -0.017936965 -0.2031400035  1.936683e-02 #> Efemp1   -0.1488280631  0.027576071 -0.031953277  0.0145686118 -7.206308e-02 #> Adgrb3    0.2572227294  0.123914398 -0.067619456  0.0652661523  2.012681e-01 #> Fn1      -0.0255747186  0.034445417  0.094843573  0.0833642077 -7.105043e-02 #> Mertk     0.0767727788  0.138501387 -0.025807046 -0.1408189951 -1.005566e-01 #> Adgrl2   -0.0240220259  0.015997072  0.003344261 -0.1110349288 -3.838102e-02 #> Fzd2     -0.0606452445 -0.017963464 -0.007685615 -0.0237867403 -3.073157e-02 #> Aldh1l1  -0.0034666362  0.117546407  0.020814691  0.0322193967  3.682676e-02 #> Adgrg6    0.1414064016  0.140698465 -0.014073069 -0.1387687972  3.506657e-02 #> Egfr      0.0558185903  0.005256354  0.075116458  0.0199596118  8.231042e-02 #> Kit       0.0087070321 -0.178334333  0.046879683 -0.0640861680  7.038962e-02 #> Ptgdr     0.0736573806  0.131322670  0.025843988 -0.0216869608 -3.697933e-02 #> Gad1     -0.0396407508  0.036907797  0.051970643 -0.0149179111  2.973331e-02 #> Tyro3    -0.0064362358 -0.054881942 -0.047964494 -0.0228024468  8.213397e-02 #> Atp13a5   0.0384860186 -0.031310490 -0.020471104 -0.0543620856  1.208858e-02 #> Ddr2     -0.0626974873 -0.136709620 -0.007516952  0.0335426958  9.787339e-02 #> Rspo3    -0.0309039275  0.007325428  0.048003881 -0.0486419449 -8.835275e-03 #> Arhgap29  0.2237371425 -0.026624138  0.051350991  0.0419043496  1.204373e-01 #> Fzd7      0.1678221524  0.048668836 -0.007165167  0.1620989999  2.228624e-01 #> Slc47a1   0.0928683087 -0.025838626 -0.004168962 -0.0462685562  1.755251e-02 #> Ptger3    0.0249441519 -0.001156395  0.066937072 -0.1144621314 -1.752300e-01 #> Bdkrb1   -0.0085581111  0.002578463  0.047835175 -0.0263849742 -1.242401e-01 #> Traf4     0.0391640386  0.047990809 -0.009616797 -0.0261957322 -5.084471e-02 #> Cx3cr1    0.0938215373 -0.153063345 -0.019751679 -0.0025127260 -2.515914e-02 #> Anxa11   -0.0691047768  0.044786100  0.101128845 -0.0897481016 -1.890360e-01 #> Adgrb1   -0.0202667639  0.032484300 -0.038693140 -0.0397780956  1.208404e-01 #> Lpar1     0.0441309496 -0.067667745 -0.099856535 -0.0865986103 -6.077921e-02 #> Gpr17    -0.1071898757 -0.026963294 -0.017954576 -0.0075553221 -4.570432e-02 #> Cxcl12   -0.0585808077 -0.018787414 -0.162147952  0.1595591740  1.395589e-01 #> Epha4     0.0768834015  0.075467766 -0.019952318  0.0502040560  3.346546e-03 #> Gpr182   -0.0332409530  0.053377236  0.059545265  0.1059979898 -9.267929e-02 #> P2ry14    0.0726907181 -0.025061899  0.079530561  0.0112854547 -6.369785e-02 #> Hcar1    -0.1633868715 -0.097974787 -0.008102099  0.0059583586  3.634126e-02 #> Ephb1     0.0710242059  0.008265060 -0.011766185 -0.0336930429 -1.246034e-01 #> Grm3     -0.1163558580 -0.089911134 -0.009700036 -0.0040474147 -3.799352e-02 #> P2ry1     0.0427740614  0.043239623  0.078023330  0.0319931904  5.880956e-05 #> Ptk7     -0.1738777322  0.052519091 -0.042623964 -0.1358588876  1.645579e-02 #> Slco1a4  -0.1660790632  0.019009683 -0.082900310  0.1029068528  2.165118e-02 #> Insrr    -0.0928055497  0.163208850  0.022016892  0.0022208850 -6.100030e-02 #> Cmklr1   -0.0590268033  0.059089742 -0.037832479 -0.0261682465  1.021090e-01 #> Fzd6      0.0814355924 -0.003491441 -0.045973029 -0.0666552074 -5.901591e-02 #> S1pr5    -0.0598604617 -0.047335127  0.119767018  0.1640621887 -1.027682e-01 #> Pdgfrb    0.0465640210  0.066835296 -0.067035620 -0.0153185467  2.285277e-02 #> Flt1     -0.0092385127 -0.042416897  0.049647706 -0.0583126319 -7.909645e-02 #> Adgrl4    0.0069503370 -0.096620230 -0.027487525  0.0796945660  4.537073e-02 #> Lpar6    -0.1398854117  0.110902226 -0.026424475 -0.0157460599  5.261836e-02 #> Epha6    -0.0369973971 -0.164994019 -0.089436246  0.0168503290 -1.203159e-01 #> Emcn      0.2115045287 -0.121183948  0.179578346  0.0537757069  7.795342e-02 #> Cldn5     0.0613105591  0.076964392  0.040354729 -0.0988317227 -5.127217e-02 #> P2ry12   -0.0989624810 -0.040632207  0.020763570 -0.0522155059  2.673458e-02 #> Adgrf5    0.0828021697  0.089861284 -0.039354838 -0.0764565689  7.172751e-02 #> P2yr13   -0.0106891485 -0.017404493  0.001497426  0.0701777053  2.367790e-03 #> Adgre1    0.1001691670 -0.058688563 -0.013093919 -0.0098932845  2.375173e-02 #> Cx3cl1   -0.0555806187 -0.006286973 -0.022344697  0.0126028107 -9.688128e-04 #> Plxnb3   -0.0627204933 -0.088464068 -0.108271845  0.0101599412  3.946018e-03 #> Flt4     -0.2133975423 -0.125710608  0.052823970  0.0710389894 -3.312774e-02 #> Slc17a7  -0.0505456723 -0.044776726  0.019705770  0.0256305387 -5.015696e-02 #> Cd300c2   0.0100762109  0.050145541  0.092825455  0.1807528684 -5.933996e-02 #> Tek      -0.1690315426 -0.006420412 -0.059917126  0.0687387921 -8.067318e-04 #> Kdr      -0.0216746530 -0.057733516 -0.015496832  0.0194170503  5.277487e-02 #> Kcnj8     0.0048492597  0.047815100 -0.027415876 -0.0174393384  3.705245e-03 #> S1pr3    -0.0133622568 -0.032569877  0.067335411  0.0517770278  8.648706e-03 #> Tie1     -0.0813937966  0.042748703  0.003829562  0.0671889582  8.277435e-02 #> Pdgfra    0.0844983769 -0.052890325  0.115692019  0.1425262203  6.502142e-03 #> Baiap2   -0.0495186221 -0.105370594  0.095621026 -0.0877162658  1.251348e-01 #> Calcrl    0.0171005829 -0.033301150  0.063428463 -0.0668652827 -2.878973e-02 #> Adrb2    -0.0545787266 -0.210736922 -0.006614800  0.1604319958  1.237050e-01 #> Ccr2      0.0486999428 -0.098751510 -0.018711936 -0.0940158727  6.600146e-02 #> Alk      -0.1281344268  0.057304179 -0.058180620  0.0231666822 -3.856565e-02 #> Tacr3    -0.0624874037 -0.060614775  0.054495520 -0.0031829469  6.899449e-02 #> Erbb3    -0.0318475367  0.051369818  0.229836184  0.3004098202 -9.301888e-02 #> Pcdh15   -0.0430571176  0.103826398 -0.111215853  0.0970499275 -3.404765e-02 #> Grm7      0.0308857561  0.034880551  0.017555921  0.1518007948  6.885951e-02 #> F2r       0.0693665195 -0.201531214  0.345891709 -0.0454395100  3.700176e-02 #> Bdkrb2    0.2295575534  0.078549079  0.100648451 -0.0856030137 -7.896300e-02 #> Adgrv1   -0.0449550964  0.041159438 -0.198280336 -0.0178788815  6.412251e-02 #> Gprc5c   -0.0656708945  0.027526430 -0.007290792  0.0359554806  1.067112e-01 #> Tbxa2r   -0.1236270098  0.057306799  0.014556965  0.0090341568 -6.702018e-02 #> Ackr1     0.2019164143 -0.234676721 -0.032979505  0.0005812258  7.227304e-02 #> Lpar2     0.0495377903  0.079276116 -0.013536164 -0.1024118476 -2.978569e-02 #> Myh11     0.0322153722 -0.043370218 -0.015074004 -0.0240286296 -3.526565e-02 #> Musk      0.0990223092  0.094426541 -0.088036548  0.0163395110 -9.953970e-02 #> Cnr1      0.0785426673  0.023099311 -0.133322489  0.1013142557 -1.995846e-01 #> C3ar1     0.0089530762  0.046399448  0.032945168 -0.1216708792 -2.978944e-02 #> S1pr4     0.0300642851 -0.023770659 -0.059571937 -0.0696792762 -2.007499e-02 #> C5ar1    -0.2073652922  0.074308233  0.060042149  0.0687461017 -3.583460e-02 #> Fpr1     -0.0221856605 -0.022539129 -0.007247489 -0.0427372570 -1.640045e-02 #> Sctr      0.0235396431  0.041648525  0.033444745 -0.0225587535 -6.691755e-02 #> Gpr158    0.0329766739 -0.008530823 -0.040119471  0.0551543138  2.482754e-02 #> Cxcr4     0.0110892309  0.010852805  0.017564773 -0.0319806229  4.485823e-03 #> Hrh2     -0.0590743981 -0.010835017 -0.080590549 -0.1044074036 -1.246771e-02 #> Slc17a6  -0.0068493293 -0.018315494  0.012681583 -0.0238077598 -3.252311e-02 #> Ppp1r3g  -0.0526824261  0.107266646  0.015914684 -0.0064860291 -5.238345e-02 #> Pln       0.0109083191 -0.003322155 -0.101150780 -0.0431099968 -3.825230e-03 #> Grin2b   -0.0462492966  0.042369776  0.063174970  0.0331090631  3.820993e-02 #> Taar7e    0.0269635584  0.032332698 -0.042802051  0.0661121035  1.026312e-02 #> Ptger2   -0.0988007030 -0.224716974 -0.050034239 -0.0078701686  6.715279e-02 #> Mc4r     -0.0564594875 -0.179600625  0.228255492 -0.2039794284 -6.088343e-02 #> Ghsr     -0.0314799375  0.100300289 -0.012627397  0.0341753911  7.570183e-02 #> Nmbr      0.1466676367 -0.204003125 -0.254970016  0.2650677475 -4.621425e-01 #>                 Dim.46       Dim.47       Dim.48        Dim.49        Dim.50 #> Mlc1     -3.609612e-02 -0.066023377 -0.053245137 -0.0005666037  0.0005694164 #> Gprc5b   -8.469528e-02  0.156788151 -0.178225691 -0.0430244562 -0.0058373110 #> Gfap     -2.304603e-03 -0.008335894  0.027302635 -0.0095727295  0.0672685467 #> Ednrb    -7.193897e-02 -0.052959499  0.073387052  0.0868422292 -0.0074431370 #> Sox9     -4.431520e-02 -0.020581213 -0.079456079  0.0278801967 -0.0388738143 #> Aqp4      6.480487e-02  0.147580811 -0.036645535  0.0332258593 -0.0662155403 #> Gjc3      7.700075e-03 -0.151583195  0.045329570  0.1172799084 -0.0156182814 #> Sox8      4.742613e-02 -0.090087077  0.163979039 -0.0479065251 -0.1451686967 #> Ntsr2    -3.653848e-02 -0.018134522 -0.048345420 -0.0309826351  0.0105251743 #> Smo       1.877413e-01  0.196898790  0.114488102  0.0718535764  0.0856293831 #> C1qb      2.697623e-02  0.004236971  0.015446251 -0.0043411963 -0.0142665905 #> Olig1    -4.165291e-02  0.009604809 -0.131364599 -0.0439190482  0.1051083608 #> C1qa      4.377265e-02  0.083205303  0.071208712 -0.0013364060  0.1146369009 #> Pth1r    -1.575574e-01  0.096925470 -0.083282442  0.0997044510  0.0510609958 #> Gabbr2   -8.843364e-02 -0.161704077 -0.017095519 -0.0747410166 -0.0106345464 #> Timp4     1.148117e-01 -0.062397296  0.066438613 -0.0242846595  0.1555480638 #> Abcc9     1.094394e-01 -0.133622774  0.100885708 -0.0725002218  0.0606758793 #> Csf1r     1.529788e-01 -0.064328988 -0.086918057  0.0570521826 -0.1610032030 #> Ntrk2    -1.568100e-01  0.020994619 -0.007712980 -0.0071612051  0.0005229980 #> Adgrg1    2.388182e-02  0.017904895  0.008883993  0.0907701719 -0.1134864979 #> Ntrk3     1.106170e-01 -0.038423826  0.166696207 -0.0390014122 -0.0124688828 #> Erbb4     1.116445e-02 -0.011645203  0.009943270 -0.0056019374  0.0400326242 #> Selplg   -5.638070e-02  0.089465919  0.004589622 -0.0548685004 -0.0583841987 #> Cspg5     5.524470e-02  0.030915217 -0.133723908 -0.0156598612 -0.0056119573 #> Dlk1     -1.691182e-02 -0.128126549  0.010692953  0.0109357761 -0.0418994030 #> Gpr37l1   1.316078e-02 -0.070534856  0.139736417 -0.1249194281  0.0115320440 #> Fgfr3     8.364816e-02 -0.053370913  0.007261560  0.0221187734 -0.0028121421 #> Slc25a18 -7.118463e-02 -0.046701857  0.177465437  0.1952373504 -0.1292617254 #> Igf1r     1.026437e-01  0.110101990  0.081509743  0.1102287335 -0.0584441439 #> S1pr1     5.567532e-02 -0.010694832 -0.040164707 -0.0608230405  0.1521623432 #> Grm5      6.201133e-02  0.058192032 -0.034622390  0.0158311712  0.0945483831 #> Axl       1.313275e-01  0.001977299 -0.020392755 -0.0276729913 -0.0806823629 #> Efemp1   -1.022657e-01  0.036512620 -0.046267284 -0.1076514739 -0.0809859402 #> Adgrb3   -4.949285e-01 -0.022663479  0.200950151 -0.0393112140 -0.1533070751 #> Fn1      -1.143007e-01 -0.048965937  0.065166511  0.0948981952  0.0548166495 #> Mertk     7.734030e-02  0.029783392 -0.056683599  0.0415095697  0.2629019425 #> Adgrl2   -1.131086e-01  0.021964402  0.067595697  0.0198870424  0.0162037952 #> Fzd2      4.293113e-02 -0.088300269  0.087094340  0.0845049126 -0.0031670489 #> Aldh1l1   5.108596e-02  0.086922550 -0.065408401 -0.0866080823 -0.1793221836 #> Adgrg6    2.944860e-02  0.106268603  0.031681147 -0.1432775296  0.0241733100 #> Egfr     -9.949434e-02 -0.040076814 -0.003998721 -0.1417275200  0.0466602180 #> Kit      -9.576071e-02  0.049670300  0.011304211  0.0139331049 -0.0969204721 #> Ptgdr     2.987458e-02  0.046214553 -0.040824686 -0.0169567198  0.0861548332 #> Gad1      9.164643e-02  0.022376024  0.025937564  0.0174945240  0.0475197611 #> Tyro3    -1.012704e-01 -0.041053530  0.044575843 -0.0065171212  0.0870308019 #> Atp13a5   9.461724e-03  0.059848088  0.141217643 -0.1080931965 -0.1725735076 #> Ddr2     -3.336392e-03 -0.119776309 -0.100137104 -0.1072134262 -0.0186774712 #> Rspo3     1.431303e-01  0.120579759 -0.012950821  0.0869925988  0.0450280875 #> Arhgap29  1.097046e-01 -0.031582415 -0.231677106 -0.2123062495 -0.0144360578 #> Fzd7      4.812392e-02  0.045110462 -0.031251585  0.0528964049  0.0759748684 #> Slc47a1   2.689901e-02 -0.027593765  0.021204320  0.0133751215  0.0038773672 #> Ptger3   -1.217134e-01  0.107218245 -0.051536892  0.1308241241  0.0220483563 #> Bdkrb1   -1.237338e-01 -0.092245230  0.033552353  0.0570350297 -0.0516797543 #> Traf4     4.195331e-02 -0.053424190  0.019911588  0.0698559999 -0.0369034440 #> Cx3cr1   -1.374479e-01  0.115105459 -0.036614082 -0.0230737572  0.0243591138 #> Anxa11   -1.211922e-01  0.108175113 -0.116850119 -0.0307037486  0.0038767990 #> Adgrb1   -7.540231e-03  0.114818114  0.031592661 -0.0394018280  0.0064328615 #> Lpar1     6.743333e-02  0.036049384  0.130893921 -0.0154479875  0.0364291955 #> Gpr17    -3.424863e-02  0.099316050 -0.073836667 -0.0715334048 -0.0687982666 #> Cxcl12    7.118673e-03  0.078789436 -0.026506266 -0.0165250610  0.0276787455 #> Epha4    -1.077804e-01  0.005086550 -0.023424819 -0.0455338281 -0.0124169517 #> Gpr182   -5.127006e-03 -0.072255659  0.020643640 -0.0844610137  0.0384675086 #> P2ry14   -2.827262e-02 -0.017776785  0.069439084  0.0761260372 -0.0174479531 #> Hcar1     8.245219e-03 -0.169307515 -0.061136870  0.1048085002 -0.0125887689 #> Ephb1     7.933501e-02  0.009227109  0.043837704  0.0663940034  0.0013681269 #> Grm3      1.054366e-01  0.120671946  0.043812672 -0.0605719915 -0.0004615742 #> P2ry1    -1.241989e-01 -0.021344066 -0.015276009 -0.0891443634  0.1655238112 #> Ptk7      3.692229e-02  0.058365021  0.075297973 -0.0905807420 -0.2444265390 #> Slco1a4   3.960095e-02  0.012265630 -0.010000152  0.1347170749 -0.0790255671 #> Insrr     3.303288e-03 -0.056063168 -0.005658957  0.0366097474  0.0985863987 #> Cmklr1   -4.452884e-02 -0.079240285 -0.013233330  0.0314729793 -0.0262771918 #> Fzd6     -7.683884e-02  0.018953054  0.024373600  0.0324010441  0.1798808272 #> S1pr5     3.522360e-02  0.089564115  0.048410357 -0.0149731097 -0.0609867657 #> Pdgfrb    4.186066e-02  0.137317609 -0.149704384  0.1605377461  0.0292368222 #> Flt1     -4.515999e-02  0.079880039 -0.024935392 -0.1129170978 -0.0617926831 #> Adgrl4    2.230768e-02 -0.017956311  0.170414455 -0.1435166252  0.0963468776 #> Lpar6    -2.674174e-02 -0.176404229  0.100057704  0.0626369705  0.0749259054 #> Epha6     7.858181e-02 -0.092516939  0.004377653  0.0306614981 -0.0255877222 #> Emcn     -1.344921e-02  0.023755042 -0.207196493  0.2694192183 -0.0485825614 #> Cldn5    -1.662330e-02 -0.158216302 -0.053101664 -0.1886431748  0.0717726190 #> P2ry12   -1.238912e-02 -0.137329994  0.034529932  0.0091707142  0.0243161908 #> Adgrf5    2.284301e-02 -0.040937827 -0.021443237  0.0466198889 -0.0056802832 #> P2yr13   -1.113402e-02  0.014574959  0.014752478  0.0086699233  0.0154175081 #> Adgre1   -6.912791e-02 -0.026799727  0.018465152 -0.0136996215  0.0878366603 #> Cx3cl1   -2.685946e-02 -0.004512758 -0.013716984  0.0712291447  0.0486563910 #> Plxnb3   -6.405360e-02 -0.149172617 -0.090804014  0.0417755528  0.0114148640 #> Flt4      5.907203e-02 -0.165345418  0.065359515 -0.0580646987  0.0415148139 #> Slc17a7   2.502915e-02 -0.016152172 -0.011883352 -0.0275565058 -0.0649342280 #> Cd300c2  -9.178146e-02  0.146457911 -0.020980943 -0.0800686876  0.0117010951 #> Tek      -1.247060e-01  0.195125143  0.165550610  0.1597793441  0.0460309093 #> Kdr       1.436761e-02  0.013748201  0.043503363  0.2167032530 -0.0962465898 #> Kcnj8     3.780850e-02 -0.025929378  0.059541479 -0.0956904279  0.0526446523 #> S1pr3    -3.972054e-02 -0.086951394 -0.095395602  0.0551027782  0.0617825207 #> Tie1      1.494018e-01  0.104714932 -0.164364053 -0.0279915791 -0.2775782010 #> Pdgfra    3.014636e-02  0.051950432  0.165056354  0.0108871135  0.1149001052 #> Baiap2    8.481868e-02  0.054147008  0.064370961 -0.0088778323  0.0647071059 #> Calcrl   -1.175377e-01  0.074866839  0.063846494  0.2647417594  0.0094264784 #> Adrb2     1.369878e-02  0.028184139  0.007398724 -0.0849416283 -0.0538219816 #> Ccr2     -4.657241e-02 -0.079828485  0.017568886 -0.0839860010 -0.0314660612 #> Alk      -1.205000e-01  0.055750041 -0.031115226 -0.0926035406 -0.0500224877 #> Tacr3    -6.684064e-02  0.115898428  0.045611750 -0.0546322233 -0.0053085325 #> Erbb3    -1.296998e-02  0.129768155 -0.043497459 -0.0888212158 -0.0727856626 #> Pcdh15    2.671940e-02  0.001984140  0.036070622  0.0317228147  0.0873590711 #> Grm7      2.012896e-02 -0.010720198 -0.124076272 -0.0436772126 -0.0242379365 #> F2r      -2.145095e-02 -0.087422879 -0.200238742  0.2059786884 -0.1690432175 #> Bdkrb2    6.887812e-02 -0.011827868  0.124269712  0.1010077276  0.0610755412 #> Adgrv1    1.165612e-01  0.135440541 -0.059904482  0.0960754086 -0.1401058307 #> Gprc5c    6.391407e-02 -0.086733937 -0.080728177  0.0642973633  0.0895423161 #> Tbxa2r   -2.620424e-01 -0.032525551 -0.039874820 -0.0101757904 -0.0547843895 #> Ackr1    -2.547614e-02  0.053859953 -0.047158504  0.1347045621 -0.0575774110 #> Lpar2     3.800211e-02 -0.018605194  0.015109368  0.0438630718 -0.0062211486 #> Myh11     3.661799e-03  0.041543829 -0.011517432 -0.0810440828 -0.0120298574 #> Musk      1.254369e-01 -0.132897852 -0.085905798  0.0486926957 -0.0761179113 #> Cnr1     -6.078101e-02  0.029842763  0.020466309  0.0304315238 -0.0967712847 #> C3ar1     1.584089e-02 -0.146050154 -0.095446285  0.0278511398 -0.1640907807 #> S1pr4     4.631400e-02  0.010700759  0.011934261 -0.1105711788  0.0220394998 #> C5ar1    -1.782270e-02 -0.165383874  0.013860161  0.2538840182  0.1089257050 #> Fpr1     -1.089135e-02 -0.002540849 -0.030889116 -0.0527753640 -0.0560091472 #> Sctr      8.630072e-02  0.028219200  0.054964188 -0.0189475737 -0.0537832914 #> Gpr158    6.188227e-02 -0.055164521 -0.073148122  0.0714465893  0.1435800291 #> Cxcr4    -6.876068e-03 -0.035561742  0.011770111  0.0233199208  0.0643347245 #> Hrh2     -4.839773e-02  0.148475076 -0.203035365 -0.0343350389  0.2645500263 #> Slc17a6  -4.883941e-02 -0.009926849 -0.019351003 -0.0292647483 -0.0139834019 #> Ppp1r3g  -1.246256e-02  0.120582253  0.028793909  0.0059616133  0.0109484360 #> Pln      -4.313203e-03  0.053020230  0.050700097 -0.0391119953  0.0283814353 #> Grin2b   -2.498571e-02  0.016206301 -0.044238756  0.0074485686  0.0857301576 #> Taar7e   -4.859692e-02 -0.108048783 -0.108460696 -0.0561999077 -0.0196165702 #> Ptger2   -1.162974e-01  0.057366116 -0.249926227  0.0827042048  0.1736190167 #> Mc4r      1.149901e-02  0.245347709  0.239972113  0.0903362531  0.0432158993 #> Ghsr      1.223699e-02 -0.026448389 -0.008868179  0.0143234793 -0.0170332587 #> Nmbr     -3.516158e-05 -0.085034858 -0.006184928  0.0429620993 -0.0695392364 #>                 Dim.51        Dim.52       Dim.53        Dim.54        Dim.55 #> Mlc1      0.0864147797  0.0386775355 -0.133413111  0.0380473547 -0.1102939152 #> Gprc5b    0.0357622186  0.0512881874 -0.068807439 -0.0481835083 -0.0437332137 #> Gfap     -0.0217852383  0.0431115841  0.009178273 -0.0011945001  0.0040812457 #> Ednrb     0.1087725419 -0.0808638138 -0.071338394  0.0744174277 -0.0570105994 #> Sox9     -0.0176324689 -0.0826078232  0.152889225 -0.0917811558  0.0779147201 #> Aqp4     -0.0203445968 -0.0488174547 -0.016860661 -0.1032182345 -0.0363172386 #> Gjc3      0.1275113456 -0.0483121278 -0.019414639  0.1850497168  0.0011071938 #> Sox8     -0.1224535096 -0.1750904596  0.026583489  0.0173817150 -0.2252728971 #> Ntsr2     0.0140366587  0.0246952728  0.078319518 -0.0935201998  0.1169457543 #> Smo      -0.1031320026 -0.0359235598 -0.133693345  0.2038910383  0.1063444765 #> C1qb      0.0521542841  0.0094092029  0.002476313 -0.0246306159  0.0789103045 #> Olig1     0.0632934579  0.1449316489 -0.041198344  0.0611857623  0.0209697656 #> C1qa     -0.0656778650 -0.0254267826 -0.010955781 -0.0322721651  0.0374617121 #> Pth1r     0.0043895416 -0.0242733733  0.043880080 -0.0091430761 -0.0828741787 #> Gabbr2   -0.1374284613  0.1593460484 -0.059018276 -0.0275923685 -0.0399142930 #> Timp4    -0.0372242762  0.0271928268 -0.046978817  0.0956635701  0.0298385358 #> Abcc9    -0.0097259150  0.0314977534 -0.059431355  0.0274230190 -0.0052770571 #> Csf1r     0.0365952849 -0.0530367985 -0.072551262 -0.1872273090  0.0377306235 #> Ntrk2    -0.0194439843  0.0458547563 -0.048510111 -0.0597154606  0.0962834845 #> Adgrg1    0.0537804033  0.0166895477 -0.177489015  0.0122632813 -0.0093721989 #> Ntrk3    -0.0107225687  0.1100880625  0.014048952  0.0036945658  0.0791101853 #> Erbb4    -0.0440979329 -0.0123564634  0.039606601  0.0756432951 -0.0160496844 #> Selplg    0.0365344378 -0.0346125185 -0.132803428  0.1123293706 -0.0386259852 #> Cspg5     0.0517471169  0.0396240554  0.097696563  0.0373313387 -0.0593615155 #> Dlk1      0.0124225637 -0.0393928657  0.007115968 -0.0081002040  0.0062991755 #> Gpr37l1  -0.1375541205 -0.1426914677 -0.060408516  0.0049487567 -0.0002983586 #> Fgfr3     0.0704441310  0.0585355837 -0.005745559  0.1263525434 -0.1804427983 #> Slc25a18  0.1478459139 -0.0337286097 -0.052206896  0.0031981546  0.0202625142 #> Igf1r    -0.0676919148  0.2215479203  0.061604277 -0.1322078028 -0.0126485227 #> S1pr1     0.0217424181  0.0562988675  0.128672369 -0.0469290099 -0.0317916341 #> Grm5      0.1267232607 -0.1821298370  0.052846292  0.0424923720  0.0076355397 #> Axl      -0.0266549669 -0.0821029583  0.157901071  0.1279416129  0.0841713056 #> Efemp1    0.0433298740  0.0100590464  0.041090086  0.1147784825 -0.0637470063 #> Adgrb3    0.0340548251 -0.1994057731 -0.051887088 -0.0113294532 -0.0464800559 #> Fn1      -0.0349162454 -0.0401352883  0.048224773  0.0975955940  0.0997022949 #> Mertk    -0.1276267847  0.0775079185 -0.288190844  0.0569550685  0.0789090251 #> Adgrl2   -0.0241442306  0.0409112631 -0.096203450  0.1597259033  0.2413268814 #> Fzd2     -0.0419992850 -0.0180222553  0.022547760  0.0522350728 -0.1547725775 #> Aldh1l1   0.0422315537 -0.0231634494  0.034038794  0.1446442523  0.0158639102 #> Adgrg6   -0.0717403643 -0.0676177911  0.148759259 -0.0519620856  0.0842916639 #> Egfr      0.0284834388  0.0211036995  0.036558208 -0.1104781039  0.0106323406 #> Kit      -0.1765353989  0.0376083486  0.021545916 -0.0218771945 -0.0990823513 #> Ptgdr     0.0148796399 -0.0376569535  0.050108165  0.0071623126  0.1663118745 #> Gad1     -0.0541977029 -0.0163372119 -0.042973321 -0.0069105205  0.0047448288 #> Tyro3    -0.0569203364  0.0612726675  0.076203210 -0.0103244686  0.1607574988 #> Atp13a5   0.0113448248 -0.0653265478 -0.020052422  0.0191948702  0.0960118564 #> Ddr2      0.1681851656  0.0887515342 -0.052155085 -0.1562335324 -0.1977053642 #> Rspo3     0.0761000666  0.0035596410 -0.139773838  0.0350979016 -0.0044469695 #> Arhgap29  0.1667256161 -0.0773465523  0.093483749 -0.1120105349  0.0800865191 #> Fzd7      0.0391600922 -0.0131202374  0.180511473  0.0186110798 -0.0531900152 #> Slc47a1  -0.0121339774  0.0097956856 -0.055939685 -0.1478033048 -0.0290117398 #> Ptger3   -0.1227445202 -0.0024991875  0.030960076  0.1176523492  0.0523231574 #> Bdkrb1   -0.0563752401 -0.0242625363 -0.087956660 -0.0940087552 -0.0667586016 #> Traf4    -0.0111792112 -0.0426464501 -0.050267124 -0.0376267512 -0.0430799491 #> Cx3cr1   -0.1162055761 -0.0069438933 -0.028212431  0.2117797684 -0.0446537063 #> Anxa11    0.0353237978  0.1567190027 -0.054605970  0.1923689361 -0.0701103530 #> Adgrb1    0.0516243637 -0.0522654985  0.071080233 -0.0161336593  0.0100539573 #> Lpar1    -0.1384795678  0.0768995198 -0.144919035 -0.2200563502 -0.0663261050 #> Gpr17    -0.0746612602  0.0197536996  0.047348650 -0.1552907405 -0.0153074045 #> Cxcl12    0.0648913479 -0.0195018206 -0.026275858 -0.0723587833 -0.0564373482 #> Epha4    -0.0843040721 -0.0892352884  0.070502520 -0.0443669373 -0.0984616705 #> Gpr182   -0.0667528492  0.0433835251 -0.018812028 -0.0795079381  0.0061116662 #> P2ry14   -0.0449297426  0.0001195871  0.041216992 -0.0290320869 -0.0599709389 #> Hcar1    -0.1029181773 -0.1187874358 -0.146846265 -0.0006462698 -0.0039605024 #> Ephb1    -0.0616231277 -0.0751957167  0.035772510  0.0283280176 -0.1165143517 #> Grm3     -0.1007750989 -0.0433463680  0.135596165 -0.2009154012  0.1526114637 #> P2ry1     0.0233721854 -0.0638652285  0.016604629  0.0815173824  0.2315074879 #> Ptk7      0.0551579326  0.0445516383 -0.030319575  0.1172336511  0.0345609210 #> Slco1a4  -0.0087573577  0.0269395471  0.009395579 -0.1086067520  0.0605262607 #> Insrr     0.1270950449  0.0333949654  0.028659257  0.0734937210 -0.0372920581 #> Cmklr1    0.0344742592 -0.0113610834  0.013208863 -0.1708795430  0.0564534510 #> Fzd6     -0.0480376453  0.0350960455  0.126015787 -0.0412247023 -0.1663803009 #> S1pr5    -0.0582889903 -0.1316655993  0.012547598 -0.1397729434 -0.0412782701 #> Pdgfrb    0.0553378559  0.0080545505  0.112178670  0.0565945132 -0.1531415817 #> Flt1     -0.0775316321  0.0033952380 -0.061223744  0.0375820168 -0.0100047921 #> Adgrl4   -0.0081703643 -0.0834951982 -0.070501790 -0.0046751832 -0.0808977607 #> Lpar6     0.1223878463  0.0904897121  0.021726169 -0.1141456456 -0.0238123549 #> Epha6    -0.1143417531 -0.1650457045  0.038605281  0.0363261512  0.1822764977 #> Emcn     -0.0386266207  0.0852658395  0.038754419 -0.0403708596  0.0141791906 #> Cldn5     0.1123573616  0.0005760496 -0.018919683  0.0838494382 -0.0193509681 #> P2ry12    0.0229225179  0.0271101977  0.248601936 -0.0514222400 -0.0730620449 #> Adgrf5    0.0353231917 -0.0305784655 -0.012003946 -0.0538631125  0.0138152743 #> P2yr13    0.0270066085 -0.0380045514  0.070438540 -0.0439513987 -0.0244272732 #> Adgre1    0.0166776146  0.0691432729  0.067586534  0.0852109952 -0.0388432612 #> Cx3cl1   -0.0709108140 -0.1656054901 -0.005206945  0.0076716132  0.0551430461 #> Plxnb3    0.1009669067  0.0442974416  0.073272872 -0.0135246931  0.0790419632 #> Flt4      0.1086011493 -0.0605052837 -0.081719541  0.1028148958 -0.1342517212 #> Slc17a7   0.0808908105  0.0051317339  0.042305490  0.0567588205 -0.0031208272 #> Cd300c2   0.0183229148  0.0463674993 -0.252995102 -0.0309029261 -0.0998193754 #> Tek      -0.0551530251 -0.0582152041  0.233546927  0.0202078696  0.0123374170 #> Kdr      -0.1234118278 -0.0380859398 -0.039075774 -0.1609766667  0.1003331397 #> Kcnj8    -0.0103127285  0.0090620487  0.038700421 -0.0007958727 -0.0718108080 #> S1pr3    -0.0179677873  0.0380877212 -0.113772651  0.0039253432  0.0231778531 #> Tie1      0.0789047663 -0.1362516867 -0.039528137  0.1252079846  0.0525015330 #> Pdgfra    0.1019353138 -0.0312812942  0.003423582  0.0652608374  0.0743515118 #> Baiap2    0.1135912593  0.0219881411 -0.196006178 -0.1041168499 -0.0063890775 #> Calcrl   -0.0500724961 -0.0178709405  0.094389259  0.0691643926 -0.1170290672 #> Adrb2    -0.0595874908 -0.0390308949  0.144321534  0.1129875063 -0.0433099847 #> Ccr2      0.0654393950  0.0474509109  0.101245875 -0.0163764868 -0.0554918076 #> Alk       0.0442256589  0.0983084350 -0.040820285 -0.0361424587 -0.0345972165 #> Tacr3     0.1237807279  0.0658279984 -0.006089670 -0.0185418645  0.0645658705 #> Erbb3    -0.0340301323 -0.0390831253 -0.037639453 -0.0582994065 -0.0701854955 #> Pcdh15   -0.0374600639 -0.0224354030 -0.019501705 -0.0307194305  0.0861771739 #> Grm7     -0.1031227969  0.3295882376  0.118844898  0.0816743708 -0.1236703326 #> F2r       0.0931193789 -0.0836869052 -0.072068031  0.0333319191  0.1457884560 #> Bdkrb2    0.1627554070  0.0323463867 -0.054462392 -0.0971855631  0.0458285246 #> Adgrv1    0.0326083983  0.0377132153  0.037772805  0.0637532060 -0.1303758168 #> Gprc5c    0.0285250798 -0.0342096719 -0.056161499  0.0352883874  0.0546336930 #> Tbxa2r   -0.0233685859 -0.0140499300 -0.110105667 -0.0845488830  0.0240069920 #> Ackr1    -0.1012257854  0.1453868666 -0.204118822 -0.1431468391 -0.0383348973 #> Lpar2     0.0507513654  0.0161347153 -0.008616978 -0.0374190895 -0.0061587505 #> Myh11    -0.0155853017 -0.0046230824 -0.093167296  0.0473299380 -0.0628617684 #> Musk     -0.2221807449 -0.0659729925  0.022494216  0.0643440995 -0.1329958905 #> Cnr1      0.1975243417  0.0187672712 -0.018177801  0.0053602430  0.0616084661 #> C3ar1    -0.0381349950 -0.0744630426  0.069071944 -0.0494524922 -0.0451792090 #> S1pr4    -0.0419322910  0.0252769481  0.068791113 -0.0812493796  0.0012319352 #> C5ar1     0.0316802085  0.0356658521  0.122734759  0.0562466352 -0.0950808980 #> Fpr1     -0.0447367180 -0.0402554942  0.030249584 -0.0404073607  0.1518325236 #> Sctr      0.0005447204 -0.0305494889 -0.038582735  0.0843803157 -0.1776756301 #> Gpr158   -0.0341123742 -0.2321943439 -0.068175887 -0.0468304160 -0.0669802745 #> Cxcr4     0.0388084855 -0.0091183998  0.050108364  0.0228397673  0.0069202841 #> Hrh2      0.1102837536 -0.4622618107 -0.083352128 -0.1182196817 -0.2069093626 #> Slc17a6   0.0508423015 -0.0074970378  0.023322623 -0.0106506421  0.0541894186 #> Ppp1r3g  -0.0049939163  0.0635975777 -0.029785943  0.0447019980  0.0430259291 #> Pln      -0.0184412729 -0.0096171260  0.082225912 -0.0304172113 -0.1192326741 #> Grin2b    0.0246089221  0.0405930431 -0.005237479 -0.0605258111 -0.0156904103 #> Taar7e   -0.1608751357  0.0471814613  0.010069119  0.0267038913  0.0625994078 #> Ptger2   -0.0328753449 -0.0262785831  0.014433540 -0.0301211417  0.0668181404 #> Mc4r      0.3421843377  0.0888456847  0.074044448 -0.1326400789 -0.0619409513 #> Ghsr     -0.0176841854  0.0245916486 -0.038920106 -0.1558940969  0.0005784895 #> Nmbr      0.2825238073 -0.0171862648  0.014508438 -0.0115176735  0.1321641075 #>                 Dim.56        Dim.57        Dim.58        Dim.59       Dim.60 #> Mlc1      0.0125631175 -0.1258394688  0.0812768551 -0.0325152883  0.031562163 #> Gprc5b   -0.0305652385 -0.1085300649  0.1563698599  0.0231201457  0.070045161 #> Gfap      0.0021355509  0.0714058083  0.0763472244  0.0650322037  0.025693299 #> Ednrb     0.0584635092 -0.0767763288  0.0033938626  0.0378251709  0.066705871 #> Sox9      0.0805272566  0.0447301351 -0.0421526508 -0.1616761853 -0.159880316 #> Aqp4      0.0037243270 -0.0993403374 -0.2890032234 -0.0982454411  0.016497111 #> Gjc3      0.0101608573 -0.0619153596 -0.1513878036  0.0363212652 -0.110972943 #> Sox8     -0.0809782644 -0.2348320443  0.1566087641 -0.1970185600  0.009194735 #> Ntsr2     0.0389614486  0.1332368717  0.0042891304  0.0609521324 -0.016232585 #> Smo       0.1625453672 -0.0931763845  0.1032452338 -0.1873871441 -0.093587081 #> C1qb     -0.0288261215 -0.0201602299 -0.0335959487 -0.0114946500 -0.017538837 #> Olig1     0.0371927417  0.1044543073  0.0352491176 -0.0223503292 -0.049835683 #> C1qa      0.0184349063 -0.1299580747 -0.0968623043 -0.0704076438  0.102272300 #> Pth1r    -0.0190940473 -0.0458870239 -0.0230064508 -0.1267705292  0.025322508 #> Gabbr2    0.1279993443 -0.0819635234  0.0471205739  0.2377004740 -0.253864197 #> Timp4    -0.0103226545  0.0003300398  0.0331626903  0.1600166279  0.029633641 #> Abcc9     0.0127921714  0.1019249124  0.0798386143  0.1099444579 -0.047089993 #> Csf1r     0.0947957477  0.0616803037  0.0983375044 -0.0100382598 -0.024199670 #> Ntrk2     0.0540820596 -0.1076362312  0.0772730011 -0.1136272052 -0.090542287 #> Adgrg1   -0.2011991797  0.1105710216  0.1585851668  0.0814053222  0.002502263 #> Ntrk3     0.0342178396 -0.0922025185  0.0889694032 -0.0793067495 -0.040569347 #> Erbb4    -0.1127841244  0.1241517211  0.0243371267 -0.1387311268  0.003192089 #> Selplg    0.0056001049  0.0113088113  0.0617843140  0.0609322583  0.058498494 #> Cspg5    -0.1066170764  0.1051521321 -0.1719944945  0.0410005258  0.169845449 #> Dlk1     -0.0234520433 -0.0789734466  0.0812137717  0.0552190654  0.088636265 #> Gpr37l1   0.0115143322 -0.0563338750 -0.0050629521  0.0208197517 -0.103656551 #> Fgfr3     0.0512952728  0.0497756409  0.0732161680  0.0359611281  0.031370725 #> Slc25a18 -0.0364136515 -0.0352914382 -0.0115305289  0.1338703486  0.092329169 #> Igf1r    -0.1892876039 -0.0229877867  0.0257016685  0.1801316021 -0.016640364 #> S1pr1     0.1306441830  0.0018101914  0.0274789829 -0.0270158147  0.004429182 #> Grm5     -0.1368760458  0.1791687318 -0.1323974260 -0.1712051647  0.007993431 #> Axl       0.0080953078  0.1027457305 -0.0555705393  0.0558114128 -0.012201843 #> Efemp1   -0.0038693103 -0.0194672109 -0.0292948458  0.0015103619 -0.009499639 #> Adgrb3    0.0418865733  0.0876056078  0.0469282415 -0.0553319753 -0.028042824 #> Fn1      -0.0897428651 -0.0093729182  0.0532934136  0.1546065148  0.073347073 #> Mertk    -0.0428843560  0.0632799155  0.0225563024 -0.1080896706 -0.083921518 #> Adgrl2    0.0117531844 -0.1089285547 -0.0845206599 -0.0329888054  0.024433420 #> Fzd2      0.0156058562  0.2045668585 -0.0374698440 -0.0113486596  0.040327474 #> Aldh1l1  -0.2382201172  0.0128442191  0.0331049428 -0.0374622942 -0.003951492 #> Adgrg6    0.0474139284  0.0184103792 -0.0454821975  0.1156513958  0.066673811 #> Egfr     -0.1069417753 -0.0812671785 -0.0024913128 -0.0072973791 -0.122554489 #> Kit       0.0300642257 -0.0327735101  0.0267065298  0.1065209672  0.025192545 #> Ptgdr    -0.0125397577 -0.0361986382  0.0673530004 -0.0020460572 -0.115916877 #> Gad1      0.0284670439 -0.0464764177 -0.0098412840  0.0544587438  0.060824305 #> Tyro3    -0.1453580209  0.1799962090  0.0752516138 -0.1401475299 -0.025668316 #> Atp13a5   0.1384154615 -0.0586404260 -0.0577130317  0.0174343417  0.006329030 #> Ddr2      0.0155556273  0.0329578665 -0.1493021151 -0.0471333999 -0.006488838 #> Rspo3     0.1616813769  0.0365731059  0.0149345127 -0.0392573731  0.115983276 #> Arhgap29  0.1680927605  0.0079360302  0.1528593729 -0.0222403790 -0.130187594 #> Fzd7      0.0011474288 -0.3060422598  0.0584027983 -0.1677444767  0.022086315 #> Slc47a1  -0.0014693147  0.0327199581 -0.0303133683 -0.0562508697 -0.012478167 #> Ptger3    0.0025240676  0.0807933396 -0.0370147991  0.1870709440  0.026449610 #> Bdkrb1   -0.0054946102  0.0028979903  0.1049069710  0.0207177154  0.244792369 #> Traf4     0.0784828597 -0.0437363600 -0.0738189224  0.0091249010  0.034223995 #> Cx3cr1   -0.0070421751  0.1107192802 -0.0099338258  0.0906263805 -0.025540025 #> Anxa11    0.0279295400 -0.1257517021  0.0385773930 -0.0172069015  0.008509316 #> Adgrb1   -0.0997161699  0.0733953598 -0.1247643052 -0.0680026604  0.123040368 #> Lpar1     0.0024810195  0.0733857149  0.0980163593 -0.1670248625  0.025164236 #> Gpr17    -0.0281835976 -0.0070786767  0.1093938914 -0.0062593664  0.084807261 #> Cxcl12   -0.0205918367 -0.0186568854 -0.1313499570 -0.0362173683  0.065591407 #> Epha4    -0.0882998594  0.0214887514  0.0584114344 -0.0378809914  0.086296819 #> Gpr182   -0.2511028389 -0.1010533342  0.1584131767  0.0759866564 -0.118515215 #> P2ry14   -0.1699238060 -0.0311742208 -0.0810930931  0.0262569617 -0.004472930 #> Hcar1     0.1129573388  0.2409686412 -0.0272745259 -0.0412985034  0.161535440 #> Ephb1     0.0961312701 -0.1512075512 -0.1332085826  0.0929246304  0.091554560 #> Grm3     -0.0437337777 -0.1426346631 -0.0521254244  0.0830198376  0.220799293 #> P2ry1     0.0033777554 -0.0724721100  0.0975151749 -0.0683411033  0.172923042 #> Ptk7      0.0547041952  0.0288532318 -0.2986611777  0.0004828615 -0.155016303 #> Slco1a4  -0.0226297908  0.0337860563  0.0835626158  0.0552278139 -0.165459302 #> Insrr    -0.2437482602  0.0676910275 -0.0780102992  0.0981906440  0.028604828 #> Cmklr1    0.0027984760  0.0086719619  0.0829172848  0.0251346197  0.093161593 #> Fzd6      0.0008739310  0.0235940308  0.0248012771 -0.0825901102 -0.107852996 #> S1pr5     0.0242998373 -0.0273065472  0.0062585725  0.0563690282  0.087205293 #> Pdgfrb    0.0529741275  0.0550393462  0.1198278997 -0.0466095825 -0.029252266 #> Flt1     -0.0986397623 -0.0248673926 -0.1682185910 -0.0347979310 -0.138943493 #> Adgrl4   -0.0433109295  0.0117893302 -0.0717634707 -0.1129017096  0.090181666 #> Lpar6    -0.0659236459 -0.1430136329 -0.0293633463 -0.0277795373 -0.025439290 #> Epha6    -0.1939758161 -0.0343699315  0.0650277523 -0.0893479263 -0.061099359 #> Emcn      0.0495065102 -0.0647088550 -0.0845519180 -0.0093167166 -0.062814480 #> Cldn5     0.0112692681 -0.0160991141 -0.0005573598  0.0446081285  0.169515921 #> P2ry12   -0.0978875638 -0.0492236037 -0.1014475097 -0.0612664767 -0.027145536 #> Adgrf5    0.0752205862  0.0467587796 -0.0148236659 -0.0584500374  0.221630755 #> P2yr13    0.0933062122 -0.0537551669 -0.0219436226 -0.0060993427  0.015400181 #> Adgre1   -0.0099158210 -0.0356890146 -0.0483830547  0.0560885311  0.016669965 #> Cx3cl1   -0.1283467969  0.0980470576 -0.0157475082  0.0216342962 -0.103819901 #> Plxnb3   -0.0130991068 -0.0026998420 -0.0277201108  0.1244705153 -0.024357665 #> Flt4      0.0995414370  0.0028472668 -0.0282088913 -0.1313477633 -0.088914796 #> Slc17a7  -0.0230888467  0.0489992760 -0.0029864940  0.0032591073  0.100060779 #> Cd300c2  -0.0458736418  0.1020948329  0.0983767433 -0.0271564174 -0.043635012 #> Tek       0.2465059035  0.0394645247  0.0940994749  0.0396530885 -0.019712450 #> Kdr      -0.0649951747  0.0812261263 -0.0048572810  0.0271083938 -0.122392433 #> Kcnj8    -0.1014553427  0.0882397342  0.0366640333 -0.0348519591 -0.041307201 #> S1pr3    -0.0902119900 -0.0249242233 -0.0544814138  0.0771760642  0.053455368 #> Tie1     -0.1069020758 -0.0915140356  0.2578190970  0.0134750468  0.033993417 #> Pdgfra    0.0643018899  0.0281471252 -0.0739105961  0.2112805124 -0.041273586 #> Baiap2    0.1104616654 -0.1474351656 -0.0222166970  0.1386394947  0.020071104 #> Calcrl    0.1244032080  0.0365418755  0.0241490890 -0.0537304520 -0.171705872 #> Adrb2    -0.0485114356  0.0123821031  0.0490913193  0.1177803595  0.003030082 #> Ccr2     -0.0608178756 -0.0375105802 -0.0153748349  0.0297278426 -0.063357335 #> Alk      -0.0432839639 -0.0834115848 -0.0841439855 -0.0300399150 -0.027021944 #> Tacr3    -0.0427312328  0.0104073009  0.0184935125  0.0296168255 -0.029295753 #> Erbb3     0.0588699886  0.2054543319  0.0256636591 -0.0818830122 -0.070049261 #> Pcdh15    0.0006348089  0.0636586879 -0.1583186965  0.0142013211 -0.041341955 #> Grm7      0.1661827875  0.0744208850  0.0398764012 -0.0497191080  0.151582905 #> F2r      -0.0014730327 -0.0614655318 -0.0526321999 -0.0541502699  0.007806200 #> Bdkrb2   -0.0575874852 -0.0402068372  0.0397186042 -0.0078895207 -0.132682144 #> Adgrv1   -0.0951414401 -0.1127886005 -0.0350161915  0.0631818594 -0.052376734 #> Gprc5c    0.0047510536  0.0459720328 -0.0499402543 -0.1094925677  0.016724648 #> Tbxa2r    0.0666518978 -0.0522195564 -0.1106764446 -0.0737239887  0.111871445 #> Ackr1    -0.1044346039 -0.0377061386 -0.2082417510 -0.0568595862 -0.002542482 #> Lpar2    -0.0362003732  0.1112685866  0.0104502969  0.0225967070  0.131476991 #> Myh11    -0.0941300214 -0.0225495709 -0.0980065710 -0.0302217744 -0.105998619 #> Musk     -0.0211486737 -0.0259382155 -0.0295046770 -0.0114267884 -0.008274967 #> Cnr1      0.0632683129 -0.0035031760  0.0319345247 -0.0468717278 -0.048588307 #> C3ar1     0.0929069437  0.1297420031  0.0669043167  0.0787876501 -0.032815816 #> S1pr4     0.0128334673  0.0216923945 -0.1612809445  0.0144505534 -0.101883147 #> C5ar1    -0.0499523644 -0.1436311727  0.0870690367 -0.0836865760 -0.020422608 #> Fpr1      0.0791205054  0.0360995729 -0.0218960276  0.0328010364  0.015369955 #> Sctr     -0.0515800467  0.0467266061  0.0524115513  0.0469323465 -0.071430313 #> Gpr158   -0.0007208232 -0.0261546051  0.0082102851  0.0925688954  0.138652309 #> Cxcr4     0.0143479027  0.0340470151  0.0416501285 -0.0382331341  0.020915839 #> Hrh2     -0.0044647236 -0.0908611357 -0.0138365251  0.2488935041 -0.199251703 #> Slc17a6   0.0151548519  0.0369575062  0.0173631601  0.0034547619 -0.002517079 #> Ppp1r3g  -0.0405298481 -0.1222379604 -0.0346799352  0.0700405209  0.118079841 #> Pln       0.0748123078  0.0483826517 -0.0389908657 -0.0116775316 -0.005489177 #> Grin2b    0.0792476734 -0.0157385827 -0.0001124593  0.2310324967 -0.024981003 #> Taar7e    0.0644724481 -0.1096456877 -0.0059358117 -0.0317436310  0.013958289 #> Ptger2   -0.1258876980 -0.0501821138  0.0072855899 -0.0695578612  0.006726419 #> Mc4r     -0.0811609986  0.1272446124  0.1350917084 -0.0333871203  0.039833203 #> Ghsr      0.0876575950  0.0571697380 -0.0141473440  0.0578700676 -0.073276938 #> Nmbr      0.0750855237 -0.0243946563 -0.0134219369 -0.0729800023 -0.049924914 #>                 Dim.61        Dim.62        Dim.63       Dim.64        Dim.65 #> Mlc1     -0.0363434655 -0.1547949294  0.0690070544  0.120829101  2.312221e-01 #> Gprc5b    0.0362279509  0.0175050913  0.0905423914  0.014155961  8.418026e-02 #> Gfap     -0.0363755013 -0.0259665488 -0.0352573003  0.007087687 -4.463271e-02 #> Ednrb     0.0713049646  0.0933871364  0.0034181948  0.061534550 -7.867310e-03 #> Sox9      0.1701790493 -0.1457135747  0.1292493435 -0.161085744  2.435420e-02 #> Aqp4      0.0609575050  0.0622959430  0.0819136872 -0.087797690  1.548329e-01 #> Gjc3      0.0507582735 -0.0633504472 -0.0534559136  0.148344015  2.691779e-02 #> Sox8     -0.1511520915 -0.1050312649 -0.0178710295  0.023132844  2.683183e-02 #> Ntsr2    -0.0086247569 -0.0831650661 -0.0577663979  0.013954495  6.752734e-02 #> Smo      -0.0625214729 -0.0251252897  0.1275467246  0.138555843  2.784213e-02 #> C1qb     -0.0690887292 -0.0793736673  0.0510743038  0.150138335 -6.531145e-02 #> Olig1    -0.0369556045 -0.0069395097  0.0357138555 -0.140644311 -1.168722e-01 #> C1qa     -0.0187377855 -0.0244912115  0.0423976662 -0.051603049  6.670225e-04 #> Pth1r     0.0028351836  0.1058943534 -0.0409482964  0.036792352 -3.652917e-02 #> Gabbr2   -0.1162459705  0.1024793225  0.0029229914 -0.187797538  1.337037e-01 #> Timp4     0.0350464414  0.0329134652  0.0198732126  0.078165490  7.515997e-02 #> Abcc9     0.0761818642 -0.0410427203 -0.0113425588 -0.011964967  8.140403e-02 #> Csf1r    -0.1169059544  0.0771002961 -0.0225656742  0.054377017  1.765171e-01 #> Ntrk2    -0.0283888316  0.0484163434 -0.0428191822  0.088102580  2.805628e-02 #> Adgrg1    0.0392042591 -0.0906504241 -0.0653489655  0.042012621 -1.912321e-03 #> Ntrk3    -0.0013109246  0.0919907867 -0.1405054212 -0.071662132  7.280188e-02 #> Erbb4    -0.0132933634  0.0697890303  0.0512855728  0.104244028 -2.272039e-02 #> Selplg   -0.0885546636  0.0075408374  0.0268323459 -0.083826466  1.102152e-01 #> Cspg5     0.0145335597 -0.0522911210 -0.2276891360  0.027749113  7.355342e-03 #> Dlk1     -0.0585290783  0.1067931285 -0.0523287905  0.076587946 -8.788101e-02 #> Gpr37l1   0.0117530280  0.0567440375  0.1439278622 -0.088012784 -6.130192e-02 #> Fgfr3    -0.0702296226  0.0171812419  0.0581130944  0.066354233 -4.197903e-02 #> Slc25a18 -0.2102427413  0.2908783066  0.0928012716 -0.025961975 -1.695964e-01 #> Igf1r     0.0517043270 -0.1226090440  0.0168146348 -0.123404477 -1.077369e-01 #> S1pr1    -0.0816224861  0.0480052674 -0.0131399092 -0.037457685 -3.773583e-02 #> Grm5     -0.0300549804  0.0519683454  0.0575651156  0.050933926 -5.897599e-02 #> Axl       0.1635970644 -0.0978900111  0.0398933074  0.025567917 -5.145290e-02 #> Efemp1    0.0726508638  0.1016542543 -0.0614805003  0.014794407 -4.386747e-02 #> Adgrb3    0.1470858854 -0.0073336295 -0.0383271997 -0.065662739  8.932871e-02 #> Fn1      -0.1058294678 -0.0347351444  0.0207403748 -0.042515046  7.406163e-02 #> Mertk     0.0749844751  0.0571316367 -0.0171342954 -0.097561389 -1.733548e-01 #> Adgrl2   -0.0907134060 -0.1606302540 -0.0666785154 -0.038661246  3.070973e-02 #> Fzd2     -0.1395293382 -0.0559231309  0.0494726955 -0.135529819 -7.924828e-02 #> Aldh1l1  -0.0629451618 -0.1819791270 -0.3694097086  0.143497760 -3.546132e-02 #> Adgrg6   -0.1256371143  0.0360689842  0.1123032643  0.061291551 -1.050019e-01 #> Egfr     -0.0394857889  0.0288213323  0.1025090990  0.131267359 -1.798244e-01 #> Kit       0.0527135237  0.0296577131 -0.0724540051  0.017279987  1.479790e-02 #> Ptgdr     0.0084029918  0.0449752574  0.0094437808  0.081641587  6.026343e-02 #> Gad1      0.0045208390 -0.0203915408  0.0270705051 -0.063888453  3.795085e-02 #> Tyro3     0.0210221152  0.1052458845 -0.0150436166 -0.230928268 -3.541155e-02 #> Atp13a5   0.0446350024 -0.0906449940  0.0413781117 -0.008833788 -6.372984e-02 #> Ddr2      0.0546973860  0.1270878853  0.0054824872  0.088908891  2.441886e-02 #> Rspo3     0.1051182550  0.0320527931 -0.1020131912  0.049037703  6.075154e-02 #> Arhgap29  0.1589068947  0.1498024091 -0.0145526341  0.072643870 -4.978069e-02 #> Fzd7     -0.0185937818 -0.1644659693  0.0270833690 -0.061888287 -6.079709e-02 #> Slc47a1  -0.0508272483 -0.1030855685 -0.0060520438  0.017414978 -1.597815e-03 #> Ptger3   -0.0584433835  0.0294209687 -0.0817687826  0.011122160 -1.180247e-02 #> Bdkrb1    0.1816189771 -0.0094979873  0.1344661849  0.022435704 -1.301310e-01 #> Traf4     0.0665581800  0.0927689433 -0.0798955499  0.003978262  1.022135e-01 #> Cx3cr1    0.1233298588 -0.0202978330  0.0433191507  0.052033919 -2.997915e-02 #> Anxa11    0.0513003949  0.0323658764  0.0162963529 -0.009965616  3.153566e-02 #> Adgrb1   -0.0095715520  0.0601539994  0.0447904115 -0.055503417  1.346521e-01 #> Lpar1     0.0005013196  0.0181735025 -0.0536482226 -0.094870360 -1.450974e-01 #> Gpr17    -0.0467366713  0.0228362735  0.0797881897  0.018781938 -3.504827e-02 #> Cxcl12   -0.0804436914 -0.0525400551 -0.0031925270 -0.054069448  2.537165e-02 #> Epha4     0.1094037039 -0.1487513500  0.1270004458 -0.072452626 -3.484660e-02 #> Gpr182   -0.0033164079 -0.0149051188  0.0422184199  0.027191957  1.812753e-05 #> P2ry14    0.0077978961 -0.0339643140  0.0291564542 -0.053040744  1.054677e-01 #> Hcar1     0.1479011252 -0.0320484046  0.0354660553 -0.009629197  8.073636e-02 #> Ephb1     0.2143238400  0.0575415770  0.3121813814 -0.036390674 -9.131967e-02 #> Grm3     -0.0735233943 -0.0074907482 -0.0401411464  0.052211165  1.398112e-01 #> P2ry1     0.0419996193 -0.0555842984  0.0004363337 -0.056879141 -3.276266e-02 #> Ptk7     -0.2107969559 -0.0048060099  0.0123056527 -0.204726002 -8.022361e-02 #> Slco1a4   0.1147361423 -0.0756270772 -0.0436023380  0.096026886 -5.075217e-02 #> Insrr    -0.1172753250  0.0424788927  0.0820528921  0.023949188  1.144644e-01 #> Cmklr1   -0.0396041090  0.0136026580  0.0010788041  0.024602600  9.070060e-02 #> Fzd6     -0.1140211764  0.1530751429 -0.0697895657  0.113688375  9.875577e-02 #> S1pr5    -0.0660805937  0.1080812139  0.0046660077  0.030912316  1.341179e-02 #> Pdgfrb   -0.0732461491  0.1501492812 -0.0527445960 -0.047087757 -2.850070e-03 #> Flt1     -0.0155193272  0.0266518562  0.0673163402  0.094393292 -1.011798e-01 #> Adgrl4   -0.0346288260  0.0425105213 -0.0108792787 -0.009631311  1.770198e-01 #> Lpar6    -0.0588805058  0.0571018410  0.0483397106  0.050578808 -6.025791e-02 #> Epha6     0.1555536626  0.2430613926 -0.1852991630 -0.029631591  1.834738e-01 #> Emcn     -0.0305888355  0.0959423664 -0.1325424252 -0.123799242 -2.558188e-02 #> Cldn5    -0.0067321275  0.0122745704  0.0127934315 -0.085871309  5.538852e-02 #> P2ry12    0.1154826304 -0.0150175459 -0.0742144472  0.019093224 -1.626320e-01 #> Adgrf5   -0.0521902166  0.0320573870 -0.0207656274 -0.063117020  1.082515e-01 #> P2yr13    0.0339352881  0.0244972272 -0.0700270533 -0.145165307  8.854780e-02 #> Adgre1    0.1423820803  0.0869281922 -0.1034038317 -0.134396462 -4.992566e-02 #> Cx3cl1   -0.0546487691  0.1214932329  0.1470428951  0.172273146  4.498589e-02 #> Plxnb3    0.0549917780 -0.1360321683  0.0950419678 -0.066517875  1.400429e-01 #> Flt4      0.1198038368 -0.0217541494 -0.0295915995  0.003615632 -6.545003e-02 #> Slc17a7  -0.1040082909 -0.0544688558  0.1011107378  0.074855289 -3.432861e-02 #> Cd300c2  -0.0852420058  0.1236184937  0.0134183798 -0.021155570  2.728315e-02 #> Tek      -0.0482992317  0.0257313910 -0.0542945457 -0.037682356 -1.068850e-01 #> Kdr       0.1058664750 -0.1358585739  0.0403373051  0.181343131  3.036184e-02 #> Kcnj8    -0.0344877640  0.0163157234  0.0543891824  0.007888845  1.081797e-01 #> S1pr3    -0.0452942301 -0.0690724372  0.0166450601 -0.039199798 -1.201898e-01 #> Tie1      0.0844206796  0.0122081981  0.0943294026 -0.169360972 -1.482741e-01 #> Pdgfra   -0.0039157415  0.0876653809  0.0170881633  0.105164240  8.138765e-02 #> Baiap2    0.0334069736 -0.0659063688 -0.2514798559 -0.073928874 -1.306925e-01 #> Calcrl   -0.0795227061 -0.0702647992 -0.0283846237  0.160238947  5.060292e-02 #> Adrb2    -0.0608379472  0.0165235825 -0.0087501827 -0.043961970  6.355782e-02 #> Ccr2      0.0450320033  0.0201140813 -0.0817428718 -0.043632859 -2.042879e-02 #> Alk       0.0193764339  0.0129192361 -0.0440073469  0.082974022 -1.287248e-02 #> Tacr3     0.1332178273  0.0295397648  0.0777628377  0.026480596  3.395530e-02 #> Erbb3    -0.0567245023  0.0240321500 -0.0815180039 -0.006732310  9.438577e-03 #> Pcdh15    0.1906372756 -0.0610292243 -0.0448330055 -0.050284579  2.352267e-02 #> Grm7      0.0193440105 -0.2034341921  0.1329459106  0.191313159  1.325848e-01 #> F2r      -0.1506523811  0.0260753897  0.1440656235  0.033552726  2.891180e-02 #> Bdkrb2    0.1140806165 -0.0002623405  0.0836713590  0.060123821  1.249961e-01 #> Adgrv1    0.2284523889  0.2460625624  0.0494842467 -0.102673594  7.705142e-02 #> Gprc5c   -0.0565288608 -0.1142209865  0.0292548153 -0.118833458  2.911910e-04 #> Tbxa2r    0.0436121427 -0.0561700454 -0.0962430534  0.150360368 -1.478006e-01 #> Ackr1     0.0134996377 -0.0343470921 -0.0174875412 -0.050907786  4.855027e-02 #> Lpar2    -0.0112034563  0.0556131690  0.0485626116 -0.067900980 -2.298362e-02 #> Myh11     0.0794628081  0.0090021298 -0.0031261657  0.076100956 -9.440891e-04 #> Musk     -0.1132664810 -0.0160927527 -0.0139378836 -0.036576131 -4.239191e-02 #> Cnr1     -0.0066558292 -0.0366830708  0.0281410669 -0.004356620  2.028521e-02 #> C3ar1     0.0155008299  0.0166105274 -0.0245486781 -0.006759377  2.784848e-02 #> S1pr4    -0.0220906316  0.0033879640  0.0141870236  0.168667541 -6.699874e-02 #> C5ar1     0.0960111160 -0.0535007413 -0.0743741347 -0.072689203  2.516896e-02 #> Fpr1      0.0329341540  0.0321719135 -0.0596426659  0.006059747 -1.256468e-02 #> Sctr      0.0695576161 -0.0531381936  0.0921986957  0.011224008 -7.011426e-02 #> Gpr158    0.0015329909  0.0548280767 -0.2227016310  0.173174901 -2.903093e-01 #> Cxcr4    -0.0016786406  0.0219833075  0.0414682025 -0.003677807 -2.395059e-03 #> Hrh2     -0.0792255225 -0.2616825076 -0.0718836525 -0.161641011  1.007261e-01 #> Slc17a6  -0.0357243084 -0.0115859619 -0.0387670457  0.050875528  6.262938e-02 #> Ppp1r3g   0.1669086391  0.0811501547 -0.0286354384  0.145831306  8.553946e-02 #> Pln       0.0684256776  0.0694085860 -0.0522243887  0.065296752  5.266343e-02 #> Grin2b    0.0523079210  0.0052384402  0.0947439856  0.100807064 -1.024327e-01 #> Taar7e   -0.0738361372  0.0002086252 -0.0930331693 -0.020204480  5.401002e-02 #> Ptger2   -0.0667717302  0.0788384479  0.2038392132  0.004995610 -1.276164e-02 #> Mc4r      0.0333960736 -0.1396369222 -0.0106242395 -0.079133700  8.469524e-04 #> Ghsr     -0.0693555261 -0.0889129111  0.0880344797  0.014366345 -4.696204e-02 #> Nmbr     -0.0965961547  0.0039125312  0.0420587836 -0.020019142 -1.199213e-01 #>                 Dim.66        Dim.67       Dim.68        Dim.69        Dim.70 #> Mlc1     -2.180444e-02  0.0509485754  0.268830108  0.2073268570  0.1481951292 #> Gprc5b    5.735700e-02  0.2503791817 -0.106428827  0.1776642000 -0.0490134765 #> Gfap     -5.313815e-02 -0.0708074923  0.037384256  0.0016725497 -0.0362639411 #> Ednrb    -7.024608e-03  0.0946853285  0.034493813  0.0576949710 -0.2285982282 #> Sox9      1.807022e-01  0.0546773712  0.070783877 -0.0382300910 -0.1177357502 #> Aqp4      1.592885e-01  0.0329768358 -0.070395176 -0.0248747928  0.0970304244 #> Gjc3     -3.323623e-02 -0.0428932266 -0.097155096  0.0356396823 -0.0362664889 #> Sox8     -5.277059e-02 -0.0702069374 -0.067654032  0.0847521498 -0.1821537499 #> Ntsr2     1.688058e-02 -0.0855470970  0.027037766 -0.0228350509  0.0865575306 #> Smo       9.069631e-02 -0.0999477249  0.015316573 -0.1035136035 -0.0903782692 #> C1qb      6.431639e-02 -0.0236558233 -0.007937257 -0.0208539151 -0.0167829225 #> Olig1     8.167612e-02 -0.0768756932 -0.008059446 -0.0014557578  0.2081991701 #> C1qa     -7.250339e-02 -0.0610496153  0.041596122  0.0134164109  0.0697352462 #> Pth1r    -1.146547e-04  0.1146435822  0.027816673  0.0507767074 -0.0367906224 #> Gabbr2   -9.455405e-02  0.1017963300 -0.011819667 -0.1079435303 -0.0572648210 #> Timp4    -3.103154e-02 -0.0536642920 -0.075443225 -0.0680516985  0.1248819977 #> Abcc9     6.328993e-02  0.0068940021 -0.128888497  0.0248664545 -0.0376274956 #> Csf1r    -3.376456e-02 -0.1376937249  0.060473759  0.0179306420 -0.0185606207 #> Ntrk2    -6.184334e-02  0.0393200132  0.056932403 -0.0378919698  0.1476871517 #> Adgrg1   -5.671942e-02  0.0739760013 -0.056784189  0.0352210481 -0.0878511515 #> Ntrk3    -1.289265e-01  0.0926089226  0.014160283 -0.0855939359 -0.0864180736 #> Erbb4    -6.175009e-02 -0.0719833111  0.039687117 -0.0576475924  0.0276273570 #> Selplg    4.532071e-02 -0.0067639082 -0.069806173  0.0635047704  0.0003958421 #> Cspg5    -9.683195e-02 -0.1085274708 -0.156940211  0.0113932006 -0.1473729815 #> Dlk1     -9.038941e-02  0.0012696048  0.064229827 -0.0637610055 -0.0074678825 #> Gpr37l1   3.819727e-02  0.0278482987 -0.096895834 -0.0523089889  0.0574720748 #> Fgfr3    -1.543647e-01  0.0321129405  0.202431531 -0.0362069394 -0.0014650356 #> Slc25a18  3.852797e-02 -0.1596785085 -0.049197666 -0.0973583053 -0.0251660525 #> Igf1r     9.880276e-02 -0.0274912042  0.069245082  0.0646948662 -0.3308105369 #> S1pr1     3.196872e-02 -0.1341877696  0.182367895  0.0858929441 -0.0704561353 #> Grm5     -1.139508e-01 -0.0324040008 -0.062967961 -0.0596359471 -0.0422567204 #> Axl      -8.913474e-02  0.1042111503  0.096248942 -0.0570438354 -0.0892342835 #> Efemp1    2.237215e-02 -0.0352328527 -0.035873485 -0.0692725147  0.0478291537 #> Adgrb3    8.725996e-02 -0.0252023723  0.034915916 -0.0935292744  0.0627254945 #> Fn1      -1.163542e-01  0.0537656999  0.044686716  0.0810373760  0.0469238872 #> Mertk    -8.647904e-02  0.1210436145 -0.088566619  0.0573608159 -0.0006104242 #> Adgrl2   -2.064289e-03 -0.1157869316  0.047864879 -0.0746061721  0.0125967135 #> Fzd2      1.633771e-01 -0.1050816395 -0.005585715  0.1005945047 -0.0007038798 #> Aldh1l1  -4.863740e-02 -0.1081526474 -0.177888569 -0.0580112239  0.1650436979 #> Adgrg6    7.030933e-02 -0.0393976569  0.070051139 -0.0385737212  0.0380361790 #> Egfr     -1.122364e-01  0.0322319403 -0.014760206  0.1431062119 -0.0302216042 #> Kit      -5.858489e-02 -0.0252964268  0.025001497 -0.0119366782  0.0824318599 #> Ptgdr    -6.424682e-02  0.0878189159 -0.067495526  0.0076604962  0.0461745449 #> Gad1      4.734447e-02  0.0249047951 -0.067107862  0.0450866515  0.0022643001 #> Tyro3     9.807800e-02  0.0569549369  0.143174619 -0.2399856277 -0.0365760436 #> Atp13a5  -2.777914e-02 -0.0928380836  0.075681991 -0.0787949787 -0.0345953792 #> Ddr2      6.543896e-02 -0.0104007773  0.004722769  0.0426247739 -0.0748795891 #> Rspo3     4.291280e-02 -0.1178230258 -0.023212467 -0.2122770140 -0.0918374535 #> Arhgap29  5.550297e-02  0.0366830170 -0.167052644  0.0906459975 -0.0263857205 #> Fzd7      1.863546e-03  0.1070347570  0.115631709 -0.0591066088 -0.0776524979 #> Slc47a1   4.684035e-02 -0.0244283416  0.001303967  0.0608170870  0.0328530568 #> Ptger3   -6.286797e-02  0.0374204689  0.082281266  0.0563592703  0.0591123992 #> Bdkrb1   -9.511756e-02 -0.0942972014 -0.018464926 -0.0993888670  0.0237951108 #> Traf4    -1.149698e-01  0.0545923176  0.040503404 -0.1057209814 -0.0515894468 #> Cx3cr1    4.448548e-02  0.1501238920 -0.012641075 -0.0187385562 -0.0722349627 #> Anxa11    2.646427e-01 -0.2760280374 -0.061635376 -0.1054860528 -0.1362392279 #> Adgrb1   -4.789822e-02  0.0011749307 -0.040811845  0.3008067472  0.0414684839 #> Lpar1    -8.238595e-02 -0.1244296704 -0.063785151 -0.0347945122  0.0845929891 #> Gpr17     2.035282e-02  0.0203824417  0.028740057 -0.0610067861  0.0577816203 #> Cxcl12   -1.468419e-01 -0.0102809200  0.123691090  0.0417879960  0.0581991990 #> Epha4     1.010654e-01 -0.1343726689 -0.136827150  0.1453590870 -0.0766896454 #> Gpr182    5.702545e-02 -0.0369997088 -0.020969974 -0.0647287082  0.1126997056 #> P2ry14   -6.944200e-02  0.0533099636  0.051846358 -0.0416923965  0.1233763291 #> Hcar1    -3.004285e-02  0.0819482274 -0.069177994 -0.0250579826 -0.0863313712 #> Ephb1    -1.421088e-01 -0.0261027951 -0.071937626  0.1863365828  0.2779048367 #> Grm3      1.369024e-01  0.0029764265 -0.018496859 -0.0901648787 -0.0458559239 #> P2ry1    -7.449036e-02  0.0898084448 -0.039822891  0.0508188865 -0.0695922339 #> Ptk7     -8.549627e-02  0.0628703488 -0.062995763  0.1150675458  0.0603093544 #> Slco1a4  -8.244239e-02  0.0009620091 -0.053798546  0.1288775536  0.0187408190 #> Insrr     1.109964e-01  0.1194547260 -0.072473511 -0.0384624547 -0.0525173643 #> Cmklr1    8.287082e-02 -0.0535498217 -0.130034823 -0.0229776114  0.0500126685 #> Fzd6      1.321660e-01  0.0144199643 -0.208261844 -0.0206463307  0.1026324326 #> S1pr5    -3.306042e-02  0.0505443319  0.029651998 -0.0259124538 -0.1753439125 #> Pdgfrb   -9.453916e-02 -0.0430714491  0.038897726  0.0860887076  0.0148144960 #> Flt1      5.291115e-02 -0.0166497237  0.080254244 -0.0311409824  0.0428088617 #> Adgrl4   -2.415542e-05  0.0173469552 -0.082244419 -0.1429460622  0.0572207401 #> Lpar6     1.255938e-05  0.0679932436  0.070519629  0.0044468281 -0.0146509063 #> Epha6     1.158855e-01 -0.1942669820  0.234264801  0.2828944622  0.0425495209 #> Emcn     -9.433091e-02 -0.1458467574  0.005451370  0.0210588089  0.0322306084 #> Cldn5    -3.915228e-02 -0.0315559801  0.127931519 -0.0429383465 -0.0204878394 #> P2ry12   -3.373338e-02  0.0708821012  0.010509976 -0.0687328407  0.0139550011 #> Adgrf5    1.810203e-02  0.0732510684 -0.004878348 -0.0464582832 -0.0190382800 #> P2yr13   -6.614625e-02 -0.1078141268  0.001570643  0.0216281907  0.1539601742 #> Adgre1   -4.179230e-02 -0.0079797822 -0.050419779  0.0082445979  0.0229729075 #> Cx3cl1   -4.625971e-02 -0.0676084560  0.096315663  0.0050563932  0.0765853026 #> Plxnb3    1.749145e-01 -0.0455347819  0.001378771 -0.0049625043  0.0214533419 #> Flt4     -5.657952e-03 -0.0598560645 -0.072707446  0.0655366145 -0.0611033774 #> Slc17a7  -9.659451e-02  0.0985333693 -0.100712126 -0.0972843882  0.0283024070 #> Cd300c2   4.687387e-02  0.0491626576 -0.009755632  0.1019862691 -0.0398527218 #> Tek       3.057949e-02  0.0143083634 -0.267661650  0.1072584158  0.0635469833 #> Kdr      -2.662782e-02  0.0638379380 -0.090074157  0.0037730731 -0.0318037031 #> Kcnj8     2.719719e-02  0.0525318342 -0.027521016 -0.0557996198  0.0574561414 #> S1pr3     2.710308e-02 -0.0415936134  0.051371790  0.0304945807  0.0021683414 #> Tie1     -3.195196e-02  0.0023658947  0.045181223 -0.0131240363  0.1439546487 #> Pdgfra    1.664750e-02  0.0550685589  0.040726360  0.1454141458 -0.1236729211 #> Baiap2    1.802067e-01  0.1307522080 -0.014527508  0.1075417272  0.0841343417 #> Calcrl    1.208724e-01  0.0920428499  0.152312768  0.0113467312 -0.0543336788 #> Adrb2     7.526892e-02  0.0386791434 -0.014336466 -0.0221495165  0.0180708207 #> Ccr2      8.311026e-03  0.0216781648 -0.035463248 -0.0201927133  0.0268575194 #> Alk       8.424806e-02 -0.0171405303  0.037199497 -0.0337643015 -0.0291163607 #> Tacr3    -4.318870e-02 -0.1983578007  0.057655428  0.0561142818 -0.0235120459 #> Erbb3    -9.843728e-02  0.0121679417  0.201440315 -0.0553532446  0.0438030341 #> Pcdh15    1.998874e-02  0.0304796649  0.058526792 -0.0349101033  0.0521330978 #> Grm7     -3.338724e-02  0.0355627120  0.020473452 -0.1000911557  0.1716592555 #> F2r       1.549603e-01  0.0655745202 -0.086818368 -0.0692260393  0.1130852388 #> Bdkrb2   -4.415963e-02 -0.0588436381 -0.086076129 -0.0863462946  0.1205577456 #> Adgrv1   -1.323651e-02  0.1439844055  0.086699551 -0.2259830019 -0.0303825980 #> Gprc5c    8.620728e-02  0.0153277340  0.110902858  0.1075562888  0.0224857705 #> Tbxa2r   -8.235208e-02  0.0098698867  0.038334444  0.0345995030 -0.0854565427 #> Ackr1    -1.831774e-02 -0.0446091558 -0.049202852 -0.0186152904 -0.0066678322 #> Lpar2     3.916925e-02  0.0520418454  0.086949587 -0.0100194352  0.0013993009 #> Myh11    -1.734374e-02  0.0464736842  0.128354362 -0.0823989557  0.0091982929 #> Musk      1.420258e-01  0.1200756088 -0.088802771 -0.0528757769  0.0411670460 #> Cnr1      1.239605e-03  0.0222121304  0.033677847  0.0112741666  0.0032176017 #> C3ar1    -1.864165e-03 -0.0398766239  0.035853029 -0.0185812194 -0.0453215077 #> S1pr4     3.929798e-02 -0.0656080479  0.074751001 -0.0045482941 -0.0710797499 #> C5ar1    -6.574640e-02 -0.1134052895 -0.055974484 -0.0661784584  0.1015930800 #> Fpr1     -1.135557e-01  0.0649296347 -0.007038102 -0.0255501626  0.0423049175 #> Sctr      1.075215e-01 -0.0775023029  0.014688768 -0.0222430807  0.0228493694 #> Gpr158    3.210956e-01  0.1827852345  0.171148003 -0.0780930999  0.2047212526 #> Cxcr4    -2.404657e-02 -0.0181956487  0.031321822  0.0409752295 -0.0410268751 #> Hrh2     -1.481572e-01 -0.0915637868  0.004560917 -0.1947067988 -0.0511252540 #> Slc17a6   1.944781e-02 -0.0245591105 -0.064260286 -0.0088208413 -0.0154390916 #> Ppp1r3g   9.623146e-03  0.0108886993 -0.054879007 -0.0573771077  0.0462825739 #> Pln      -7.934541e-02  0.0241018518 -0.053936350 -0.0058742348  0.0062657235 #> Grin2b    8.801095e-03 -0.3010850306  0.078458310 -0.0510765245  0.0073081916 #> Taar7e   -7.515084e-02  0.0884732178 -0.050378275 -0.0004016495 -0.0794989187 #> Ptger2   -1.640076e-01 -0.0832545165 -0.128242094 -0.1058812083 -0.1898248819 #> Mc4r     -1.354755e-02  0.1309691658  0.074115489 -0.0553346191  0.0977042140 #> Ghsr     -1.043267e-01  0.0778342550 -0.039263466 -0.1128103024  0.0377625361 #> Nmbr      1.072201e-02  0.0774311468 -0.098071576 -0.1144985782  0.0181678188 #>                Dim.71       Dim.72        Dim.73       Dim.74        Dim.75 #> Mlc1     -0.060559691 -0.050950656  0.1022928436 -0.018755257 -0.1273852264 #> Gprc5b   -0.063104300  0.286250740 -0.0251856093 -0.038993956  0.0550875457 #> Gfap      0.065110279 -0.064439665 -0.0196306516  0.024552527  0.0119924509 #> Ednrb    -0.058516847  0.062645785 -0.0124203832 -0.038077283  0.0711736577 #> Sox9      0.082880214  0.035369083 -0.0739366722 -0.174569439 -0.0932799709 #> Aqp4     -0.032531480 -0.007643029 -0.0158767950 -0.113869475  0.0285774774 #> Gjc3      0.091675499 -0.039255337 -0.0040948021 -0.043561623 -0.0178024173 #> Sox8      0.116895229  0.066927753 -0.0972443985 -0.144672002  0.0168731617 #> Ntsr2    -0.015591112 -0.031524694 -0.0188671179  0.129121017 -0.0847018061 #> Smo      -0.224692032 -0.139799582 -0.1127574648 -0.013620345  0.0438908379 #> C1qb     -0.023277221 -0.083978585  0.0705403411 -0.162778227 -0.0148112351 #> Olig1    -0.053148196 -0.019962569 -0.0173464567 -0.072584330  0.0160094417 #> C1qa      0.039426648 -0.043254062  0.0631424835 -0.139113119  0.0205276659 #> Pth1r    -0.001187810  0.040533385 -0.0966006225  0.062951631 -0.1350839075 #> Gabbr2    0.046118872  0.012660744  0.0108177333 -0.044401072  0.0521251448 #> Timp4    -0.053006936 -0.110923467  0.1081139190  0.134769024 -0.0782112181 #> Abcc9    -0.007908647  0.014986630  0.0726891459 -0.066747179  0.1131103049 #> Csf1r     0.036190447 -0.008103598  0.0031644822  0.175836367  0.0805081945 #> Ntrk2     0.098648011  0.021707565  0.1659145137  0.147629244  0.0951983529 #> Adgrg1    0.024699669 -0.049958349  0.0173139360  0.002571492 -0.1207213763 #> Ntrk3    -0.057384905 -0.083562959 -0.0061604841 -0.179030823 -0.2691322738 #> Erbb4     0.010490645  0.047744514  0.1047638152 -0.028263450  0.0888599345 #> Selplg    0.042660938 -0.028439026 -0.0688687418  0.038770248  0.0401933829 #> Cspg5    -0.004519161 -0.055718106 -0.0271939542 -0.145355323  0.0468352442 #> Dlk1     -0.110660337  0.125386364  0.0777297668  0.069799658  0.0040221451 #> Gpr37l1  -0.078073292  0.110938679 -0.0595206938  0.040679380 -0.1031500316 #> Fgfr3    -0.088658454 -0.052835057  0.2319331029 -0.082535380  0.0624165765 #> Slc25a18 -0.065393512  0.038525963 -0.1580529219 -0.030167095  0.0821272433 #> Igf1r    -0.028591882  0.009023995  0.0770125327  0.056612838  0.0422655194 #> S1pr1     0.131751483 -0.178023590 -0.1113031726 -0.068278231  0.0293735256 #> Grm5      0.098687651  0.026115014  0.1762127827  0.039227284  0.0011007656 #> Axl       0.065805353  0.136747191 -0.0286514220  0.059956125  0.0617320661 #> Efemp1   -0.076220229 -0.129121931 -0.0562871224 -0.032787618  0.0289195308 #> Adgrb3    0.064041974  0.031469693 -0.0031008663 -0.157229323 -0.0410974684 #> Fn1       0.036286143  0.024180024 -0.0368936210 -0.078434365 -0.0193022541 #> Mertk     0.092169020  0.071722932 -0.0440574324 -0.010117281  0.0654870000 #> Adgrl2   -0.131856018 -0.028217458 -0.1340055799 -0.083751561  0.0149735164 #> Fzd2      0.115837403  0.094488379  0.0940590424  0.143806481  0.0211136055 #> Aldh1l1  -0.038335766  0.155998884  0.0142125899  0.031282719  0.0308590798 #> Adgrg6    0.055784075  0.070004096  0.0956388265 -0.059866370  0.0264481726 #> Egfr     -0.076453803 -0.064555290 -0.1362988360  0.046202873  0.1516301307 #> Kit       0.076757025 -0.048191096  0.0097628019 -0.015261147 -0.0029335677 #> Ptgdr    -0.029265026  0.002897508 -0.0690502261 -0.103131874  0.1510723175 #> Gad1     -0.047986395 -0.069248504 -0.0703758795  0.009887484 -0.0341162883 #> Tyro3    -0.030631130 -0.122470370  0.1276345734  0.079224103 -0.0248482228 #> Atp13a5   0.099169748 -0.077913932  0.0090822790  0.079108650  0.0275004530 #> Ddr2     -0.018975384 -0.058400662  0.0375447418  0.029753810 -0.0556353252 #> Rspo3     0.049313998  0.159672913  0.1039126727 -0.090252886 -0.2950482581 #> Arhgap29 -0.020959942 -0.107418816  0.0481068763  0.003069581  0.0944723651 #> Fzd7      0.101548628  0.111416672  0.2088554802  0.277222595  0.1188329761 #> Slc47a1   0.051708942  0.013968140  0.0593560566  0.084578114 -0.0629012098 #> Ptger3    0.051468349 -0.039737984 -0.0573526099 -0.049698682 -0.0162281929 #> Bdkrb1    0.127761941 -0.138731126  0.1608980963 -0.075051234  0.0590207919 #> Traf4    -0.063344704 -0.012534809  0.0203937363  0.144560887  0.0463399743 #> Cx3cr1    0.143654151  0.031789858 -0.0047925510  0.020867781  0.0621503244 #> Anxa11    0.009388242 -0.033943951  0.1442159699  0.105662335  0.0049519296 #> Adgrb1    0.150684850 -0.162891246 -0.2254326478  0.105044561 -0.0944318070 #> Lpar1    -0.058870535 -0.024864632 -0.1245706115  0.004371882 -0.1295023517 #> Gpr17     0.027053603  0.059960360  0.0420375037 -0.001731964  0.0365777244 #> Cxcl12    0.101076179  0.125139444 -0.0374556342 -0.257389544 -0.0221984599 #> Epha4    -0.294763563 -0.075414276 -0.0277372962  0.026642616  0.0518827275 #> Gpr182    0.133006977 -0.001128710 -0.0548371742 -0.011982830 -0.0443853979 #> P2ry14    0.026657020  0.076195817 -0.0076906024  0.117600171  0.0460448912 #> Hcar1    -0.059214971  0.039174103 -0.0936225281 -0.040445328  0.1625684908 #> Ephb1    -0.101019819 -0.046744247  0.1529176941  0.021629283 -0.1404678211 #> Grm3      0.109301186 -0.029724067 -0.1228539379  0.055711961  0.1192337728 #> P2ry1    -0.180612427 -0.026837031  0.0109558247  0.083601305  0.0408412516 #> Ptk7     -0.010507897 -0.064895990  0.1458587935  0.051389172  0.1265438662 #> Slco1a4   0.010247809 -0.082895546  0.0001276429 -0.027588189 -0.0934805234 #> Insrr    -0.082158744  0.037805907  0.0795378949 -0.008487538 -0.0445181066 #> Cmklr1   -0.004152000 -0.023137470  0.1257604252  0.003100938 -0.0263894946 #> Fzd6     -0.081008714 -0.025902064  0.0844757620  0.010606930  0.0006235811 #> S1pr5    -0.022733316  0.047537196 -0.0512570357  0.011060552 -0.0124225958 #> Pdgfrb    0.009121902  0.008915702 -0.1023114767 -0.176491732 -0.1017082329 #> Flt1      0.031452419 -0.013018861 -0.0501526701  0.009772905 -0.0350141819 #> Adgrl4   -0.005513909  0.087751651 -0.0044220610  0.009775016  0.0089576878 #> Lpar6    -0.009826361 -0.078178309  0.0020631523 -0.100706026 -0.0036210347 #> Epha6    -0.121894975  0.055095684  0.2062313111 -0.166419465  0.1678945872 #> Emcn      0.043449920 -0.028290495 -0.0304780762  0.005189266  0.1157880487 #> Cldn5     0.035189418  0.078680386 -0.0467720459 -0.017826302  0.0386936431 #> P2ry12   -0.178236825  0.093585603  0.0011242759 -0.081253246 -0.1264142502 #> Adgrf5   -0.077603642 -0.026613754 -0.0067177286  0.062230559  0.0813823346 #> P2yr13   -0.079648099  0.062733282 -0.1485847766  0.200841669 -0.0352454412 #> Adgre1    0.023379592  0.011143278 -0.0376802157  0.002915943  0.0124277978 #> Cx3cl1   -0.037397708  0.109724067 -0.0842579078  0.135686249  0.1131269610 #> Plxnb3    0.124569927 -0.183848448 -0.0120186075 -0.077876821  0.0107417823 #> Flt4      0.094907782 -0.032516940 -0.1425573097  0.070694990  0.1707816625 #> Slc17a7   0.104236653 -0.213271141  0.0138193008  0.074494125 -0.0968776258 #> Cd300c2   0.049152009 -0.018961612  0.0194293868  0.003806559  0.0687467162 #> Tek      -0.007670036  0.107529236  0.2391819060 -0.050292116  0.0018261780 #> Kdr      -0.019381754 -0.002021575  0.0451753736 -0.054807464  0.0224094181 #> Kcnj8    -0.005558235  0.012980134 -0.0277121970 -0.047229748 -0.1231623118 #> S1pr3    -0.127394091  0.021648696  0.0175628003 -0.017508824 -0.0248130574 #> Tie1      0.008215865 -0.146948617 -0.0485479008  0.039243866 -0.1254431631 #> Pdgfra   -0.090384602 -0.056379918  0.0331875230  0.073043289 -0.1358707139 #> Baiap2    0.103627350  0.164105029  0.0565464234  0.037955166 -0.0261337736 #> Calcrl   -0.030020670 -0.109678204 -0.1254510999  0.163198581 -0.0862017149 #> Adrb2     0.002161610  0.088005914 -0.0241958440 -0.025731530 -0.0285909318 #> Ccr2     -0.208463359  0.044159734 -0.1422987412  0.140113228 -0.1372275759 #> Alk      -0.084746657 -0.036533273  0.0464469251 -0.012244701 -0.0149087274 #> Tacr3     0.077760336  0.128150600  0.0022168409  0.036205854 -0.0953883249 #> Erbb3    -0.144530162  0.030135373  0.0767444070  0.037887542  0.0086161100 #> Pcdh15    0.014829554  0.007248258 -0.0211172492  0.112911203  0.0301431138 #> Grm7     -0.047209521  0.105826237 -0.1215784923 -0.089147272  0.1116265036 #> F2r      -0.030329587  0.028170487  0.0749223907 -0.112193761 -0.0218313770 #> Bdkrb2    0.137587609  0.033391732  0.0002635216 -0.029210482  0.0628804221 #> Adgrv1   -0.016049451 -0.027250083 -0.0180509832 -0.044595126  0.1089364143 #> Gprc5c   -0.114962935  0.215002898 -0.0340260345  0.044331893 -0.1009861606 #> Tbxa2r   -0.089298824 -0.111843703  0.0940002112  0.061147276  0.0245176681 #> Ackr1    -0.128625115 -0.022980789  0.0332587304  0.040003594  0.0439962906 #> Lpar2    -0.024285271  0.024547820  0.0321658867 -0.008548279 -0.0394970902 #> Myh11     0.050344685  0.010990289 -0.1060057159  0.047070393  0.0278885561 #> Musk     -0.125214290 -0.169802429  0.0001039446 -0.035932161  0.0812629584 #> Cnr1      0.038376210  0.116879598 -0.0127700809 -0.001983683 -0.0331605346 #> C3ar1    -0.125735276  0.069509768 -0.0910894863  0.174240351 -0.1569059637 #> S1pr4    -0.054025801  0.046655947  0.0790624390 -0.101284971 -0.1315372025 #> C5ar1     0.079675134  0.013193643 -0.0797084519  0.059000007  0.0752920821 #> Fpr1     -0.104878749 -0.017347497 -0.0208630069 -0.104059744 -0.0468103471 #> Sctr     -0.050468735  0.069985910 -0.0151862557 -0.022359392 -0.0080035183 #> Gpr158    0.131369538 -0.113953865 -0.1356260208 -0.041406388 -0.0023394918 #> Cxcr4    -0.008670854 -0.009210456 -0.0005997615 -0.007249846 -0.0286132290 #> Hrh2     -0.130491936 -0.119811469  0.1015890625 -0.039165314  0.0176380121 #> Slc17a6   0.060163594 -0.041283659 -0.0479424058  0.047416627  0.0093347458 #> Ppp1r3g  -0.066629853 -0.013792342 -0.0585162403  0.126508444 -0.0662379240 #> Pln       0.079018611 -0.028710834  0.0087757763 -0.005087685  0.1033973260 #> Grin2b   -0.111822627  0.243692045 -0.1578893097 -0.082824719  0.1513802580 #> Taar7e   -0.047234773 -0.035073135  0.0476735877 -0.050495762 -0.0040686524 #> Ptger2    0.106915541  0.010806603 -0.0462962406  0.062192881 -0.1690984676 #> Mc4r     -0.216306566 -0.155642589 -0.0712733495 -0.066852618  0.2659486098 #> Ghsr     -0.003243523  0.092192635 -0.0514766228 -0.050259131  0.0318545930 #> Nmbr     -0.030472123  0.138068709 -0.0914862322  0.021187606  0.0183807215 #>                 Dim.76        Dim.77        Dim.78        Dim.79        Dim.80 #> Mlc1     -0.0363355712 -0.0145850457  4.619688e-02 -0.0827422236 -0.2286119280 #> Gprc5b    0.0378449691  0.1408382865 -2.108614e-01  0.0589767365 -0.0211923850 #> Gfap     -0.0358361030 -0.0318860948 -3.667653e-02  0.0377614621  0.0083006782 #> Ednrb     0.0544582259 -0.0790516103 -1.767260e-01  0.0612266925 -0.0966505028 #> Sox9     -0.0423490415  0.1829919235  1.022337e-01 -0.0440008623  0.0249128488 #> Aqp4     -0.0490670917  0.0312792174  1.604871e-01 -0.0203047670 -0.0206999055 #> Gjc3      0.0040269543 -0.0118508993  2.115296e-03 -0.1311189707  0.1275781304 #> Sox8      0.0154296858  0.0921118891  1.099499e-01  0.2129670877  0.1750382804 #> Ntsr2     0.0555101521  0.0334074512 -8.656427e-02  0.0011841208  0.0452857527 #> Smo       0.0047894203  0.1232687312 -9.303399e-04 -0.0271568814  0.0253260703 #> C1qb      0.0478372170  0.0304290715  6.717821e-02 -0.0494929893  0.0201865056 #> Olig1     0.0494195615 -0.0382916207  2.342742e-02 -0.1271106990 -0.1839703352 #> C1qa      0.0611427730 -0.0092837490  6.203749e-02  0.0273246218 -0.0082114823 #> Pth1r    -0.1096084532 -0.0674148034  4.511431e-02 -0.0849483486  0.0447609778 #> Gabbr2   -0.1130569980  0.0846608280  1.968073e-01 -0.0555984294 -0.0731710691 #> Timp4     0.1263856775 -0.0030835233 -1.645243e-02  0.1049776872  0.0892833384 #> Abcc9     0.1826401727  0.1421652865 -7.319609e-02 -0.0560503173 -0.0030302058 #> Csf1r     0.0046355290  0.0641369775 -9.832798e-02 -0.0448371208 -0.0245870961 #> Ntrk2     0.2037201363  0.0217331969  2.091932e-02  0.0244895404  0.3759422328 #> Adgrg1   -0.0578984680 -0.0573947087  8.177562e-02  0.0470807182  0.1292144826 #> Ntrk3    -0.0710488939 -0.2061473876 -1.524915e-01 -0.0565253864 -0.0302339522 #> Erbb4    -0.0953303470  0.1293148032 -1.501850e-01 -0.1623917938  0.0463883134 #> Selplg   -0.2322851583  0.0297233284 -8.647665e-02  0.0434054587  0.0473792620 #> Cspg5    -0.1518318569  0.0900088395 -3.953102e-02  0.1227085636  0.0071160477 #> Dlk1      0.0625768921 -0.0003054694 -4.654048e-02 -0.0176091706 -0.0935692458 #> Gpr37l1   0.0264995083  0.0239750508 -1.288843e-01 -0.0690497219 -0.1208690615 #> Fgfr3     0.0465398498  0.1401291817  2.132495e-01  0.0372214881 -0.0861244140 #> Slc25a18 -0.0435888626 -0.1779055393 -4.778637e-02 -0.0052799722 -0.2224713545 #> Igf1r     0.0747048584  0.1654967803  1.210928e-01 -0.0715755555 -0.0604122390 #> S1pr1     0.0442306278 -0.1133540339 -1.197171e-01 -0.0932948193  0.0303706699 #> Grm5     -0.1338209139  0.2319024076 -3.959755e-02 -0.0485246500 -0.0323851915 #> Axl       0.0826296026 -0.1164918690 -8.938248e-03 -0.0857293880  0.0123623205 #> Efemp1    0.0316806632  0.0619865727  8.706941e-02  0.0998284791  0.0273842532 #> Adgrb3    0.0682007357  0.0325455170 -3.481689e-02 -0.0512028188 -0.0031584051 #> Fn1      -0.0038519258  0.0455066318  1.842734e-02  0.0248713324 -0.0198623485 #> Mertk    -0.0198082836 -0.1637886302 -1.210735e-02  0.0711536213 -0.0633425862 #> Adgrl2    0.0720700714  0.1563693141 -5.897087e-02 -0.0815778607 -0.0447727688 #> Fzd2     -0.0966759738 -0.0939515765 -1.197041e-02 -0.0813943337  0.1076128857 #> Aldh1l1  -0.0013086915 -0.1275540425  1.506279e-01 -0.0072982955 -0.0930111260 #> Adgrg6    0.0530038219 -0.0658479530 -1.388035e-01  0.1545743274  0.0585043790 #> Egfr     -0.2603799282  0.0468905204  8.295931e-02 -0.0641833853  0.0688460234 #> Kit       0.0450426937  0.0182436506  3.543153e-02 -0.0458470023 -0.0606077450 #> Ptgdr     0.0929971881  0.0886538028  3.662809e-02  0.1243810600 -0.1552982897 #> Gad1      0.0844120085 -0.1252449059  1.205522e-02  0.1359940178  0.0097745236 #> Tyro3    -0.1444913632 -0.0586614776  6.465287e-02  0.3048110683 -0.0540606896 #> Atp13a5  -0.0552501205 -0.0218025098 -2.288236e-02 -0.0035680573 -0.0627137145 #> Ddr2     -0.0508719870 -0.1007551405 -2.958171e-02 -0.1442772472  0.0556476249 #> Rspo3     0.0338330458 -0.0542197124 -6.765473e-02 -0.1873662386  0.0046042496 #> Arhgap29  0.0807445491 -0.0001153793  8.071399e-02  0.1030840002 -0.0644647035 #> Fzd7     -0.0436997161 -0.0548530561 -4.980433e-02 -0.0374893985 -0.0748534653 #> Slc47a1   0.0087582645 -0.0517938717 -5.079785e-03  0.0241306334 -0.0435709406 #> Ptger3    0.0368987806  0.0688256562 -5.803567e-02 -0.0936473395  0.0746865433 #> Bdkrb1    0.0329121080 -0.1000481608  5.177176e-02  0.0166607719 -0.0518769411 #> Traf4     0.0398456972  0.0330790356 -1.965694e-02  0.1185728816  0.0764863235 #> Cx3cr1   -0.0410060213 -0.1130256354  3.264678e-02 -0.0284754493  0.0344127890 #> Anxa11   -0.0414437162  0.0792399040 -4.027865e-02  0.0206615906 -0.1181902216 #> Adgrb1    0.2729268719 -0.0388388740  6.540292e-02  0.0576916634 -0.2010228841 #> Lpar1    -0.0415085486  0.0348881853  1.091373e-01  0.0553319100  0.1421372606 #> Gpr17     0.0032016089 -0.0198702249 -1.672234e-02 -0.2128814855 -0.0753817921 #> Cxcl12    0.0095354248  0.0284045785 -1.582160e-01  0.1804325939 -0.0054606697 #> Epha4     0.1978961841 -0.1485884850 -1.287429e-01 -0.2141727029  0.2116429636 #> Gpr182   -0.0162499074 -0.0161425738 -1.476342e-01 -0.1221477943 -0.0473299512 #> P2ry14   -0.0772437717 -0.0623492782 -1.124091e-02  0.0470685012  0.0023902668 #> Hcar1     0.0021060685 -0.0089962935  5.536445e-02 -0.0355671638 -0.1393775600 #> Ephb1    -0.1992170360  0.0780243628  7.084537e-04 -0.0410192452  0.0079085436 #> Grm3     -0.1316824466 -0.1233140069  1.505651e-01 -0.1331179247 -0.1339327576 #> P2ry1    -0.1007682917  0.0222584599  7.551530e-02 -0.0813933903 -0.0470920059 #> Ptk7     -0.0525628308  0.0512145288 -2.747049e-02 -0.0689726023  0.0315609010 #> Slco1a4  -0.0933132472  0.0471517140 -1.358988e-01 -0.0179708094 -0.1019919126 #> Insrr     0.0821974479 -0.0141710807  7.455271e-03  0.0085840246  0.0680143345 #> Cmklr1   -0.0432580214  0.0222173019  1.213038e-02  0.1202270029 -0.0410927874 #> Fzd6      0.0250430289 -0.0273719775  8.057744e-02 -0.0080968344  0.0002633071 #> S1pr5     0.1699856207  0.0151161592 -6.826067e-02  0.1135536878  0.0283736078 #> Pdgfrb   -0.0702083431 -0.0335570848  1.184078e-01 -0.0371727515  0.0370642654 #> Flt1      0.0410303616 -0.1623786561 -1.061110e-01  0.0929263722 -0.0335727245 #> Adgrl4   -0.0744578770  0.0643895826  2.897772e-02 -0.0423981794  0.0217017849 #> Lpar6     0.0578828676 -0.0697921425  3.960271e-02 -0.0172022802  0.0439216471 #> Epha6    -0.1740711124 -0.1260203832 -3.443853e-02  0.0245462517  0.0084451230 #> Emcn      0.1117072284  0.0748040016 -1.105911e-01  0.0015341114  0.0447229918 #> Cldn5     0.0158847440  0.0769490294  2.268918e-02 -0.0397490744  0.0291013802 #> P2ry12    0.1389404589 -0.0256037950  8.026131e-02 -0.0104299034 -0.0502138053 #> Adgrf5   -0.0142220032  0.0021463003  1.644623e-01 -0.0830476018  0.0576580532 #> P2yr13   -0.0096114960  0.1231481736 -1.506480e-01  0.0791215869 -0.0527619195 #> Adgre1    0.0339938167 -0.0827248192  1.140248e-02 -0.0704072565 -0.0600671676 #> Cx3cl1    0.1739816415 -0.0550031446  1.601526e-01 -0.0393460397 -0.0062745083 #> Plxnb3   -0.0539509892 -0.0451823625 -4.287604e-02  0.0847098335  0.0802834011 #> Flt4     -0.0012230056 -0.1052873187  6.401684e-02  0.0739900899 -0.0256397021 #> Slc17a7   0.0190030184  0.0388135682 -1.137889e-01  0.0583866880 -0.1111693785 #> Cd300c2  -0.0120538397 -0.0223582199 -5.733176e-02 -0.0143223030  0.0248971829 #> Tek      -0.0095093428 -0.0562624922 -1.506817e-02  0.0961611427  0.0091508760 #> Kdr      -0.1193318122 -0.0169945768 -6.778868e-02 -0.0663464302 -0.1384546129 #> Kcnj8    -0.0330823272  0.0377115301  4.100845e-02 -0.0309045506  0.0059744366 #> S1pr3     0.1257233369  0.0415924694 -3.368253e-02  0.0691431969  0.0985217164 #> Tie1     -0.0001737544 -0.0578651194  7.836068e-02 -0.0024042144  0.1279032672 #> Pdgfra   -0.0599125953  0.0539507418  2.392577e-02  0.0391562760  0.1095946997 #> Baiap2    0.0559107795 -0.0383318910  1.374346e-01  0.0043857533 -0.0629922296 #> Calcrl   -0.0064588693 -0.0931802310  1.298936e-01  0.0490509106 -0.0429053004 #> Adrb2     0.0108691063  0.0490653556  4.380074e-03 -0.0305979681  0.0101463145 #> Ccr2     -0.0578373929  0.1054229795 -4.599388e-02  0.0205562403 -0.0246245682 #> Alk       0.0116086383  0.0948584740 -7.040831e-02  0.1534694864 -0.0183842735 #> Tacr3     0.0711322798  0.0499749534  1.289962e-01  0.0737663570 -0.0121843993 #> Erbb3     0.0941613621 -0.0054133025 -1.042618e-02 -0.0885299818 -0.1220656048 #> Pcdh15   -0.0286616954 -0.0341530564  2.503556e-05  0.1763402366  0.0342324909 #> Grm7     -0.0547467637 -0.1627361311 -5.901421e-02  0.1642366139  0.0436076926 #> F2r       0.0004674493 -0.1074030976  7.598153e-02  0.1260301835  0.0188770088 #> Bdkrb2    0.0217584627 -0.0137170807 -6.977910e-02  0.0282272397  0.0050616562 #> Adgrv1    0.0494049139 -0.0389058136 -1.316207e-01  0.0057301486  0.1323432794 #> Gprc5c   -0.0443731621 -0.0687569505 -7.860086e-02  0.0994528214  0.0433155886 #> Tbxa2r   -0.0365319183 -0.0197471560 -2.088756e-02  0.1132764609 -0.0726937623 #> Ackr1     0.0800119932  0.0792421576  2.676663e-02 -0.0402310903  0.0087411884 #> Lpar2     0.1056304559 -0.0029641070  1.780869e-01 -0.0332162486  0.0793253784 #> Myh11     0.0144281911 -0.0464288788 -1.411834e-03 -0.0459868790 -0.0051649687 #> Musk      0.0656672619 -0.0476787296 -8.177055e-02 -0.0239648061 -0.0786758229 #> Cnr1     -0.0014192105  0.0035849168  9.162548e-02 -0.0276969549 -0.0279960472 #> C3ar1    -0.1311069797  0.0716111422 -6.570013e-02  0.1243819813 -0.0162806350 #> S1pr4     0.0319407828 -0.1083394571 -8.205955e-02  0.0475249731 -0.0523493951 #> C5ar1     0.0835207283  0.1059874838 -5.281588e-02 -0.0417692154 -0.0841209585 #> Fpr1      0.1169890643  0.0335406649  1.362155e-01 -0.0828701932  0.0543940443 #> Sctr      0.0197145876  0.0658662605  5.272389e-02  0.1860293442 -0.2439555775 #> Gpr158   -0.0886371498  0.3145306831 -9.340059e-02 -0.0316687474  0.0494743274 #> Cxcr4    -0.0703100779 -0.0429129596 -1.127758e-02 -0.0206795470 -0.0176666130 #> Hrh2     -0.0248799200 -0.1901193315  1.679709e-02 -0.0012646053 -0.0182938290 #> Slc17a6   0.0088166909 -0.0707498438 -4.748368e-02 -0.0799726348  0.1049215432 #> Ppp1r3g  -0.1641733705 -0.0507014230  8.750264e-02 -0.0354750424  0.0893140330 #> Pln       0.0002424275  0.0612874494 -2.284823e-03 -0.0627246611 -0.0895280165 #> Grin2b   -0.1601821140 -0.0397917030  1.420783e-01  0.0381312596  0.1261084076 #> Taar7e   -0.1158512547 -0.1101975798 -8.198578e-02 -0.0595354115  0.0256896070 #> Ptger2    0.0186546780  0.0693885108  1.935567e-02  0.0205028835 -0.0709532479 #> Mc4r     -0.0692233244 -0.0130575857 -1.383449e-01 -0.0001251354  0.0326516777 #> Ghsr     -0.1002845603  0.0157519532 -7.428544e-03  0.0214926474  0.1154889747 #> Nmbr      0.0116987931 -0.0560298097 -1.098731e-02 -0.0983196070  0.0451396033 #>                Dim.81        Dim.82        Dim.83        Dim.84        Dim.85 #> Mlc1     -0.093735387  0.1200973176 -0.0160785957  0.1336642551  0.0793526409 #> Gprc5b   -0.004330739  0.0230413421  0.0047498014  0.0884552400  0.0105176609 #> Gfap      0.051426761 -0.0628112513 -0.0209238625  0.0023613787  0.0108277007 #> Ednrb    -0.150908441 -0.0282064825  0.1678329384 -0.0291582135  0.2441313287 #> Sox9      0.070901568 -0.0612837992 -0.0745932300  0.0142183784 -0.0576132217 #> Aqp4     -0.078194229  0.2058795931 -0.0184833864 -0.0194567997 -0.0230407479 #> Gjc3      0.092813453 -0.0538281269  0.0600185714  0.0885473595 -0.1089634311 #> Sox8     -0.122443709  0.0952410306  0.1252869154  0.0398065303 -0.1503193599 #> Ntsr2    -0.014035892 -0.1323497662 -0.0533465028  0.0758342228 -0.0500524979 #> Smo      -0.165099942 -0.0210943075 -0.1108363230  0.2040286379  0.0990239405 #> C1qb     -0.059329219 -0.1098273049  0.0024608868 -0.1270682887 -0.0514775681 #> Olig1     0.074402136 -0.0806522540 -0.1521452273  0.0221041139 -0.0168247154 #> C1qa      0.008506292 -0.0303846703  0.0025777237  0.0729904963 -0.0705206723 #> Pth1r    -0.097529836 -0.0777161834  0.0593022443 -0.1261974022  0.0080101626 #> Gabbr2    0.050500647 -0.1376070838  0.1828769780  0.0042395710  0.0860778897 #> Timp4    -0.053985809 -0.0103088207 -0.0349899576 -0.0009470189  0.0785925946 #> Abcc9    -0.084000979  0.0481453110  0.0300460317 -0.0303041154 -0.0358995446 #> Csf1r    -0.023856999  0.0072382401 -0.0193290958 -0.0060316055  0.0270143678 #> Ntrk2     0.057003878  0.0271395619 -0.0373520180 -0.0591720512  0.0719077231 #> Adgrg1   -0.032633384  0.0523410286 -0.1092554370 -0.2119288979 -0.1244712114 #> Ntrk3     0.184167727 -0.0052183942 -0.0457542903  0.1335193784  0.1305230486 #> Erbb4     0.022719586  0.0403344003  0.0106936040  0.0114230827 -0.0931475983 #> Selplg    0.119420394  0.0019057928  0.0201809859 -0.0117402780 -0.0017012819 #> Cspg5    -0.055727227 -0.0341658044  0.1250707131  0.1442527391 -0.0420218035 #> Dlk1     -0.018414694 -0.0275189532 -0.0010024202 -0.0649090699 -0.1129470891 #> Gpr37l1  -0.068786541 -0.2576964841  0.0489630383  0.0434810435  0.0071331021 #> Fgfr3     0.132117015  0.1804626755  0.0093820869 -0.1255848657 -0.0741670774 #> Slc25a18  0.017735221  0.1511728119  0.0283768842 -0.1208252332  0.0110099331 #> Igf1r     0.122323547 -0.0220986197 -0.0153538013  0.0580046362 -0.1251907183 #> S1pr1     0.098165575  0.0717365792  0.0788429479  0.0464750260 -0.0898707564 #> Grm5      0.158893312 -0.0245137518  0.0598589637 -0.0420515081  0.2497392118 #> Axl      -0.098346838  0.0372442597 -0.0503337550 -0.0532898638  0.1678125967 #> Efemp1    0.068470705 -0.0804955997  0.0308911141  0.1443210531 -0.0128082459 #> Adgrb3   -0.113504658  0.0293691951 -0.0464523296  0.0478208033  0.0528604849 #> Fn1      -0.036487071  0.0489999345 -0.1096257886 -0.0575619377  0.0453148701 #> Mertk     0.029489096  0.0029953317  0.0426388017 -0.0288841273 -0.1268492175 #> Adgrl2    0.002953736 -0.1020826135  0.1090301988 -0.2094479581 -0.0557262594 #> Fzd2     -0.138129078 -0.0217151728  0.0256563905  0.0817216866 -0.0202232053 #> Aldh1l1   0.053356541 -0.0384042048 -0.0170205676  0.0409807696  0.0707628310 #> Adgrg6    0.004449662 -0.0505498312 -0.0829132231  0.0657147804 -0.0201166244 #> Egfr     -0.133535664 -0.1243481550 -0.4432832708 -0.0106905826  0.1482925886 #> Kit       0.026742829  0.0314906484 -0.0115530882 -0.0278371370 -0.0041457159 #> Ptgdr     0.005354746  0.1040894668  0.0141634041 -0.0576823501 -0.0605783251 #> Gad1     -0.056547558 -0.0361165158 -0.0132463950 -0.0237646789  0.0006399957 #> Tyro3    -0.076695541  0.1344567982  0.0465629212 -0.1483871063 -0.1150626940 #> Atp13a5   0.063483461 -0.0221045012  0.0630452534 -0.0553326727 -0.0812343112 #> Ddr2     -0.027766826 -0.0580709862  0.1198700458  0.0091584849  0.0144595563 #> Rspo3     0.113088557  0.2164508702 -0.0493329731 -0.0042624743  0.0401556101 #> Arhgap29  0.034794911  0.1340649463  0.0975341849 -0.0484821398 -0.0176624386 #> Fzd7      0.030534888 -0.0737895048  0.0298190523  0.0445103314 -0.0266417723 #> Slc47a1   0.002414622 -0.0116127627  0.1881597736 -0.0575984497  0.0338414335 #> Ptger3    0.020971315 -0.0858008902  0.0471187179 -0.0972593225  0.0115405388 #> Bdkrb1   -0.005632865  0.0015174666 -0.1083891291  0.3034279659 -0.0571970683 #> Traf4     0.127200387  0.0290749941 -0.2078394820  0.1385487525 -0.0061526142 #> Cx3cr1    0.073344614  0.0202269269 -0.0344100298  0.0327389794  0.1356894848 #> Anxa11   -0.205003102  0.0218770431 -0.1147588917 -0.0467618665 -0.0096104694 #> Adgrb1   -0.010245871 -0.0289001310 -0.0406959418  0.0850357347 -0.1399789458 #> Lpar1    -0.100519996 -0.0296181051 -0.0303608873  0.0284140963  0.1079446603 #> Gpr17    -0.037413183 -0.0409449419  0.1066698878 -0.0904712564 -0.0042850736 #> Cxcl12    0.166303218 -0.0741088720 -0.0987652140 -0.1045173035  0.0379263063 #> Epha4     0.236215472  0.1187559210 -0.1014044458 -0.2576374317 -0.0288992920 #> Gpr182   -0.007325424  0.1239147034  0.0567236821 -0.0303465614 -0.0172635204 #> P2ry14    0.026060228  0.0623355729 -0.1191555344  0.1284210156 -0.0615401150 #> Hcar1    -0.017866841 -0.0878042377 -0.0253030057  0.0218291965 -0.1156933762 #> Ephb1    -0.006609463  0.0556474977  0.0607459593 -0.1802441884  0.0067445497 #> Grm3      0.087976984 -0.0172607813 -0.0414884321 -0.0473811798  0.1605742802 #> P2ry1    -0.046186003  0.1353774255  0.0579385318  0.1446826680 -0.0586571090 #> Ptk7     -0.096323825  0.1641962315  0.0216347633  0.0616541843 -0.0307671660 #> Slco1a4  -0.092257226  0.0641209606  0.0799656090  0.1018008345 -0.0074273235 #> Insrr    -0.059080030 -0.0670002809 -0.0310309035  0.1380043199  0.0266727706 #> Cmklr1   -0.061271398 -0.0383254611 -0.0126749000 -0.1366653701 -0.0442663116 #> Fzd6      0.053287406 -0.1081961814  0.0797959776 -0.0092843009  0.0709059583 #> S1pr5    -0.101201473  0.0273667827  0.0480230199 -0.0692913512  0.1770706385 #> Pdgfrb   -0.051505924  0.0364359113 -0.1830693271 -0.0753629471  0.0507032542 #> Flt1     -0.038053300  0.0767461723  0.0208032046 -0.0537280068 -0.0615250878 #> Adgrl4    0.026253555 -0.0268851874 -0.0377383111 -0.0297586542  0.0100685614 #> Lpar6     0.071099049 -0.0220534155  0.0066036776  0.0916356476  0.0322774410 #> Epha6    -0.023285186 -0.1823371659 -0.0069725568 -0.0382722419  0.0177770319 #> Emcn     -0.185055908  0.0024771658  0.0003246873 -0.0001023792  0.1275890844 #> Cldn5    -0.005991687  0.0458753655 -0.1251857613 -0.0118347265  0.0297507920 #> P2ry12   -0.197614091  0.0387684568  0.0214227613 -0.0147775014  0.0438934561 #> Adgrf5    0.010745935 -0.1632673109  0.1081391279 -0.0029739122  0.0350290076 #> P2yr13    0.179447022  0.0572060389 -0.0278561314  0.1064854478 -0.1103962367 #> Adgre1   -0.052122112  0.0176002566  0.1360406511  0.1011271489  0.0047794617 #> Cx3cl1    0.098913594  0.0786969858  0.1179818711  0.1422956979 -0.0695686299 #> Plxnb3    0.002883744  0.0072856985  0.0137006839  0.0883121522  0.1875815346 #> Flt4      0.096013501 -0.0247383588 -0.1021594334 -0.1251698885 -0.0021921914 #> Slc17a7  -0.256499781 -0.0782267820 -0.0653459735 -0.0471411164 -0.0838828422 #> Cd300c2   0.015434046  0.0945279368  0.0423602416  0.0735319305 -0.0023573835 #> Tek       0.065209708 -0.0462791237  0.0200272894  0.1305409348 -0.0477164219 #> Kdr       0.004992421  0.0467759451 -0.0132908062  0.0838992391 -0.0444099964 #> Kcnj8    -0.006457918  0.0137809431  0.0077145057  0.0735818538 -0.0634035547 #> S1pr3     0.080031181  0.0215036975 -0.0091979488  0.1529445656  0.1258799645 #> Tie1     -0.009394909 -0.1332618374  0.2182733559  0.1134867086  0.1495459134 #> Pdgfra   -0.024210376 -0.1301655468 -0.0157326771 -0.1138978194 -0.0861137852 #> Baiap2   -0.086956494 -0.0217690733 -0.2253096697 -0.0436361141 -0.0404289886 #> Calcrl    0.095010135  0.0287122339  0.0330597124 -0.0030495130 -0.0184638459 #> Adrb2    -0.004960049  0.1767430408 -0.0227114221  0.0274593626 -0.0143647826 #> Ccr2      0.068857935  0.1079559698  0.0220579132  0.0950169039 -0.0317731027 #> Alk       0.115865387  0.0844081755  0.0250473222 -0.0431262849  0.0344749285 #> Tacr3    -0.051025366 -0.1259265507  0.0828404405 -0.0514782206 -0.0486880966 #> Erbb3    -0.150982847 -0.0644175904 -0.0784411207  0.0645418493 -0.0734840167 #> Pcdh15   -0.118717951  0.2693692684  0.0205868683 -0.0427408517  0.2768821344 #> Grm7     -0.092151484 -0.1024376606  0.1144558682 -0.1056192634 -0.0453776912 #> F2r       0.105792536  0.0144681129 -0.1002946522  0.0456532091 -0.0794064443 #> Bdkrb2    0.006001383 -0.0459385959  0.0088333126 -0.0305198133 -0.0526452216 #> Adgrv1   -0.026158465 -0.2056272141 -0.1198631418  0.0233466285 -0.2518471017 #> Gprc5c   -0.023790564 -0.0678341827  0.1192417349  0.0314452670 -0.0645376975 #> Tbxa2r    0.140387432 -0.1359503411  0.0385701747  0.0276742671  0.0093499153 #> Ackr1    -0.029065291 -0.0578602700  0.0755327226 -0.0082264946  0.0336118587 #> Lpar2    -0.062835829 -0.0388571222  0.0238483036  0.0313594088  0.0680303424 #> Myh11     0.024970701  0.0200975461  0.1009525960 -0.0326637175 -0.0211099112 #> Musk      0.063985092  0.0535659480 -0.0550955508 -0.0079134786  0.0937532730 #> Cnr1     -0.013906595 -0.0051928058 -0.0156992706  0.0061304241  0.0403338016 #> C3ar1     0.040076607  0.0062155089 -0.1244926028 -0.0492635936 -0.0471373831 #> S1pr4    -0.065958029 -0.0107962960 -0.0762538210  0.0620445279 -0.0655559389 #> C5ar1    -0.063637211 -0.0071225936 -0.0490415793 -0.1249847305  0.0498359527 #> Fpr1     -0.007449543  0.0349705591  0.0454274730 -0.0330372227  0.0021663403 #> Sctr      0.217948125 -0.2021586654 -0.0313647208 -0.0323918549  0.2127553516 #> Gpr158   -0.010826408  0.0262009227  0.0733116753  0.0279112388 -0.1041623031 #> Cxcr4    -0.076691016  0.0345196880  0.0775273150 -0.0060655988 -0.0866485357 #> Hrh2     -0.099014764 -0.0467100393  0.0278380198 -0.0417478197 -0.0970706786 #> Slc17a6  -0.082618502  0.0339428623 -0.0348717086  0.0473219326  0.0196922049 #> Ppp1r3g   0.013087120  0.0001441324  0.0678246439 -0.0276088484 -0.1342479581 #> Pln      -0.060753126 -0.0002540803 -0.0455250134  0.0102654582 -0.0195768585 #> Grin2b   -0.069454630  0.1341492975  0.0771539648  0.1749918653 -0.0473794907 #> Taar7e   -0.032709596  0.0944560187 -0.0695272893 -0.0133027666 -0.0999029114 #> Ptger2    0.044539693  0.0204023883 -0.0229346732  0.0242302762  0.0367794357 #> Mc4r      0.013592632  0.0278544767  0.0774813171  0.0160754232  0.0464084266 #> Ghsr      0.057581076  0.0104375508  0.0562762594 -0.0150781170  0.0521752668 #> Nmbr     -0.027601323 -0.0431472576 -0.0146725241  0.0152135724 -0.1101811620 #>                 Dim.86        Dim.87        Dim.88       Dim.89        Dim.90 #> Mlc1     -0.0446194521 -1.805083e-02  0.1484667185  0.078401733 -2.924862e-02 #> Gprc5b    0.0747662202 -4.475160e-02 -0.2115922857 -0.105664583 -5.921809e-02 #> Gfap      0.0155304162  1.903392e-02 -0.0666472414  0.066194824 -2.246512e-02 #> Ednrb     0.0512531207  3.987415e-03  0.2369214973  0.166821179 -2.950391e-02 #> Sox9     -0.0350224532  1.287844e-01  0.0315784750  0.088571993 -1.438889e-03 #> Aqp4     -0.0409703527 -7.632461e-02 -0.0185938481 -0.174663056  1.345998e-02 #> Gjc3      0.0253485452  7.446386e-02  0.1748230538  0.056229272  9.247124e-02 #> Sox8     -0.0600121991  7.987573e-02  0.0152099579 -0.044230580 -1.182730e-01 #> Ntsr2    -0.0328373691  5.558512e-02  0.0091378822  0.059867405  1.238556e-02 #> Smo       0.0026082270 -8.615144e-05  0.1097382639  0.004404282  9.167016e-02 #> C1qb     -0.0463971696 -7.029504e-02  0.0017497232  0.029113934  5.680070e-02 #> Olig1     0.0475466556 -2.586215e-02 -0.1024841085 -0.158382061 -6.533709e-02 #> C1qa      0.0327250841  7.903381e-02 -0.0883805004 -0.004993833 -1.239920e-04 #> Pth1r    -0.0340636713 -7.034020e-02  0.0232577748  0.073222547 -2.297609e-02 #> Gabbr2    0.2467788563 -2.335529e-01  0.1066481236  0.009390707  1.378517e-01 #> Timp4     0.0344405694 -2.093301e-01 -0.2507068893  0.093717686  4.694750e-02 #> Abcc9    -0.1654077683  1.239701e-02  0.0133393661 -0.106839592  8.088886e-02 #> Csf1r    -0.0911006034  6.607610e-02 -0.0175853355 -0.083767182 -2.424711e-02 #> Ntrk2     0.0909720851  1.162075e-01  0.2498873675 -0.060203665 -5.733222e-02 #> Adgrg1    0.1604057654 -7.367918e-02 -0.0786447060 -0.011826503  1.166184e-01 #> Ntrk3    -0.0702398451 -1.291608e-01  0.0514904569 -0.189859230 -2.138488e-01 #> Erbb4    -0.1204752552 -7.039966e-02 -0.0068576943  0.092890744  2.754632e-02 #> Selplg   -0.0754350766  6.230948e-02  0.1336268565  0.063006232 -6.318817e-02 #> Cspg5    -0.0887596276 -1.065305e-01 -0.0557288014  0.051694191 -2.038485e-02 #> Dlk1     -0.0114570157  1.415152e-01  0.0767420697 -0.054251363  6.092212e-02 #> Gpr37l1   0.0100927556  1.574754e-01 -0.0523048732  0.085128714 -4.366962e-02 #> Fgfr3    -0.1019314966 -5.537155e-02  0.0190798414 -0.033899780 -9.996322e-02 #> Slc25a18  0.0111218317  5.032591e-02 -0.0940290665 -0.121073844  5.010449e-02 #> Igf1r     0.2054869791  1.404098e-01  0.0338512596 -0.087277620 -2.845034e-02 #> S1pr1    -0.0150071577 -1.081918e-01 -0.0680190781 -0.125823251  8.775953e-02 #> Grm5     -0.0681448131  2.929161e-02 -0.0651909556 -0.098733711  1.579165e-01 #> Axl       0.0590108802 -1.080991e-01  0.0771046579  0.007894065 -5.397611e-02 #> Efemp1   -0.1154580606  7.907215e-03 -0.0424233822 -0.051372093  2.600285e-02 #> Adgrb3    0.0321149563  3.287189e-02 -0.1250068947 -0.125439970  1.612462e-02 #> Fn1      -0.0263861792  2.825983e-02  0.0102674758  0.053535815  5.371041e-02 #> Mertk     0.0636284756  7.375500e-02  0.0038191254  0.140573724  1.177747e-01 #> Adgrl2   -0.0228908889 -7.787807e-02 -0.0810190261 -0.055962182 -1.500475e-01 #> Fzd2     -0.0043931382  3.327012e-02 -0.0681692424 -0.068827869  7.152434e-02 #> Aldh1l1   0.0710862542 -7.769703e-02  0.0582722364 -0.140624588 -4.983157e-02 #> Adgrg6   -0.0118591507 -7.894166e-02  0.1372651343 -0.110852399 -7.310954e-02 #> Egfr      0.0322822638  8.828886e-02 -0.0575830224  0.045389255 -3.166876e-02 #> Kit      -0.0063283850  4.850125e-02  0.0058902801  0.006787918 -4.666146e-02 #> Ptgdr    -0.0033795743  7.205373e-02 -0.0338538620  0.010687341  2.218572e-02 #> Gad1      0.0649317004  1.052728e-01 -0.0169077529 -0.087712485 -4.638314e-02 #> Tyro3    -0.1936872100  8.286322e-02  0.0596594836  0.158670818 -1.697447e-01 #> Atp13a5   0.0536887501 -7.139742e-02 -0.0006019162  0.032278164  3.367556e-02 #> Ddr2     -0.0118138792  7.599040e-02  0.0981873588 -0.011273135 -5.016877e-02 #> Rspo3     0.1926614623  2.216777e-01 -0.1237669286  0.190032935 -1.532177e-01 #> Arhgap29  0.0512842017  9.375010e-02  0.0144832564 -0.055482717  7.913907e-04 #> Fzd7     -0.0348546237 -7.435300e-02 -0.1377184601 -0.034325478  6.582313e-02 #> Slc47a1   0.0337073209 -4.600745e-02  0.0360188574 -0.002719568  7.251633e-03 #> Ptger3   -0.1665172671  6.925160e-02  0.0112721993 -0.057882229  3.436207e-02 #> Bdkrb1   -0.0149827331  3.956890e-02  0.0256329102  0.080174603  1.338152e-01 #> Traf4     0.1010347149 -4.021194e-02 -0.1354731048  0.051532783 -1.349484e-02 #> Cx3cr1    0.0009525478 -1.017464e-01  0.0049169613 -0.031228771 -1.107590e-01 #> Anxa11    0.1317304674 -5.213404e-02 -0.0008196147  0.104542851  9.760599e-02 #> Adgrb1    0.0569615285 -1.567489e-01  0.1746398448  0.167423492  6.489188e-02 #> Lpar1     0.0635439589 -1.292604e-01  0.0833577119 -0.042971513  2.382378e-02 #> Gpr17    -0.0424124024 -4.348071e-02  0.0262955726  0.025745022  8.425356e-02 #> Cxcl12    0.0010679019  4.864325e-02  0.0606862789  0.094669791  1.066750e-01 #> Epha4    -0.0821875289 -9.604508e-02  0.0612775936  0.120227765 -9.518840e-02 #> Gpr182   -0.0479715697  5.451215e-02  0.0271839533  0.042579190  8.562556e-03 #> P2ry14    0.1085034671 -5.430043e-02 -0.0155609584  0.050346184 -1.591596e-01 #> Hcar1    -0.0067979095 -3.439027e-02 -0.0022340629 -0.100960193 -8.404609e-02 #> Ephb1     0.0371327572 -5.541361e-02 -0.0188839748 -0.140323806 -2.243897e-02 #> Grm3      0.0389587964  1.446795e-01  0.0760903847  0.065248793 -5.862115e-02 #> P2ry1     0.0009032442 -5.571599e-02 -0.0329558709 -0.078559184 -2.140956e-01 #> Ptk7      0.1021790718  3.947358e-02 -0.1292614587  0.205451999 -1.922064e-01 #> Slco1a4  -0.1230216987  1.620591e-02 -0.0164715384  0.075624971 -7.504246e-02 #> Insrr    -0.0618564389  7.917756e-02 -0.0133765712 -0.053179434 -6.474554e-03 #> Cmklr1    0.0876965432 -1.905926e-01  0.0410382644  0.036860903 -1.367721e-01 #> Fzd6     -0.0606310055 -4.110305e-02 -0.0606122265  0.085063856 -1.423208e-01 #> S1pr5    -0.0333697225 -1.651912e-01 -0.2398338827  0.079263455  9.648839e-02 #> Pdgfrb    0.0722589193  6.142832e-02 -0.0268860101  0.071009120 -4.138239e-02 #> Flt1      0.0094090193 -3.079724e-02  0.0182186890 -0.075639673  1.047349e-03 #> Adgrl4   -0.0209377846  3.113586e-03  0.0128197093  0.070877993  5.843472e-02 #> Lpar6    -0.0402961268  7.686132e-02 -0.1282588895  0.008005590 -1.463135e-01 #> Epha6     0.1305479186  1.104275e-01 -0.1029818180 -0.055884161  1.073548e-01 #> Emcn     -0.0470831763  7.510201e-02  0.0362258487 -0.038194179 -2.105266e-01 #> Cldn5     0.0565542902  2.510552e-02  0.0315876240 -0.009298534  7.189559e-02 #> P2ry12    0.1143582937 -3.988627e-02 -0.0035901726  0.001953338  8.302300e-02 #> Adgrf5   -0.0461115669 -2.655683e-02 -0.0344487892 -0.023655936 -4.777138e-02 #> P2yr13    0.0125318115  5.569178e-02 -0.0420937780 -0.015805057  4.400681e-02 #> Adgre1    0.0117089575  1.161404e-01  0.0513334851  0.058824367  6.150708e-02 #> Cx3cl1    0.0525073828  2.093352e-02 -0.0754721673  0.169348562 -1.571408e-01 #> Plxnb3   -0.0205279486 -7.604818e-02 -0.0924020758 -0.006464499 -9.795533e-02 #> Flt4      0.1073713796 -1.297346e-02 -0.0427496857 -0.127412189 -1.227490e-01 #> Slc17a7   0.0565152861  2.272088e-01  0.0271522871 -0.229408843 -4.701083e-02 #> Cd300c2   0.0274907928  1.143450e-02  0.0065890129 -0.130221505 -7.010812e-02 #> Tek       0.0560011841  4.294065e-02  0.1335633219 -0.014078586  4.149950e-02 #> Kdr      -0.0201259418 -6.527167e-02 -0.0735287909 -0.018974185 -7.516299e-02 #> Kcnj8     0.0372905862 -1.116525e-02 -0.0252264071  0.044301430 -6.266965e-05 #> S1pr3    -0.0299521998  1.025287e-01  0.0882538463 -0.159986219 -2.502918e-02 #> Tie1     -0.0717360114  2.639144e-02 -0.1375540330  0.157961502  1.553215e-04 #> Pdgfra    0.0233506937  8.200833e-02  0.0038740056  0.095441443 -9.966319e-02 #> Baiap2   -0.4645124859 -6.708663e-03 -0.0683163507  0.095760104  4.075181e-02 #> Calcrl   -0.0755337762  2.884843e-02 -0.1971094832 -0.147954534  1.646196e-01 #> Adrb2     0.0232551104  2.182670e-02  0.0442128864 -0.031119813  7.749773e-03 #> Ccr2      0.0187758578  1.423078e-01 -0.0401214290  0.009916639  1.618989e-01 #> Alk       0.0094736307 -2.479994e-02 -0.0290829866  0.131559455  7.399575e-02 #> Tacr3     0.0475557748  2.828127e-02 -0.0447900242 -0.074897727 -1.551180e-01 #> Erbb3    -0.0116597367 -7.930685e-02  0.1488984855 -0.011857314 -2.676202e-02 #> Pcdh15   -0.0269552105  5.885912e-02  0.1059472583 -0.106230546  6.587346e-02 #> Grm7      0.0826025860  2.463791e-01 -0.1404234949  0.082048046 -3.615954e-02 #> F2r       0.1026273597 -4.818283e-02  0.0852606440  0.082413081  1.522432e-01 #> Bdkrb2   -0.0542236247 -6.360083e-02  0.0038745014 -0.025688396  3.332960e-02 #> Adgrv1   -0.1021722586 -1.422461e-01  0.0437448145 -0.056937217 -5.939909e-02 #> Gprc5c    0.0495495077 -1.119429e-01  0.0529993738 -0.084594579  4.060084e-02 #> Tbxa2r   -0.0121577529  7.251028e-03 -0.0883168339  0.064150475 -3.959664e-03 #> Ackr1     0.0079071318  5.988393e-02  0.0151373969  0.031453858  8.095278e-03 #> Lpar2     0.0043291299  8.080011e-02 -0.0356883105 -0.054470181 -1.099391e-02 #> Myh11    -0.0567735403  7.492579e-02 -0.1033736082 -0.045153914  5.432581e-02 #> Musk     -0.0627212129  8.387976e-02  0.0950492391  0.076878746  6.558108e-02 #> Cnr1     -0.0356711740 -5.338342e-02  0.0150921884 -0.018300402 -7.110529e-03 #> C3ar1    -0.0302378107 -2.663406e-02  0.0970212512  0.013354996  1.387947e-02 #> S1pr4     0.0777441924 -8.961595e-02 -0.0089304346 -0.026649657 -5.290134e-02 #> C5ar1     0.0334688763 -9.575626e-02  0.0356289138  0.058512222 -5.330371e-02 #> Fpr1      0.0178616196  6.087678e-02 -0.0822492653  0.025762868  1.574356e-01 #> Sctr     -0.0927803997  2.562672e-02  0.1087190230  0.024505202 -1.272342e-01 #> Gpr158    0.2804129926 -1.019917e-01  0.0460595008  0.011958022 -1.576415e-01 #> Cxcr4    -0.0124775636 -1.470519e-02  0.0210273618  0.013932847 -5.098411e-02 #> Hrh2      0.0527114067  1.065130e-01 -0.0018334120 -0.032959941 -3.524109e-02 #> Slc17a6   0.0356926463 -1.842255e-02 -0.1074389264 -0.015823678  8.473616e-02 #> Ppp1r3g  -0.0880604154  7.780899e-02  0.1949952894 -0.178453914  5.251934e-02 #> Pln      -0.0454816248  5.586009e-02 -0.0074355584  0.082752732 -4.942930e-02 #> Grin2b   -0.1556732114 -1.328897e-01  0.0514727255  0.102723982  6.283657e-03 #> Taar7e   -0.0604679604 -4.507736e-02 -0.0121886825  0.016353812  1.261960e-01 #> Ptger2   -0.0399916191 -4.134145e-02  0.0832987494 -0.094119195  3.060327e-02 #> Mc4r      0.1444646087 -1.640418e-02  0.0906481710  0.043195372  1.538470e-01 #> Ghsr     -0.0199047909  4.445657e-02 -0.0162983411 -0.028989517 -2.208633e-02 #> Nmbr     -0.0466640465 -6.363597e-02  0.0567610241  0.083868530 -6.956039e-02 #>                 Dim.91        Dim.92        Dim.93        Dim.94       Dim.95 #> Mlc1      5.274630e-02  0.1119067244 -0.0058843186 -0.1260245979 -0.062133638 #> Gprc5b    7.451196e-02 -0.0725239516 -0.0177110790  0.0422678106 -0.071748323 #> Gfap     -5.426800e-03 -0.0009118004  0.0203838019  0.0130710924 -0.058933794 #> Ednrb     1.270626e-01  0.1975129564  0.0128232313 -0.0401348038  0.069795811 #> Sox9      5.300940e-02 -0.0635346464  0.0548853394  0.0165461293  0.159258768 #> Aqp4     -1.517101e-02  0.0242932969  0.0024132074  0.0041561978  0.106669459 #> Gjc3     -9.228729e-02  0.1188491227  0.1082725892  0.0010672864  0.038196259 #> Sox8      7.469424e-02 -0.0440096699 -0.0868163694 -0.0280494469 -0.032285235 #> Ntsr2    -7.869387e-02 -0.0087441775  0.0994052047 -0.0470564988 -0.144997227 #> Smo      -4.865835e-02  0.0229379884 -0.1074756153  0.0354601048  0.116596708 #> C1qb     -2.074106e-02 -0.2393448345  0.0478761536 -0.0007524227 -0.014477896 #> Olig1     2.768440e-02 -0.1600840106  0.0088878639 -0.0040873489  0.022958611 #> C1qa      1.876587e-02  0.0138978653 -0.1212664358 -0.0558055109 -0.142545337 #> Pth1r    -1.809017e-01 -0.0452984472  0.0533957458 -0.1415904704 -0.004328204 #> Gabbr2   -2.182466e-02 -0.1128847191 -0.2304138433  0.1243715447  0.033183363 #> Timp4    -7.359871e-02 -0.0360900616 -0.0049517074 -0.1501054501  0.090362088 #> Abcc9     8.776331e-02  0.0521360242 -0.0085283136  0.1391603416 -0.022712588 #> Csf1r     5.100531e-02  0.0336142928 -0.0756824900  0.0037381114  0.020710353 #> Ntrk2    -2.417711e-01 -0.0812715030 -0.0043631322 -0.0081213750 -0.056854403 #> Adgrg1    1.346017e-01  0.1223961668 -0.2295753563 -0.0956746527 -0.090149156 #> Ntrk3    -2.374724e-02  0.0825801855  0.0551206233 -0.0290736291 -0.130174134 #> Erbb4    -3.835613e-02  0.1237293510  0.0517807023  0.0236626175 -0.100207753 #> Selplg    1.132267e-02 -0.0604731000  0.0723855567  0.0915252382  0.056802808 #> Cspg5    -1.119734e-01 -0.0693898022 -0.0016051719  0.0264069705 -0.095290874 #> Dlk1      4.919871e-02 -0.1741299554  0.0699417797  0.0420140222 -0.008967707 #> Gpr37l1   9.515550e-02 -0.0730644077  0.0446836441 -0.1253609433  0.053643619 #> Fgfr3     8.425444e-02  0.0039412239  0.0165419726  0.1590987135  0.146860270 #> Slc25a18 -8.814109e-02 -0.0135399639  0.0272595990  0.1088374133  0.056437595 #> Igf1r    -4.728995e-02  0.1028665732  0.2451292333 -0.1436671287  0.033086226 #> S1pr1     3.220078e-02  0.1448388548  0.1727089120  0.1872601124 -0.065810688 #> Grm5      6.983273e-02  0.0348919967 -0.0362557012 -0.1906023454  0.076228672 #> Axl       1.282342e-02  0.0774643176 -0.0002670706  0.0420034959  0.065182132 #> Efemp1   -1.303980e-01  0.0291655882 -0.0676869394  0.1547113193  0.187009834 #> Adgrb3   -3.224509e-02 -0.0544250128  0.0636919755 -0.0352234089  0.030183741 #> Fn1       1.095986e-02  0.0106850902  0.0123097978 -0.0392558434 -0.059979499 #> Mertk    -2.603184e-02  0.0188830892 -0.0363736098  0.0531165931  0.065029966 #> Adgrl2    6.419857e-02  0.0192476777  0.0609166898 -0.0268072961 -0.085087072 #> Fzd2      8.308113e-02 -0.0315091534 -0.0327257804  0.1299755197 -0.034626714 #> Aldh1l1   1.701282e-01 -0.0218071514 -0.1163273732 -0.0991568679  0.113192050 #> Adgrg6   -1.381625e-02 -0.0163830487 -0.0108848847 -0.0801376177  0.093141983 #> Egfr      9.556956e-02  0.0637854932 -0.0820240368  0.1227685775 -0.234172750 #> Kit       1.397337e-02  0.0074008920 -0.0111842346 -0.0473228962  0.040086813 #> Ptgdr    -1.496378e-01  0.1521258459  0.0043817332  0.0317115304  0.022757113 #> Gad1     -8.320921e-03 -0.0205413619  0.0208210785  0.0027575052  0.052196651 #> Tyro3     4.202130e-02 -0.0118759845 -0.1515579464 -0.0986512932  0.016103211 #> Atp13a5   5.137613e-02  0.0122029177  0.0166656726 -0.0367414591 -0.098132582 #> Ddr2      1.067384e-03 -0.0715132707 -0.0892093482 -0.0760200095  0.057334832 #> Rspo3     3.153281e-02 -0.1485852682 -0.0797618400  0.1017012014 -0.126598079 #> Arhgap29  3.673274e-02 -0.0313719339 -0.0092522089 -0.1041883214 -0.098033034 #> Fzd7     -8.768548e-02 -0.0556027811 -0.0340580667  0.0854028316  0.011053845 #> Slc47a1  -1.049590e-02 -0.0380321766  0.1020534531 -0.0740588261  0.064150133 #> Ptger3    8.999965e-02  0.0201227608 -0.0866566116  0.0150350012  0.068411317 #> Bdkrb1   -3.517196e-03  0.0177256164 -0.1910225702 -0.0084693673 -0.002411413 #> Traf4    -3.597948e-02  0.0169164589  0.1174897496  0.0671280949  0.185864850 #> Cx3cr1   -5.266623e-02  0.0399290009  0.1858021886  0.0158711747  0.111509837 #> Anxa11    3.333925e-02 -0.0208656309  0.0301249996 -0.0459639935 -0.052587851 #> Adgrb1    9.867209e-02 -0.2357833506 -0.0256168656  0.1360881588 -0.015569375 #> Lpar1     2.985648e-02  0.1592898623  0.2317965357  0.0136643880  0.178270900 #> Gpr17    -1.592767e-01  0.2122786878 -0.0493877360 -0.0910875088 -0.004874026 #> Cxcl12    1.513376e-02 -0.0099646162  0.0797348008 -0.0463832317 -0.040245633 #> Epha4    -4.408341e-02  0.0771809879 -0.1840034099  0.1428032845  0.042768029 #> Gpr182    7.206805e-02 -0.0692460810  0.0941783248  0.0670536943  0.009681566 #> P2ry14   -1.366635e-01 -0.0484745097  0.0587505754  0.1375289381 -0.091776111 #> Hcar1    -1.679301e-01 -0.0291004491 -0.0604382372 -0.1695048047 -0.113575750 #> Ephb1     5.449130e-02 -0.0570568594  0.0088434925 -0.0410839852  0.062984098 #> Grm3      1.422796e-01  0.0382414120 -0.1080238100 -0.0181992123  0.132527789 #> P2ry1    -1.234986e-04  0.0352800912  0.0061337002  0.0148423810  0.040628383 #> Ptk7     -3.400042e-02  0.1043124267 -0.0023697917 -0.0434795872 -0.127352696 #> Slco1a4  -1.102402e-01 -0.0510245545 -0.0154378755  0.0652769290  0.127281908 #> Insrr    -1.279034e-01 -0.0198141057 -0.0402604398  0.0917762751  0.120392818 #> Cmklr1   -6.111989e-02  0.0239326991  0.1557921105 -0.0467046857 -0.031457352 #> Fzd6      2.392842e-01  0.1070139799  0.1032530179  0.0594508148 -0.117127669 #> S1pr5    -1.698502e-01  0.0064873071 -0.0314512754 -0.0047582822 -0.088842584 #> Pdgfrb   -8.903590e-02  0.0554026147  0.0112335976 -0.0554802232  0.097785036 #> Flt1     -8.397945e-02  0.1104478313 -0.1445429372 -0.0585623138  0.085627628 #> Adgrl4    5.147395e-02 -0.0077315055 -0.0228087263  0.1125072990  0.015768241 #> Lpar6     2.688989e-02  0.0025936378 -0.0909584982 -0.0205692378  0.023886774 #> Epha6    -8.426374e-02  0.0083902484  0.0610022002  0.0535833669  0.043927727 #> Emcn     -3.379956e-02 -0.1881030057 -0.1108758191  0.0219499761  0.040543646 #> Cldn5     5.164176e-03 -0.0582697060  0.0315810714 -0.0780171074 -0.009205243 #> P2ry12   -3.672288e-04  0.0195319771  0.0371205083  0.0553671931 -0.054466839 #> Adgrf5    3.637698e-02  0.0418984353  0.0651674492  0.1303545172 -0.023513050 #> P2yr13   -1.053792e-02  0.2155203696 -0.1715896097 -0.1840113796  0.026579646 #> Adgre1    1.579639e-02  0.1910967722 -0.0406083345 -0.0335323958 -0.060401049 #> Cx3cl1    1.264855e-01 -0.0212992628  0.1466435162 -0.1492039960  0.055354754 #> Plxnb3    2.288169e-02  0.1594962174 -0.1326319356 -0.1112995400 -0.008911806 #> Flt4      2.436691e-03 -0.0625747141  0.1160129047 -0.1579802723 -0.025707302 #> Slc17a7  -2.162611e-02  0.1501026508  0.1773487521  0.0284518061 -0.002662220 #> Cd300c2   9.373069e-03  0.0455778645  0.0651040413 -0.0580099884  0.013556195 #> Tek       1.179705e-01  0.0442479816 -0.0622206196  0.0017044543 -0.073825263 #> Kdr       2.954364e-02 -0.0778192837  0.0419985628  0.1193363711  0.012406760 #> Kcnj8    -1.139091e-01 -0.0112078354  0.0632968271 -0.0711670943 -0.025603391 #> S1pr3     1.651888e-01 -0.0941163033 -0.0543558259 -0.0878114038  0.060274450 #> Tie1      2.183940e-02 -0.0929299554  0.1221934973  0.0714904304 -0.035429824 #> Pdgfra    4.470313e-02 -0.0704080579 -0.0366466912 -0.0660518979  0.070267173 #> Baiap2   -5.007352e-02  0.0964096735  0.0653049088 -0.0439186303  0.099053514 #> Calcrl    5.086396e-02 -0.0443910277 -0.0632429601 -0.0755402623 -0.170827488 #> Adrb2    -8.531171e-02 -0.0235390834  0.0277281774 -0.0281566993 -0.012074353 #> Ccr2     -1.111422e-02  0.0798895460 -0.0142434512  0.0499987246  0.051588246 #> Alk       8.818340e-02 -0.0064481907  0.1489984479  0.0272100256 -0.002052568 #> Tacr3    -2.423263e-02  0.1858740584 -0.0864598644  0.1845241189  0.011070858 #> Erbb3     8.649665e-02  0.0403412424 -0.0080201021  0.0573785690 -0.067445700 #> Pcdh15    1.793187e-01 -0.0904384341  0.1222951706  0.2295291974 -0.205263012 #> Grm7      4.082372e-02  0.0645856989  0.0246271920  0.0779872938  0.118455276 #> F2r       2.593090e-02  0.1970133776  0.1180674408  0.1078030635 -0.035225472 #> Bdkrb2    4.564745e-02  0.0071894322 -0.0718710495  0.0627660964 -0.032027913 #> Adgrv1    3.446076e-01  0.0422527952  0.0312952274 -0.1030285349 -0.094754773 #> Gprc5c    2.988676e-03  0.0616420471 -0.0758919905  0.0202860957 -0.054501685 #> Tbxa2r    1.076748e-01 -0.0119957490  0.0666507185  0.0809035397  0.074280864 #> Ackr1    -9.688354e-03  0.1109129947 -0.0213916976  0.0203904193 -0.052891145 #> Lpar2    -1.743762e-02  0.0145641239  0.0126481211 -0.0354632132 -0.110595369 #> Myh11    -1.829092e-03 -0.0306573803 -0.0995110444  0.0341511540  0.001283886 #> Musk     -6.212793e-02 -0.0801629560  0.0638048127 -0.1806913031 -0.159469306 #> Cnr1      5.976242e-03 -0.0178971737 -0.0075423455 -0.0488774634  0.055390504 #> C3ar1     3.295826e-02  0.0129418092 -0.0200485611  0.0907133802  0.096648532 #> S1pr4    -3.719727e-02 -0.0622030391 -0.1293827367 -0.0283849392  0.078226450 #> C5ar1     1.801483e-03  0.0308498187  0.0473987344 -0.0730893051  0.069828518 #> Fpr1      7.931787e-02  0.0837330351  0.0236887889  0.0098323219 -0.135110079 #> Sctr     -2.198100e-01  0.0260801526 -0.0583525288  0.1126435113 -0.251303669 #> Gpr158    2.018869e-02  0.0735612563 -0.1174086930  0.1017593704 -0.026547291 #> Cxcr4     2.807854e-02 -0.0252815960 -0.0357495237  0.0205471203  0.064926506 #> Hrh2     -4.505155e-02  0.0547656474  0.0717706742  0.0838867644  0.014215480 #> Slc17a6   1.118016e-01  0.0334324949  0.0303828133 -0.0459640930  0.084925433 #> Ppp1r3g  -1.845598e-01 -0.0806323697  0.0278996958  0.0034614065 -0.203229312 #> Pln      -5.207526e-02 -0.0141919704  0.0136697737  0.0119358138  0.022949312 #> Grin2b    3.785940e-02 -0.0624963454  0.1174093742 -0.1673219285 -0.129418076 #> Taar7e    5.297093e-02 -0.1448636627  0.1009128563 -0.0668147619  0.087798126 #> Ptger2    6.293152e-02 -0.0018785182  0.0015214838 -0.0097059538 -0.053563140 #> Mc4r     -2.186995e-02 -0.1983943923 -0.0134706415 -0.1139875981  0.068989559 #> Ghsr      2.851065e-05  0.0086599489 -0.0222297196 -0.0583938753 -0.002155070 #> Nmbr     -3.243908e-02 -0.0140878731 -0.0506366406  0.0631695680 -0.002616482 #>                 Dim.96        Dim.97        Dim.98        Dim.99       Dim.100 #> Mlc1     -0.0443537762  0.0360484369  0.0819819508  1.260459e-01  0.0450089853 #> Gprc5b   -0.0510558926 -0.0167780274 -0.0765372383 -5.747994e-02  0.0109242827 #> Gfap     -0.0172649627 -0.0325150875 -0.1045522993  2.849920e-02 -0.0343928321 #> Ednrb     0.1799824844 -0.0266675468  0.0126936581  1.502550e-01  0.0914827465 #> Sox9     -0.0776139391 -0.1348317883  0.0272543567 -1.218634e-01  0.0578865312 #> Aqp4     -0.0108937623  0.1450361285  0.2153831763 -5.214377e-02  0.0292030131 #> Gjc3     -0.0711227766 -0.0237886291  0.0343921640 -8.717850e-02  0.0005867661 #> Sox8     -0.0219504626  0.1839473385 -0.0055640059  8.358220e-02 -0.0472305015 #> Ntsr2    -0.0632400181 -0.0132755552 -0.0229996979  1.290156e-02 -0.1622541807 #> Smo       0.0446726332  0.0240068066 -0.1061320550 -1.462967e-01 -0.0498647005 #> C1qb     -0.0711368702  0.0638066014  0.1014940176  7.417651e-02  0.2129650839 #> Olig1     0.1893899465 -0.0113085427  0.0271378206  7.785833e-02 -0.0509245967 #> C1qa     -0.0449503731 -0.0960650048 -0.0771657285  4.181065e-02 -0.0754157023 #> Pth1r    -0.0108889896  0.0968962403 -0.0397244781 -3.021003e-02  0.1744126574 #> Gabbr2   -0.1127715258  0.1773201109 -0.1029834145  1.209036e-01 -0.0706423471 #> Timp4    -0.0469308197 -0.0136558665  0.1427075714  7.442107e-02  0.2083804252 #> Abcc9    -0.0868392638  0.0548558733  0.1813730140 -9.282117e-02 -0.1516930779 #> Csf1r     0.0597065849 -0.0116122845  0.0336615327 -1.838982e-02 -0.0626278245 #> Ntrk2     0.0889879882  0.0814695626  0.0465132494  4.193621e-02  0.0532033928 #> Adgrg1   -0.0046413805 -0.1743434429 -0.1574148804 -2.932602e-01 -0.1899499941 #> Ntrk3    -0.0935254436 -0.2637648766  0.2785446170 -2.392332e-02 -0.0058407785 #> Erbb4    -0.1687700521 -0.0341593112 -0.2247057880  1.110902e-01  0.0796625842 #> Selplg    0.0437971895 -0.0463517396  0.0465568388  6.566697e-02 -0.0708426139 #> Cspg5    -0.0097326391  0.0375980393  0.1274219462  7.434923e-02 -0.0581365681 #> Dlk1     -0.0550064886 -0.1046811997  0.0624809226  3.654155e-02 -0.0024350514 #> Gpr37l1   0.0557102606 -0.0889941638 -0.1141913728  1.594975e-01 -0.0369676530 #> Fgfr3     0.0586096854 -0.0269485012 -0.0181944486 -6.419439e-02  0.1628006771 #> Slc25a18 -0.0754009255  0.1231508326  0.0387336149  4.379239e-02 -0.0008650515 #> Igf1r    -0.0071980557  0.1371319776  0.0010901707  1.028243e-01  0.1415628044 #> S1pr1    -0.0586984413  0.1770275465 -0.1479985976 -1.284361e-01 -0.1350629013 #> Grm5     -0.0112312693  0.1778657338 -0.0605667870  1.595176e-01 -0.1533531628 #> Axl       0.0868458539  0.0655911386 -0.0048398865 -1.126509e-01 -0.1559221555 #> Efemp1   -0.0309381034 -0.1439380354 -0.0925716241  7.542845e-02  0.0478113886 #> Adgrb3   -0.0560734659  0.0039267328 -0.0026751082 -1.309427e-01 -0.0333891198 #> Fn1      -0.0239286942 -0.0205363547  0.0211027429 -2.125365e-02 -0.0460118361 #> Mertk     0.0395005414  0.0640619585  0.1031300535 -5.733631e-02  0.1335469428 #> Adgrl2    0.0195788504  0.0789741627 -0.0008308767  2.853738e-03 -0.0062170128 #> Fzd2     -0.0065199766 -0.1310735935  0.1572681321  8.776131e-02  0.0552191702 #> Aldh1l1  -0.0224101512  0.0292154700 -0.0378982746 -9.869550e-03  0.1135695271 #> Adgrg6   -0.0555596044  0.0919334192 -0.0236862783  2.818611e-03 -0.0003815807 #> Egfr     -0.1078294613  0.1540900612  0.1981852096 -1.919934e-02  0.0780892047 #> Kit       0.0523865550 -0.0386807889  0.0162609700 -1.247745e-02  0.0111076131 #> Ptgdr     0.1490205337 -0.0648832054 -0.0358539783  1.555095e-01 -0.1691839548 #> Gad1      0.1130041785  0.0439577095  0.1340075342 -6.451207e-02 -0.0300128673 #> Tyro3     0.0373603761  0.1074132990  0.1054368777 -4.662024e-02 -0.0365530052 #> Atp13a5   0.0073141075  0.0294909094  0.0357624918  1.460249e-02  0.0689017805 #> Ddr2     -0.0841406286  0.1473669490 -0.0089520103 -1.673733e-01  0.0827914374 #> Rspo3     0.0742247994  0.2529983374 -0.0580867643 -6.847477e-03 -0.0299330728 #> Arhgap29 -0.0269153620 -0.1034054972 -0.0060879314  3.061664e-02 -0.0037196932 #> Fzd7      0.0826427421 -0.0354264650  0.1027051543 -8.486209e-02 -0.0869939679 #> Slc47a1   0.0377543892 -0.0122535769 -0.0236616772 -9.365409e-02 -0.0203153213 #> Ptger3   -0.0761078960  0.0401885677 -0.0211771590 -1.105876e-01  0.1265538944 #> Bdkrb1   -0.0360341989  0.0180912458 -0.0813510345  3.149664e-02 -0.0125204111 #> Traf4    -0.0841528360  0.0417908160 -0.0470187449 -5.853414e-03  0.0402492851 #> Cx3cr1    0.0121677778  0.0283883732  0.0090845478 -7.015568e-02 -0.0086359019 #> Anxa11   -0.1266526962 -0.0901204568  0.1300161597  4.910297e-02 -0.0988169775 #> Adgrb1    0.0715700958  0.0673534814 -0.0393200976 -1.013340e-01  0.0162896611 #> Lpar1    -0.0002344535  0.0775491634 -0.0357163481  7.684334e-02 -0.1244453280 #> Gpr17     0.0571312823 -0.0167074981  0.1165888236 -1.667889e-01 -0.0238835701 #> Cxcl12    0.1057562688  0.0050510973  0.1631412288  4.178168e-02 -0.0218110911 #> Epha4     0.0391504682  0.0103309385 -0.0521921360  2.497589e-01  0.0326497811 #> Gpr182    0.0126087893  0.1296180784  0.0151222552 -7.079531e-02  0.0402807391 #> P2ry14    0.1392576242  0.0009081532 -0.1124062478  9.233882e-02 -0.1015120121 #> Hcar1    -0.0067673809  0.0410951436 -0.0203082511  1.203454e-01  0.1064953338 #> Ephb1     0.0149729283 -0.0202305784 -0.0350631704 -3.970236e-02 -0.1435495491 #> Grm3     -0.0594710151 -0.1637695938 -0.1229371505  6.062457e-02  0.0349878895 #> P2ry1    -0.1005179917  0.1687439529 -0.0487013462 -9.843553e-02  0.0611132939 #> Ptk7      0.0957404922 -0.0178864154 -0.0425020642 -7.592525e-02  0.0114444663 #> Slco1a4  -0.0626315893  0.0201931781  0.0744170417  9.867970e-02 -0.0053665358 #> Insrr     0.0944776078  0.0335998295  0.0432814485 -5.041559e-02 -0.0815594033 #> Cmklr1   -0.0783381406  0.0509605751 -0.1146788289 -1.831444e-02 -0.0341116091 #> Fzd6      0.1052248180  0.0788448872 -0.0421288772 -1.087229e-01  0.0585974004 #> S1pr5    -0.0013298678  0.0368014566  0.0470516154 -8.905017e-02  0.0877678767 #> Pdgfrb   -0.1018702817 -0.0594929075  0.0011852843  9.373763e-02 -0.0681029985 #> Flt1     -0.0794881609 -0.0767376686 -0.0352270387  1.701944e-02 -0.0593478010 #> Adgrl4    0.0715719036 -0.0024930768 -0.0026283303 -7.695242e-02 -0.0081116497 #> Lpar6    -0.0338539052 -0.0699560815 -0.1013519424  1.572401e-02 -0.0209834505 #> Epha6     0.1292911044  0.0639261186 -0.0787368065 -7.881928e-02  0.0730507215 #> Emcn     -0.0630136885 -0.0387701346 -0.1296581708 -2.786186e-02 -0.0795758492 #> Cldn5     0.0089685139  0.0378101412  0.0372486792  5.591290e-03  0.0116931295 #> P2ry12    0.0407785955 -0.0067044142 -0.0493437175  1.554941e-02 -0.1460416692 #> Adgrf5    0.0356186631 -0.0929036549 -0.0431651800 -2.943058e-02 -0.0265416805 #> P2yr13   -0.1024577086  0.1104307839 -0.0186240317 -1.499583e-01  0.2366327278 #> Adgre1   -0.0207542755  0.1252825896 -0.0217732142  2.833754e-02 -0.0388424267 #> Cx3cl1   -0.3294128886  0.0023821356  0.2061062819 -2.316771e-02 -0.2453750441 #> Plxnb3    0.1697384800  0.1661675573 -0.0152867680  8.637727e-02 -0.0701051213 #> Flt4      0.0586426204  0.0176883428 -0.0125178126  3.461665e-02 -0.0392505043 #> Slc17a7   0.0828733051  0.0429671987 -0.1974277477 -6.446599e-02  0.1643070653 #> Cd300c2  -0.0481613197 -0.0563445727 -0.0710774534  7.344774e-03 -0.0100193949 #> Tek      -0.0089852611  0.0414927826  0.0590540015 -1.597511e-02  0.0268458258 #> Kdr       0.0779024612  0.0734437579 -0.0069344954  1.293320e-02  0.0015974350 #> Kcnj8     0.0818562748 -0.0584210918 -0.1080648007  7.424314e-02  0.1278848916 #> S1pr3     0.1318715326  0.0812680530 -0.0165760443 -8.612860e-02 -0.0265361090 #> Tie1      0.0033508741  0.1083100692 -0.0006694247  2.620638e-02  0.0579725541 #> Pdgfra   -0.0387369696  0.0588450248 -0.0787371045 -2.944948e-02 -0.1049359760 #> Baiap2   -0.0775217698  0.1349416427 -0.1636373601  1.108546e-01 -0.1079669366 #> Calcrl    0.1419570347  0.0208696070 -0.0293084541  1.669668e-01  0.0357484666 #> Adrb2    -0.0365630186 -0.0082632953 -0.0670394928  6.155158e-02  0.0227936987 #> Ccr2      0.0858909799 -0.0021885373  0.0625329152 -2.820142e-02  0.0099452840 #> Alk       0.0458290549 -0.0734565716 -0.1648546419  5.582668e-02 -0.0792551027 #> Tacr3     0.0265660569 -0.0436933519  0.0850627227  9.230092e-02  0.0687709599 #> Erbb3     0.1245836146  0.1412833680  0.0164346809  1.122492e-01 -0.0665527368 #> Pcdh15   -0.2529142945 -0.1004256139 -0.1432620596  1.004588e-01  0.2194278503 #> Grm7     -0.1397368781  0.1089594413  0.0379568219  1.443681e-02 -0.0322724861 #> F2r      -0.0423929786  0.0566388736 -0.0074588355  1.282994e-02  0.0393546109 #> Bdkrb2    0.0781244052  0.0162706420 -0.0392946792 -9.185904e-03  0.1108206463 #> Adgrv1   -0.0356076159  0.0738471856 -0.0006103067  9.597895e-02  0.0121626521 #> Gprc5c   -0.2042111942 -0.0003886170 -0.0891583759  8.981869e-02 -0.0085222955 #> Tbxa2r    0.0088643166  0.0266243067  0.0670353931 -7.072588e-02 -0.1360094300 #> Ackr1    -0.0123965578 -0.1484398276  0.0494395270 -4.358139e-02  0.0026337024 #> Lpar2    -0.0224920176 -0.1120428877 -0.0551356136 -3.575251e-02  0.0088337743 #> Myh11     0.0404946186  0.0164047386 -0.0386613025  2.024687e-02 -0.0207320428 #> Musk     -0.0524175931  0.0439845020 -0.0106651062 -9.185905e-02 -0.0704663974 #> Cnr1     -0.0508017667  0.0555751164 -0.0332689232  6.523213e-03 -0.0693199266 #> C3ar1     0.1046549965  0.0508510489  0.0800600990 -3.385654e-02 -0.0109808954 #> S1pr4    -0.0717778678  0.0565913811 -0.1038866351 -1.688067e-02  0.0660013158 #> C5ar1    -0.0336764016  0.0003741751 -0.0131256422 -9.364569e-02  0.0141209369 #> Fpr1      0.0418202715  0.1105538549  0.0453254973  3.427520e-02  0.0066593880 #> Sctr     -0.1433701071  0.0896402281 -0.1137159324 -2.522357e-01 -0.0207737837 #> Gpr158    0.0562321374 -0.0563950797  0.1171726660  4.753825e-02 -0.0126591675 #> Cxcr4     0.0118897498 -0.1273500733 -0.0736292578  9.587281e-05 -0.0497375321 #> Hrh2     -0.0696668100 -0.0344627831  0.0156450293 -1.724896e-02  0.0246493820 #> Slc17a6   0.0333474238  0.0239279656  0.0496821502  1.116024e-01 -0.0052144861 #> Ppp1r3g   0.0152166395  0.0842415215  0.0323072063  8.383231e-02 -0.2180193222 #> Pln       0.0560646403 -0.0693041040  0.0316120048 -3.325110e-02  0.0144415377 #> Grin2b    0.3086303995 -0.1369938155 -0.0702822115 -1.924546e-01  0.0952752006 #> Taar7e    0.0299564845  0.0113191149 -0.1575437408 -7.225802e-02 -0.0143840271 #> Ptger2    0.0687272492 -0.0360582887 -0.0043759260  1.268787e-02  0.0203538675 #> Mc4r     -0.0853855671  0.0217886780  0.0046874230 -3.175744e-02 -0.0417995305 #> Ghsr      0.0217415657  0.0229802934 -0.0204775738  2.456220e-02  0.0040153451 #> Nmbr     -0.0143240610 -0.0464849471 -0.0352151903 -1.932095e-02  0.0324894853 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":null,"dir":"Reference","previous_headings":"","what":"my_arowMeans — my_arowMeans","title":"my_arowMeans — my_arowMeans","text":"my_arowMeans","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"my_arowMeans — my_arowMeans","text":"","code":"my_arowMeans(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"my_arowMeans — my_arowMeans","text":"x data use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"my_arowMeans — my_arowMeans","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"my_arowMeans — my_arowMeans","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  my_arowMeans(m) #>  [1]  0.2884262 -0.5417610 -0.2227548  0.1578376  0.2002051  0.1017837 #>  [7] -0.6461654  0.8037910 -0.3705254 -0.4083799"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":null,"dir":"Reference","previous_headings":"","what":"my_growMeans — my_growMeans","title":"my_growMeans — my_growMeans","text":"my_growMeans","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"my_growMeans — my_growMeans","text":"","code":"my_growMeans(x, offset = 0.1)"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"my_growMeans — my_growMeans","text":"x data use offset offset","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"my_growMeans — my_growMeans","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"my_growMeans — my_growMeans","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  my_growMeans(abs(m)) #>  [1] 0.6858454 0.4898760 0.5735737 0.6441830 0.5510774 0.7287629 0.7224097 #>  [8] 0.4566198 0.8709865 0.6379915"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":null,"dir":"Reference","previous_headings":"","what":"my_rowMeans — my_rowMeans","title":"my_rowMeans — my_rowMeans","text":"my_rowMeans","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"my_rowMeans — my_rowMeans","text":"","code":"my_rowMeans(x, method = c(\"arithmic\", \"geometric\"), offset = 0.1)"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"my_rowMeans — my_rowMeans","text":"x data use method method either \"arithmic\" \"geometric\" offset offset","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"my_rowMeans — my_rowMeans","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"my_rowMeans — my_rowMeans","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  my_rowMeans(m) #>  [1]  0.31935467 -0.11429801  0.06630945 -0.38510854 -0.38755999 -0.08956358 #>  [7]  0.84401809 -0.06373938  0.25949145 -0.02899145"},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":null,"dir":"Reference","previous_headings":"","what":"nnDT_to_kNN — nnDT_to_kNN","title":"nnDT_to_kNN — nnDT_to_kNN","text":"Convert nearest network data.table kNN object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"nnDT_to_kNN — nnDT_to_kNN","text":"","code":"nnDT_to_kNN(nnDT)"},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"nnDT_to_kNN — nnDT_to_kNN","text":"nnDT nearest neighbor network data.table format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"nnDT_to_kNN — nnDT_to_kNN","text":"kNN object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"nnDT_to_kNN — nnDT_to_kNN","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_nn <- getNearestNetwork(g, output = \"data.table\", name = \"custom_NN\") #> The NN network type was not specified, default to the #>  first: \"sNN\"  nnDT_to_kNN(g_nn) #> k-nearest neighbors for 624 objects (k=3). #> Distance metric:  #>  #> Available fields: dist, id, k, sort"},{"path":"https://drieslab.github.io/GiottoClass/reference/nnNetObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 nnNetObj — nnNetObj-class","title":"S4 nnNetObj — nnNetObj-class","text":"Framework store nearest neighbor network information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnNetObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 nnNetObj — nnNetObj-class","text":"nnNetObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnNetObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 nnNetObj — nnNetObj-class","text":"name name nnNetObj nn_type type nearest neighbor network igraph igraph object containing network information feat_type feature type data spat_unit spatial unit data provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnNetObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 nnNetObj — nnNetObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"nnNetObj\") #> An object of class nnNetObj : \"sNN.pca\" #> --| Contains nearest neighbor network generated with: sNN  #> ----| for feat_type: rna  #> ----|     spat_unit: aggregate  #> ----|     provenance: z0 z1  #>  #> IGRAPH 859f76e DNW- 462 3021 --  #> + attr: name (v/c), weight (e/n), distance (e/n), shared (e/n), rank #> | (e/n) #> + edges from 859f76e (vertex names): #> [1] 240649020551054330404932383065726870513->335295524680090725199231409883288198017 #> [2] 240649020551054330404932383065726870513->77151711298730578178892667721058396928  #> [3] 240649020551054330404932383065726870513->322879686187630160969459793861944841206 #> [4] 240649020551054330404932383065726870513->31072896077757820678000109671990674373  #> [5] 240649020551054330404932383065726870513->102184699197574201819246996094734116255 #> [6] 240649020551054330404932383065726870513->17685062374745280598492217386845129350  #> + ... omitted several edges #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto object history — objHistory","title":"Giotto object history — objHistory","text":"Print return giotto object history","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto object history — objHistory","text":"","code":"objHistory(object, summarized = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto object history — objHistory","text":"object giotto object summarized logical. whether print summarized","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto object history — objHistory","text":"list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto object history — objHistory","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  objHistory(g) #> Steps and parameters used: #> <0_normalize> #>   gobject           : mini_visium #>   expression_values : raw #>   norm_methods      : standard #>   library_size_norm : TRUE #>   scalefactor       : 6000 #>   log_norm          : TRUE #>   log_offset        : 1 #>   logbase           : 2 #>   scale_feats       : TRUE #>   scale_cells       : TRUE #>   scale_order       : first_feats #>   theta             : 100 #>   update_slot       : scaled #>   verbose           : T #> <1_subset> #>   gobject         : gobject #>   spat_unit       : spat_unit #>   feat_type       : feat_type #>   cell_ids        : selected_cell_ids #>   feat_ids        : selected_feat_ids #>   poly_info       : poly_info #>   spat_unit_fsub  : spat_unit_fsub #>   feat_type_ssub  : feat_type_ssub #>   verbose         : verbose #>   toplevel_params : 2 #> <2_filter> #>   gobject                : mini_visium #>   expression_values      : raw #>   expression_threshold   : 1 #>   feat_det_in_min_cells  : 5 #>   min_det_feats_per_cell : 20 #>   spat_unit_fsub         : :all: #>   feat_type_ssub         : :all: #>   tag_cells              : FALSE #>   tag_cell_name          : tag #>   tag_feats              : FALSE #>   tag_feats_name         : tag #>   verbose                : T #> <3_feat_stats> #>   gobject             : mini_visium #>   expression_values   : normalized #>   detection_threshold : 0 #>   return_gobject      : TRUE #>   verbose             : TRUE #> <4_cell_stats> #>   gobject             : mini_visium #>   expression_values   : normalized #>   detection_threshold : 0 #>   return_gobject      : TRUE #>   verbose             : TRUE #> <5_hvf> #>   gobject              : mini_visium #>   expression_values    : normalized #>   method               : cov_groups #>   reverse_log_scale    : FALSE #>   logbase              : 2 #>   expression_threshold : 0 #>   nr_expression_groups : 20 #>   zscore_threshold     : 1.5 #>   HVFname              : hvf #>   difference_in_cov    : 0.1 #>   var_threshold        : 1.5 #>   set_seed             : TRUE #>   seed_number          : 1234 #>   save_param           : list() #>   default_save_name    : HVFplot #>   return_gobject       : TRUE #>   verbose              : TRUE #> <6_pca> #>   gobject           : mini_visium #>   expression_values : normalized #>   reduction         : cells #>   return_gobject    : TRUE #>   center            : TRUE #>   scale_unit        : TRUE #>   ncp               : 100 #>   method            : irlba #>   method_params     : BiocParallel::SerialParam() #>   rev               : FALSE #>   set_seed          : TRUE #>   seed_number       : 1234 #>   verbose           : TRUE #>   ...               :  #> <7_umap> #>   gobject              : mini_visium #>   expression_values    : normalized #>   reduction            : cells #>   dim_reduction_to_use : pca #>   dimensions_to_use    : 1:10 #>   return_gobject       : TRUE #>   n_neighbors          : 40 #>   n_components         : 2 #>   n_epochs             : 400 #>   min_dist             : 0.01 #>   n_threads            : NA #>   spread               : 5 #>   set_seed             : TRUE #>   seed_number          : 1234 #>   verbose              : TRUE #>   toplevel_params      : 2 #>   ...                  :  #> <8_tsne> #>   gobject              : mini_visium #>   expression_values    : normalized #>   reduction            : cells #>   dim_reduction_to_use : pca #>   dimensions_to_use    : 1:10 #>   return_gobject       : TRUE #>   dims                 : 2 #>   perplexity           : 30 #>   theta                : 0.5 #>   do_PCA_first         : FALSE #>   set_seed             : TRUE #>   seed_number          : 1234 #>   verbose              : TRUE #>   ...                  :  #> <9_nn_network> #>   gobject              : mini_visium #>   type                 : sNN #>   dim_reduction_to_use : pca #>   dimensions_to_use    : 1:5 #>   expression_values    : normalized #>   return_gobject       : TRUE #>   k                    : 10 #>   minimum_shared       : 5 #>   top_shared           : 3 #>   verbose              : TRUE #>   ...                  :  #> <10_cluster> #>   gobject           : mini_visium #>   name              : leiden_clus #>   nn_network_to_use : sNN #>   network_name      : sNN.pca #>   resolution        : 0.1 #>   weight_col        : weight #>   partition_type    : RBConfigurationVertexPartition #>   n_iterations      : 1000 #>   return_gobject    : TRUE #>   set_seed          : TRUE #>   seed_number       : 1234 #> <11_delaunay_spatial_network> #>   dimensions used            : dimensions: sdimx and sdimy #>   method                     : deldir #>   maximum distance threshold : auto #>   name of spatial network    : Delaunay_network #> <12_spatial_network> #>   k neighbours               : 10 #>   dimensions used            : all #>   maximum distance threshold : 400 #>   name of spatial network    : spatial_network #> <13_create_metafeat> #>   gobject           : mini_visium #>   expression_values : normalized #>   feat_clusters     : cluster_genes #>   stat              : mean #>   name              : cluster_metagene #>   return_gobject    : TRUE #> <14_pca> #>   gobject           : mini_visium #>   expression_values : normalized #>   reduction         : cells #>   name              : custom_pca #>   feats_to_use      : my_spatial_genes #>   return_gobject    : TRUE #>   center            : TRUE #>   scale_unit        : TRUE #>   ncp               : 100 #>   method            : irlba #>   method_params     : BiocParallel::SerialParam() #>   rev               : FALSE #>   set_seed          : TRUE #>   seed_number       : 1234 #>   verbose           : TRUE #>   ...               :  #> <15_umap> #>   gobject              : mini_visium #>   expression_values    : normalized #>   reduction            : cells #>   dim_reduction_to_use : pca #>   dim_reduction_name   : custom_pca #>   dimensions_to_use    : 1:20 #>   name                 : custom_umap #>   return_gobject       : TRUE #>   n_neighbors          : 40 #>   n_components         : 2 #>   n_epochs             : 400 #>   min_dist             : 0.01 #>   n_threads            : NA #>   spread               : 5 #>   set_seed             : TRUE #>   seed_number          : 1234 #>   verbose              : TRUE #>   toplevel_params      : 2 #>   ...                  :  #> <16_nn_network> #>   gobject              : mini_visium #>   type                 : sNN #>   dim_reduction_to_use : pca #>   dim_reduction_name   : custom_pca #>   dimensions_to_use    : 1:20 #>   expression_values    : normalized #>   name                 : custom_NN #>   return_gobject       : TRUE #>   k                    : 5 #>   minimum_shared       : 5 #>   top_shared           : 3 #>   verbose              : TRUE #>   ...                  :  #> <17_cluster> #>   gobject           : mini_visium #>   name              : custom_leiden #>   nn_network_to_use : sNN #>   network_name      : custom_NN #>   resolution        : 0.15 #>   weight_col        : weight #>   partition_type    : RBConfigurationVertexPartition #>   n_iterations      : 1000 #>   return_gobject    : TRUE #>   set_seed          : TRUE #>   seed_number       : 1234 #> <18_spatial_deconvolution> #>   method used              : DWLS #>   deconvolution name       : DWLS #>   expression values        : normalized #>   logbase                  : 2 #>   cluster column used      : leiden_clus #>   number of cells per spot : 50 #>   used cut off             : 2 #> <19_spatial_deconvolution> #>   method used              : DWLS #>   deconvolution name       : DWLS #>   expression values        : normalized #>   logbase                  : 2 #>   cluster column used      : leiden_clus #>   number of cells per spot : 50 #>   used cut off             : 2 #> <20_spatial_deconvolution> #>   method used              : DWLS #>   deconvolution name       : DWLS #>   expression values        : normalized #>   logbase                  : 2 #>   cluster column used      : leiden_clus #>   number of cells per spot : 50 #>   used cut off             : 2 objHistory(g, summarized = TRUE) #> Processing steps: #> 0_normalize #> 1_subset #> 2_filter #> name info: tag tag #> 3_feat_stats #> 4_cell_stats #> 5_hvf #> name info: hvf HVFplot #> 6_pca #> 7_umap #> 8_tsne #> 9_nn_network #> 10_cluster #> name info: leiden_clus sNN.pca #> 11_delaunay_spatial_network #> name info: Delaunay_network #> 12_spatial_network #> name info: spatial_network #> 13_create_metafeat #> name info: cluster_metagene #> 14_pca #> name info: custom_pca #> 15_umap #> name info: custom_pca custom_umap #> 16_nn_network #> name info: custom_pca custom_NN #> 17_cluster #> name info: custom_leiden custom_NN #> 18_spatial_deconvolution #> name info: DWLS #> 19_spatial_deconvolution #> name info: DWLS #> 20_spatial_deconvolution #> name info: DWLS"},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto object name information — objName-generic","title":"Giotto object name information — objName-generic","text":"access set name slot fo S4 subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto object name information — objName-generic","text":"","code":"# S4 method for class 'ANY' objName(x)  # S4 method for class 'list' objName(x)  # S4 method for class 'nameData' objName(x)  # S4 method for class 'giottoPoints' objName(x)  # S4 method for class 'giottoLargeImage' objName(x)  # S4 method for class 'giottoImage' objName(x)  # S4 method for class 'list' objName(x) <- value  # S4 method for class 'nameData' objName(x) <- value  # S4 method for class 'giottoImage' objName(x) <- value  # S4 method for class 'giottoLargeImage' objName(x) <- value  # S4 method for class 'giottoPoints' objName(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto object name information — objName-generic","text":"x Giotto S4 class subobject name data value value set object name","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto object name information — objName-generic","text":"name slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Giotto object name information — objName-generic","text":"objName(nameData): Get name information objName(giottoPoints): Get name giottoPoints objName(giottoPoints) <- value: Set name giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto object name information — objName-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  objName(g) #> [1] \"normalized\""},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":null,"dir":"Reference","previous_headings":"","what":"Name wrangling for subobject lists — objectlist_name_utils","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"Name wrangling subobject lists","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"","code":"assign_objnames_2_list(obj_list, force_replace = FALSE)  assign_listnames_2_obj(obj_list)  .uniquify_dups(x, sep = \".\", what = \"\", verbose = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"obj_list list containing giotto subobjects force_replace logical. default = FALSE. Whether replace names objects name already name x character vector sep character. Separator used making names unique. Default \".\" character (optional). Description character vector input used printing verbose messages made unique verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"","code":"if (FALSE) { # \\dontrun{ e <- new(\"exprObj\") a <- replicate(3L, e) # name the objects objName(a) <- letters[1:3]  # assign the object stored names to the list names(a) a <- assign_objnames_2_list(a) names(a)  # assign list names to the object b <- list(\"name_to_set\" = new(\"exprObj\"), \"name2\" = new(\"exprObj\")) objName(b) b <- assign_listnames_2_obj(b) objName(b)   # ensure that character values are unique input <- c(\"a\", \"b\", \"b\", \"c\", \"a\", \"a\", \"a\") .uniquify_dups(input, verbose = FALSE) } # }"},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read metadata of an ometif — ometif_metadata","title":"Read metadata of an ometif — ometif_metadata","text":"Use python package tifffile get XML metadata .ome.tif file. R package xml2 used work retrieve specific nodes xml data extract data.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read metadata of an ometif — ometif_metadata","text":"","code":"ometif_metadata(   path,   node = NULL,   output = c(\"data.frame\", \"xml\", \"list\", \"structure\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read metadata of an ometif — ometif_metadata","text":"path character. filepath .ome.tif image node character vector. Specific xml node get. terms can added get node specific hierarchy. output character. One \"data.frame\" return data.frame attributes information xml node, \"xmL\" xml2 representation node, \"list\" R native list (note many items list may overlapping names make indexing difficult), \"structure\" invisibly return NULL, print structure XML document node.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read metadata of an ometif — ometif_metadata","text":"list image metadata information","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_to_tif.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert ome.tif to tif — ometif_to_tif","title":"Convert ome.tif to tif — ometif_to_tif","text":"Simple converter .ome.tif .tif format. Utilizes python tifffile package. Performs image conversions one page time. Wrap loop lapply one image page.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_to_tif.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert ome.tif to tif — ometif_to_tif","text":"","code":"ometif_to_tif(   input_file,   output_dir = file.path(dirname(input_file), \"tif_exports\"),   page,   overwrite = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_to_tif.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert ome.tif to tif — ometif_to_tif","text":"input_file character. Filepath ome.tif convert output_dir character. Directory write .tif . Defaults new folder directory called \"tif_exports\" page numeric. page tif open (needed). provided, \"_%04d\" formatted suffix added output filename. overwrite logical. Default = FALSE. Whether overwrite filename already exists.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_to_tif.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert ome.tif to tif — ometif_to_tif","text":"returns written filepath invisibly","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapImagesToMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"overlapImagesToMatrix — overlapImagesToMatrix","title":"overlapImagesToMatrix — overlapImagesToMatrix","text":"create count matrix based overlap results calculateOverlapPolygonImages","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapImagesToMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"overlapImagesToMatrix — overlapImagesToMatrix","text":"","code":"overlapImagesToMatrix(   gobject,   name = \"raw\",   poly_info = \"cell\",   feat_info = \"protein\",   name_overlap = \"images\",   aggr_function = \"sum\",   image_names = NULL,   spat_locs_name = \"raw\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapImagesToMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"overlapImagesToMatrix — overlapImagesToMatrix","text":"gobject giotto object name name overlap count matrix poly_info polygon information feat_info feature information name_overlap name overlap aggr_function function aggregate image information (default = sum) image_names names images used spat_locs_name name spatial centroids / locations associated matrix return_gobject return giotto object (default: TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapImagesToMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"overlapImagesToMatrix — overlapImagesToMatrix","text":"giotto object data.table aggregated information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"overlapToMatrix — overlapToMatrix","title":"overlapToMatrix — overlapToMatrix","text":"create count matrix based overlap results calculateOverlap","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"overlapToMatrix — overlapToMatrix","text":"","code":"# S4 method for class 'giotto' overlapToMatrix(   x,   name = \"raw\",   poly_info = NULL,   feat_info = NULL,   type = c(\"point\", \"intensity\"),   count_info_column = NULL,   aggr_function = \"sum\",   return_gobject = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'giottoPolygon' overlapToMatrix(   x,   feat_info = \"rna\",   type = c(\"point\", \"intensity\"),   count_info_column = NULL,   output = c(\"Matrix\", \"data.table\"),   ... )  # S4 method for class 'SpatVector' overlapToMatrix(   x,   col_names = NULL,   row_names = NULL,   count_info_column = NULL,   output = c(\"Matrix\", \"data.table\"),   verbose = TRUE,   ... )  # S4 method for class 'data.table' overlapToMatrix(x, aggr_function = \"sum\", output = c(\"Matrix\", \"data.table\"))"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"overlapToMatrix — overlapToMatrix","text":"x object containing overlaps info. Can giotto object SpatVector points data.table overlaps generated calculateOverlap name name overlap count matrix poly_info character. Polygon information use feat_info character. Feature information use type character. Type overlap data (either 'point' 'intensity') count_info_column column count information aggr_function function aggregate image information (default = sum) return_gobject return giotto object (default: TRUE) verbose verbose ... additional params pass methods output data format/class return results col_names, row_names character vector. (optional) Set row col names expected exist. fixes dimensions matrix since overlaps information directly report rows cols values detected.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"overlapToMatrix — overlapToMatrix","text":"giotto object count matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"overlapToMatrix — overlapToMatrix","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" gpoly <- getPolygonInfo(g,     polygon_name = \"aggregate\",     return_giottoPolygon = TRUE ) gpoints <- getFeatureInfo(g, return_giottoPoints = TRUE)  # calculate all transcripts overlapped out_all <- calculateOverlap(gpoly, gpoints) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information  overlapToMatrix(out_all) #> Warning: [overlapToMatrix] expected col_names and row_names #>  not provided together. Points aggregation Matrix output #>  may be missing some cols and rows where no detections #>  were found. #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>   [[ suppressing 33 column names ‘100210519278873141813371229408401071444’, ‘101161259912191124732236989250178928032’, ‘101488859781016188084173008420811094152’ ... ]] #>                                                                                 #> Abcc9      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ackr1      .  . . 3 . .  . 1  .  1  7  . 2 2 1 .  .  . .  .  . . 1  . . 5 . . . #> Ackr3      .  . 2 . . .  . .  .  1  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adcyap1r1  .  . 1 4 1 4  5 4  1  1  6  7 2 1 2 1  1  2 .  2  2 2 1  3 1 1 2 3 . #> Adgra1     .  . 1 1 1 .  . 1  .  .  .  . 1 . . .  .  . .  2  . . 1  . . . . . . #> Adgra2     1  . . . . .  . .  .  .  .  . . . . .  .  . 2  .  . . .  . . . . . . #> Adgra3     .  1 . . . .  2 1  1  .  .  2 . . 2 .  .  . .  .  . . .  . . . . . . #> Adgrb1     .  . . 3 . 1  . 3  .  6  6  1 2 . . 1  1  3 .  1  . 3 5  1 1 . 1 . . #> Adgrb3     .  . . . . 3  . 2  1  1  3  1 . 1 . .  .  . .  .  . . .  2 . 2 3 1 . #> Adgre1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . 1 . . #> Adgrf2     .  . . . . 1  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Adgrf4     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrf5     4  . . . 1 .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrg1     2  . . . 1 .  4 .  2  .  .  . . . . .  1  . .  1  . . .  . . . 1 . . #> Adgrg2     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrg4     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrg6     .  . . . . .  1 .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrl1     1  . 1 1 3 1  . 4  1  .  1  6 3 2 2 1  .  1 .  .  1 . 1  1 . 2 . . . #> Adgrl2     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrl3     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrl4     2  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrv1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . 1 . . #> Adora1     .  1 1 1 . .  . .  1  1  .  1 . . 1 .  4  2 .  .  1 . 1  . 1 . . 1 . #> Adora2a    .  . . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Adora2b    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adra1a     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adra1b     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adra1d     .  . . . . .  . 1  .  1  1  . . 1 . .  .  2 .  .  . . 2  1 . 1 . . . #> Adra2a     .  . . . . .  . 1  .  .  .  . . . . 1  .  . .  .  . . .  1 . . . . . #> Adra2b     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adrb1      .  . . . . .  . .  .  1  2  . . . . .  .  . .  .  . . .  . . . . . . #> Adrb2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Agtr1a     .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Aldh1l1    .  . . . 1 .  1 .  1  1  .  . . . . .  .  . .  2  . . .  . . . . . . #> Alk        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Amigo2     1  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  1 . . . . . #> Anxa11     .  . . 1 . 1  . 1  .  1  2  . 1 . 1 .  .  . 1  .  1 . 1  . 2 . . . . #> Aplnr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Aqp4       .  1 . . . .  3 .  4  .  .  . . . . .  1  1 . 11  . . .  . . . 1 . . #> Arhgap29   2  . . . 1 .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Ascl1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Atp13a5    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Avpr2      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Axl        .  . . . . .  1 .  2  .  .  . . . . .  .  . 3  .  . . .  . . . . . . #> Baiap2     .  1 5 2 1 2  . 3  .  4  7  1 4 1 1 .  .  2 .  1  1 5 2  5 . . . 1 . #> Bdkrb1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Bdkrb2     .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Blank-104  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-127  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-128  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-139  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-145  .  . . . . .  . .  .  1  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-148  .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Blank-152  .  . . . . .  . .  .  .  .  . 1 . . .  .  . .  .  . . .  . . . . . . #> Blank-155  .  . . 1 . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-161  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-45   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . 1 . . . #> Blank-57   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-69   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-80   .  . . . . .  . 1  .  .  .  . . . . 1  .  . .  .  . . .  . . . . . . #> Blank-83   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-95   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Brs3       .  1 . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> C1qa       .  1 . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 3 #> C1qb       .  3 . . . .  . .  .  .  .  . . . . .  .  . .  .  . . 1  . . . . . 4 #> C3ar1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> C5ar1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> C5ar2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Calcrl     .  . . . . .  . .  1  .  .  . . . . .  .  . 2  .  . . .  . . . . . . #> Casr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . 1 . . . #> Cckbr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ccr1       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ccr10      .  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Ccr2       .  1 . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ccr9       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Cd300c2    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Celsr1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . 1 . . #> Celsr2     .  1 . 5 1 2  1 3  .  2  3  2 3 1 2 1  .  4 .  .  . . 2  3 . 1 1 1 . #> Celsr3     .  . . . . .  . 1  .  .  .  . 1 1 . .  .  . .  4  . 1 1  . . . . . . #> Cenpe      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Chrm1      .  . . 6 . 1  . 2  .  1  .  2 1 1 1 1  .  1 .  .  1 1 3  3 1 2 . . . #> Chrm3      .  . . . . .  . 1  .  1  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Chrm4      .  . 2 . . .  . .  .  .  .  . . 1 . .  .  . .  .  . . 1  . . . . 1 . #> Chrm5      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Cldn5      5  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Cmklr1     .  . . . . .  1 .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Cnr1       .  . . . . .  . .  .  1  .  1 . . . .  .  . .  .  1 . .  . . . . 2 1 #> Crhr1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Crhr2      .  . . . . .  . 1  .  .  1  . . . . .  .  . .  .  . . .  . . . . . . #> Csf1r      .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . . 1  . . . . . 7 #> Cspg5      .  . . . 5 1 12 .  9  .  3  2 1 1 . 1  .  . .  3  1 2 2  . . . 7 . . #> Cx3cl1     .  . 1 5 1 .  1 5  1  2  2  7 2 4 . 3  .  3 1  2  3 5 6  6 1 4 . 3 . #> Cx3cr1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 3 #> Cxcl12     3  . . . 2 .  . .  .  .  1  . 1 . . .  .  3 9  4  . . 1  . 1 3 . 1 . #> Cxcr4      .  . . . 1 .  . .  .  .  .  . . . . .  .  . .  3  . . .  . . . . . . #> Cysltr2    1  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ddr1       .  6 . . . 1  . .  3  .  2  . . 1 . .  2  . .  3  . . 1  . . . . . . #> Ddr2       .  . 1 . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Dlk1       .  . . . . .  . .  .  .  .  . . . . .  4  . .  .  . . .  . . . 1 1 . #> Drd1       .  . . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Drd2       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Drd5       .  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Ednra      .  . . . . .  . .  1  .  .  . . . . .  .  . .  1  . . .  1 . . . . . #> Ednrb      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Efemp1     .  . . . . .  . .  2  .  .  . . . . .  .  . 3  .  . . .  . . . . . . #> Egfr       .  . . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . 1 . #> Emcn       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Eomes      .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Epha1      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Epha10     .  1 1 1 . .  . .  .  .  2  . 2 . . .  .  . .  .  . . .  . . . . . . #> Epha2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Epha3      .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . 1 .  1 . . . . . #> Epha4      .  . 1 2 1 1  . 3  1  .  3  1 1 2 2 1  1  3 .  .  1 2 4  3 2 1 . 1 . #> Epha5      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  1 . . . . . #> Epha6      .  . 1 . . 1  . .  .  1  3  1 . 3 . 1  .  1 .  .  1 . 2  2 . . . 2 . #> Epha7      .  . 1 . . 1  . 2  .  2  2  5 . 2 3 3  .  . 2  .  2 3 .  2 . . . 1 . #> Epha8      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ephb1      .  2 . . 1 .  . 1  .  .  .  . . . . .  1  . .  .  . . .  . . . 2 . . #> Ephb2      .  . . 1 . .  . .  .  1  .  . . . 1 .  .  . .  .  . . .  . . 1 . . . #> Ephb3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  1 . . . . . #> Ephb6      .  . . . . .  . .  .  .  .  . . . . .  .  1 .  1  1 . 2  . . . . 1 1 #> Erbb2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Erbb3      .  1 . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Erbb4      .  . . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  1 . . . . . #> F2r        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> F2rl3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Fgfr2      .  6 . . . .  . .  1  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Fgfr3      .  . . . 1 .  3 .  3  .  .  . . . . .  .  . .  1  . . .  . . . 1 . . #> Fgfrl1     .  . . . 1 .  . .  4  .  .  . . . . .  .  . .  2  . . .  . . . . . . #> Flt1      10  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Flt3       .  . . . . .  . .  .  .  1  . . . . .  .  . .  .  . . .  1 . . . . . #> Flt4       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Fn1        1  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Fpr1       .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Fzd1       .  . . . . .  . .  2  .  .  . . . . .  .  . .  .  1 . .  . . . . . . #> Fzd10      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Fzd2       .  . . . . .  1 .  .  .  .  . . . . .  .  . 1  .  . . .  . . . 1 . . #> Fzd3       .  1 . 1 1 2  . 1  1  .  .  2 2 2 . 1  1  . 1  .  . 2 1  2 1 2 . 1 . #> Fzd4       1  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Fzd5       .  1 . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  1 . . . . . #> Fzd6       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . 1 . . #> Fzd7       .  . . . . .  . 1  .  1  .  . . . . .  .  . .  .  . . .  2 . . . . . #> Fzd8       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . 1 1 . . . #> Fzd9       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gabbr1     .  2 4 1 1 1  . 4  2  3 10  5 3 2 1 1  .  2 .  3  1 4 3  6 . 6 2 . 2 #> Gabbr2     .  . 3 2 . 1  . 1  .  .  3  1 3 1 3 2  .  2 .  .  2 2 2  1 1 5 . . 1 #> Gad1       .  . 2 1 . 2  . 3  1  1  .  . . . . 1  .  . .  .  1 . 2  2 . . . . . #> Galr1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . 1  . . . . . . #> Gcgr       .  . . . . .  . .  .  .  1  . . . . .  .  . .  .  . . .  . . . . . . #> Gfap       1 12 . . 6 .  . .  1  2  .  . 1 . . . 21  . . 13  . . .  . . . 1 . . #> Ghsr       .  . . . . .  . .  .  .  .  . . . . 1  .  . .  .  . . .  1 . . . . . #> Gipr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gjc3       . 15 . . . .  . .  .  .  .  . . . . .  6  . .  .  . . .  . . . . . . #> Glp2r      .  . . . . .  . .  .  2  5  2 2 . . .  .  1 .  .  . 2 1  2 1 . . 1 . #> Gpbar1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gper1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr1       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr101     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr135     .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . 1 .  . . . . . . #> Gpr139     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr146     .  . . . . .  . .  .  .  .  . 1 1 . .  .  . 1  .  . . .  . . . . . . #> Gpr153     .  1 . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Gpr156     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr157     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr158     .  . 4 . 1 2  . 1  .  .  1  . 1 . 2 .  .  . .  .  . . 1  1 . 1 . . . #> Gpr160     1  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr161     .  . . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr162     .  . 1 1 . 1  . 2  .  1  .  1 . 2 . .  .  3 .  1  . 2 .  . . . . . 1 #> Gpr17      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr173     .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Gpr176     .  . . . . .  . 1  .  .  1  . . . . .  .  1 .  .  . 1 .  . . . . 1 . #> Gpr182     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr183     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr20      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr21      .  . . . . .  . .  .  1  .  . . . . .  2  . .  .  . . .  . . 1 . . 1 #> Gpr22      .  . . 2 1 .  . 2  .  1  1  . 2 1 . .  .  1 .  .  . 2 2  1 . 1 . 1 . #> Gpr26      .  . 1 . . .  . .  .  2  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr27      .  . . . 1 .  . 1  .  .  .  1 . . . .  .  . .  1  1 . .  . . . . . . #> Gpr34      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr37      .  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Gpr37l1    .  . . . 1 . 10 .  9  .  .  . . . . .  .  . .  5  . 1 .  . . . 2 . . #> Gpr4       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr45      .  . . . . .  . .  .  .  2  . . 1 . .  .  . .  .  . . .  . . . . . . #> Gpr52      .  . . . . .  . 1  .  .  3  1 . . . .  .  . .  .  . . .  . . 1 . . . #> Gpr55      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr6       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr61      .  . 1 1 . .  . 1  .  .  1  . . . . .  .  . .  .  . . .  . . . . 1 . #> Gpr62      .  1 . . . .  . .  .  .  .  1 . . . .  1  . .  .  . . 1  1 . . . . . #> Gpr63      .  . . . . .  1 .  .  .  2  . . . . .  .  1 .  .  . . .  . . . . 1 . #> Gpr75      .  . . . 1 .  . .  .  .  1  . . . 1 .  .  . .  .  . 3 .  . . . . . . #> Gpr83      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr85      .  . . . . 2  . 1  .  .  .  3 1 . . .  .  1 .  .  . 2 2  . . . . . . #> Gprc5b     . 17 . . 2 .  1 1  4  .  5  . 1 . . .  7  1 .  1  . . 1  . . . 1 . . #> Gprc5c     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gramd3     .  . . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Grin2b     .  . 3 5 2 2  . 4  .  1  5  3 2 . 1 .  .  1 .  .  . 2 5  1 . 1 . 2 . #> Grm1       .  . 1 . . .  . 2  .  2  4  1 . . 1 .  .  1 .  .  . . 1  . . 1 . . . #> Grm2       .  . . 1 . .  . 1  .  2  2  2 1 1 . .  .  . .  1  . . 2  1 . 1 . . . #> Grm3       1  6 . . . .  . .  2  .  .  . . . . .  3  . .  .  . . .  . . . 1 . . #> Grm4       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Grm5       .  . 1 5 2 3  . 2  .  5  7  1 3 . 2 1  .  2 1  .  . 1 1  3 . 1 . . . #> Grm7       .  . 3 1 1 2  . 2  .  3  4  4 2 . 1 .  1  2 .  .  2 . .  1 1 . . 2 . #> Grpr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Hcar1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Hcrtr2     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Hrh1       .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Hrh2       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Hrh3       .  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . 1 . . . #> Htr1a      .  . . . 1 1  . 1  .  .  .  . . 1 . 1  .  . .  .  . . .  . . . . . . #> Htr1b      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Htr2a      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Htr4       .  . . . . .  . .  .  .  3  1 . . . .  .  1 .  .  . . .  1 . . . . . #> Htr5a      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Htr5b      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Htr6       .  . . . . .  . .  .  .  1  . . . . .  .  . .  .  . . .  . . . . . . #> Htr7       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Igf1r      5  1 1 1 1 .  . 1  .  .  1  . . . . .  1  . 1  3  . . .  1 . . 1 1 1 #> Insr       .  1 1 . . .  . 1  .  2  3  1 3 . . 1  1  1 .  .  . . .  . 1 . . . . #> Insrr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Kcnj8      .  . . . 1 1  . .  .  1  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Kdr        4  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Kiss1r     .  . . . . .  . .  .  .  .  . . . . 1  .  . .  .  . . .  . . . . . . #> Kit        .  . . . 1 .  . .  .  .  .  . . . . .  .  . 2  2  . . .  . . . . . . #> Lgr4       .  . . . 1 .  1 .  1  .  1  3 . . . .  .  . 3  1  . . .  . . . 1 1 . #> Lgr6       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Lhcgr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Lmod1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Lmtk2      .  . 2 1 . .  . .  .  .  2  1 2 3 . 3  .  3 .  .  . . .  2 . . . . . #> Lpar1      .  4 . . 1 .  . .  .  .  .  . . . . .  2  . 1  .  . . .  . . . . . . #> Lpar2      .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Lpar4      .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Lpar6      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Man1a      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Mas1       .  . 2 2 . 3  . .  .  1  .  . . . 1 .  .  . .  .  2 . .  . . 1 . 1 . #> Mc4r       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Mc5r       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Mchr1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Mertk      .  . . . 2 .  2 .  3  .  .  . . . . .  .  . .  1  . . .  . . . 1 . 1 #> Mlc1       .  1 . . 1 .  2 .  .  .  .  . . . . .  .  . .  1  . . .  1 . . . . . #> Mrgpre     .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . . .  . . . . . . #> Mrgprf     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Musk       .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Myh11      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Nmbr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Npy1r      .  . 1 . . .  . 1  .  .  1  . . 1 1 .  .  . 1  .  1 . .  . . 1 . 1 . #> Npy2r      .  . . 1 . 2  . 2  .  1  1  1 . . 1 1  .  1 .  .  1 1 2  1 . 1 . 3 . #> Nrp1       .  . . . . 1  . 2  3  .  .  2 1 . . 2  .  . .  1  1 . 1  1 1 . . . 3 #> Nrp2       .  1 1 . . .  . 1  .  1  .  . 1 . 2 .  .  . .  1  1 . .  . . 2 1 . . #> Ntrk2      1  1 . 1 1 .  4 .  7  1  1  2 1 . . .  .  . .  9  . 1 .  . . . 2 . . #> Ntrk3      .  . 3 5 1 4  . 3  .  6  4  3 1 2 3 2  .  3 .  .  4 4 3  4 1 2 . 1 . #> Ntsr2      1  2 . . 1 .  3 . 10  .  .  . . . . .  1  . .  5  . . .  . . . 1 . . #> Olig1      . 15 . . . 1  . .  1  .  .  . . . . .  3  1 .  .  . . .  . 1 . . . . #> Opn3       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Opn5       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Oprm1      .  . . . . 1  . .  .  1  .  . . . . .  .  . .  .  . . .  . . . . . . #> Oxtr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> P2ry1      .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> P2ry12     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . 2  . . . . . 4 #> P2ry14     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> P2ry2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> P2ry4      .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . . .  . . . . . . #> P2ry6      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> P2yr13     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . 1  . . . . . 3 #> Pcdh15     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Pdgfra     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Pdgfrb     .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Peg10      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Pln        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Plxnb3     .  . . . . .  . .  .  .  .  . . . . .  2  . .  .  . . .  . . . . . . #> Ppp1r3g    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Prokr2     .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . 1  1 . . . . . #> Ptafr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptgdr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptger2     .  . 1 . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptger3     .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptger4     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptgfr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Pth1r      .  . . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptk7       .  . . . . .  . .  .  1  1  . . . . .  .  . 1  1  . . .  . . . . . . #> Ret        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Rho        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ror1       .  . . 1 . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ror2       .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Rrh        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Rspo3      .  . 1 . . .  . .  .  .  .  . . . 1 1  .  1 .  .  2 . 1  . . . . . . #> Rxfp3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ryk        .  . . 1 . .  . 1  1  .  3  1 . . 1 .  1  . .  1  . . .  . . . . . 2 #> S1pr1      1  . . . 1 .  3 .  3  .  .  . . . . .  .  . .  .  . . .  . . . 2 . . #> S1pr2      .  1 . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> S1pr3      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> S1pr4      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> S1pr5      .  3 . . . .  . .  .  .  .  . . . . .  2  . .  .  . . .  . . . . . . #> Sctr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Selplg     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 6 #> Sema4d     .  9 . 1 . .  . 1  .  .  2  2 2 . 1 .  .  . .  .  1 . .  . . 1 . 1 . #> Slc15a3    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Slc17a6    .  . . . . .  . .  .  .  .  . . . . .  .  . .  5  . . .  . . . . . . #> Slc17a7    .  . 7 7 4 4  3 7  . 10 25 11 8 7 7 4  . 11 .  1 10 7 7 11 2 5 . 5 . #> Slc17a8    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Slc25a18   .  . . . . .  1 1  1  .  .  . . . . .  1  . .  2  . . 1  . . . 4 . . #> Slc32a1    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Slc47a1    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Slco1a4    1  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Smo        .  . . 1 . .  . .  .  1  .  . . . . .  .  . .  .  . . .  1 . . . . . #> Sox8       .  3 . . . .  . 1  .  2  .  1 . 1 . .  2  . .  .  . . .  . 2 . . . . #> Sox9       .  . . . 6 .  1 1  .  1  .  . . . . .  1  . .  1  . . .  . . . . . . #> Sstr1      .  . . . . 1  . 3  .  2  .  1 3 . . 1  .  . .  .  1 2 .  2 . 1 . 1 . #> Sstr2      .  . . . . .  . 1  .  .  2  . . . . .  .  . .  .  . . 1  . . 1 . 1 . #> Sstr3      .  . . . . .  . .  .  .  1  . 1 . . .  .  . .  .  . 2 1  1 . . . . . #> Sstr4      .  . . . . 1  1 1  .  .  .  1 1 3 2 .  .  1 .  .  . 1 1  . . . . . . #> Syt4       .  . . 1 . .  . 1  .  .  .  . 1 . . .  .  1 .  .  . 1 1  2 . . . 1 . #> Taar2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Taar3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . 1 . #> Taar6      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Taar7e     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tacr1      .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . . .  . . . . . . #> Tacr3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tas1r1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tas1r3     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tas2r135   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tbxa2r     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tek        2  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tie1       2  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Timp4      .  1 . . . .  1 .  1  .  .  . . . . .  .  . .  2  . . .  . . . . . . #> Tjap1      .  . . . . 1  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Tmem108    .  . . 2 . 3  . 4  .  1  5  3 1 1 2 .  .  . .  .  . 2 2  1 1 . . . . #> Traf4      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Trhr       .  . 2 1 . 1  . .  .  .  2  1 1 . 1 .  .  4 .  .  . . 1  1 . 1 . . . #> Tyro3      .  9 . . . .  1 .  .  .  .  . . 1 1 .  .  . .  .  . . .  . . . . . . #> Uts2r      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> V1ra8      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Vipr1      .  . . . . .  . .  .  .  .  . 1 . . .  .  1 .  .  . . .  . . . . . . #> Vmn1r40    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Vmn1r43    .  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Vmn1r46    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Vmn1r50    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Vmn2r1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #>                            #> Abcc9      .  . . . ...... #> Ackr1      .  . . . ...... #> Ackr3      .  . . . ...... #> Adcyap1r1  1  2 . 2 ...... #> Adgra1     .  2 . . ...... #> Adgra2     .  . . . ...... #> Adgra3     .  . 1 1 ...... #> Adgrb1     .  . . . ...... #> Adgrb3     3  1 . . ...... #> Adgre1     .  . . . ...... #> Adgrf2     .  . . . ...... #> Adgrf4     .  . . . ...... #> Adgrf5     .  . . . ...... #> Adgrg1     4  . . . ...... #> Adgrg2     .  . . . ...... #> Adgrg4     .  . . . ...... #> Adgrg6     .  . . . ...... #> Adgrl1     1  4 . . ...... #> Adgrl2     .  . . . ...... #> Adgrl3     .  . . . ...... #> Adgrl4     .  . . . ...... #> Adgrv1     .  . . . ...... #> Adora1     .  1 . 1 ...... #> Adora2a    .  . . . ...... #> Adora2b    .  . . . ...... #> Adra1a     .  . . . ...... #> Adra1b     .  . . . ...... #> Adra1d     .  1 . . ...... #> Adra2a     .  . . . ...... #> Adra2b     .  . . . ...... #> Adrb1      .  . . . ...... #> Adrb2      .  . . . ...... #> Agtr1a     .  1 . . ...... #> Aldh1l1    4  . . . ...... #> Alk        .  . . . ...... #> Amigo2     .  . . . ...... #> Anxa11     .  . . . ...... #> Aplnr      .  . . . ...... #> Aqp4       3  . . . ...... #> Arhgap29   .  1 . . ...... #> Ascl1      .  . . . ...... #> Atp13a5    1  . . . ...... #> Avpr2      .  . . . ...... #> Axl        2  . . . ...... #> Baiap2     .  1 . . ...... #> Bdkrb1     .  . . . ...... #> Bdkrb2     .  . . . ...... #> Blank-104  .  . . . ...... #> Blank-127  .  . . . ...... #> Blank-128  .  . . . ...... #> Blank-139  .  . . . ...... #> Blank-145  .  . . . ...... #> Blank-148  .  . . . ...... #> Blank-152  .  . . . ...... #> Blank-155  .  . . . ...... #> Blank-161  .  . . . ...... #> Blank-45   .  . . . ...... #> Blank-57   .  . . . ...... #> Blank-69   .  . . . ...... #> Blank-80   .  . . . ...... #> Blank-83   .  . . . ...... #> Blank-95   .  . . . ...... #> Brs3       .  . . . ...... #> C1qa       .  . 5 . ...... #> C1qb       .  . 6 . ...... #> C3ar1      .  . . . ...... #> C5ar1      .  . . . ...... #> C5ar2      .  . . . ...... #> Calcrl     .  . . . ...... #> Casr       .  . . . ...... #> Cckbr      .  . . . ...... #> Ccr1       .  . . . ...... #> Ccr10      .  . . . ...... #> Ccr2       .  . . . ...... #> Ccr9       .  . . . ...... #> Cd300c2    .  . . . ...... #> Celsr1     .  . . . ...... #> Celsr2     .  1 . . ...... #> Celsr3     .  1 . . ...... #> Cenpe      .  . . . ...... #> Chrm1      .  1 . . ...... #> Chrm3      .  . . . ...... #> Chrm4      .  . . . ...... #> Chrm5      .  . . . ...... #> Cldn5      .  . . . ...... #> Cmklr1     .  . . . ...... #> Cnr1       .  . . . ...... #> Crhr1      .  . . . ...... #> Crhr2      .  . . . ...... #> Csf1r      .  . 3 . ...... #> Cspg5      5  1 . . ...... #> Cx3cl1     .  3 . . ...... #> Cx3cr1     .  . 3 . ...... #> Cxcl12     .  . . . ...... #> Cxcr4      .  . . . ...... #> Cysltr2    .  . . . ...... #> Ddr1       .  2 . . ...... #> Ddr2       .  . . . ...... #> Dlk1       .  . . . ...... #> Drd1       .  . . . ...... #> Drd2       .  . . . ...... #> Drd5       .  . . . ...... #> Ednra      .  . . . ...... #> Ednrb      2  . . . ...... #> Efemp1     .  . . . ...... #> Egfr       .  1 . . ...... #> Emcn       .  . . . ...... #> Eomes      .  . . . ...... #> Epha1      .  . . . ...... #> Epha10     .  . . . ...... #> Epha2      .  . . . ...... #> Epha3      .  . . . ...... #> Epha4      .  1 . . ...... #> Epha5      .  . . . ...... #> Epha6      .  . . . ...... #> Epha7      .  1 . . ...... #> Epha8      .  . . . ...... #> Ephb1      .  1 . . ...... #> Ephb2      .  . . . ...... #> Ephb3      1  . . . ...... #> Ephb6      .  . 1 . ...... #> Erbb2      .  . . . ...... #> Erbb3      .  . . . ...... #> Erbb4      .  . . 1 ...... #> F2r        .  . . . ...... #> F2rl3      .  . . . ...... #> Fgfr2      1  . . . ...... #> Fgfr3      7  . 1 . ...... #> Fgfrl1     1  . . . ...... #> Flt1       .  1 . . ...... #> Flt3       .  1 . . ...... #> Flt4       .  . . . ...... #> Fn1        .  . . . ...... #> Fpr1       .  . . . ...... #> Fzd1       .  . . . ...... #> Fzd10      .  . . . ...... #> Fzd2       .  . . . ...... #> Fzd3       2  . . . ...... #> Fzd4       .  1 . . ...... #> Fzd5       .  . . . ...... #> Fzd6       .  . . . ...... #> Fzd7       .  . . . ...... #> Fzd8       .  . . . ...... #> Fzd9       .  . . . ...... #> Gabbr1     3  3 1 . ...... #> Gabbr2     .  2 . . ...... #> Gad1       1  . . . ...... #> Galr1      .  . . . ...... #> Gcgr       .  . . . ...... #> Gfap       1  . 2 2 ...... #> Ghsr       .  . . . ...... #> Gipr       .  . . . ...... #> Gjc3       .  . . . ...... #> Glp2r      .  . . . ...... #> Gpbar1     .  . . . ...... #> Gper1      .  . . . ...... #> Gpr1       .  . . . ...... #> Gpr101     .  . . . ...... #> Gpr135     .  . . . ...... #> Gpr139     .  . . . ...... #> Gpr146     1  . . . ...... #> Gpr153     .  . . . ...... #> Gpr156     .  . . . ...... #> Gpr157     .  . . . ...... #> Gpr158     .  . . . ...... #> Gpr160     .  . . . ...... #> Gpr161     .  . . . ...... #> Gpr162     1  . . . ...... #> Gpr17      .  . . . ...... #> Gpr173     .  . . . ...... #> Gpr176     .  . . . ...... #> Gpr182     .  . . . ...... #> Gpr183     .  . . . ...... #> Gpr20      .  . . . ...... #> Gpr21      .  . . . ...... #> Gpr22      .  . . . ...... #> Gpr26      .  . . . ...... #> Gpr27      .  . . . ...... #> Gpr34      .  . . . ...... #> Gpr37      .  . . . ...... #> Gpr37l1    6  . . . ...... #> Gpr4       .  . . . ...... #> Gpr45      .  1 . . ...... #> Gpr52      .  . . . ...... #> Gpr55      .  . . . ...... #> Gpr6       .  . . . ...... #> Gpr61      .  . . . ...... #> Gpr62      .  . . . ...... #> Gpr63      .  . . . ...... #> Gpr75      .  . . . ...... #> Gpr83      .  . . . ...... #> Gpr85      .  1 . . ...... #> Gprc5b     2  1 . . ...... #> Gprc5c     .  . . . ...... #> Gramd3     .  . . . ...... #> Grin2b     .  2 . . ...... #> Grm1       .  1 . . ...... #> Grm2       .  . . . ...... #> Grm3       4  . . . ...... #> Grm4       .  . . . ...... #> Grm5       .  2 . . ...... #> Grm7       .  3 . . ...... #> Grpr       .  . . . ...... #> Hcar1      .  . . . ...... #> Hcrtr2     .  . . . ...... #> Hrh1       .  . . . ...... #> Hrh2       .  . . . ...... #> Hrh3       .  . . . ...... #> Htr1a      .  . . . ...... #> Htr1b      .  . . . ...... #> Htr2a      .  . . . ...... #> Htr4       .  1 . . ...... #> Htr5a      .  . . . ...... #> Htr5b      .  . . . ...... #> Htr6       .  . . . ...... #> Htr7       .  . . . ...... #> Igf1r      2  1 . . ...... #> Insr       3  1 . . ...... #> Insrr      .  . . . ...... #> Kcnj8      .  . . . ...... #> Kdr        .  1 . . ...... #> Kiss1r     .  . . . ...... #> Kit        .  . . . ...... #> Lgr4       2  . 1 . ...... #> Lgr6       .  . . . ...... #> Lhcgr      .  . . . ...... #> Lmod1      .  . . . ...... #> Lmtk2      .  2 1 . ...... #> Lpar1      .  . . . ...... #> Lpar2      .  . . . ...... #> Lpar4      .  1 . . ...... #> Lpar6      .  . . . ...... #> Man1a      .  . . . ...... #> Mas1       .  . . . ...... #> Mc4r       .  . . . ...... #> Mc5r       .  . . . ...... #> Mchr1      .  . . . ...... #> Mertk      3  . . . ...... #> Mlc1       1  . . . ...... #> Mrgpre     .  . . . ...... #> Mrgprf     .  . . . ...... #> Musk       .  . . . ...... #> Myh11      .  . . . ...... #> Nmbr       .  . . . ...... #> Npy1r      .  . . . ...... #> Npy2r      .  1 . . ...... #> Nrp1       .  3 . . ...... #> Nrp2       .  . . . ...... #> Ntrk2      3  . . 1 ...... #> Ntrk3      .  . 1 . ...... #> Ntsr2     13  . . . ...... #> Olig1      .  . . . ...... #> Opn3       .  . . . ...... #> Opn5       .  . . . ...... #> Oprm1      .  . . . ...... #> Oxtr       .  . . . ...... #> P2ry1      .  . . . ...... #> P2ry12     .  . 5 . ...... #> P2ry14     .  . . . ...... #> P2ry2      .  . . . ...... #> P2ry4      .  . . . ...... #> P2ry6      .  . . . ...... #> P2yr13     .  . 1 1 ...... #> Pcdh15     .  . . . ...... #> Pdgfra     .  . . . ...... #> Pdgfrb     1  . . . ...... #> Peg10      .  . . . ...... #> Pln        .  . . . ...... #> Plxnb3     .  . . . ...... #> Ppp1r3g    .  . . . ...... #> Prokr2     .  . . . ...... #> Ptafr      .  . . . ...... #> Ptgdr      .  . . . ...... #> Ptger2     .  . . . ...... #> Ptger3     .  . . . ...... #> Ptger4     .  . . . ...... #> Ptgfr      .  . . . ...... #> Pth1r      .  . . . ...... #> Ptk7       .  1 . . ...... #> Ret        .  . . . ...... #> Rho        .  . . . ...... #> Ror1       .  . . . ...... #> Ror2       .  . . . ...... #> Rrh        .  . . . ...... #> Rspo3      .  . . . ...... #> Rxfp3      .  . . . ...... #> Ryk        .  1 . . ...... #> S1pr1      3  . . . ...... #> S1pr2      .  . . . ...... #> S1pr3      .  . . . ...... #> S1pr4      .  . . . ...... #> S1pr5      .  . . . ...... #> Sctr       .  . . . ...... #> Selplg     .  . 2 . ...... #> Sema4d     .  1 . . ...... #> Slc15a3    .  . 1 . ...... #> Slc17a6    .  . . . ...... #> Slc17a7    . 16 1 . ...... #> Slc17a8    .  . . . ...... #> Slc25a18   1  . . . ...... #> Slc32a1    .  . . . ...... #> Slc47a1    .  . . . ...... #> Slco1a4    .  . . . ...... #> Smo        .  . . . ...... #> Sox8       1  . . . ...... #> Sox9       1  . 2 1 ...... #> Sstr1      .  1 . . ...... #> Sstr2      .  . . . ...... #> Sstr3      .  1 . . ...... #> Sstr4      .  1 . . ...... #> Syt4       .  2 . . ...... #> Taar2      .  . . . ...... #> Taar3      .  . . . ...... #> Taar6      .  . . . ...... #> Taar7e     .  . . . ...... #> Tacr1      .  . . . ...... #> Tacr3      .  . . . ...... #> Tas1r1     .  . . . ...... #> Tas1r3     .  . . . ...... #> Tas2r135   .  . . . ...... #> Tbxa2r     .  . . . ...... #> Tek        .  . . . ...... #> Tie1       .  . . . ...... #> Timp4      .  . . . ...... #> Tjap1      .  . . . ...... #> Tmem108    .  1 . . ...... #> Traf4      .  . . . ...... #> Trhr       .  1 . . ...... #> Tyro3      .  . . . ...... #> Uts2r      .  . . . ...... #> V1ra8      .  . . . ...... #> Vipr1      .  . . . ...... #> Vmn1r40    .  . . . ...... #> Vmn1r43    .  . . . ...... #> Vmn1r46    .  . . . ...... #> Vmn1r50    .  . . . ...... #> Vmn2r1     .  . . . ...... #>  #>  .....suppressing 429 columns in show(); maybe adjust options(max.print=, width=) #>  .............................."},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":null,"dir":"Reference","previous_headings":"","what":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"create count matrix based overlap results calculateOverlapRaster, calculateOverlapSerial, calculateOverlapParallel aggregate information multiple polygon layers (e.g. z-stacks) together","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"","code":"overlapToMatrixMultiPoly(   gobject,   name = \"raw\",   poly_info = \"cell\",   feat_info = \"rna\",   new_poly_info = \"multi\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"gobject giotto object name name overlap count matrix poly_info vector polygon information feat_info feature information new_poly_info name new aggregated polygon information return_gobject return giotto object (default: TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"giotto object count matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  overlapToMatrixMultiPoly(g, poly_info = \"z0\") #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #>   [multi][rna] raw #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"overlaps-generic — overlaps-generic","title":"overlaps-generic — overlaps-generic","text":"Access list overlaps information object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"overlaps-generic — overlaps-generic","text":"","code":"# S4 method for class 'giottoPolygon' overlaps(x, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"overlaps-generic — overlaps-generic","text":"x object name (optional) name overlaps information retrieve","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"overlaps-generic — overlaps-generic","text":"list overlaps object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"overlaps-generic — overlaps-generic","text":"overlaps(giottoPolygon): Get overlaps information giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"overlaps-generic — overlaps-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  overlaps(g) #> $rna #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 32071, 4  (geometries, attributes) #>  extent      : 6400.441, 6900.032, -5149.827, -4699.984  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID feat_ID feat_ID_uniq stack #>  type        :                     <chr>   <chr>        <int> <int> #>  values      : 323754550002953984063006~  Selplg           87     1 #>                323754550002953984063006~   Fgfr3          122     1 #>                323754550002953984063006~    Gfap          138     1 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":null,"dir":"Reference","previous_headings":"","what":"pDataDT — pDataDT","title":"pDataDT — pDataDT","text":"show cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"pDataDT — pDataDT","text":"","code":"pDataDT(gobject, spat_unit = NULL, feat_type = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"pDataDT — pDataDT","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"pDataDT — pDataDT","text":"data.table cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"pDataDT — pDataDT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  pDataDT(g) #>                 cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                  <char>     <int>    <int>      <num>      <num>       <num> #>   1: AACTCGATGGCGCAGT-1         1      265   41.79811  1057.9308           2 #>   2: GGCTGGCTAGCTTAAA-1         1      279   44.00631  1064.7493           5 #>   3: GACGCCTGTTGCAGGG-1         1      219   34.54259   964.9294           2 #>   4: GAGGGCATCGCGTATC-1         1      294   46.37224  1142.7664           2 #>   5: TCAACACATTGGGTAA-1         1      261   41.16719  1063.3517           2 #>  ---                                                                         #> 620: GGTAGTGCTCGCACCA-1         1      179   28.23344   768.4749           5 #> 621: AAGCTCGTGCCAAGTC-1         1      195   30.75710   756.0675           5 #> 622: TATTCAATTCTAATCC-1         1      247   38.95899   921.8264           5 #> 623: TTCAAAGTCTCTAGCC-1         1      384   60.56782   916.5929           6 #> 624: TTGAATATGGACTTTC-1         1      380   59.93691   912.3051           6 #>      custom_leiden #>              <num> #>   1:             4 #>   2:             3 #>   3:             3 #>   4:             3 #>   5:             3 #>  ---               #> 620:             4 #> 621:             4 #> 622:             4 #> 623:             7 #> 624:             4"},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Preview a Giotto spatial object — plot-generic","title":"Preview a Giotto spatial object — plot-generic","text":"S4 generic previewing Giotto's image subcellular objects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preview a Giotto spatial object — plot-generic","text":"","code":"# S4 method for class 'giottoImage,missing' plot(x, y, ...)  # S4 method for class 'giottoLargeImage,missing' plot(   x,   y,   col,   max_intensity,   mar,   asRGB = FALSE,   legend = FALSE,   axes = TRUE,   maxcell = 5e+05,   smooth = TRUE,   ... )  # S4 method for class 'giottoAffineImage,missing' plot(x, y, ...)  # S4 method for class 'giottoPolygon,missing' plot(   x,   point_size = 0.6,   type = c(\"poly\", \"centroid\"),   max_poly = getOption(\"giotto.plot_max_poly\", 1e+06),   ... )  # S4 method for class 'giottoPoints,missing' plot(x, point_size = 0, feats = NULL, raster = TRUE, raster_size = 600, ...)  # S4 method for class 'spatLocsObj,missing' plot(x, y, ...)  # S4 method for class 'dimObj,missing' plot(x, dims = c(1, 2), ...)  # S4 method for class 'spatialNetworkObj,missing' plot(x, y, ...)  # S4 method for class 'affine2d,missing' plot(x, y, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Preview a Giotto spatial object — plot-generic","text":"x giotto image, giottoPolygon, giottoPoints object y used. ... additional parameters pass col character. Colors. default grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1) max_intensity (optional) value treat maximum intensity color scale mar numeric vector length 4 set margins plot (make space legend). default (3, 5, 1.5, 1) asRGB (optional) logical. Force RGB plotting automatically detected legend logical character. FALSE legend drawn. character value can used indicate legend drawn. example \"topright\" \"bottomleft\" axes logical. Draw axes? maxcell positive integer. Maximum number cells use plot smooth logical. TRUE cell values smoothed point_size size points plotting giottoPoints type plot: either 'poly' (default) polygon 'centroid' max_poly numeric. type specified, maximum number polygons plot automatically switching centroids plotting. Default 1e4. value settable using options(\"giotto.plot_max_poly\") feats specific features plot within giottoPoints object (defaults NULL, meaning available features) raster default = TRUE, whether plot points rasterized plot size based raster_size param. See details. FALSE, plots via terra::plot() raster_size Default 600. used raster TRUE dims dimensions plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Preview a Giotto spatial object — plot-generic","text":"plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Preview a Giotto spatial object — plot-generic","text":"[giottoPoints raster plotting] Fast plotting points information rasterizing information using terra::rasterize(). terra SpatVectors, faster scattermore plotting. plotting raster, col colors map whole image level, opposed mapping individual points, raster = FALSE Allows following additional params plotting specific feats input: force_size logical. raster_size param caps 1:1 spatial extent, also minimum resulting px dim 100. ignore constraints, set force_size = FALSE dens logical. Show point density using count statistic per rasterized cell. (Default = FALSE). param affects col param defaults. TRUE, col grDevices::hcl.colors(256). FALSE, \"black\" \"white\" used. background (optional) background color. Usually used col color mapping sufficient. Note col param base::plot() graphical params available ...","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Preview a Giotto spatial object — plot-generic","text":"plot(x = giottoImage, y = missing): Plot magick-based giottoImage object. ... param passes .plot_giottoimage_mg plot(x = giottoLargeImage, y = missing): Plot terra-based giottoLargeImage object. ... param passes .plot_giottolargeimage plot(x = giottoPolygon, y = missing): Plot terra-based giottoPolygon object. ... param passes plot plot(x = giottoPoints, y = missing): terra-based giottoPoint object. ... param passes plot plot(x = spatLocsObj, y = missing): Plot spatLocsObj plot(x = dimObj, y = missing): Plot dimObj plot(x = spatialNetworkObj, y = missing): Plot spatialNetworkObj plot(x = affine2d, y = missing): Plot affine2d. blue start, red end","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Preview a Giotto spatial object — plot-generic","text":"","code":"######### giottoLargeImage plotting ######### if (FALSE) { # \\dontrun{ gimg <- GiottoData::loadSubObjectMini(\"giottoLargeImage\") gimg <- GiottoClass:::.update_giotto_image(gimg) # only needed if out of date plot(gimg) plot(gimg, col = grDevices::hcl.colors(256)) plot(gimg, max_intensity = 100) } # }  ######### giottoPolygon plotting ######### gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") plot(gpoly)  plot(gpoly, type = \"centroid\")   ######### giottoPoints plotting ######### gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  # ----- rasterized plotting ----- # # plot points binary plot(gpoints)  # plotting all features maps colors on an image level plot(gpoints, col = grDevices::hcl.colors(n = 256)) # only 2 colors are used  plot(gpoints, col = \"green\", background = \"purple\")   # plot points density (by count) plot(gpoints, dens = TRUE, raster_size = 300)   # force_size = TRUE to ignore default constraints on too big or too small # (see details) plot(gpoints, dens = TRUE, raster_size = 80, force_size = TRUE)   # plot specific feature(s) plot(gpoints, feats = featIDs(gpoints)[seq_len(4)])   # ----- vector plotting ----- # # non-rasterized plotting (slower, but higher quality) plot(gpoints, raster = FALSE)   # vector plotting maps colors to transcripts plot(gpoints, raster = FALSE, col = grDevices::rainbow(nrow(gpoints)))   # plot specific feature(s) plot(gpoints, feats = featIDs(gpoints)[seq_len(4)], raster = FALSE)   ######### spatLocsObj plotting ######### sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") plot(sl)   ######### dimObj plotting ######### d <- GiottoData::loadSubObjectMini(\"dimObj\") plot(d)  plot(d, dims = c(3, 5))"},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot a giotto image object — plotGiottoImage","title":"Plot a giotto image object — plotGiottoImage","text":"Display giotto image viewer panel. Image object plot can specified providing giotto object containing image (gobject), image object name (image_name), image object type (image_type). Alternatively, image objects can directly plotted respective associated params.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot a giotto image object — plotGiottoImage","text":"","code":"plotGiottoImage(   gobject = NULL,   image_name = NULL,   image_type = NULL,   giottoImage = NULL,   giottoLargeImage = NULL,   largeImage_crop_params_list = NULL,   largeImage_max_intensity = NULL,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot a giotto image object — plotGiottoImage","text":"gobject gobject containing giotto image object image_name name giotto image object image_type type giotto image object plot giottoImage giottoImage object plot directly giottoLargeImage giottoLargeImage object plot directly largeImage_crop_params_list (optional) named list params focusing specified region giottoLargeImage. largeImage_max_intensity (optional) assign override value treat maximum intensity color scale plotting giottoLargeImage ... additional params pass image object specific plotting functions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot a giotto image object — plotGiottoImage","text":"image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"largeimage-specific-additional-params","dir":"Reference","previous_headings":"","what":"largeImage-specific additional params","title":"Plot a giotto image object — plotGiottoImage","text":"largeImage_crop_params_list accepts named list following possible params define region interest (ROI) plot either terra extent object x y min max bounds given numerics: crop_extent – terra extent object define crop ROI xmax_crop – x max ROI xmin_crop – x min ROI ymax_crop – y max ROI ymin_crop – y min ROI largeImage_max_intensity accepts numeric value set max value plotting color scale. Can used case high outlier intensity values image preview alternative color scaling desired.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot a giotto image object — plotGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  plotGiottoImage(g,     image_type = \"largeImage\", image_name = \"dapi_z0\",     largeImage_max_intensity = 200 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial polygons stamp — polyStamp","title":"Spatial polygons stamp — polyStamp","text":"Takes given stamp polygon places spatial location provided.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial polygons stamp — polyStamp","text":"","code":"polyStamp(   stamp_dt,   spatlocs,   id_col = \"cell_ID\",   x_col = \"sdimx\",   y_col = \"sdimy\",   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial polygons stamp — polyStamp","text":"stamp_dt data.table x y vertices polygon stamped. Column names expected 'x' 'y' respectively spatlocs spatial locations x y coordinates polygons stamped. Column names 'cell_ID', 'sdimx' 'sdimy' default id_col column spatlocs use IDs (default 'cell_ID') x_col column spatlocs use x locations (default 'sdimx') y_col column spatlocs use y locations (default 'sdimy') verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial polygons stamp — polyStamp","text":"data.table polygon vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial polygons stamp — polyStamp","text":"","code":"# stamp shapes hex <- hexVertices(radius = 1) spatlocs <- data.table::data.table(     sdimx = rnorm(10, mean = 5, sd = 20),     sdimy = rnorm(10, mean = 5, sd = 20),     cell_ID = paste0(\"spot_\", seq_len(10)) ) random_hex <- polyStamp(hex, spatlocs) #> 10 polygons generated random_hex_poly <- createGiottoPolygon(random_hex) #>   Selecting col \"poly_ID\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(random_hex_poly)   # make a grid of shapes e <- c(0, 1000, 0, 1000) tg <- triGrid(extent = e, ccd = 100, id_prefix = \"bin_\")  r <- rectVertices(dims = c(x = 60, y = 50))  rect_grid_dt <- polyStamp(stamp_dt = r, spatlocs = tg) #> 104 polygons generated rect_poly <- createGiottoPolygon(rect_grid_dt) #>   Selecting col \"poly_ID\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(rect_poly)"},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert polygon to raster — polygon_to_raster","title":"Convert polygon to raster — polygon_to_raster","text":"convert polygon raster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert polygon to raster — polygon_to_raster","text":"","code":"polygon_to_raster(polygon, field = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert polygon to raster — polygon_to_raster","text":"polygon SpatVector polygon rasterize field character. Name attribute polygon used rasterizing assign values. Passing NULL uses first attribute.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert polygon to raster — polygon_to_raster","text":"list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert polygon to raster — polygon_to_raster","text":"","code":"df <- data.frame(x = 1:5, y = c(1, 4, 4, 3, 1)) d <- data.frame(id = 1, name = \"polygon_1\") my_polygon <- terra::vect(as.matrix(df), type = \"polygons\", atts = d)  polygon_to_raster(my_polygon) #> $raster #> class       : SpatRaster  #> dimensions  : 3, 4, 1  (nrow, ncol, nlyr) #> resolution  : 1, 1  (x, y) #> extent      : 1, 5, 1, 4  (xmin, xmax, ymin, ymax) #> coord. ref. :   #> source(s)   : memory #> name        : poly_i  #> min value   :      1  #> max value   :      1  #>  #> $ID_vector #> 1  #> 1  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Provenance information — prov-generic","title":"Provenance information — prov-generic","text":"access set provenance slot S4 subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Provenance information — prov-generic","text":"","code":"# S4 method for class 'provData' prov(x)  # S4 method for class 'provData' prov(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Provenance information — prov-generic","text":"x Giotto S4 class subobject value value set provenance","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Provenance information — prov-generic","text":"provenance slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Provenance information — prov-generic","text":"prov(provData): Get provenance information prov(provData) <- value: Set provenance information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Provenance information — prov-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  prov(g) #> [1] \"z0\" \"z1\""},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":null,"dir":"Reference","previous_headings":"","what":"R spatial conversions — r_spatial_conversions","title":"R spatial conversions — r_spatial_conversions","text":"R spatial conversions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R spatial conversions — r_spatial_conversions","text":"","code":"# S4 method for class 'sf' as.sp(x)  # S4 method for class 'SpatVector' as.sp(x)  # S4 method for class 'stars' as.sp(x)  # S4 method for class 'Spatial' as.sp(x)  # S4 method for class 'giottoPolygon' as.sp(x, drop = TRUE)  # S4 method for class 'giottoPoints' as.sp(x, drop = TRUE)  # S4 method for class 'SpatVector' as.sf(x)  # S4 method for class 'Spatial' as.sf(x)  # S4 method for class 'stars' as.sf(x)  # S4 method for class 'sf' as.sf(x)  # S4 method for class 'giottoPolygon' as.sf(x, drop = TRUE)  # S4 method for class 'giottoPoints' as.sf(x, drop = TRUE)  # S4 method for class 'SpatVector' as.stars(x)  # S4 method for class 'sf' as.stars(x)  # S4 method for class 'Spatial' as.stars(x)  # S4 method for class 'stars' as.stars(x)  # S4 method for class 'giottoPolygon' as.stars(x, drop = TRUE)  # S4 method for class 'giottoPoints' as.stars(x, drop = TRUE)  # S4 method for class 'SpatVector' as.terra(x)  # S4 method for class 'sf' as.terra(x)  # S4 method for class 'stars' as.terra(x, type = c(\"vector\", \"raster\"))  # S4 method for class 'Spatial' as.terra(x)  # S4 method for class 'giottoPolygon' as.terra(x, drop = TRUE)  # S4 method for class 'giottoPoints' as.terra(x, drop = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R spatial conversions — r_spatial_conversions","text":"x object coerce drop TRUE, returned object desired object type instead wrapped giottoPoints giottoPolygon object type whether data 'vector' 'raster'","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"R spatial conversions — r_spatial_conversions","text":"sf, sp, stars terra","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R spatial conversions — r_spatial_conversions","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  as.sf(g) #> Simple feature collection with 79761 features and 3 fields #> Geometry type: POINT #> Dimension:     XY #> Bounding box:  xmin: 6400.037 ymin: -5149.983 xmax: 6900.032 ymax: -4699.978 #> CRS:           NA #> First 10 features: #>    feat_ID global_z feat_ID_uniq                   geometry #> 1     Mlc1        0            1 POINT (6400.037 -4966.651) #> 2   Gprc5b        0            2 POINT (6400.041 -4965.377) #> 3     Gfap        0            3 POINT (6400.078 -5081.453) #> 4     Gfap        0            4 POINT (6400.084 -5038.288) #> 5    Ednrb        0            5 POINT (6400.172 -4816.516) #> 6     Gfap        0            6 POINT (6400.172 -5077.041) #> 7     Gfap        0            7 POINT (6400.189 -5080.815) #> 8     Sox9        0            8 POINT (6400.228 -4770.126) #> 9     Gfap        0            9 POINT (6400.246 -5096.167) #> 10  Gprc5b        0           10 POINT (6400.278 -4928.655)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine objects by rows (Giotto-related) — rbind-generic","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"row bind two objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"","code":"# S4 method for class 'cellMetaObj,cellMetaObj' rbind2(x, y, ...)  # S4 method for class 'featMetaObj,featMetaObj' rbind2(x, y, ...)  # S4 method for class 'spatLocsObj,spatLocsObj' rbind2(x, y, ...)  # S4 method for class 'giottoPolygon,giottoPolygon' rbind2(x, y, add_list_ID = TRUE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"x item 1 rbind y item 2 rbind ... additional params pass methods add_list_ID whether generate list_ID column giottoPolygons append different names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"object appended rows","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"rbind2(x = giottoPolygon, y = giottoPolygon): Append giottoPolygon objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  rbind2(g, g) #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 924, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    :"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_hetero.html","id":null,"dir":"Reference","previous_headings":"","what":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","title":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","text":"Append two giotto polygons together different names Performed recursively rbind2 rbind. Generates additional list_ID attribute based original names. object name also becomes combination previous names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_hetero.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","text":"","code":"rbind2_giotto_polygon_hetero(x, y, new_name, add_list_ID = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_hetero.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","text":"x giottoPolygon 1 y giottoPolygon 2 add_list_ID whether include name origin giottoPolygons new 'list_ID' attribute","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_hetero.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_homo.html","id":null,"dir":"Reference","previous_headings":"","what":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","title":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","text":"Append two giotto polygons together name. Performed recursively rbind2 rbind","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_homo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","text":"","code":"rbind2_giotto_polygon_homo(x, y)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_homo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","text":"x giottoPolygon 1 y giottoPolygon 2","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_homo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read cell metadata — readCellMetadata","title":"Read cell metadata — readCellMetadata","text":"read cell metadata list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read cell metadata — readCellMetadata","text":"","code":"readCellMetadata(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read cell metadata — readCellMetadata","text":"data_list nested list cell metadata information default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read cell metadata — readCellMetadata","text":"cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read cell metadata — readCellMetadata","text":"","code":"df <- data.frame(     cell_ID = c(\"cell_1\", \"cell_2\", \"cell_3\"),     annotation = c(\"cell_type_1\", \"cell_type_1\", \"cell_type_2\") ) temporal_dir <- tempdir() write.csv(df, paste0(temporal_dir, \"/metadata.csv\"), row.names = FALSE)  readCellMetadata(paste0(temporal_dir, \"/metadata.csv\")) #>  #> List item [1]: #>  spat_unit: cell #>  feat_type: rna #> [[1]] #> An object of class cellMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #> dimensions: 3 2  #>  #>    cell_ID  annotation #>     <char>      <char> #> 1:  cell_1 cell_type_1 #> 2:  cell_2 cell_type_1 #> 3:  cell_3 cell_type_2 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read dimensional reduction data — readDimReducData","title":"Read dimensional reduction data — readDimReducData","text":"read dimension reduction results list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read dimensional reduction data — readDimReducData","text":"","code":"readDimReducData(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   reduction = c(\"cells\", \"feats\"),   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read dimensional reduction data — readDimReducData","text":"data_list (nested) list dimension reduction input data default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use reduction whether dim reduction performed 'cels' 'feats' provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read dimensional reduction data — readDimReducData","text":"dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read dimensional reduction data — readDimReducData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"dimObj\")  readDimReducData(x) #> [[1]] #> An object of class dimObj : \"pca\" #> --| Contains dimension reduction generated with: pca  #> ----| for feat_type: rna  #> ----|     spat_unit: aggregate  #>  #>    100 dimensions for 462 data points #>  #> Additional included info: #> [1] \"eigenvalues\" \"loadings\"    #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read expression data — readExprData","title":"Read expression data — readExprData","text":"Read nested list expression data inputs order generate list giotto-native exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read expression data — readExprData","text":"","code":"readExprData(   data_list,   sparse = TRUE,   cores = determine_cores(),   default_feat_type = NULL,   verbose = TRUE,   provenance = NULL,   expression_matrix_class = c(\"dgCMatrix\", \"DelayedArray\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read expression data — readExprData","text":"data_list (nested) list expression input data sparse (boolean, default = TRUE) read matrix data sparse manner cores number cores use default_feat_type (optional) default feat_type use verbose verbose provenance (optional) provenance information expression_matrix_class class expression matrix use (e.g. 'dgCMatrix', 'DelayedArray')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read expression data — readExprData","text":"exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read expression data — readExprData","text":"mylistA = list('' = matrix(seq(5)), 'b' = matrix(seq(5))) depth(mylistA) mylistB = list(= list('' = matrix(seq(5)), 'b' = matrix(seq(5))), B = list('c' = matrix(seq(5)),'d' = matrix(seq(5)))) depth(mylistB) mylistC = list('RNA' = list('RAW' = list('cell' = matrix(seq(5)), 'nucleus' = matrix(seq(6,10))), 'NORM' = list('cell' = matrix(seq(11,15)), 'nucleus' = matrix(seq(20,25)))), 'PROT' = list('RAW' = list('cell' = matrix(seq(16,20))))) depth(mylistC) mymatD = matrix(data = seq(4))","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read expression data — readExprData","text":"","code":"x <- matrix(seq_len(100), nrow = 10) temporal_dir <- tempdir() write.csv(x, paste0(temporal_dir, \"/mymatrix.csv\"))  readExprData(paste0(temporal_dir, \"/mymatrix.csv\")) #> list depth of 1 #>  #> List item [1]: #>  spat_unit: cell #>  feat_type: rna #>  name: raw #> [[1]] #> An object of class exprObj : \"raw\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #>  #> contains: #> 10 x 10 sparse Matrix of class \"dgCMatrix\" #>                                #> 1 1 11 21 31 41 51 61 71 81 91 #> 2 2 12 22 32 42 52 62 72 82 92 #> 3 3 13 23 33 43 53 63 73 83 93 #> 4 4 14 24 34 44 54 64 74 84 94 #>  #>  ........suppressing 2 rows in show(); maybe adjust options(max.print=, width=) #>                                   #> 7   7 17 27 37 47 57 67 77 87  97 #> 8   8 18 28 38 48 58 68 78 88  98 #> 9   9 19 29 39 49 59 69 79 89  99 #> 10 10 20 30 40 50 60 70 80 90 100 #>  #>  First four colnames: #>  V1 V2 V3 V4  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Read expression matrix — readExprMatrix","title":"Read expression matrix — readExprMatrix","text":"Function read expression matrix sparse matrix.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read expression matrix — readExprMatrix","text":"","code":"readExprMatrix(   path,   cores = determine_cores(),   transpose = FALSE,   feat_type = \"rna\",   expression_matrix_class = c(\"dgCMatrix\", \"DelayedArray\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read expression matrix — readExprMatrix","text":"path path expression matrix cores number cores use transpose transpose matrix feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") expression_matrix_class class expression matrix use (e.g. 'dgCMatrix', 'DelayedArray')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read expression matrix — readExprMatrix","text":"sparse matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read expression matrix — readExprMatrix","text":"expression matrix needs unique column names row names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read expression matrix — readExprMatrix","text":"","code":"x <- matrix(seq_len(100), nrow = 10) temporal_dir <- tempdir() write.csv(x, paste0(temporal_dir, \"/mymatrix.csv\"))  readExprMatrix(paste0(temporal_dir, \"/mymatrix.csv\")) #> 10 x 10 sparse Matrix of class \"dgCMatrix\" #>   [[ suppressing 10 column names ‘V1’, ‘V2’, ‘V3’ ... ]] #>                                   #> 1   1 11 21 31 41 51 61 71 81  91 #> 2   2 12 22 32 42 52 62 72 82  92 #> 3   3 13 23 33 43 53 63 73 83  93 #> 4   4 14 24 34 44 54 64 74 84  94 #> 5   5 15 25 35 45 55 65 75 85  95 #> 6   6 16 26 36 46 56 66 76 86  96 #> 7   7 17 27 37 47 57 67 77 87  97 #> 8   8 18 28 38 48 58 68 78 88  98 #> 9   9 19 29 39 49 59 69 79 89  99 #> 10 10 20 30 40 50 60 70 80 90 100"},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read feature information — readFeatData","title":"Read feature information — readFeatData","text":"Function read lists feature information data output list generated giottoPoints objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read feature information — readFeatData","text":"","code":"readFeatData(data_list, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read feature information — readFeatData","text":"data_list (nested) list input data read verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read feature information — readFeatData","text":"list giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read feature information — readFeatData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"giottoPoints\")  readFeatData(list(x)) #> pointslist is a list without names #> [ rna ] Process point info... #> $rna #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3 #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read feature metadata — readFeatMetadata","title":"Read feature metadata — readFeatMetadata","text":"read feature metadata listt","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read feature metadata — readFeatMetadata","text":"","code":"readFeatMetadata(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read feature metadata — readFeatMetadata","text":"data_list nested list feature metadata information default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read feature metadata — readFeatMetadata","text":"featMetadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read feature metadata — readFeatMetadata","text":"","code":"df <- data.frame(     feat_ID = c(\"feat_1\", \"feat_2\", \"feat_3\"),     geneID = c(\"gene_1\", \"gene_1\", \"gene_2\") ) temporal_dir <- tempdir() write.csv(df, paste0(temporal_dir, \"/metadata.csv\"), row.names = FALSE)  readFeatMetadata(paste0(temporal_dir, \"/metadata.csv\")) #> list depth of 2 #>  #> List item [1]: #>  spat_unit: cell #>  feat_type: rna #> [[1]] #> An object of class featMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #>  #>    feat_ID geneID #>     <char> <char> #> 1:  feat_1 gene_1 #> 2:  feat_2 gene_1 #> 3:  feat_3 gene_2 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — readGiottoInstructions","title":"deprecated — readGiottoInstructions","text":"Retrieves instruction associated provided parameter","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — readGiottoInstructions","text":"","code":"readGiottoInstructions(giotto_instructions, param = NULL, default)"},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — readGiottoInstructions","text":"giotto_instructions giotto object result createGiottoInstructions() param parameter retrieve default default object return parameter retrieve exist","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — readGiottoInstructions","text":"specific parameter","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"deprecated — readGiottoInstructions","text":"","code":"readGiottoInstructions(     giotto_instructions = createGiottoInstructions(),     param = \"show_plot\" ) #> Warning: `readGiottoInstructions()` was deprecated in GiottoClass 0.3.5. #> ℹ Please use `instructions()` instead. #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> [1] TRUE"},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read nearest neighbor network data — readNearestNetData","title":"Read nearest neighbor network data — readNearestNetData","text":"read nearest network results list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read nearest neighbor network data — readNearestNetData","text":"","code":"readNearestNetData(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read nearest neighbor network data — readNearestNetData","text":"data_list (nested) list input data read default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read nearest neighbor network data — readNearestNetData","text":"nnNetObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read nearest neighbor network data — readNearestNetData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"nnNetObj\")  readNearestNetData(x) #> [[1]] #> An object of class nnNetObj : \"sNN.pca\" #> --| Contains nearest neighbor network generated with: sNN  #> ----| for feat_type: rna  #> ----|     spat_unit: aggregate  #> ----|     provenance: z0 z1  #>  #> IGRAPH 859f76e DNW- 462 3021 --  #> + attr: name (v/c), weight (e/n), distance (e/n), shared (e/n), rank #> | (e/n) #> + edges from 859f76e (vertex names): #> [1] 240649020551054330404932383065726870513->335295524680090725199231409883288198017 #> [2] 240649020551054330404932383065726870513->77151711298730578178892667721058396928  #> [3] 240649020551054330404932383065726870513->322879686187630160969459793861944841206 #> [4] 240649020551054330404932383065726870513->31072896077757820678000109671990674373  #> [5] 240649020551054330404932383065726870513->102184699197574201819246996094734116255 #> [6] 240649020551054330404932383065726870513->17685062374745280598492217386845129350  #> + ... omitted several edges #>  #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read list of polygons information — readPolygonData","title":"Read list of polygons information — readPolygonData","text":"Function extract list polygons given raw input either mask tabular data. Calls respective createGiottoPolygons functions.  giottoPolygon object passed edits made updating name slot list named.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read list of polygons information — readPolygonData","text":"","code":"readPolygonData(   data_list,   default_name = \"cell\",   input = \"guess\",   polygon_mask_list_params = NULL,   polygon_dfr_list_params = NULL,   calc_centroids = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read list of polygons information — readPolygonData","text":"data_list read polygon results list default_name default name assign polygonlist list. polygonlist unnamed list default_name used part template generating indexed default names. input type input used. set 'guess', uses 'mask' polygonlist type character 'table' polygonlist dataframe-like polygon_mask_list_params parameters using 'mask' workflow polygon_dfr_list_params parameters using 'table' workflow calc_centroids whether centroids calculated polygon creation verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read list of polygons information — readPolygonData","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read list of polygons information — readPolygonData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  readPolygonData(x) #> polygonlist is not a list #> [ cell ] Process polygon info... #> $aggregate #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    : rna #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read spatial enrichment — readSpatEnrichData","title":"Read spatial enrichment — readSpatEnrichData","text":"read spatial enrichment results list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read spatial enrichment — readSpatEnrichData","text":"","code":"readSpatEnrichData(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read spatial enrichment — readSpatEnrichData","text":"data_list (nested) list spatial enrichment input data default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read spatial enrichment — readSpatEnrichData","text":"spatEnrObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read spatial enrichment — readSpatEnrichData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatEnrObj\")  readSpatEnrichData(x) #> [[1]] #> An object of class spatEnrObj : \"cluster_metagene\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>    ------------------------ #>  #> preview: #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #>  #> ...first 20 remaining colnames: #>  #>    #>  #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read spatial location data — readSpatLocsData","title":"Read spatial location data — readSpatLocsData","text":"read spatial locations/coordinates nested list generate list Giotto spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read spatial location data — readSpatLocsData","text":"","code":"readSpatLocsData(   data_list,   default_spat_unit = NULL,   provenance = NULL,   cores = determine_cores(),   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read spatial location data — readSpatLocsData","text":"data_list (nested) list spatial locations input data default_spat_unit (optional) default spat_unit use provenance (optional) provenance information cores many cores use verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read spatial location data — readSpatLocsData","text":"list spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read spatial location data — readSpatLocsData","text":"","code":"df <- data.frame(     feat_ID = c(\"feat_1\", \"feat_2\", \"feat_3\"),     sdimx = c(1, 2, 3), sdimy = c(1, 2, 1) ) temporal_dir <- tempdir() write.csv(df, paste0(temporal_dir, \"/spatlocs.csv\"), row.names = FALSE)  readSpatLocsData(paste0(temporal_dir, \"/spatlocs.csv\")) #> list depth of 1 #>  #> List item [1]: #>  spat_unit: cell #>  name: raw #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> [[1]] #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"cell\" #> provenance: cell  #> dimensions: 3 3  #> preview   : #>    sdimx sdimy cell_ID #>    <int> <int>  <char> #> 1:     1     1  feat_1 #> 2:     2     2  feat_2 #> 3:     3     1  feat_3 #>  #> ranges: #>      sdimx sdimy #> [1,]     1     1 #> [2,]     3     2 #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read spatial networks — readSpatNetData","title":"Read spatial networks — readSpatNetData","text":"read spatial networks data list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read spatial networks — readSpatNetData","text":"","code":"readSpatNetData(   data_list,   default_spat_unit = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read spatial networks — readSpatNetData","text":"data_list (nested) list spatial network input data default_spat_unit (optional) default spat_unit use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read spatial networks — readSpatNetData","text":"spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read spatial networks — readSpatNetData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatialNetworkObj\", idx = 2)  readSpatNetData(x) #> [[1]] #> An object of class spatialNetworkObj : \"kNN_network\" #> Contains spatial network generated with: dbscan  #> spat_unit : \"aggregate\" #> provenance: z0 z1  #>    2211 connections (filtered) #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/read_data_params.html","id":null,"dir":"Reference","previous_headings":"","what":"read_data_params — read_data_params","title":"read_data_params — read_data_params","text":"read_data_params","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/read_data_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_data_params — read_data_params","text":"data_list (nested) list input data read default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/read_data_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read_data_params — read_data_params","text":"data params","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":null,"dir":"Reference","previous_headings":"","what":"Reconnect a GiottoClass object — reconnect","title":"Reconnect a GiottoClass object — reconnect","text":"Reconnect GiottoClass object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reconnect a GiottoClass object — reconnect","text":"","code":"# S4 method for class 'giottoLargeImage' reconnect(x, path = NULL, ...)  # S4 method for class 'giottoImage' reconnect(x, path = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reconnect a GiottoClass object — reconnect","text":"x object reconnect path character. (optional) New filepath associate object. needed filepath normally carried object path changed. ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reconnect a GiottoClass object — reconnect","text":"GiottoClass object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reconnect a GiottoClass object — reconnect","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  reconnect(g_image) #> An object of class giottoLargeImage : \"alignment\" #> Image extent            : 2364.5, 6522.5, -5425.25, -2620.75 (xmin, xmax, ymin, ymax) #> Original image extent   : 2364.5, 6522.5, -5425.25, -2620.75 (xmin, xmax, ymin, ymax) #> Scale factor            : 13.2420382165605, 13.2287735849057 (x, y) #> Resolution              : 0.0755170755170755, 0.0755927972900695 (x, y) #> Layers                  : 4  #> Estimated max intensity : 174  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoData/Mini_datasets/Visium/VisiumObject/Images/alignment_spatRaster'"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Reconnect images with dead pointers — reconnectGiottoImage","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"reconnect gobject's dead image pointers using filepaths original source image files","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"","code":"reconnectGiottoImage(   gobject,   auto_reconnect = TRUE,   reconnect_type = c(\"all\", \"image\", \"largeImage\"),   image_name = NULL,   largeImage_name = NULL,   image_path = NULL,   largeImage_path = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"gobject giotto object auto_reconnect automatically reconnect images TRUE. manual FALSE reconnect_type type image reconnect auto_reconnect = TRUE image_name names images reconnect largeImage_name name large images reconnect image_path named list paths images reconnect giottoImages largeImage_path named list paths images reconnect giottoLargeImages verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"giotto object updated image pointer","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"Inputs can either given image name (image_name/largeImage_name) filepath (image_path/largeImage_path) args named list filepath argument alone. auto_reconnect = TRUE additional params need supplied. long giotto image objects directly created using filepaths, filepaths stored within image objects referenced reconnection. Issues arise giotto image objects created directly underlying image handling package objects (magick raster objects) image files moved since giotto image object generated. cases, use manual reconnection setting auto_reconnect = FALSE.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  reconnectGiottoImage(g, reconnect_type = \"largeImage\") #> Attempting automatic reconnection... #> largeImage(s) discovered... #> --> alignment : filepath found #>  #> --> image : filepath found #>  #>  #> done #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoImage_MG.html","id":null,"dir":"Reference","previous_headings":"","what":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","title":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","text":"reconnect giottoImage image pointer broken","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoImage_MG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","text":"","code":"reconnect_giottoImage_MG(giottoImage, image_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoImage_MG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","text":"giottoImage giottoImage reconnect image_path path source file giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoImage_MG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","text":"reconnected giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","title":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","text":"reconnect giottoLargeImage image pointer broken","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","text":"","code":"reconnect_giottoLargeImage(giottoLargeImage, image_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","text":"giottoLargeImage giottoLargeImage reconnect image_path path source file giottoLargeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","text":"reconnected giottoLargeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":null,"dir":"Reference","previous_headings":"","what":"reconnect_image_object — reconnect_image_object","title":"reconnect_image_object — reconnect_image_object","text":"Reconnect giotto image object dead image pointer using filepath original image source","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reconnect_image_object — reconnect_image_object","text":"","code":"reconnect_image_object(image_object, image_type, image_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reconnect_image_object — reconnect_image_object","text":"image_object giotto image object image_type type giotto image object image_path path image source reconnect image object ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reconnect_image_object — reconnect_image_object","text":"reconnected image_object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"reconnect_image_object — reconnect_image_object","text":"simple wrapper function image object-specific reconnection functions include functionality find specific image objects giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate rectangular polygon vertices — rectVertices","title":"Generate rectangular polygon vertices — rectVertices","text":"Generates vertex coordinates rectangle dimensions given dims param.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate rectangular polygon vertices — rectVertices","text":"","code":"rectVertices(dims)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate rectangular polygon vertices — rectVertices","text":"dims named vector style c(x = numeric, y = numeric) defines width (x) height (y) generated rectangle polygon.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate rectangular polygon vertices — rectVertices","text":"data.table rectangle vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate rectangular polygon vertices — rectVertices","text":"","code":"rectVertices(c(x = 1, y = 2)) #>        x     y #>    <num> <num> #> 1:     0     0 #> 2:     0     2 #> 3:     1     2 #> 4:     1     0"},{"path":"https://drieslab.github.io/GiottoClass/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. GiottoUtils getDistinctColors, getMonochromeColors, getRainbowColors","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reexports.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Objects exported from other packages — reexports","text":"character vector hexadecimal distinct colors","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reexports.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Objects exported from other packages — reexports","text":"","code":"getDistinctColors(n = 5) #> [1] \"#377EB8\" \"#4DAF4A\" \"#A65628\" \"#BC80BD\" \"#FFED6F\""},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial relationships between geometries — relate","title":"Spatial relationships between geometries — relate","text":"relate() returns logical matrix indicating presence absence specific spatial relationships geometries x y.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial relationships between geometries — relate","text":"","code":"# S4 method for class 'giottoSpatial,giottoSpatial' relate(   x,   y,   relation,   pairs = TRUE,   na.rm = TRUE,   output = c(\"data.table\", \"matrix\"),   use_names = TRUE,   ... )  # S4 method for class 'giotto,giottoSpatial' relate(   x,   y,   ...,   what = c(\"polygon\", \"spatlocs\", \"points\"),   spat_unit = NULL,   feat_type = NULL,   spat_locs_name = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial relationships between geometries — relate","text":"x spatial object records test y spatial object records test relations relation character. One \"intersects\", \"touches\", \"crosses\", \"overlaps\", \"within\", \"contains\", \"covers\", \"coveredby\", \"disjoint\". \"DE-9IM\" string \"FF*FF****\". See wikipedia geotools doc pairs logical. TRUE two-column matrix returned indices cases requested relation TRUE. especially helpful dealing many geometries returned value generally much smaller na.rm logical. TRUE pairs=TRUE, geometries x related geometry y omitted output character. \"data.table\" \"matrix\". \"data.table\" possible pairs=TRUE use_names logical. TRUE, pairs=TRUE, output=\"data.table\" IDs geometries used. ... additional args pass character. type spatial data giotto object relate. One \"polygon\", \"spatlocs\", \"points\" spat_unit spatial unit feat_type feature type spat_locs_name name spatlocs use = \"spatlocs\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial relationships between geometries — relate","text":"data.table output=\"data.table\". matrix output=\"matrix\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial relationships between geometries — relate","text":"","code":"g <- GiottoData::loadGiottoMini(\"viz\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" activeSpatUnit(g) <- \"aggregate\" sl <- g[[\"spatial_locs\"]][[1]] gpoints <- g[[\"feat_info\"]][[1]] gpoly <- g[[\"spatial_info\"]][[1]]  res1 <- relate(gpoints, gpoly, relation = \"intersects\") res2 <- relate(gpoints, gpoly, relation = \"intersects\", use_names = FALSE)  selection <- system.file(\"extdata/viz_interactive_select.csv\",     package = \"GiottoClass\" ) select_polys <- createGiottoPolygon(data.table::fread(selection)) #>   Selecting col \"name\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively res <- relate(g, select_polys, relation = \"intersects\") g[,res[y == \"polygon1\", x]] #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 25 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used g[,res[y == \"polygon2\", x]] #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 90 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used g[,res[y == \"polygon3\", x]] #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 245 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove cell annotation — removeCellAnnotation","title":"Remove cell annotation — removeCellAnnotation","text":"Removes cell annotation Giotto object specific feature modality (default = 'rna')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove cell annotation — removeCellAnnotation","text":"","code":"removeCellAnnotation(   gobject,   spat_unit = NULL,   feat_type = NULL,   columns = NULL,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove cell annotation — removeCellAnnotation","text":"gobject giotto object spat_unit spatial unit feat_type feature type columns names columns remove return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove cell annotation — removeCellAnnotation","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Remove cell annotation — removeCellAnnotation","text":"return_gobject = FALSE, return cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove cell annotation — removeCellAnnotation","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  annotation <- c(     \"1\" = \"cell_type_1\",     \"2\" = \"cell_type_2\",     \"3\" = \"cell_type_3\",     \"4\" = \"cell_type_4\",     \"5\" = \"cell_type_5\",     \"6\" = \"cell_type_6\",     \"7\" = \"cell_type_7\",     \"8\" = \"cell_type_8\" )  g <- annotateGiotto(g,     annotation_vector = annotation,     cluster_column = \"leiden_clus\" )  g <- removeCellAnnotation(g, columns = \"cell_types\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove feature annotation — removeFeatAnnotation","title":"Remove feature annotation — removeFeatAnnotation","text":"Removes feature annotation Giotto object specific feature modality","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove feature annotation — removeFeatAnnotation","text":"","code":"removeFeatAnnotation(   gobject,   spat_unit = NULL,   feat_type = NULL,   columns = NULL,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove feature annotation — removeFeatAnnotation","text":"gobject giotto object spat_unit spatial unit feat_type feature type columns names columns remove return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove feature annotation — removeFeatAnnotation","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Remove feature annotation — removeFeatAnnotation","text":"return_gobject = FALSE, return gene metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove feature annotation — removeFeatAnnotation","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  g <- removeFeatAnnotation(g, columns = \"hvf\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — replaceGiottoInstructions","title":"deprecated — replaceGiottoInstructions","text":"Function replace instructions giotto object. call initialize giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — replaceGiottoInstructions","text":"","code":"replaceGiottoInstructions(gobject, instructions = NULL, init_gobject = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — replaceGiottoInstructions","text":"gobject giotto object instructions new instructions (e.g. result createGiottoInstructions) init_gobject (boolean, default = TRUE) initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — replaceGiottoInstructions","text":"giotto object replaces instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"deprecated — replaceGiottoInstructions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  replaceGiottoInstructions(     gobject = g,     instructions = createGiottoInstructions() ) #> Warning: `replaceGiottoInstructions()` was deprecated in GiottoClass 0.3.5. #> ℹ Please use `instructions()` instead. #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace part of an object with [<- — replace_bracket","title":"Replace part of an object with [<- — replace_bracket","text":"Replace values Giotto Classes. Providing empty brackets x[] <- value usually replace entire contained data representation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace part of an object with [<- — replace_bracket","text":"","code":"# S4 method for class 'coordDataDT,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'metaData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'dimObj,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'exprData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'spatNetData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'nnData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'enrData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'spatGridData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'giottoPoints,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'giottoPolygon,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'giottoLargeImage,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'giottoImage,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'affine2d,missing,missing,ANY' x[i, j] <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace part of an object with [<- — replace_bracket","text":"x Giotto S4 object replace information , j indices specifying elements replace. Indices numeric character vectors empty value values(s) set","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replace part of an object with [<- — replace_bracket","text":"x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"-lt-methods","dir":"Reference","previous_headings":"","what":"`[<-` methods","title":"Replace part of an object with [<- — replace_bracket","text":"Assign coordinates slot giotto S4 Assign metaDT slot giotto S4 Assign coordinates slot giotto S4 dimObj Assign exprMat slot giotto S4 Assign networkDT slot giotto S4 Assign igraph slot giotto S4 Assign enrichDT slot giotto S4 Assign gridDT slot giotto S4 Assign spatVector slot giotto S4 Assign spatVector slot giottoPolygon Assign affine slot affine2d","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Replace part of an object with [<- — replace_bracket","text":"","code":"gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  gpoints[] <- gpoints[]"},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace part of an object with $<- — replace_dollar","title":"Replace part of an object with $<- — replace_dollar","text":"Replace values Giotto Classes using $<- operator.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace part of an object with $<- — replace_dollar","text":"","code":"# S4 method for class 'giotto' x$name <- value  # S4 method for class 'coordDataDT' x$name <- value  # S4 method for class 'spatEnrObj' x$name <- value  # S4 method for class 'dimObj' x$name <- value  # S4 method for class 'metaData' x$name <- value  # S4 method for class 'terraVectData' x$name <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace part of an object with $<- — replace_dollar","text":"x Giotto S4 object replace columns name literal character string (possibly backtick quoted). normally matched colnames. value values(s) set column","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replace part of an object with $<- — replace_dollar","text":"x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"-lt-methods","dir":"Reference","previous_headings":"","what":"`$<-` methods","title":"Replace part of an object with $<- — replace_dollar","text":"Set values colname giotto S4 data.table coordinates slot. Works via data.table methods Set values colname giotto S4 spatEnrObj. Set entries misc slot giotto S4 dimObj. Set values colname giotto S4 data.table metaDT slot. Works via data.table methods Set values colname giotto S4 spatVector slot.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Replace part of an object with $<- — replace_dollar","text":"","code":"gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  gpoints$new_col <- sprintf(\"feat_%d\", seq(nrow(gpoints)))"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":null,"dir":"Reference","previous_headings":"","what":"Rescale an object — rescale","title":"Rescale an object — rescale","text":"Rescale object spatially. Z dimension scaling supported types subobjects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rescale an object — rescale","text":"","code":"# S4 method for class 'giotto' rescale(   x,   fx = 1,   fy = fx,   x0,   y0,   spat_unit = \":all:\",   feat_type = \":all:\",   images = \":all:\" )  # S4 method for class 'spatLocsObj' rescale(x, fx = 1, fy = fx, fz = fx, x0, y0, z0)  # S4 method for class 'data.frame' rescale(   x,   fx = 1,   fy = fx,   fz = fx,   x0,   y0,   z0,   geom = c(\"sdimx\", \"sdimy\", \"sdimz\") )  # S4 method for class 'giottoPolygon' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'giottoPoints' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'giottoImage' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'giottoLargeImage' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'giottoAffineImage' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'affine2d' rescale(x, fx = 1, fy = fx, x0, y0)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rescale an object — rescale","text":"x object fx numeric > 0. horizontal scaling factor fy numeric > 0. vertical scaling factor x0 numeric. x-coordinate center rescaling. missing, center extent x used y0 numeric. y-coordinate center rescaling. missing, center extent x used spat_unit character vector. spatial units affect feat_type character vector. feature types affect images character vector. Images affect fz numeric > 0. z scaling factor (supported objects) z0 numeric. z-coordinate center rescaling. missing, center extent x used (supported objects) geom character. Named vector colnames x, y, (z) coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rescale an object — rescale","text":"re-scaled object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Rescale an object — rescale","text":"giotto object, \"::\" token can passed spat_unit, feat_type, images arguments affect available items.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Rescale an object — rescale","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  rescale(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"rescalePolygons — rescalePolygons","title":"rescalePolygons — rescalePolygons","text":"Rescale individual polygons x y factor","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rescalePolygons — rescalePolygons","text":"","code":"rescalePolygons(   gobject,   poly_info = \"cell\",   name = \"rescaled_cell\",   fx = 0.5,   fy = 0.5,   calculate_centroids = TRUE,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rescalePolygons — rescalePolygons","text":"gobject giotto object poly_info polygon information name name name new polygon layer fx x-scaling factor fy y-scaling factor calculate_centroids calculate centroids return_gobject return giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rescalePolygons — rescalePolygons","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"rescalePolygons — rescalePolygons","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  rescalePolygons(g, poly_info = \"aggregate\") #> Setting polygon info [rescaled_cell] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate rescaled_cell  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Row and column names — row-plus-colnames-generic","title":"Row and column names — row-plus-colnames-generic","text":"Retrieve set row column names object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Row and column names — row-plus-colnames-generic","text":"","code":"# S4 method for class 'giotto' colnames(x)  # S4 method for class 'exprObj' colnames(x)  # S4 method for class 'cellMetaObj' colnames(x)  # S4 method for class 'featMetaObj' colnames(x)  # S4 method for class 'spatEnrObj' colnames(x)  # S4 method for class 'spatLocsObj' colnames(x)  # S4 method for class 'dimObj' colnames(x)  # S4 method for class 'giotto' rownames(x)  # S4 method for class 'exprObj' rownames(x)  # S4 method for class 'dimObj' rownames(x)  # S4 method for class 'metaData' rownames(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row and column names — row-plus-colnames-generic","text":"x object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Row and column names — row-plus-colnames-generic","text":"character vector row col names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Row and column names — row-plus-colnames-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  colnames(g) #>                                         2  #> \"240649020551054330404932383065726870513\"  #>                                         3  #> \"274176126496863898679934791272921588227\"  #>                                         4  #> \"323754550002953984063006506310071917306\"  #>                                         5  #>  \"87260224659312905497866017323180367450\"  #>                                         6  #>  \"17817477728742691260808256980746537959\"  #>                                         7  #> \"182132384503107798660396708280285136358\"  #>                                         9  #> \"316289522368890354495930310222776908199\"  #>                                        10  #> \"318995879282318989627235045690211636294\"  #>                                        11  #> \"104570855383158731814075192607294301741\"  #>                                        12  #> \"115370283894795045523368609208878185314\"  #>                                        13  #> \"123860671559578247432410194986927758864\"  #>                                        14  #> \"126981423897188762239468136959275655616\"  #>                                        15  #> \"134398773695365619188678200952912609063\"  #>                                        16  #>  \"15242486364109501724975900940581726845\"  #>                                        17  #> \"152684748256642370929802439227360458069\"  #>                                        18  #> \"153751792203577791006158581642177087065\"  #>                                        19  #>  \"16326589507615554063401897357427439030\"  #>                                        20  #> \"165786478473465185470745991122188406667\"  #>                                        21  #> \"167710327060928309829388429279250508392\"  #>                                        22  #> \"172181421897607556322673704318102678295\"  #>                                        23  #> \"176844289786228093052039491926955764947\"  #>                                        24  #> \"182235958169292445695483205478317795477\"  #>                                        25  #> \"183227745956657225549068107012033843521\"  #>                                        26  #> \"186988931894710833920932112634285943415\"  #>                                        27  #> \"190687643154627893064711601675234362640\"  #>                                        28  #>  \"20548793658722995878220914240286086757\"  #>                                        29  #> \"206702762285684421190019779213421380201\"  #>                                        30  #> \"216701996099683814512199402223708471323\"  #>                                        31  #>  \"21934936165997373583174173761929761438\"  #>                                        32  #> \"230344318208995342827768566280706457626\"  #>                                        33  #> \"251905496166492083168644493421091558216\"  #>                                        34  #> \"262996653580953175020435707363716649390\"  #>                                        35  #>  \"27666206735695437393204421885258583706\"  #>                                        37  #> \"286906689872367261752702769926754066848\"  #>                                        38  #> \"288822108801800165318171357739905375883\"  #>                                        39  #> \"301054712356664458042996323827909441002\"  #>                                        40  #> \"304842190541754537761816256358565562302\"  #>                                        41  #> \"318439340668767417720582355350205310941\"  #>                                        42  #> \"335295524680090725199231409883288198017\"  #>                                        43  #>  \"35118346554513854436644695033199584696\"  #>                                        44  #>  \"41054036480225512911591384807281320971\"  #>                                        45  #>  \"43731708947199618294982749003938483862\"  #>                                        46  #>  \"48024672048124996997588408479044670509\"  #>                                        47  #>  \"51348907619842676963078202479438175138\"  #>                                        49  #>  \"67532821514617092397935003422482443295\"  #>                                        50  #>  \"77151711298730578178892667721058396928\"  #>                                        51  #>  \"77782228870577724567477221255169934206\"  #>                                        52  #>   \"8777587181320516093160667806451882030\"  #>                                        53  #>  \"95838678880751873613229512065975406368\"  #>                                        54  #>  \"95947958963963707263153541936375959179\"  #>                                        55  #>   \"9668748337336721830701975018211142813\"  #>                                        56  #>  \"97411078642927912684859796714759494710\"  #>                                        57  #> \"101161259912191124732236989250178928032\"  #>                                        58  #> \"110615983935499449765434338770904504245\"  #>                                        59  #> \"110858042010405247711695373195937122852\"  #>                                        60  #> \"110900719814678261966908552089216814729\"  #>                                        61  #>  \"12925323527075390484710711277617599454\"  #>                                        63  #> \"137348923180371322628727011975895485209\"  #>                                        64  #> \"138859376429590720661963324654447571708\"  #>                                        65  #> \"140543565961583233746802451796981444137\"  #>                                        66  #> \"143386081176260440019925196855300710659\"  #>                                        67  #> \"143408196806895889016075556052288734233\"  #>                                        68  #> \"145421744145915784890159499930205641713\"  #>                                        69  #> \"148336156782096202859532636956126767457\"  #>                                        70  #> \"150082699777048696177232440639953146354\"  #>                                        71  #>  \"15247055772869406897093633424720409278\"  #>                                        72  #>  \"15834776842182822801451197571763335013\"  #>                                        73  #> \"170833460535439412738579124041592991444\"  #>                                        74  #> \"173780780834031059819946658163431921979\"  #>                                        75  #> \"174306823762889142173283452439684229948\"  #>                                        76  #> \"175540604452034099044348476236813150837\"  #>                                        77  #> \"177757177666889772027017950398587309639\"  #>                                        78  #>  \"17868848607867654301368031294266874310\"  #>                                        79  #> \"180947508370750255585892730777436680945\"  #>                                        80  #> \"187952627468949069447188707715308813657\"  #>                                        81  #>   \"1900302715660571356090444774019116326\"  #>                                        82  #> \"203192161403397797138670022274582721699\"  #>                                        83  #> \"206016050634629330546630679047044021073\"  #>                                        85  #> \"214394514156259228118188949454902817376\"  #>                                        86  #> \"221669638772738575000116137509912039310\"  #>                                        87  #> \"224458376429228506642398057779371677646\"  #>                                        88  #> \"226912346807310637711937183879196326571\"  #>                                        89  #> \"227232155811404089141823608874580791245\"  #>                                        91  #> \"236677629222667262221261861475728542818\"  #>                                        93  #> \"244015124549889909957742476033146111487\"  #>                                        94  #> \"244247765904337326625465691380839405459\"  #>                                        95  #> \"244448312826260498647079278647004353269\"  #>                                        96  #> \"244840145612854293464477850603474951260\"  #>                                        97  #> \"262797098003740683881650619022037793005\"  #>                                        98  #> \"265185306239991354232232246957204545228\"  #>                                        99  #> \"266413162898429280572455841453688616870\"  #>                                       101  #> \"275784684664527332374777211328350223506\"  #>                                       102  #> \"277057315125198906319398446608128392905\"  #>                                       104  #> \"291975341311453330406711526698967834209\"  #>                                       105  #> \"295193149306421749943849825086053455411\"  #>                                       106  #>  \"30222355550742125173065032035537805062\"  #>                                       107  #> \"304560432600831995659079356647103974886\"  #>                                       108  #>  \"30571638947438619177947320407779261750\"  #>                                       109  #> \"306415949245581212081161219410047325001\"  #>                                       110  #> \"311565496674213535805029947713320284697\"  #>                                       111  #> \"314397389362641167108869069386457433770\"  #>                                       112  #>   \"3188909098022617910378369321966273882\"  #>                                       113  #> \"322879686187630160969459793861944841206\"  #>                                       114  #> \"330850389163886577071114668277958486114\"  #>                                       115  #> \"334199301045926627171760429217123408914\"  #>                                       116  #> \"339814056401091912617621500767389941735\"  #>                                       117  #>  \"36648998424868029072860674954666559763\"  #>                                       118  #>  \"39033692777509843205319060807429911979\"  #>                                       119  #>   \"3942785923272820952395109293003259310\"  #>                                       120  #>  \"47275912178029130797780898068213599096\"  #>                                       121  #>  \"56815638009315000170441964570512336625\"  #>                                       122  #>  \"57203625626451579261315887898923502046\"  #>                                       123  #>  \"62669443199671326763841071380380779477\"  #>                                       124  #>  \"64228015236811922665804882776457047292\"  #>                                       126  #>  \"68418314542386876178693610244900595267\"  #>                                       127  #>  \"70219882915166469874938407731799217344\"  #>                                       128  #>  \"75660428514717127988983246148828583482\"  #>                                       129  #>  \"75682347267697870039469591993208007445\"  #>                                       130  #>  \"87903363874776475366779322866396664731\"  #>                                       131  #>  \"88743795534206169429467675642537392511\"  #>                                       133  #>   \"9538866320245722231901445225545432644\"  #>                                       134  #>  \"96091484747656303270745913028146994621\"  #>                                       135  #> \"116860147088450350976374609398998546737\"  #>                                       136  #> \"133061403473432310288273623600023558748\"  #>                                       137  #> \"137154375879163008723188861204335796821\"  #>                                       138  #> \"185903314401459366597627436588666236388\"  #>                                       139  #> \"217996462208701069168232210617040322639\"  #>                                       140  #> \"226667648171626631993624597360362535576\"  #>                                       141  #> \"254829253202043893331055483138743800247\"  #>                                       142  #> \"271967915636064836314881508293335292245\"  #>                                       143  #> \"273673567134859598195435250950149370161\"  #>                                       144  #> \"305306955532868686456926844192964831687\"  #>                                       145  #> \"307030440204593378842812081935039092344\"  #>                                       146  #> \"311587331826654155209560142756469108973\"  #>                                       147  #>  \"44197902970141946871502798467323259089\"  #>                                       148  #>  \"44721220002773982161418195292536576043\"  #>                                       150  #>  \"65855854848879329159292019718060662708\"  #>                                       151  #>  \"76322781861215450124167009829890606622\"  #>                                       152  #>  \"11065258297873257226330942251431244138\"  #>                                       153  #> \"118071411587380747913796380721014165557\"  #>                                       154  #> \"123540785709544435621019288242840920053\"  #>                                       156  #> \"130428604684362047522418850101908720496\"  #>                                       157  #> \"134509424346276649608483685115101376571\"  #>                                       158  #> \"136341171141277731884608634279863298546\"  #>                                       160  #> \"137356600627014280700323828086313714576\"  #>                                       161  #> \"151798130004305208790801168757831384604\"  #>                                       162  #> \"162684318525520950869468479178769741207\"  #>                                       163  #> \"164424478098970510930576318421517316799\"  #>                                       164  #> \"166456955228473064319115194076209471689\"  #>                                       165  #> \"168376325588102040437463621554621047372\"  #>                                       166  #> \"179297712006471333306826676970515917851\"  #>                                       167  #>  \"19311588976622944909682910864587104989\"  #>                                       168  #> \"204611834270911643022584999768859598082\"  #>                                       169  #> \"212501669348639182111017279862555064555\"  #>                                       171  #> \"222047855782557501653245982274520432658\"  #>                                       173  #> \"231212643322278795528005770495251497705\"  #>                                       174  #> \"233229703476821612486041386363745481186\"  #>                                       175  #>  \"23470744401352443589618734383441183930\"  #>                                       176  #> \"234988593327199604253479621078255555503\"  #>                                       177  #> \"250481714349085757816071122854700489348\"  #>                                       178  #> \"254538897036257180617662178141894962698\"  #>                                       179  #> \"257184545464839903394564555141875300987\"  #>                                       180  #> \"266246243070401825856501948379131507953\"  #>                                       181  #> \"280661554698226730422771895627995747059\"  #>                                       182  #> \"283821893476134729825893155000887153128\"  #>                                       183  #> \"286146294981380023269011675378975275188\"  #>                                       184  #> \"292254379263157279159966458654907155929\"  #>                                       185  #> \"293900582929631255788566880963197704396\"  #>                                       186  #> \"296019945099320175547230863498668480924\"  #>                                       187  #> \"307915098305811968258082436904262060268\"  #>                                       188  #>  \"31072896077757820678000109671990674373\"  #>                                       189  #> \"324637742389179243201282186318588452049\"  #>                                       190  #> \"324877467507432389063800715005904969237\"  #>                                       191  #>  \"32535304551014256860916796345005841454\"  #>                                       192  #> \"325896428237586114830946437310469001833\"  #>                                       193  #>  \"32944790627105381861829233020285020883\"  #>                                       194  #> \"331580323004945087311483453179965743309\"  #>                                       195  #> \"331675815801204232182324913632094035806\"  #>                                       196  #> \"334356931858742201981142004419227940530\"  #>                                       198  #>  \"42056064196611141769700924475836317519\"  #>                                       199  #>  \"59141517931138845718061638546803837463\"  #>                                       200  #>  \"77541886028463256801311974652160917274\"  #>                                       201  #>  \"79668971589879493465166271739355011800\"  #>                                       202  #>  \"90740652120142025598838838824737408007\"  #>                                       203  #>  \"93766399603521973873598911761678204002\"  #>                                       204  #>  \"94915957193797412218079317943892351685\"  #>                                       205  #> \"101488859781016188084173008420811094152\"  #>                                       206  #> \"102184699197574201819246996094734116255\"  #>                                       207  #> \"107393799088150693125543893285009932508\"  #>                                       208  #> \"111687473021757662663527126267334037424\"  #>                                       209  #> \"112201175467804501210529603201546927780\"  #>                                       210  #> \"115235047525370533075441381313256765131\"  #>                                       211  #> \"119102272531447353986749088457842353881\"  #>                                       212  #> \"121108122402850896937802185181656711412\"  #>                                       213  #> \"122906612256038341059239630042273244949\"  #>                                       214  #> \"126809950897128716226739975254707226975\"  #>                                       215  #> \"126827073040370531574124290326181150621\"  #>                                       216  #> \"129220219089532886548658463773454811807\"  #>                                       217  #> \"130416595705865355812306620146726096256\"  #>                                       218  #> \"130720172120660644879676230721263100142\"  #>                                       219  #> \"134503679556257538045105223616434677584\"  #>                                       220  #> \"134512816139291924739198129882869576276\"  #>                                       222  #>  \"14225193593112604305545027950864785906\"  #>                                       223  #>  \"14615917600474753437497051666515185188\"  #>                                       224  #> \"146715357009983465209963560859286180117\"  #>                                       225  #> \"147103070941083943163952951858791268261\"  #>                                       226  #> \"150338819641781846748929553541898461633\"  #>                                       227  #> \"160318430812610433362422897343020317434\"  #>                                       228  #> \"166788256632929614638779193211391658357\"  #>                                       229  #> \"167818783196654344295653476753505898360\"  #>                                       230  #> \"185055418446250460085953045917995887188\"  #>                                       231  #> \"186404099358317212811882499608798243906\"  #>                                       232  #> \"188179457167181317036865075745680501410\"  #>                                       233  #> 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rowMeans_flex","text":"rowMeans_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowMeans_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rowMeans_flex — rowMeans_flex","text":"","code":"rowMeans_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rowMeans_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rowMeans_flex — rowMeans_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowMeans_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rowMeans_flex — rowMeans_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowMeans_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"rowMeans_flex — rowMeans_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  rowMeans_flex(m) #>  [1] -0.03455096  0.08871945 -0.29999737  0.47536178 -0.66005505 -0.03974135 #>  [7] -0.45622412 -0.14340232 -0.50460708  0.45589154"},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"rowSums_flex — rowSums_flex","title":"rowSums_flex — rowSums_flex","text":"rowSums_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rowSums_flex — rowSums_flex","text":"","code":"rowSums_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rowSums_flex — rowSums_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rowSums_flex — rowSums_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"rowSums_flex — rowSums_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  rowSums_flex(m) #>  [1] -0.2852256 -4.7180057  3.5983422 -1.4346828  2.0426869  2.0530418 #>  [7] -4.1031143 -3.5399338  1.3677829  9.0450398"},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"saveGiotto — saveGiotto","title":"saveGiotto — saveGiotto","text":"Saves Giotto object specific folder structure","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"saveGiotto — saveGiotto","text":"","code":"saveGiotto(   gobject,   foldername = \"saveGiottoDir\",   dir = getwd(),   method = c(\"RDS\", \"qs\"),   method_params = list(),   overwrite = FALSE,   image_filetype = \"PNG\",   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"saveGiotto — saveGiotto","text":"gobject Giotto object foldername Folder name dir Directory create folder method method save main object method_params additional method parameters RDS qs overwrite Overwrite existing folders image_filetype image filetype use, see writeRaster. Default \"PNG\". TIFF outputs, try \"COG\" verbose verbose ... additional parameters writeRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"saveGiotto — saveGiotto","text":"Creates directory Giotto object information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"saveGiotto — saveGiotto","text":"Works together loadGiotto save re-load Giotto objects. Additional method_params need provided list go saveRDS qsave","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"saveGiotto — saveGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  saveGiotto(gobject = g, dir = tempdir(), overwrite = TRUE) #> Folder already exist and overwrite = TRUE, #>  overwrite folder #> 1. Start writing feature information #> 2. Start writing spatial information #> For spatial information: cell #> 3. Start writing image information #> For image information: alignment #> For image information: image #> [1] TRUE"},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cell metadata — setCellMetadata","title":"Set cell metadata — setCellMetadata","text":"Function set cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cell metadata — setCellMetadata","text":"","code":"setCellMetadata(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cell metadata — setCellMetadata","text":"gobject giotto object x cellMetaObj list cellMetaObj set. Passing NULL reset specified set cell metadata giotto object. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cell metadata — setCellMetadata","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cell metadata — setCellMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" m1 <- getCellMetadata(g, output = \"data.table\") m2 <- data.frame(     cell_ID = m1$cell_ID,     new_column = sample(letters, 624, replace = TRUE) )  setCellMetadata(gobject = g, x = createCellMetaObj(m2)) #> > Cell metadata for spat_unit \" cell \" and feat_type \" rna \" already exists and #>  will be replaced with new metadata. #> Setting cell metadata [cell][rna] #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":null,"dir":"Reference","previous_headings":"","what":"Set dimension reduction data — setDimReduction","title":"Set dimension reduction data — setDimReduction","text":"Function dimension reduction information Giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set dimension reduction data — setDimReduction","text":"","code":"setDimReduction(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   name = \"pca\",   reduction = c(\"cells\", \"feats\"),   reduction_method = c(\"pca\", \"umap\", \"tsne\"),   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set dimension reduction data — setDimReduction","text":"gobject giotto object x dimObj list dimObj set. Passing NULL remove specified set dimension reduction information gobject spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name reduction results reduction reduction cells features reduction_method reduction method (e.g. \"pca\") provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set dimension reduction data — setDimReduction","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set dimension reduction data — setDimReduction","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" dimred <- getDimReduction(g)  setDimReduction(gobject = g, x = dimred) #> > pca already exists and will be replaced with #>  new dimension reduction object #> Setting dimension reduction [cell][rna] pca #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":null,"dir":"Reference","previous_headings":"","what":"Set expression data — setExpression","title":"Set expression data — setExpression","text":"Function set expression values giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set expression data — setExpression","text":"","code":"setExpression(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   name = \"raw\",   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set expression data — setExpression","text":"gobject giotto object x exprObj list exprObj set. Passing NULL remove specified set expression data giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name expression information provenance provenance information (optional) information giotto object. Pass NULL remove expression object verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set expression data — setExpression","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set expression data — setExpression","text":"","code":"g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" m <- matrix(rnorm(100), nrow = 10) colnames(m) <- paste0(\"cell_\", seq_len(10)) rownames(m) <- paste0(\"feat_\", seq_len(10))  g <- setExpression(gobject = g, x = createExprObj(m, name = \"raw\")) #> Setting expression [cell][rna] raw"},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feature info — setFeatureInfo","title":"Set feature info — setFeatureInfo","text":"Set giotto polygon spatVector features","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feature info — setFeatureInfo","text":"","code":"setFeatureInfo(   gobject,   x,   feat_type = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feature info — setFeatureInfo","text":"gobject giotto object x giottoPoints object list giottoPoints set. Passing NULL remove specified giottoPoints object giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feature info — setFeatureInfo","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set feature info — setFeatureInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" featinfo <- getFeatureInfo(g, return_giottoPoints = TRUE)  setFeatureInfo(gobject = g, x = featinfo) #> > \" rna \" already exists and will be #>  replaced with new giotto points #> Setting feature info [rna] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feature metadata — setFeatureMetadata","title":"Set feature metadata — setFeatureMetadata","text":"Function set feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feature metadata — setFeatureMetadata","text":"","code":"setFeatureMetadata(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feature metadata — setFeatureMetadata","text":"gobject giotto object x featMetaObj list featMetaObj set. Passing NULL reset specified set feature metadata giotto object. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feature metadata — setFeatureMetadata","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set feature metadata — setFeatureMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" m1 <- getFeatureMetadata(g, output = \"data.table\") m2 <- data.frame(     feat_ID = m1$feat_ID,     new_column = paste0(\"gene_\", m1$feat_ID) )  setFeatureMetadata(gobject = g, x = createFeatMetaObj(m2)) #> Setting feature metadata [cell][rna] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Set giotto subobjects into giotto object — setGiotto","title":"Set giotto subobjects into giotto object — setGiotto","text":"Set giotto subobjects giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set giotto subobjects into giotto object — setGiotto","text":"","code":"# S4 method for class 'giotto,list' setGiotto(gobject, x, verbose = TRUE, ...)  # S4 method for class 'giotto,cellMetaObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,featMetaObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,exprObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,giottoPoints' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,giottoPolygon' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,dimObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,spatLocsObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,spatEnrObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,nnNetObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,spatialNetworkObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,giottoLargeImage' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,giottoImage' setGiotto(gobject, x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set giotto subobjects into giotto object — setGiotto","text":"gobject giotto object x giottoSubobject set verbose verbose ... additional params pass specific Giotto setter functions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set giotto subobjects into giotto object — setGiotto","text":"giottoSubobject","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set giotto subobjects into giotto object — setGiotto","text":"","code":"g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_expression <- GiottoData::loadSubObjectMini(\"exprObj\")  setGiotto(gobject = g, x = g_expression) #> Setting expression [aggregate][rna] normalized #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 462 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [aggregate][rna] normalized #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Set giotto image object — setGiottoImage","title":"Set giotto image object — setGiottoImage","text":"Directly attach giotto image giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set giotto image object — setGiottoImage","text":"","code":"setGiottoImage(gobject, image, image_type = NULL, name = NULL, verbose = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set giotto image object — setGiottoImage","text":"gobject giotto object image giotto image object attached without modification giotto object image_type deprecated name name giotto image object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set giotto image object — setGiottoImage","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set giotto image object — setGiottoImage","text":"Use care! function directly attaches giotto image objects gobject without modifications spatial positioning values within image object generally needed order plot correct location relative modalities spatial data.  general-purpose method attaching image objects, see addGiottoImage","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set giotto image object — setGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" gimg <- getGiottoImage(gobject = g)  setGiottoImage(g, NULL, name = objName(gimg)) #> NULL passed to `image` param #>  removing specified image #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : dapi_z1 polyT_z0 polyT_z1  #>  #>  #> Use objHistory() to see steps and params used setGiottoImage(gobject = g, image = gimg) #> > image 'dapi_z0' already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set multiomics integration results — setMultiomics","title":"Set multiomics integration results — setMultiomics","text":"Set multiomics integration result Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set multiomics integration results — setMultiomics","text":"","code":"setMultiomics(   gobject = NULL,   result,   spat_unit = NULL,   feat_type = NULL,   integration_method = \"WNN\",   result_name = \"theta_weighted_matrix\",   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set multiomics integration results — setMultiomics","text":"gobject Giotto object result matrix result multiomics integration (e.g. theta weighted values runWNN) spat_unit spatial unit (e.g. 'cell') feat_type (e.g. 'rna_protein') integration_method multiomics integration method used. Default = 'WNN' result_name Default = 'theta_weighted_matrix' verbose verbose ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set multiomics integration results — setMultiomics","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set multiomics integration results — setMultiomics","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  setMultiomics(     gobject = g, result = matrix(rnorm(100), nrow = 10),     spat_unit = \"cell\", feat_type = \"rna_protein\" ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Set nearest neighbor network — setNearestNetwork","title":"Set nearest neighbor network — setNearestNetwork","text":"Set NN-network Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set nearest neighbor network — setNearestNetwork","text":"","code":"setNearestNetwork(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   nn_type = \"sNN\",   name = \"sNN.pca\",   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set nearest neighbor network — setNearestNetwork","text":"gobject giotto object x nnNetObj list nnNetObj. Passing NULL remove specified set nearest neighbor network information gobject spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_type \"kNN\" \"sNN\" name name NN network used yet supported. provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set nearest neighbor network — setNearestNetwork","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set nearest neighbor network — setNearestNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" dimred <- getNearestNetwork(gobject = g) #> The NN network type was not specified, default to the #>  first: \"sNN\" #> The NN network name was not specified, default to the #>  first: \"sNN.pca\"  setNearestNetwork(gobject = g, x = dimred) #> > 'sNN.pca' already exists and will be replaced with #>  new nearest neighbor network #> Setting nearest neighbor network [cell][rna] sNN.pca #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"Set polygon info — setPolygonInfo","title":"Set polygon info — setPolygonInfo","text":"Set polygon information Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set polygon info — setPolygonInfo","text":"","code":"setPolygonInfo(   gobject,   x,   name = \"cell\",   centroids_to_spatlocs = FALSE,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set polygon info — setPolygonInfo","text":"gobject giotto object x single object named list objects set polygon information (see details) name (optional, character) name assign polygon spatial unit polygon might define. used single giottoPolygon objects. Names taken named list multiple polygons. centroids_to_spatlocs centroid information discovered, whether additionally set set spatial locations (default = FALSE) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set polygon info — setPolygonInfo","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set polygon info — setPolygonInfo","text":"Inputs can provided either single objects named lists objects. list named, generic name template 'cell_i' applied.  input character string, assumed filepath.  required formatting reading tabular data objects, see createGiottoPolygonsFromDfr details.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set polygon info — setPolygonInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" polyinfo <- getPolygonInfo(g, return_giottoPolygon = TRUE)  setPolygonInfo(gobject = g, x = polyinfo) #> > \" z0 \" already exists and will be replaced #>  with new giotto polygon #> Setting polygon info [z0] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial enrichment — setSpatialEnrichment","title":"Set spatial enrichment — setSpatialEnrichment","text":"Function set spatial enrichment slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial enrichment — setSpatialEnrichment","text":"","code":"setSpatialEnrichment(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   name = \"enrichment\",   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial enrichment — setSpatialEnrichment","text":"gobject giotto object x spatEnrObj list spatEnrObj set. Passing NULL remove specified set spatial enrichment information gobject. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name spatial enrichment results. Default \"DWLS\" provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial enrichment — setSpatialEnrichment","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set spatial enrichment — setSpatialEnrichment","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spatenrich <- GiottoData::loadSubObjectMini(\"spatEnrObj\")  g <- setSpatialEnrichment(g, spatenrich) #> > \" cluster_metagene \" already exists and will be replaced with new spatial #>  enrichment results #> Setting spatial enrichment [aggregate][rna] cluster_metagene"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial grid — setSpatialGrid","title":"Set spatial grid — setSpatialGrid","text":"Function set spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial grid — setSpatialGrid","text":"","code":"setSpatialGrid(   gobject,   spatial_grid,   spat_unit = NULL,   feat_type = NULL,   name = NULL,   verbose = TRUE,   set_defaults = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial grid — setSpatialGrid","text":"gobject giotto object spatial_grid spatial grid object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name spatial grid verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial grid — setSpatialGrid","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set spatial grid — setSpatialGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5) sg <- getSpatialGrid(g, return_grid_Obj = TRUE) #> The grid name was not specified, default to the first: \"spatial_grid\"  setSpatialGrid(gobject = g, spatial_grid = sg) #> > \" spatial_grid \" already exists and will be replaced with new spatial grid #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial locations — setSpatialLocations","title":"Set spatial locations — setSpatialLocations","text":"Function set spatial location slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial locations — setSpatialLocations","text":"","code":"setSpatialLocations(   gobject,   x,   spat_unit = NULL,   name = \"raw\",   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial locations — setSpatialLocations","text":"gobject giotto object x spatLocsObj list spatLocsObj. Passing NULL remove specified set spatial locations data. spat_unit spatial unit (e.g. \"cell\") name name spatial locations, default \"raw\" provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial locations — setSpatialLocations","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set spatial locations — setSpatialLocations","text":"Spatial information set nested location described tagged spat_unit name information. alternative location can also specified respective params function.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set spatial locations — setSpatialLocations","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" x <- getSpatialLocations(g, output = \"data.table\") sl <- data.frame(cell_ID = x$cell_ID, sdimx = rnorm(624), sdimy = rnorm(624))  setSpatialLocations(gobject = g, x = createSpatLocsObj(sl, name = \"raw\")) #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> > raw already exists and will be replaced with new spatial #>  locations #> Setting spatial locations [cell] raw #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial network — setSpatialNetwork","title":"Set spatial network — setSpatialNetwork","text":"Function set spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial network — setSpatialNetwork","text":"","code":"setSpatialNetwork(   gobject,   x,   spat_unit = NULL,   name = NULL,   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial network — setSpatialNetwork","text":"gobject giotto object x spatialNetworkObj list spatialNetworkObj set. Passing NULL removes specified set spatial network information gobject. spat_unit spatial unit (e.g. \"cell\") name name spatial network provenance provenance name verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial network — setSpatialNetwork","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set spatial network — setSpatialNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spatnet <- getSpatialNetwork(g)  setSpatialNetwork(gobject = g, x = spatnet) #> > \" Delaunay_network \" already exists and will be replaced with new spatial #>  network #> Setting spatial network [cell] Delaunay_network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":null,"dir":"Reference","previous_headings":"","what":"set_default_feat_type — set_default_feat_type","title":"set_default_feat_type — set_default_feat_type","text":"Function guess default feature type. Also see activeFeatType() methods-instructions.R way manually assign default","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"set_default_feat_type — set_default_feat_type","text":"","code":"set_default_feat_type(gobject, feat_type = NULL, spat_unit)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"set_default_feat_type — set_default_feat_type","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") spat_unit spatial unit (e.g. \"cell\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"set_default_feat_type — set_default_feat_type","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"set_default_feat_type — set_default_feat_type","text":"","code":"g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  set_default_feat_type(gobject = g, spat_unit = \"cell\", feat_type = \"rna\") #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":null,"dir":"Reference","previous_headings":"","what":"set_default_spat_unit — set_default_spat_unit","title":"set_default_spat_unit — set_default_spat_unit","text":"Function guess default spatial unit. Also see activeSpatUnit() methods-instructions.R way manually assign default","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"set_default_spat_unit — set_default_spat_unit","text":"","code":"set_default_spat_unit(gobject, spat_unit = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"set_default_spat_unit — set_default_spat_unit","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"set_default_spat_unit — set_default_spat_unit","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"set_default_spat_unit — set_default_spat_unit","text":"","code":"g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  set_default_spat_unit(gobject = g, spat_unit = \"cell\") #> [1] \"cell\""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set multiomics integration results — set_multiomics","title":"Set multiomics integration results — set_multiomics","text":"Set multiomics integration result Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set multiomics integration results — set_multiomics","text":"","code":"set_multiomics(   gobject,   result,   spat_unit = NULL,   feat_type = NULL,   integration_method = \"WNN\",   result_name = \"theta_weighted_matrix\",   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set multiomics integration results — set_multiomics","text":"gobject Giotto object result matrix result multiomics integration (e.g. theta weighted values runWNN) spat_unit spatial unit (e.g. 'cell') feat_type (e.g. 'rna_protein') integration_method multiomics integration method used. Default = 'WNN' result_name Default = 'theta_weighted_matrix' verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set multiomics integration results — set_multiomics","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set multiomics integration results — set_multiomics","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  set_multiomics(     gobject = g, result = matrix(rnorm(100), nrow = 10),     spat_unit = \"cell\", feat_type = \"rna_protein\" ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated — seuratToGiotto","title":"Deprecated — seuratToGiotto","text":"Deprecated. Please use either seuratToGiottoV4 seuratToGiottoV5","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated — seuratToGiotto","text":"","code":"seuratToGiotto(   sobject,   spatial_assay = \"Spatial\",   dim_reduction = c(\"pca\", \"umap\"),   subcellular_assay = \"Vizgen\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deprecated — seuratToGiotto","text":"sobject Input Seurat object convert Giotto object spatial_assay Specify name spatial assay slot Seurat. Default \"Spatial\". dim_reduction Specify dimensional reduction computations fetch subcellular_assay Specify name subcellular assay input object. Default \"Vizgen\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deprecated — seuratToGiotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"Convert Seurat V4 object Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"","code":"seuratToGiottoV4(   sobject,   spatial_assay = \"Spatial\",   dim_reduction = c(\"pca\", \"umap\"),   subcellular_assay = \"Vizgen\",   sp_network = NULL,   nn_network = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"sobject Input Seurat object convert Giotto object spatial_assay Specify name spatial assay slot Seurat. Default \"Spatial\". dim_reduction Specify dimensional reduction computations fetch input Seurat object. Default \"c('pca', 'umap')\". subcellular_assay Specify name subcellular assay input sp_network sp_network nn_network nn_network verbose logical. Default TRUE object. Default \"Vizgen\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"Giotto object converted Seurat object computations stored .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"","code":"m_expression <- Matrix::Matrix(rnorm(100), nrow = 10, sparse = TRUE) s <- Seurat::CreateSeuratObject(counts = m_expression)  seuratToGiottoV5(s, spatial_assay = \"RNA\") #> Warning: data layer is not found and counts layer is used #> Images for RNA assay not found in the data. #>                         Skipping image processing. #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 10, 10 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized #> spatial locations ---------------- #>   [cell] raw #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV5.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","title":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","text":"Convert Seurat V5 object Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV5.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","text":"","code":"seuratToGiottoV5(   sobject,   spatial_assay = \"Spatial\",   dim_reduction = c(\"pca\", \"umap\"),   subcellular_assay = \"SCT\",   sp_network = NULL,   nn_network = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV5.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","text":"sobject Input Seurat object convert Giotto object spatial_assay Specify name spatial assay slot Seurat. Default \"Spatial\". dim_reduction Specify dimensional reduction computations fetch input Seurat object. Default \"c('pca', 'umap')\". subcellular_assay Specify name subcellular assay input sp_network sp_network nn_network nn_network verbose logical. Default TRUE object. Default \"Vizgen\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV5.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","text":"Giotto object converted Seurat object computations stored .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply a shear tranform — shear","title":"Apply a shear tranform — shear","text":"Apply shear transformation spatial object. Currently works 2D transforms. implementation applies shear along one axis adding value axis multiplicative factor fx fy applied.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply a shear tranform — shear","text":"","code":"# S4 method for class 'spatLocsObj' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'SpatVector' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'giottoPoints' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'giottoPolygon' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'giottoLargeImage' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'giottoAffineImage' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'affine2d' shear(x, fx = 0, fy = 0, x0, y0, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply a shear tranform — shear","text":"x object fx numeric. x shear fy numeric. y shear x0 numeric. x-origin shear y0 numeric. y-origin shear ... additional args pass (none implemented)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply a shear tranform — shear","text":"shear transformed object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply a shear tranform — shear","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  plot(shear(sl, fx = 2))   # equivalent affine transform shear_m <- diag(rep(1, 3)) shear_m[2, 1] <- 2 plot(affine(sl, shear_m))  plot(shear(sl, fx = 2, x0 = 0, y0 = 0))"},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":null,"dir":"Reference","previous_headings":"","what":"Show methods for Giotto classes — show","title":"Show methods for Giotto classes — show","text":"Show methods Giotto classes","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show methods for Giotto classes — show","text":"","code":"# S4 method for class 'giotto' show(object)  # S4 method for class 'packedGiotto' show(object)  # S4 method for class 'exprObj' show(object)  # S4 method for class 'cellMetaObj' show(object)  # S4 method for class 'featMetaObj' show(object)  # S4 method for class 'dimObj' show(object)  # S4 method for class 'nnNetObj' show(object)  # S4 method for class 'spatLocsObj' show(object)  # S4 method for class 'spatialNetworkObj' show(object)  # S4 method for class 'spatialGridObj' show(object)  # S4 method for class 'spatEnrObj' show(object)  # S4 method for class 'giottoPolygon' show(object)  # S4 method for class 'packedGiottoPolygon' show(object)  # S4 method for class 'giottoPoints' show(object)  # S4 method for class 'packedGiottoPoints' show(object)  # S4 method for class 'giottoImage' show(object)  # S4 method for class 'giottoLargeImage' show(object)  # S4 method for class 'affine2d' show(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show methods for Giotto classes — show","text":"object object show","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show methods for Giotto classes — show","text":"giotto slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show methods for Giotto classes — show","text":"","code":"sl <- data.frame(seq(10), seq(10), letters[seq(10)]) |>     createSpatLocsObj(verbose = FALSE) show(sl) #> An object of class spatLocsObj : \"test\" #> spat_unit : \"cell\" #> dimensions: 10 3  #> preview   : #>    sdimx sdimy cell_ID #>    <int> <int>  <char> #> 1:     1     1       a #> 2:     2     2       b #> 3:     3     3       c #>  #> ranges: #>      sdimx sdimy #> [1,]     1     1 #> [2,]    10    10 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoCellMetadata — showGiottoCellMetadata","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"shows available cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"","code":"showGiottoCellMetadata(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"gobject giotto object nrows number rows print metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"prints name small subset available metadata","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoCellMetadata(g) #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>          An object of class cellMetaObj  #>          spat_unit : \"cell\" #>          feat_type : \"rna\" #>          provenance: cell  #>          dimensions: 4 7  #>           #>                        cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                         <char>     <int>    <int>      <num>      <num>       <num> #>          1: AACTCGATGGCGCAGT-1         1      265   41.79811  1057.9308           2 #>          2: GGCTGGCTAGCTTAAA-1         1      279   44.00631  1064.7493           5 #>          3: GACGCCTGTTGCAGGG-1         1      219   34.54259   964.9294           2 #>             custom_leiden #>                     <num> #>          1:             4 #>          2:             3 #>          3:             3 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoDimRed — showGiottoDimRed","title":"showGiottoDimRed — showGiottoDimRed","text":"shows available dimension reductions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoDimRed — showGiottoDimRed","text":"","code":"showGiottoDimRed(gobject, nrows = 3, ncols = 2)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoDimRed — showGiottoDimRed","text":"gobject giotto object nrows number coordinates rows print ncols number coordinates columns print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoDimRed — showGiottoDimRed","text":"prints name small subset available dimension reduction coordinates","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoDimRed — showGiottoDimRed","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoDimRed(g) #> Dim reduction on cells: #>  -------------------------  #>  #> . #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>       ├──Dim reduction type \"pca\" #>       │  ├──S4 dimObj \"pca\" coordinates:   (624 rows 100 cols) #>       │  │                            Dim.1      Dim.2 #>       │  │     AAAGGGATGTAGCAAG-1  0.801127   2.874369 #>       │  │     AAATGGCATGTCTTGT-1  6.995542  -2.010611 #>       │  │     AAATGGTCAATGTGCC-1 -7.813633 -12.305266 #>       │  │   #>       │  └──S4 dimObj \"custom_pca\" coordinates:   (624 rows 100 cols) #>       │                                Dim.1     Dim.2 #>       │        AAAGGGATGTAGCAAG-1 -0.4547083  3.383001 #>       │        AAATGGCATGTCTTGT-1 -6.2679882  1.503456 #>       │        AAATGGTCAATGTGCC-1 10.2690789 -7.006071 #>       │      #>       ├──Dim reduction type \"umap\" #>       │  ├──S4 dimObj \"umap\" coordinates:   (624 rows 2 cols) #>       │  │                             Dim.1      Dim.2 #>       │  │     AAAGGGATGTAGCAAG-1  -3.975629   4.401250 #>       │  │     AAATGGCATGTCTTGT-1 -16.788569 -20.950487 #>       │  │     AAATGGTCAATGTGCC-1  27.206731  -9.034316 #>       │  │   #>       │  └──S4 dimObj \"custom_umap\" coordinates:   (624 rows 2 cols) #>       │                                Dim.1      Dim.2 #>       │        AAAGGGATGTAGCAAG-1  -3.731145  -3.665592 #>       │        AAATGGCATGTCTTGT-1 -14.201382 -23.566582 #>       │        AAATGGTCAATGTGCC-1  29.736043   6.478635 #>       │      #>       └──Dim reduction type \"tsne\" #>          └──S4 dimObj \"tsne\" coordinates:   (624 rows 2 cols) #>                                        Dim.1      Dim.2 #>                AAAGGGATGTAGCAAG-1 -3.4389554  -1.690378 #>                AAATGGCATGTCTTGT-1  0.4290782 -18.060330 #>                AAATGGTCAATGTGCC-1 17.8533998  12.975694 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoExpression — showGiottoExpression","title":"showGiottoExpression — showGiottoExpression","text":"shows available matrices","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoExpression — showGiottoExpression","text":"","code":"showGiottoExpression(gobject, nrows = 4, ncols = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoExpression — showGiottoExpression","text":"gobject giotto object nrows number rows print matrix (ignored sparse matrices) ncols number columns print matrix (ignored sparse matrices)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoExpression — showGiottoExpression","text":"prints name small subset available matrices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoExpression — showGiottoExpression","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoExpression(g) #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>       ├──Expression data \"raw\" values: #>       │     An object of class exprObj : \"raw\" #>       │     spat_unit : \"cell\" #>       │     feat_type : \"rna\" #>       │     provenance: cell  #>       │      #>       │     contains: #>       │     634 x 624 sparse Matrix of class \"dgCMatrix\" #>       │                                              #>       │     Gna12  1 2 1 1 9 1 3 5 3 . . 10 7 ...... #>       │     Ccnd2  . 1 1 . . 1 . 1 1 . .  . 3 ...... #>       │     Btbd17 . 1 1 1 . . 2 . . . .  . . ...... #>       │      #>       │      ........suppressing 611 columns and 628 rows in show(); maybe adjust options(max.print=, width=) #>       │                                                    #>       │     Gm19935       . 1 . . . . . . . . 1 . . ...... #>       │     9630013A20Rik . . . . . . . . . . 1 . . ...... #>       │     2900040C04Rik 1 . . . . . . . . 1 . . . ...... #>       │      #>       │      First four colnames: #>       │      AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 #>       │      AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  #>       │   #>       ├──Expression data \"normalized\" values: #>       │     An object of class exprObj : \"normalized\" #>       │     spat_unit : \"cell\" #>       │     feat_type : \"rna\" #>       │     provenance: cell  #>       │      #>       │     contains: #>       │     634 x 624 sparse Matrix of class \"dgCMatrix\" #>       │                                                                                                 #>       │     Gna12  3.783033 3.929306 3.213481 3.625522 5.749157 2.399595 4.127923 4.693522 5.299374 . . #>       │     Ccnd2  .        3.021024 3.213481 .        .        2.399595 .        2.578969 3.785883 . . #>       │     Btbd17 .        3.021024 3.213481 3.625522 .        .        3.583641 .        .        . . #>       │                                     #>       │     Gna12  5.683074 5.036423 ...... #>       │     Ccnd2  .        3.871485 ...... #>       │     Btbd17 .        .        ...... #>       │      #>       │      ........suppressing 611 columns and 628 rows in show(); maybe adjust options(max.print=, width=) #>       │                                                                                #>       │     Gm19935       .        3.021024 . . . . . . . .        3.103487 . . ...... #>       │     9630013A20Rik .        .        . . . . . . . .        3.103487 . . ...... #>       │     2900040C04Rik 3.783033 .        . . . . . . . 3.488189 .        . . ...... #>       │      #>       │      First four colnames: #>       │      AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 #>       │      AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  #>       │   #>       └──Expression data \"scaled\" values: #>             An object of class exprObj  #>             for spatial unit: \"cell\" and feature type: \"rna\" #>               Provenance: cell #>              #>             contains: #>             634 x 624 dense matrix of class \"dgeMatrix\" #>              #>                          [,1]       [,2]        [,3]       [,4] #>             Gna12   0.3648960  0.3883749  0.02397458  0.2635371 #>             Ccnd2  -0.9726302  0.5135323  0.59882469 -0.8883955 #>             Btbd17 -0.6902939  1.0914525  1.12309944  1.3267401 #>             Sox9   -0.8344595 -1.0154377 -0.84282003 -0.7614102 #>              #>              First four colnames: #>              AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 #>              AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoFeatInfo — showGiottoFeatInfo","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"show available giotto spatial feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"","code":"showGiottoFeatInfo(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"SpatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoFeatInfo(g) #> For Feature info:  rna  #>  #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  source      : rna_feature_spatVector.shp #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3 #>  #> ----------------------------- #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoFeatMetadata — showGiottoFeatMetadata","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"shows available feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"","code":"showGiottoFeatMetadata(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"gobject giotto object nrows number rows print metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"prints name small subset available metadata","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoFeatMetadata(g) #> ├──Spatial unit \"z0\" #> │  └──Feature type \"rna\" #> │        An object of class featMetaObj  #> │        spat_unit : \"z0\" #> │        feat_type : \"rna\" #> │        provenance: z0  #> │         #> │           feat_ID #> │            <char> #> │        1:    Mlc1 #> │        2:  Gprc5b #> │        3:    Gfap #> │      #> ├──Spatial unit \"z1\" #> │  └──Feature type \"rna\" #> │        An object of class featMetaObj  #> │        spat_unit : \"z1\" #> │        feat_type : \"rna\" #> │        provenance: z1  #> │         #> │           feat_ID #> │            <char> #> │        1:    Mlc1 #> │        2:  Gprc5b #> │        3:    Gfap #> │      #> └──Spatial unit \"aggregate\" #>    └──Feature type \"rna\" #>          An object of class featMetaObj  #>          spat_unit : \"aggregate\" #>          feat_type : \"rna\" #>          provenance: z0 z1  #>           #>             feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det hvg_orig #>              <char>    <int>      <num>      <num>     <num>         <num>   <char> #>          1:    Mlc1       80   17.31602   526.5915  1.139808      6.582394       no #>          2:  Gprc5b      138   29.87013   944.0153  2.043323      6.840690       no #>          3:    Gfap      151   32.68398  1229.1943  2.660594      8.140359      yes #>                   var    hvf #>                 <num> <char> #>          1:  1.815718    yes #>          2:  2.388911    yes #>          3: 12.899599    yes #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoImageNames — showGiottoImageNames","title":"showGiottoImageNames — showGiottoImageNames","text":"Prints available giotto images attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoImageNames — showGiottoImageNames","text":"","code":"showGiottoImageNames(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoImageNames — showGiottoImageNames","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoImageNames — showGiottoImageNames","text":"prints names available giotto image objects","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoImageNames — showGiottoImageNames","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoImageNames(g) #> Image type: largeImage  #>  #> --> Name: dapi_z0  #> --> Name: dapi_z1  #> --> Name: polyT_z0  #> --> Name: polyT_z1  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — showGiottoInstructions","title":"deprecated — showGiottoInstructions","text":"Function display instructions giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — showGiottoInstructions","text":"","code":"showGiottoInstructions(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — showGiottoInstructions","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — showGiottoInstructions","text":"named vector giotto instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"deprecated — showGiottoInstructions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoInstructions(g) #> Warning: `showGiottoInstructions()` was deprecated in GiottoClass 0.3.5. #> ℹ Please use `instructions()` instead. #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : TRUE #> return_plot      : FALSE #> save_plot        : FALSE #> save_dir         : NA #> plot_format      : png #> dpi              : 300 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoNearestNetworks — showGiottoNearestNetworks","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"shows available nearest neighbor networks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"","code":"showGiottoNearestNetworks(gobject, nrows = 3)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"gobject giotto object nrows number network rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"prints name small subset available nearest neighbor network info","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoNearestNetworks(g) #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>       └──NN network type \"sNN\" #>          ├──S4 nnNetObj \"sNN.pca\"   (3748 rows) #>          │                      from                 to    weight distance shared  rank #>          │                    <char>             <char>     <num>    <num>  <int> <int> #>          │     1: AAAGGGATGTAGCAAG-1 CAGTGTCCGCAGAATG-1 0.3777898 1.646975      9     1 #>          │     2: AAAGGGATGTAGCAAG-1 ACGTAGATTGCTGATG-1 0.2318818 3.312541      6     2 #>          │     3: AAAGGGATGTAGCAAG-1 CGTACCTGATAGGCCT-1 0.3122768 2.202287      6     3 #>          │   #>          └──S4 nnNetObj \"custom_NN\"   (1872 rows) #>                                 from                 to    weight distance shared  rank #>                               <char>             <char>     <num>    <num>  <int> <int> #>                1: AAAGGGATGTAGCAAG-1 AACTGGGTCCCGACGT-1 0.1492788 5.698874      2     1 #>                2: AAAGGGATGTAGCAAG-1 CAGCTCGTGCTTGTGT-1 0.1507539 5.633328      1     2 #>                3: AAAGGGATGTAGCAAG-1 CGTACCTGATAGGCCT-1 0.1566434 5.383926      1     3 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"shows available spatial enrichment results","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"","code":"showGiottoSpatEnrichments(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"gobject giotto object nrows number rows print spatial enrichment data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"prints name small subset available data.table","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoSpatEnrichments(g) #> Spatial unit:  aggregate   #>  #> --> Feature type:  rna   #>  #> ----> Name  cluster_metagene :  #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #> 4: 4.093622 0.5886051 0.1962017 0.5886051     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #> 4:  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatGrids — showGiottoSpatGrids","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"Prints available spatial grids attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"","code":"showGiottoSpatGrids(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"gobject giotto object nrows number rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"prints name available spatial grids","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  showGiottoSpatGrids(g) #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>       └──S4 spatialGridObj \"spatial_grid\"   (388800 rows) #>                x_start y_start  x_end y_end gr_name gr_x_name gr_y_name #>                  <num>   <num>  <num> <num>  <char>    <char>    <char> #>             1:  3067.5   -5445 3072.5 -5440    gr_1    gr_x_1    gr_y_1 #>             2:  3072.5   -5445 3077.5 -5440    gr_2    gr_x_2    gr_y_1 #>             3:  3077.5   -5445 3082.5 -5440    gr_3    gr_x_3    gr_y_1 #>             4:  3082.5   -5445 3087.5 -5440    gr_4    gr_x_4    gr_y_1 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatLocs — showGiottoSpatLocs","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"shows available spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"","code":"showGiottoSpatLocs(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"gobject giotto object nrows number rows print spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"prints name small subset available data.table","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoSpatLocs(g) #> └──Spatial unit \"cell\" #>    └──S4 spatLocsObj \"raw\" coordinates:   (624 rows) #>          An object of class spatLocsObj  #>          provenance: cell #>              ------------------------ #>             sdimx sdimy            cell_ID #>             <int> <int>             <char> #>          1:  5477 -4125 AAAGGGATGTAGCAAG-1 #>          2:  5959 -2808 AAATGGCATGTCTTGT-1 #>          3:  4720 -5202 AAATGGTCAATGTGCC-1 #>          4:  5202 -5322 AAATTAACGGGTAGCT-1 #>           #>          ranges: #>               sdimx sdimy #>          [1,]  3069 -5442 #>          [2,]  6441 -2568 #>           #>           #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatNetworks — showGiottoSpatNetworks","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"Prints available spatial networks attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"","code":"showGiottoSpatNetworks(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"gobject giotto object nrows number rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"prints names small subset available spatial network info","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoSpatNetworks(g) #> └──Spatial unit \"cell\" #>    ├──S4 spatialNetworkObj \"Delaunay_network\"   (1770 rows) #>    │                      from                 to sdimx_begin sdimy_begin sdimx_end #>    │                    <char>             <char>       <num>       <num>     <num> #>    │     1: AAAGGGATGTAGCAAG-1 TCAAACAACCGCGTCG-1        5477       -4125      5340 #>    │     2: AAAGGGATGTAGCAAG-1 ACGATCATACATAGAG-1        5477       -4125      5546 #>    │     3: AAAGGGATGTAGCAAG-1 TATGCTCCCTACTTAC-1        5477       -4125      5408 #>    │     4: AAAGGGATGTAGCAAG-1 TTGTTCAGTGTGCTAC-1        5477       -4125      5615 #>    │        sdimy_end distance      weight #>    │            <num>    <num>       <num> #>    │     1:     -4125 137.0000 0.007299270 #>    │     2:     -4244 137.5573 0.007269700 #>    │     3:     -4244 137.5573 0.007269700 #>    │     4:     -4125 138.0000 0.007246377 #>    │   #>    └──S4 spatialNetworkObj \"spatial_network\"   (3288 rows) #>                           from                 to sdimx_begin sdimy_begin sdimx_end #>                         <char>             <char>       <int>       <int>     <int> #>          1: AAAGGGATGTAGCAAG-1 TCAAACAACCGCGTCG-1        5477       -4125      5340 #>          2: AAAGGGATGTAGCAAG-1 ACGATCATACATAGAG-1        5477       -4125      5546 #>          3: AAAGGGATGTAGCAAG-1 TATGCTCCCTACTTAC-1        5477       -4125      5408 #>          4: AAAGGGATGTAGCAAG-1 TTGTTCAGTGTGCTAC-1        5477       -4125      5615 #>             sdimy_end distance      weight #>                 <int>    <num>       <num> #>          1:     -4125 137.0000 0.007246377 #>          2:     -4244 137.5573 0.007217233 #>          3:     -4244 137.5573 0.007217233 #>          4:     -4125 138.0000 0.007194245 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatialInfo — showGiottoSpatialInfo","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"show available giotto spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"","code":"showGiottoSpatialInfo(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"SpatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoSpatialInfo(g) #> For Spatial info:  z0  #>  #> An object of class giottoPolygon #> spat_unit : \"z0\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 498, 1  (geometries, attributes) #>  extent      : 6399.244, 6903.243, -5152.39, -4694.868  (xmin, xmax, ymin, ymax) #>  source      : z0_spatInfo_spatVector.shp #>  coord. ref. :   #>  names       :                                 poly_ID #>  type        :                                   <chr> #>  values      :  40951783403982682273285375368232495429 #>                240649020551054330404932383065726870513 #>                274176126496863898679934791272921588227 #>  centroids   : calculated #>  overlaps    : rna #> ----------------------------- #>   #> For Spatial info:  z1  #>  #> An object of class giottoPolygon #> spat_unit : \"z1\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 504, 1  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.873  (xmin, xmax, ymin, ymax) #>  source      : z1_spatInfo_spatVector.shp #>  coord. ref. :   #>  names       :                                 poly_ID #>  type        :                                   <chr> #>  values      :  40951783403982682273285375368232495429 #>                 17685062374745280598492217386845129350 #>                223553142498364321238189328942498473503 #>  centroids   : calculated #>  overlaps    : rna #> ----------------------------- #>   #> For Spatial info:  aggregate  #>  #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  source      : aggregate_spatInfo_spatVector.shp #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    : rna #> ----------------------------- #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGrids.html","id":null,"dir":"Reference","previous_headings":"","what":"Show Spatial Grids — showGrids","title":"Show Spatial Grids — showGrids","text":"Show Spatial Grids","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGrids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show Spatial Grids — showGrids","text":"","code":"showGrids(...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGrids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show Spatial Grids — showGrids","text":"... Arguments passed showGiottoSpatGrids gobject giotto object nrows number rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGrids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show Spatial Grids — showGrids","text":"prints name available spatial grids","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"Show networks — showNetworks","title":"Show networks — showNetworks","text":"Show networks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show networks — showNetworks","text":"","code":"showNetworks(...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show networks — showNetworks","text":"... Arguments passed showGiottoSpatNetworks gobject giotto object nrows number rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show networks — showNetworks","text":"prints names small subset available spatial network info","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":null,"dir":"Reference","previous_headings":"","what":"showProcessingSteps — showProcessingSteps","title":"showProcessingSteps — showProcessingSteps","text":"shows sequential processing steps performed Giotto object summarized format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showProcessingSteps — showProcessingSteps","text":"","code":"showProcessingSteps(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showProcessingSteps — showProcessingSteps","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showProcessingSteps — showProcessingSteps","text":"list processing steps names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showProcessingSteps — showProcessingSteps","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showProcessingSteps(g) #> Warning: `showProcessingSteps()` was deprecated in GiottoClass 0.4.0. #> ℹ Please use `objHistory()` instead. #> ℹ objHistory with arg `summarized = TRUE` replaces this functionality #> Processing steps: #> 0_normalize #> 1_subset #> 2_filter #> name info: tag tag #> 3_feat_stats #> 4_cell_stats #> 5_hvf #> name info: hvf HVFplot #> 6_pca #> 7_umap #> 8_tsne #> 9_nn_network #> 10_cluster #> name info: leiden_clus sNN.pca #> 11_delaunay_spatial_network #> name info: Delaunay_network #> 12_spatial_network #> name info: spatial_network #> 13_create_metafeat #> name info: cluster_metagene #> 14_pca #> name info: custom_pca #> 15_umap #> name info: custom_pca custom_umap #> 16_nn_network #> name info: custom_pca custom_NN #> 17_cluster #> name info: custom_leiden custom_NN #> 18_spatial_deconvolution #> name info: DWLS #> 19_spatial_deconvolution #> name info: DWLS #> 20_spatial_deconvolution #> name info: DWLS"},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Slice giotto object by spat_unit and feat_type — sliceGiotto","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"Extract specific spatial units feature types giotto object independent giotto objects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"","code":"sliceGiotto(gobject, spat_unit = \":all:\", feat_type = \":all:\", verbose = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"gobject giotto object spat_unit character vector. Spatial units slice . \"::\" means keeping output feat_type character vector. Feature types slice . \"::\" means keeping output verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" res <- sliceGiotto(g, spat_unit = \"aggregate\") force(res) #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 462 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"smoothGiottoPolygons — smoothGiottoPolygons","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"Smooths Giotto polygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"","code":"smoothGiottoPolygons(   gpolygon,   vertices = 20,   k = 3,   set_neg_to_zero = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"gpolygon giotto polygon object vertices number vertices k k set_neg_to_zero set negative values zero (default: TRUE) ... additional params pass spline","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"Smoothed Giotto polygon object reduced vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"","code":"gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  smoothGiottoPolygons(gpolygon = gpoly) #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6391.72, 6903.433, 0, 0  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    : NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatEnrObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 spatEnrObj Class — spatEnrObj-class","title":"S4 spatEnrObj Class — spatEnrObj-class","text":"Framework store spatial enrichment results","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatEnrObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 spatEnrObj Class — spatEnrObj-class","text":"spatEnrObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatEnrObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 spatEnrObj Class — spatEnrObj-class","text":"name name enrichment object method method used perform spatial enrichment enrichDT spatial enrichment data.table spat_unit spatial unit feat_type feature type provenance provenance information misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatEnrObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 spatEnrObj Class — spatEnrObj-class","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatEnrObj\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial and feature IDs — spatIDs-generic","title":"Spatial and feature IDs — spatIDs-generic","text":"Get cell IDs (termed spatial IDs better reflect single-cell level) feature IDs giotto object subobject. [giotto object specific] applied giotto object, functions pull cell_ID feat_ID slots. values within slots updated whenever object data changed , importantly, whenever active spat_unit feat_type set (see activeSpatUnit() activeFeatType()). New values slots specific active spat_unit feat_type detected either subcellular level (giottoPolygon giottoPoints) aggregate level (expression matrix) data, preference latter exists. aware current behavior, values returned byspatIDs() featIDs() regarded minimal set expected IDs within giotto slots, always exact set ordering.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial and feature IDs — spatIDs-generic","text":"","code":"# S4 method for class 'giotto' spatIDs(x, spat_unit = NULL, subset, negate = FALSE, quote = TRUE, ...)  # S4 method for class 'exprObj' spatIDs(x, ...)  # S4 method for class 'spatLocsObj' spatIDs(x, ...)  # S4 method for class 'cellMetaObj' spatIDs(x, ...)  # S4 method for class 'spatialNetworkObj' spatIDs(x, ...)  # S4 method for class 'dimObj' spatIDs(x, ...)  # S4 method for class 'giottoPolygon' spatIDs(x, use_cache = TRUE, uniques = TRUE, ...)  # S4 method for class 'spatEnrObj' spatIDs(x, ...)  # S4 method for class 'nnNetObj' spatIDs(x, ...)  # S4 method for class 'giotto' featIDs(x, feat_type = NULL, subset, negate = FALSE, quote = TRUE, ...)  # S4 method for class 'exprObj' featIDs(x, ...)  # S4 method for class 'featMetaObj' featIDs(x, ...)  # S4 method for class 'giottoPoints' featIDs(x, use_cache = TRUE, uniques = TRUE, ...)  # S4 method for class 'spatEnrObj' featIDs(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial and feature IDs — spatIDs-generic","text":"x object spat_unit (optional) specify spatial unit subset logical expression find subset features. negate logical. TRUE IDs subset selected quote logical. TRUE, subset param quoted substitute(). Set FALSE calling function, although may recommended since NSE output can unexpected used interactively. ... additional params pass used subset param. spatID(), pass spatValues(). featID(), currently pass fDataDT(). use_cache use cached IDs available (gpoly gpoints ) uniques return unique ID values (currently gpoly gpoints ) feat_type (optional) specify feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial and feature IDs — spatIDs-generic","text":"character vector cell/spatial IDs feature IDs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial and feature IDs — spatIDs-generic","text":"","code":"g <- GiottoData::loadGiottoMini(\"vis\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spatIDs(g) #>   [1] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" #>   [4] \"AAATTAACGGGTAGCT-1\" \"AACAACTGGTAGTTGC-1\" \"AACAGGAAATCGAATA-1\" #>   [7] \"AACAGGATGGGCCGCG-1\" \"AACCATGGGATCGCTA-1\" \"AACCCAGAGACGGAGA-1\" #>  [10] \"AACCGAGCTTGGTCAT-1\" \"AACCGTTGTGTTTGCT-1\" \"AACGATAGAAGGGCCG-1\" #>  [13] \"AACGATATGTCAACTG-1\" \"AACGCGGTCTCCAGCC-1\" \"AACGTCAGACTAGTGG-1\" #>  [16] \"AACTCGATGGCGCAGT-1\" \"AACTGATATTAGGCCT-1\" \"AACTGGGTCCCGACGT-1\" #>  [19] \"AACTTGCCCGTATGCA-1\" \"AAGAGATGAATCGGTA-1\" \"AAGCTCGTGCCAAGTC-1\" #>  [22] \"AAGGAGCGGTTGGTGC-1\" \"AAGGCGCGTAAAGCTT-1\" \"AAGGCTGTGCTCATCG-1\" #>  [25] \"AAGTAGAAGACCGGGT-1\" \"AAGTAGTGACGCGAGG-1\" \"AATCCAAGGGCCTGAG-1\" #>  [28] \"AATGACTGTCAGCCGG-1\" \"AATGCAACCGGGTACC-1\" \"AATGGTTCTCACAAGC-1\" #>  [31] \"AATTTGGTTCCAAAGA-1\" \"ACAACAGCATGAGCTA-1\" \"ACAACGGTCCCTGCGA-1\" #>  [34] \"ACAAGGACAAGAGGTT-1\" \"ACACAAAGACGGGTGG-1\" \"ACACACTTTCTACACG-1\" #>  [37] \"ACACCCAGCATGCAGC-1\" \"ACACCCGAGAAATCCG-1\" \"ACACCTTAAGTAGGGC-1\" #>  [40] \"ACACGAGACTCCTTCT-1\" \"ACACGGGAACTTAGGG-1\" \"ACATAATAAGGCGGTG-1\" #>  [43] \"ACCAAGAACGCGTGTC-1\" \"ACCACAAGTTTCTATC-1\" \"ACCCTTCATCTGCGAA-1\" #>  [46] \"ACCGACTGAGTCCCAC-1\" \"ACCTAATCGACTTCCT-1\" \"ACGATCATACATAGAG-1\" #>  [49] \"ACGCATTCGTGAGTAC-1\" \"ACGCCAGATGATTTCT-1\" \"ACGCGGGCCAAGGACA-1\" #>  [52] \"ACGGAATTTAGCAAAT-1\" \"ACGTAGATTGCTGATG-1\" \"ACGTGCGCCTCGTGCA-1\" #>  [55] \"ACGTTTAGTTGTGATC-1\" \"ACTACCAGCTCTCTGG-1\" \"ACTATTCGTCCGTGGT-1\" #>  [58] \"ACTCAATAAAGGCACG-1\" \"ACTGCCGTCGTAACTC-1\" \"ACTGTAGCACTTTGGA-1\" #>  [61] \"ACTGTCCAGGATTATA-1\" \"ACTGTCTTCTTTAGAA-1\" \"ACTGTGCTAGTAGATC-1\" #>  [64] \"ACTTAGTACGACAAGA-1\" \"ACTTCGCCATACGCAC-1\" \"ACTTGGGACCCGGTGG-1\" #>  [67] \"ACTTTCCTATAGCTTC-1\" \"AGAACGTGGTACATTC-1\" \"AGACCATGGGATACAA-1\" #>  [70] \"AGACCCGCCCTCCTCG-1\" \"AGACTAGCCTTCCAGA-1\" \"AGAGCGGGCTAATCAT-1\" #>  [73] \"AGAGCGTACAAGCTCG-1\" \"AGATAACTTCAGGGCC-1\" \"AGATACGACTTCATAT-1\" #>  [76] \"AGATCTCAGGTGTGAT-1\" \"AGATGACTCGCCCACG-1\" \"AGCACCAGTACTCACG-1\" #>  [79] \"AGCACTTAAGGACGCC-1\" \"AGCATCGTCGATAATT-1\" \"AGCCCTAAGCGAAGTT-1\" #>  [82] \"AGCGACATCCCATTCA-1\" \"AGCGACCAACGATATT-1\" \"AGCGGGAAGGGTCCAT-1\" #>  [85] \"AGCTATTTAATCCAAC-1\" \"AGGACATCGCACGTCG-1\" \"AGGCCACCCGTTATGA-1\" #>  [88] \"AGGCCCATTGTACAGG-1\" \"AGGCTATGGTTAGCTT-1\" \"AGGGCGTGATCGGCTA-1\" #>  [91] \"AGGGCTGCAGTTACAG-1\" \"AGGGTTTAGTTCGGGA-1\" \"AGGTAACCTCCTATTC-1\" #>  [94] \"AGGTACGATATTGCCA-1\" \"AGGTAGGTACAAAGCT-1\" \"AGGTTGAGGCACGCTT-1\" #>  [97] \"AGTAATGTCTTGCCGC-1\" \"AGTAGGTAACATACAT-1\" \"AGTATAATACTAGGCA-1\" #> [100] \"AGTCAGCCACCGCCTG-1\" \"AGTCGGCCCAAACGAC-1\" \"AGTCTTCTCCTCAAAT-1\" #> [103] \"AGTTCCTACAGAATTA-1\" \"AGTTTCGCAGGTCGGA-1\" \"ATAAAGGCTCGGTCGT-1\" #> [106] \"ATAACGGAGTCCAACG-1\" \"ATAATAGTGTAGGGAC-1\" \"ATACCACGGGCAACTT-1\" #> [109] \"ATACTAGCATGACCCT-1\" \"ATAGACGAAGAGAAAG-1\" \"ATAGAGTACTGGGACA-1\" #> [112] \"ATAGGGATATCCTTGA-1\" \"ATAGGTTGGGCAGATG-1\" \"ATATCTTAGGGCCTTC-1\" #> [115] \"ATATTCCCACAGGTCA-1\" \"ATATTGCTGTCAAAGT-1\" \"ATATTTAACCCTCAAG-1\" #> [118] \"ATCAATCTGGGCTGCA-1\" \"ATCACTTCATCCTCGC-1\" \"ATCCAACGCAGTCATA-1\" #> [121] \"ATCGACTCTTTCCGTT-1\" \"ATCGCACGCCGGGAGA-1\" \"ATCTCCCTGCAATCTA-1\" #> [124] \"ATCTGGTTAAGACTGT-1\" \"ATCTGTAATTGTACCC-1\" \"ATCTTGACCTGCAACG-1\" #> [127] \"ATGAAGCCAAGGAGCC-1\" \"ATGACGCCGGCTCTAA-1\" \"ATGAGGAGTGTTAATC-1\" #> [130] \"ATGATCGGGAATAGAC-1\" \"ATGCACTACCGCATTG-1\" \"ATGCATGATCCAGGAT-1\" #> [133] \"ATGCCGGTCTTGCATA-1\" \"ATGCGACAGTCCCATT-1\" \"ATGCTCAGTGTTGCAT-1\" #> [136] \"ATGGATTGACCAAACG-1\" \"ATGTGCATCCGACGCA-1\" \"ATGTTACGAGCAATAC-1\" #> [139] \"ATTAATACTACGCGGG-1\" \"ATTAATTCGGTCACTC-1\" \"ATTACTAGCCTCTTGC-1\" #> [142] \"ATTAGATTGATAGCGG-1\" \"ATTATGCCATAGGGAG-1\" \"ATTCCTCCGCCAGTGC-1\" #> [145] \"ATTCTCGTCTCTTTAG-1\" \"ATTGAAGATCTTAGTG-1\" \"ATTGCTGCTCCTCCAT-1\" #> [148] \"ATTGGGAATATCTTGG-1\" \"ATTTAACTCGTATTAC-1\" \"ATTTACAGTTTACTGG-1\" #> [151] \"ATTTGTTCCAGGGCTC-1\" \"CAAACGGTCGCACTTT-1\" \"CAAACTATTGAGCTTC-1\" #> [154] \"CAAATTGTCAGCAAGC-1\" \"CAACGACCCGTTTACA-1\" \"CAACGGTTCTTGATAC-1\" #> [157] \"CAACTCCTTGATCCCG-1\" \"CAAGCAACGTCGGAGT-1\" \"CAAGCACCAAATGCCT-1\" #> [160] \"CAATAAACCTTGGCCC-1\" \"CAATTAAGGGTGATGA-1\" \"CACACAGGGATAGATT-1\" #> [163] \"CACAGCACCCACGGCA-1\" \"CACAGCTAGGGAGTGA-1\" \"CACCATCGGAGGAGAC-1\" #> [166] \"CACCCACACGTCACCC-1\" \"CACCGCCAGAAGGTTT-1\" \"CACCTAATCAGTTTAC-1\" #> [169] \"CACCTCGATGGTGGAC-1\" \"CACGAAAGTTAGTCCC-1\" \"CACGCACAGCGCAGCT-1\" #> [172] \"CACGCAGCGAGGCTTT-1\" \"CACTAAAGTTGCCTAT-1\" \"CACTCAGCTCTTGAGG-1\" #> [175] \"CACTGTCCAAGTGAGA-1\" \"CACTTAATCAGACGGA-1\" \"CACTTCGCCACAGGCT-1\" #> [178] \"CAGAGCATGAGCTTGC-1\" \"CAGATACTAACATAGT-1\" \"CAGCTCACTGAGACAT-1\" #> [181] \"CAGCTCGTGCTTGTGT-1\" \"CAGCTTAGTAGGTAGC-1\" \"CAGTGTCCGCAGAATG-1\" #> [184] \"CAGTTCAAATTGACAC-1\" \"CATACAAAGCCGAACC-1\" \"CATAGTAGCATAGTAG-1\" #> [187] \"CATCATCTACCCGGAC-1\" \"CATCGCCCGCGGCCAA-1\" \"CATGAACCGACATTTG-1\" #> [190] \"CATGATGCACAATTCT-1\" \"CATGCGTTAGACAGAA-1\" \"CATGCTGGCTCCAATT-1\" #> [193] \"CATGGCAGGAAGATCG-1\" \"CATGGTCTAGATACCG-1\" \"CATTACGTCGGCCCGT-1\" #> [196] \"CATTATGCTTGTTGTG-1\" \"CCAAACAGAACCCTCG-1\" \"CCAACGATGCACTGAT-1\" #> [199] \"CCAAGACTTCTGCGAA-1\" \"CCAAGCGTAACTCGTA-1\" \"CCAAGGAACAGAGAGG-1\" #> [202] \"CCAATAGTGCCGTCGA-1\" \"CCAATTGAATGTTAAT-1\" \"CCACGAGAAGAGAATC-1\" #> [205] \"CCAGGGACGTGGCCTC-1\" \"CCATAAACAACCCGAC-1\" \"CCATAGGTTGGCGTGG-1\" #> [208] \"CCATCCATACCAAGTC-1\" \"CCATGCCTGTTTAGTA-1\" \"CCATGCTCTGCAGGAA-1\" #> [211] \"CCATTAGCGATAATCC-1\" \"CCATTCCCTGCCCACA-1\" \"CCCGACCATAGTCCGC-1\" #> [214] \"CCCGCCATGCTCCCGT-1\" \"CCCGTCAGCGTCTGAC-1\" \"CCCTCATTCTGGAATT-1\" #> [217] \"CCCTGAAATGAGTTGA-1\" \"CCGAAAGTGGTGAGCA-1\" \"CCGCCGGTCAACACAC-1\" #> [220] \"CCGGAATGGTTTCAGT-1\" \"CCGGCGCATATTGGAT-1\" \"CCGGGACCCGCAGAGA-1\" #> [223] \"CCGGGCGGTCTCGTCA-1\" \"CCGTACCCAAGCGCCA-1\" \"CCGTGCCCATGACGGC-1\" #> [226] \"CCTACGGCTCAGTCGA-1\" \"CCTACTGCTTACACTT-1\" \"CCTAGTTAGTCGCATG-1\" #> [229] \"CCTATGGGTTACCGTC-1\" \"CCTCACCAATCTTGAC-1\" \"CCTCCGACAATTCAAG-1\" #> [232] \"CCTCGAAGTGGACGGG-1\" \"CCTCGCCAGCAAATTA-1\" \"CCTCTAATCTGCCAAG-1\" #> [235] \"CCTCTCTCCCATCTAG-1\" \"CCTCTGGCCTAGACGG-1\" \"CCTGAATATTTACATA-1\" #> [238] \"CCTGCTATTTGAGAAG-1\" \"CCTGGCTAGACCCGCC-1\" \"CCTGTCACCCGGGCTC-1\" #> [241] \"CCTTCTTGATCCAGTG-1\" \"CGAACGCCCAGTGCCG-1\" \"CGAAGTTGCTCTGTGT-1\" #> [244] \"CGAGAGATGTGAACCT-1\" \"CGAGCGTTGATCAGCC-1\" \"CGAGCTGGGCTTTAGG-1\" #> [247] \"CGAGGCTAAATATGGC-1\" \"CGCAAACACGAGTTAC-1\" \"CGCAATTACTTTCGGT-1\" #> [250] \"CGCAATTAGGGTAATA-1\" \"CGCAATTCTACAATAA-1\" \"CGCATTAGCTAATAGG-1\" #> [253] \"CGCGCCCGACTTAATA-1\" \"CGCGTTCATGAAATAC-1\" \"CGCTATACCGCCCACT-1\" #> [256] \"CGCTATTCAATGTATG-1\" \"CGCTCGACATAATGAT-1\" \"CGCTCTCCGTAGATTA-1\" #> [259] \"CGCTGTGACGCCGCAC-1\" \"CGCTTCCACTGAAATC-1\" \"CGCTTTCATACCGGTG-1\" #> [262] \"CGGAGTTTGAGAGACA-1\" \"CGGCACTCAAGAAAGT-1\" \"CGGCCACGCACAAAGT-1\" #> [265] \"CGGGATCAATGTAAGA-1\" \"CGGGCAGCTAAACCGC-1\" \"CGGTGTACTTGATCCC-1\" #> [268] \"CGTACCTGATAGGCCT-1\" \"CGTAGCGAATTGTCAG-1\" \"CGTATTAAGAGATCTA-1\" #> [271] \"CGTCAGTGCGCACAAG-1\" \"CGTCTGGAAGGGCCCG-1\" \"CGTGTCCCATTCGCGA-1\" #> [274] \"CGTTGTTTCAATTCCC-1\" \"CGTTTAAGCGGAGCAC-1\" \"CGTTTCGCTCATTACA-1\" #> [277] \"CTAATTCGCACGCGCT-1\" \"CTAATTTCAACAACAC-1\" \"CTACGCACGGAGTACC-1\" #> [280] \"CTACTGCCACCTGACC-1\" \"CTAGCATAGTATAATG-1\" \"CTAGTGAAGGACAGGA-1\" #> [283] \"CTAGTTGGGCCCGGTA-1\" \"CTATCGGGTCTCAACA-1\" \"CTATGTCACTAGCCCA-1\" #> [286] \"CTATGTCTATTGAAAC-1\" \"CTCAGGACTCACCTGT-1\" \"CTCATGGCTCACAATC-1\" #> [289] \"CTCATTTGATGGGCGG-1\" \"CTCCGGCCTAATATGC-1\" \"CTCCTAAGTTATGTCT-1\" #> [292] \"CTCGAGGTCGAACAGT-1\" \"CTCGCACCTATATAGT-1\" \"CTCGGTCCGTAGCCTG-1\" #> [295] \"CTCTCACAATCGATGA-1\" \"CTCTGCGAAGCAAGCA-1\" \"CTCTGGACGCCTGGTG-1\" #> [298] \"CTCTGTTTGAGGATTC-1\" \"CTGAAAGAGATCCGAC-1\" \"CTGCACCTGGAACCGC-1\" #> [301] \"CTGGAAATGGATGCTT-1\" \"CTGTATGGTGTAGAAA-1\" \"CTGTTCACTGCCTGTG-1\" #> [304] \"CTGTTCATCTCACGGG-1\" \"CTTAACTTCGAAGTAC-1\" \"CTTACACGGTATTCCA-1\" #> [307] \"CTTACACTGGGAAATA-1\" \"CTTATGTTGACTACCA-1\" \"CTTCATAGCTCAAGAA-1\" #> [310] \"CTTCTTACGTCGTATA-1\" \"CTTGTACTTGTTGACT-1\" \"CTTGTTTATGTAGCCA-1\" #> [313] \"CTTTAACTTTCAAAGG-1\" \"CTTTGGCTTTAGTAAA-1\" \"GAAACAGCCATGCAGT-1\" #> [316] \"GAAACTCTAATGAAGG-1\" \"GAAAGTGACTAACTGC-1\" \"GAAATCGCGCGCAACT-1\" #> [319] \"GAAATGGCGGTGTTAG-1\" \"GAAATTCACATCGCTG-1\" \"GAACACACATCAACCA-1\" #> [322] \"GAACGACCGAATGATA-1\" \"GAAGAACGGTGCAGGT-1\" \"GAAGCGTGAGGAATTT-1\" #> [325] \"GAAGCTTGCTGACCGC-1\" \"GAAGTGCTGGATAGCT-1\" \"GAATCGACATGGTCAC-1\" #> [328] \"GAATCGCCGGACACGG-1\" \"GAATGTTGGGTAATCT-1\" \"GAATTATAGTGAAAGG-1\" #> [331] \"GAATTTCTCGCTGCAG-1\" \"GACAACGCAGCTTACG-1\" \"GACACAAGGGAAGAAA-1\" #> [334] \"GACCAGAGCCCTGTAG-1\" \"GACGCCTGTTGCAGGG-1\" \"GACGTGTAGGGATTAT-1\" #> [337] \"GACTAAGATCATGCAC-1\" \"GACTAAGTAGGCTCAC-1\" \"GAGACTGATGGGTAGA-1\" #> [340] \"GAGATCTGCTTGGCAT-1\" \"GAGATCTGTCACTCCG-1\" \"GAGCATCATCCCTGGG-1\" #> [343] \"GAGCGAGGGAGTACCG-1\" \"GAGCTCTCGGACCTAA-1\" \"GAGGAATGGAGAGGTT-1\" #> [346] \"GAGGCTATCAAAGTCG-1\" \"GAGGGCATCGCGTATC-1\" \"GAGGTACATCCATCTT-1\" #> [349] \"GAGTACGGGTATACAA-1\" \"GATAAATCGGTGGATG-1\" \"GATATCTCATGCAATA-1\" #> [352] \"GATCATTCCAAACATT-1\" \"GATCCCTTTATACTGC-1\" \"GATCGACACTATCTGA-1\" #> [355] \"GATCGGTGGCCATAAC-1\" \"GATGCTACAAGCGCCT-1\" \"GATGGCGCACACATTA-1\" #> [358] \"GATGTTTGTGCGAGAT-1\" \"GATTCCCTTGTCGCAG-1\" \"GATTCCGCGTTTCCGT-1\" #> [361] \"GCAAATATTACGCTTT-1\" \"GCAAGTGCACAGAGAA-1\" \"GCACTAGTCGCGCTAT-1\" #> [364] \"GCAGGACTATAGAATA-1\" \"GCATCCCTAACTTTGA-1\" \"GCCCACCAAGGCTGTC-1\" #> [367] \"GCCCAGTTGGTATGCC-1\" \"GCCCGCGCGTTTGACA-1\" \"GCCGAAATTCCTACGT-1\" #> [370] \"GCCTAGCGATCTGACC-1\" \"GCCTATTCCGATATAG-1\" \"GCCTTCAGCCCTACCG-1\" #> [373] \"GCGAAGCCATACCCGT-1\" \"GCGAGTTCTGCAAAGA-1\" \"GCGCTAATTGAATAGA-1\" #> [376] \"GCGGGAACCAGGCCCT-1\" \"GCGGTCCCTAGACGCA-1\" \"GCGTCGAAATGTCGGT-1\" #> [379] \"GCTAATACCGAATGCC-1\" \"GCTAGTTTCATTGAGG-1\" \"GCTCTAAACCCTGACG-1\" #> [382] \"GCTCTATGTTACGTGC-1\" \"GCTCTCGGGTACCGAA-1\" \"GCTGCTCTCCGGACAC-1\" #> [385] \"GCTGGCATATTCACCT-1\" \"GCTTGATGATAATCAG-1\" \"GGAGAAGTCATTGGCA-1\" #> [388] \"GGAGTGCCGCCCTGGA-1\" \"GGATTCAGTACGGTGG-1\" \"GGCAATAGTCAATGAG-1\" #> [391] \"GGCACTCCACTGGGCA-1\" \"GGCATACAGGTAGCGG-1\" \"GGCGGAGTAATATTAG-1\" #> [394] \"GGCGGTAGGATCATTG-1\" \"GGCGTCCTATCCGCTG-1\" \"GGCTATTAAGTTGTAT-1\" #> [397] \"GGCTCGTGCCACCAGC-1\" \"GGCTCTGCTCCAACGC-1\" \"GGCTGGCTAGCTTAAA-1\" #> [400] \"GGGACTGCATAGATAG-1\" \"GGGAGAACTCACAGTA-1\" \"GGGAGTTAATGAGGCG-1\" #> [403] \"GGGCGATATGTGTGAA-1\" \"GGGCGGTCCTATTGTC-1\" \"GGGCGTACATTTATAT-1\" #> [406] \"GGGCTGCCTAGGGCGA-1\" \"GGGCTGGTTAGTCGCG-1\" \"GGGTATGTATGCACTT-1\" #> [409] \"GGGTCACCGTGACGGT-1\" \"GGGTGTTTCAGCTATG-1\" \"GGTAACTATGTATCTG-1\" #> [412] \"GGTAGTGCTCGCACCA-1\" \"GGTATTGCCGAGTTTA-1\" \"GGTCGGTAATTAGACA-1\" #> [415] \"GGTGAGATGCAGATAA-1\" \"GGTGCGGATAAGTGGC-1\" \"GGTTAGGCTTGGAGAA-1\" #> [418] \"GGTTTACAATCTCAAT-1\" \"GGTTTGAGTGCTGGAA-1\" \"GTAAGCGGGCAGTCAG-1\" #> [421] \"GTAAGTAGGGTATACC-1\" \"GTACGAGATTGCGACA-1\" \"GTACTAAGATTTGGAG-1\" #> [424] \"GTACTGAGGTCGTAAC-1\" \"GTACTGCATGAAGCGT-1\" \"GTACTTGGGCACTTCT-1\" #> [427] \"GTAGACGTCGTTACAT-1\" \"GTATAGGACTCAGTAG-1\" \"GTATCAGCTTGGGTTC-1\" #> [430] \"GTCAAAGTTTACATAG-1\" \"GTCACTCTCCAAATCT-1\" \"GTCAGAATAGTCTATG-1\" #> [433] \"GTCATGCACCTCCGTT-1\" \"GTCATGGACATGACTA-1\" \"GTCCCAACGTAAAGTA-1\" #> [436] \"GTCCGGCTGAATTGCG-1\" \"GTCGGATATCTCAGAC-1\" \"GTCGTCAATTATAAGG-1\" #> [439] \"GTGAAACGTGCTCCAC-1\" \"GTGCAACAAATGTGGC-1\" \"GTGCACGAAAGTGACT-1\" #> [442] \"GTGCGGGTCTCCAAAT-1\" \"GTGCTCAAGTACTGTC-1\" \"GTGGACGTGCTGAGAC-1\" #> [445] \"GTGGGCTTAGACACAC-1\" \"GTTCACAGGAGTCTAG-1\" \"GTTCCAGTCTGACCAT-1\" #> [448] \"GTTCTTCCCTCGATGT-1\" \"GTTGCACGGAGTTTCG-1\" \"GTTGTCGTGTTAGTTG-1\" #> [451] \"GTTTCCTGGAGGGTGA-1\" \"GTTTGACCAAATCCTA-1\" \"GTTTGGCCGCTCAGCG-1\" #> [454] \"TAAATGAATCCGTTTC-1\" \"TAACAAAGGGAGAAGC-1\" \"TAACGCTTTGAGAGCG-1\" #> [457] \"TAACTATCGAAGGTCC-1\" \"TAACTCCATGGAGGCT-1\" \"TAAGGAACTTGTGGGA-1\" #> [460] \"TAAGGCAACATAAGAT-1\" \"TAATACACAGTAGTAT-1\" \"TAATATTGAAATTCGC-1\" #> [463] \"TACAAGTCTCGTGCAT-1\" \"TACCAGCTAGGTTTAA-1\" \"TACCTCACGCTTGTAC-1\" #> [466] \"TACGAACACGACTTCA-1\" \"TACGAGAACTTCACGT-1\" \"TACGATGTTGATCATC-1\" #> [469] \"TACGTGCACTATGCTG-1\" \"TAGAGCTACGAAGAAC-1\" \"TAGAGTCTAAGCGAAC-1\" #> [472] \"TAGCTAAGTCCGGGAG-1\" \"TAGGGTGTTTCAAGAG-1\" \"TAGGTGAGCCCTACTC-1\" #> [475] \"TAGGTTCGAGTTCGTC-1\" \"TAGTGCCCTCCAGAGT-1\" \"TAGTTTATTCTTGCTT-1\" #> [478] \"TATAAATCCACAAGCT-1\" \"TATAAGTGAGGATAGC-1\" \"TATACACGCAAAGTAT-1\" #> [481] \"TATCCATATCATGCGA-1\" \"TATCCTGCATGGGAAT-1\" \"TATCGATGATTAAACG-1\" #> [484] \"TATGCTCCCTACTTAC-1\" \"TATGGATGTGCTACGC-1\" \"TATGGCCCGGCCTCGC-1\" #> [487] \"TATGGGTACGTATCGT-1\" \"TATTCAATTCTAATCC-1\" \"TATTCGTGCCAGAATA-1\" #> [490] \"TATTTAGTCTAGATCG-1\" \"TATTTGTTACCCTTTA-1\" \"TCAAACAACCGCGTCG-1\" #> [493] \"TCAAACTTAGATTGTT-1\" \"TCAACACATTGGGTAA-1\" \"TCAACCATGTTCGGGC-1\" #> [496] \"TCACAGGTTATTGGGC-1\" \"TCACGCATTGTAGATC-1\" \"TCACGGTCATCGCACA-1\" #> [499] \"TCAGCAAATGCATCTC-1\" \"TCAGGGTGTAACGTAA-1\" \"TCAGGTTCTTTGAGAA-1\" #> [502] \"TCAGTACTGACCCGCG-1\" \"TCATCACTCGAGCTCG-1\" \"TCATCCCAGAGGGTGG-1\" #> [505] \"TCCACAATGGTTTACG-1\" \"TCCAGGCGAGTACGGT-1\" \"TCCCAAAGACGAAGGA-1\" #> [508] \"TCCCAGCTTTAGTCTG-1\" \"TCCCAGGCTTAGCTAA-1\" \"TCCCGCGTACTCCTGG-1\" #> [511] \"TCCCGGGTGTGCTGCT-1\" \"TCCCGTCAGTCCCGCA-1\" \"TCCCTGGCTCGCTGGA-1\" #> [514] \"TCCGATAATTGCCATA-1\" \"TCCGATGACTGAGCTC-1\" \"TCCGATGGTGCGACAT-1\" #> [517] \"TCCGATTACATTGCCG-1\" \"TCCTCTACGAGATGGC-1\" \"TCCTTCAGTGGTCGAA-1\" #> [520] \"TCCTTTCTTACGCTTA-1\" \"TCGAAATTTAGGACCA-1\" \"TCGCATCCCTAAGTGT-1\" #> [523] \"TCGCCGGTCGATCCGT-1\" \"TCGCGTCCAGAAGGTC-1\" \"TCGCTCGATATATTCC-1\" #> [526] \"TCGCTGGGCGGATTGT-1\" \"TCGCTGTGCGTAAATC-1\" \"TCGGAATGCGCTCTGA-1\" #> [529] \"TCGGAGTACATGAGTA-1\" \"TCGTATAGTGCAATTA-1\" \"TCGTCCGCTGGCGTCT-1\" #> [532] \"TCTACCGTCCACAAGC-1\" \"TCTAGCATCTTCGATG-1\" \"TCTAGTTATCAGAAGA-1\" #> [535] \"TCTATCATGCAGTTAC-1\" \"TCTATCGGTCGCAACA-1\" \"TCTATTACGCTGGCGA-1\" #> [538] \"TCTCTAATAGCTGGTA-1\" \"TCTGAACCGGTCGGCT-1\" \"TCTTACAGAGGTACCG-1\" #> [541] \"TCTTACGGCATCCGAC-1\" \"TCTTCGATACCAATAA-1\" \"TCTTGATGCGTAGCGA-1\" #> [544] \"TCTTGGTAACACCAAA-1\" \"TGAAACTTATGCAAGC-1\" \"TGACCCACGTTAGACA-1\" #> [547] \"TGAGAATGCTTTACCG-1\" \"TGATCGGTTTGACCCT-1\" \"TGATCTCCGGCGCCAG-1\" #> [550] \"TGATTCGTCTATCACT-1\" \"TGATTTCCTCCTGACG-1\" \"TGCAAGAATGACGTAA-1\" #> [553] \"TGCAGGATCGGCAAAG-1\" \"TGCATGGATCGGATCT-1\" \"TGCCACCTGGCGAAAC-1\" #> [556] \"TGCCTGATCAAACGAT-1\" \"TGCGCAAAGCATTTGG-1\" \"TGCGCGATTAACGGAG-1\" #> [559] \"TGCGGAGTAAAGGTGC-1\" \"TGCGGCATAGTTCAAC-1\" \"TGCGGTGAAATTTCAT-1\" #> [562] \"TGCTGGTTGGACAATT-1\" \"TGGAAGACGAACACCA-1\" \"TGGAAGGATAAAGATG-1\" #> [565] \"TGGAGTGATGCGATGA-1\" \"TGGCCAAACTGAAGTA-1\" \"TGGCCGTATATTGACC-1\" #> [568] \"TGGCTTTGGGTAGACA-1\" \"TGGGAAATGCCTTTCC-1\" \"TGGGCACGTTCTATGG-1\" #> [571] \"TGGGCCACAAGAGCGC-1\" \"TGGTTCGTAGCAAAGG-1\" \"TGTAGTGATCTATAAT-1\" #> [574] \"TGTCCCGACATAGCAC-1\" \"TGTCCTAAGTCACCGC-1\" \"TGTCTACAGTTTCTGT-1\" #> [577] \"TGTGACTACGCCAGTC-1\" \"TGTGTCGCGAGTTGCA-1\" \"TGTTCTTCCATTGACT-1\" #> [580] \"TGTTTCGGTACTTCTC-1\" \"TTAACCAACCCTCCCT-1\" \"TTAAGCGCCTGACCCA-1\" #> [583] \"TTAATCAGTACGTCAG-1\" \"TTAATGTAGACCAGGT-1\" \"TTAATTTCAGACGCGG-1\" #> [586] \"TTACAACTACGCATCC-1\" \"TTACATCGTGGCCTGG-1\" \"TTACCATTGATTACCC-1\" #> [589] \"TTAGCAACATGGATGT-1\" \"TTATATTTGGCAATCC-1\" \"TTATCCAATCGAACTC-1\" #> [592] \"TTATCTGTATCATAAC-1\" \"TTATGACAAACTGGAT-1\" \"TTATTAGGGAAGCATC-1\" #> [595] \"TTCAAAGTCTCTAGCC-1\" \"TTCAACGACCCGACCG-1\" \"TTCAAGCCGAGCTGAG-1\" #> [598] \"TTCATGGCGCAACAGG-1\" \"TTCCTCGAGGGTGTCT-1\" \"TTCGACGGGAAGGGCG-1\" #> [601] \"TTCGCACTCGCGTGCT-1\" \"TTCGTACTCCAGAACG-1\" \"TTCTACTTGCGAGGGC-1\" #> [604] \"TTCTAGGCCAATTGTG-1\" \"TTCTTAGTGAACGGTG-1\" \"TTCTTAGTGGCTCAGA-1\" #> [607] \"TTCTTGTAACCTAATG-1\" \"TTGAAGAATTCCCAGG-1\" \"TTGAATATGGACTTTC-1\" #> [610] \"TTGATCTAACTTTGTC-1\" \"TTGATTATGCAGATGA-1\" \"TTGCACGGAGCAGCAC-1\" #> [613] \"TTGCTCCCATACCGGA-1\" \"TTGCTGAAGGAACCAC-1\" \"TTGCTGATCATGTTCG-1\" #> [616] \"TTGGATTGGGTACCAC-1\" \"TTGGCTCGCATGAGAC-1\" \"TTGGGACACTGCCCGC-1\" #> [619] \"TTGGGCGGCGGTTGCC-1\" \"TTGTAATCCGTACTCG-1\" \"TTGTATCACACAGAAT-1\" #> [622] \"TTGTCGTTCAGTTACC-1\" \"TTGTGGCCCTGACAGT-1\" \"TTGTTCAGTGTGCTAC-1\" spatIDs(g, subset = nr_feats <= 200) #>  [1] \"GTCGTCAATTATAAGG-1\" \"TCGTATAGTGCAATTA-1\" \"GAGTACGGGTATACAA-1\" #>  [4] \"TCTTACAGAGGTACCG-1\" \"GTTGTCGTGTTAGTTG-1\" \"GTACTTGGGCACTTCT-1\" #>  [7] \"CGCTATTCAATGTATG-1\" \"AATGGTTCTCACAAGC-1\" \"CTTCATAGCTCAAGAA-1\" #> [10] \"CAACGGTTCTTGATAC-1\" \"ACACCCGAGAAATCCG-1\" \"CACTGTCCAAGTGAGA-1\" #> [13] \"CATAGTAGCATAGTAG-1\" \"CAACTCCTTGATCCCG-1\" \"AAGTAGAAGACCGGGT-1\" #> [16] \"TACGTGCACTATGCTG-1\" \"GTATCAGCTTGGGTTC-1\" \"TAACAAAGGGAGAAGC-1\" #> [19] \"TTACATCGTGGCCTGG-1\" \"TCTGAACCGGTCGGCT-1\" \"TATAAGTGAGGATAGC-1\" #> [22] \"TGCTGGTTGGACAATT-1\" \"TATAAATCCACAAGCT-1\" \"CGCTCGACATAATGAT-1\" #> [25] \"TTCAACGACCCGACCG-1\" \"GTCACTCTCCAAATCT-1\" \"TTCTACTTGCGAGGGC-1\" #> [28] \"CTGTTCATCTCACGGG-1\" \"TTCTTGTAACCTAATG-1\" \"GCTTGATGATAATCAG-1\" #> [31] \"TTGGCTCGCATGAGAC-1\" \"GCCCAGTTGGTATGCC-1\" \"TCGTCCGCTGGCGTCT-1\" #> [34] \"TTCTAGGCCAATTGTG-1\" \"ATGAAGCCAAGGAGCC-1\" \"CCCGTCAGCGTCTGAC-1\" #> [37] \"GACTAAGATCATGCAC-1\" \"TGGTTCGTAGCAAAGG-1\" \"CTGTTCACTGCCTGTG-1\" #> [40] \"CGTACCTGATAGGCCT-1\" \"GAATGTTGGGTAATCT-1\" \"CACACAGGGATAGATT-1\" #> [43] \"TAACTATCGAAGGTCC-1\" \"GGGCGTACATTTATAT-1\" \"ATCGCACGCCGGGAGA-1\" #> [46] \"TATGCTCCCTACTTAC-1\" \"TCCTCTACGAGATGGC-1\" \"TTGATTATGCAGATGA-1\" #> [49] \"GTAAGTAGGGTATACC-1\" \"CGCAAACACGAGTTAC-1\" \"TGGCCGTATATTGACC-1\" #> [52] \"ACTGTAGCACTTTGGA-1\" \"GCTCTCGGGTACCGAA-1\" \"CACCGCCAGAAGGTTT-1\" #> [55] \"TCCCAAAGACGAAGGA-1\" \"TTATATTTGGCAATCC-1\" \"AGCACCAGTACTCACG-1\" #> [58] \"CGTGTCCCATTCGCGA-1\" \"GATCCCTTTATACTGC-1\" \"ATAGGTTGGGCAGATG-1\" #> [61] \"CAATTAAGGGTGATGA-1\" \"TCGCGTCCAGAAGGTC-1\" \"GGCGTCCTATCCGCTG-1\" #> [64] \"TCAGCAAATGCATCTC-1\" \"GAGATCTGTCACTCCG-1\" \"CAGCTTAGTAGGTAGC-1\" #> [67] \"CGAAGTTGCTCTGTGT-1\" \"CTCTGGACGCCTGGTG-1\" \"AGGGTTTAGTTCGGGA-1\" #> [70] \"CTCTCACAATCGATGA-1\" \"TCGGAGTACATGAGTA-1\" \"TTACCATTGATTACCC-1\" #> [73] \"CCTCTCTCCCATCTAG-1\" \"GCGCTAATTGAATAGA-1\" \"GGTAGTGCTCGCACCA-1\" #> [76] \"AAGCTCGTGCCAAGTC-1\" spatIDs(g, subset = Dim.1 > 25, dim_reduction_to_use = \"umap\") #>  [1] \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" \"AAGGCTGTGCTCATCG-1\" #>  [4] \"ACCACAAGTTTCTATC-1\" \"ACCTAATCGACTTCCT-1\" \"ACTTGGGACCCGGTGG-1\" #>  [7] \"AGTTCCTACAGAATTA-1\" \"ATATTTAACCCTCAAG-1\" \"ATTGAAGATCTTAGTG-1\" #> [10] \"CAAACGGTCGCACTTT-1\" \"CAGCTCACTGAGACAT-1\" \"CCAACGATGCACTGAT-1\" #> [13] \"CCATTCCCTGCCCACA-1\" \"CCTCCGACAATTCAAG-1\" \"CGAAGTTGCTCTGTGT-1\" #> [16] \"CGCTCTCCGTAGATTA-1\" \"CGGGCAGCTAAACCGC-1\" \"CGTTTCGCTCATTACA-1\" #> [19] \"CTTACACGGTATTCCA-1\" \"CTTTGGCTTTAGTAAA-1\" \"GAAATGGCGGTGTTAG-1\" #> [22] \"GAAGCTTGCTGACCGC-1\" \"GCAGGACTATAGAATA-1\" \"GGCACTCCACTGGGCA-1\" #> [25] \"GGGCTGGTTAGTCGCG-1\" \"GTTCACAGGAGTCTAG-1\" \"TACGAACACGACTTCA-1\" #> [28] \"TACGAGAACTTCACGT-1\" \"TATGGGTACGTATCGT-1\" \"TCCAGGCGAGTACGGT-1\" #> [31] \"TCCCAGCTTTAGTCTG-1\" \"TCGAAATTTAGGACCA-1\" \"TTGATCTAACTTTGTC-1\"  featIDs(g) #>   [1] \"Gna12\"         \"Ccnd2\"         \"Btbd17\"        \"Sox9\"          #>   [5] \"Sez6\"          \"Serpinf1\"      \"S100a6\"        \"Col1a1\"        #>   [9] \"Vwf\"           \"Esam\"          \"Npas1\"         \"Tiam1\"         #>  [13] \"Bcam\"          \"Hmgn2\"         \"Rab3b\"         \"Inmt\"          #>  [17] \"Ddr1\"          \"Homer3\"        \"Cp\"            \"Calb2\"         #>  [21] \"Man1a\"         \"Efnb3\"         \"Hlf\"           \"Gstm7\"         #>  [25] \"Cavin1\"        \"Sst\"           \"Hapln2\"        \"Hspb1\"         #>  [29] \"Ndrg1\"         \"Nid1\"          \"Kit\"           \"Pvalb\"         #>  [33] \"Tmbim1\"        \"Crip1\"         \"Tek\"           \"Elovl1\"        #>  [37] \"Cyba\"          \"Itih3\"         \"Cnp\"           \"Hap1\"          #>  [41] \"Clic1\"         \"Stx1a\"         \"Arpp19\"        \"Dio2\"          #>  [45] \"Id3\"           \"Crlf1\"         \"Ttc9b\"         \"Carhsp1\"       #>  [49] \"Cabp7\"         \"Fam163b\"       \"Rarres2\"       \"Syn2\"          #>  [53] \"Ick\"           \"Prox1\"         \"Adssl1\"        \"Vipr2\"         #>  [57] \"Gltp\"          \"Amotl1\"        \"Bcas1\"         \"Aldh1a2\"       #>  [61] \"Tppp3\"         \"Sirt2\"         \"Lpl\"           \"Cers2\"         #>  [65] \"Qdpr\"          \"Stk32c\"        \"Lbp\"           \"Hsd11b1\"       #>  [69] \"Vtn\"           \"Stac2\"         \"Plxdc1\"        \"Igfbp4\"        #>  [73] \"Dbndd2\"        \"Pltp\"          \"Slc12a4\"       \"Cadps2\"        #>  [77] \"Erbb3\"         \"Pmp22\"         \"Kcnab3\"        \"Myh11\"         #>  [81] \"Plod1\"         \"Etnppl\"        \"Arhgef25\"      \"Rcn3\"          #>  [85] \"Vip\"           \"Utrn\"          \"Grm1\"          \"Reep3\"         #>  [89] \"Fabp7\"         \"Dcn\"           \"Slc17a8\"       \"Dusp6\"         #>  [93] \"Kitl\"          \"Ccn2\"          \"Timp3\"         \"Ascl1\"         #>  [97] \"Unc5b\"         \"Vsir\"          \"Gamt\"          \"Ptprb\"         #> [101] \"Csrp2\"         \"Adarb1\"        \"Rnf130\"        \"Nefh\"          #> [105] \"Aebp1\"         \"Sept4\"         \"Gria1\"         \"Sypl\"          #> [109] \"Arsg\"          \"Cacng4\"        \"Rab37\"         \"Itgb4\"         #> [113] \"Aspa\"          \"Cygb\"          \"Rflnb\"         \"Doc2b\"         #> [117] \"Gfap\"          \"Npas3\"         \"Serpina3n\"     \"Clmn\"          #> [121] \"Prkch\"         \"Fbln5\"         \"Akr1c18\"       \"Gng4\"          #> [125] \"Sema4d\"        \"Cxcl14\"        \"Hexb\"          \"Iqgap2\"        #> [129] \"Crhbp\"         \"Rab3c\"         \"Thbs4\"         \"Serinc5\"       #> [133] \"Erbin\"         \"Prkcd\"         \"Pdlim2\"        \"Ednrb\"         #> [137] \"Cpne6\"         \"Sema5a\"        \"Matn2\"         \"Nptxr\"         #> [141] \"Enpp2\"         \"Efcab6\"        \"Ppp1r1a\"       \"Litaf\"         #> [145] \"Il1rap\"        \"Apod\"          \"Cpox\"          \"Grik1\"         #> [149] \"Clic6\"         \"Nr4a1\"         \"Igfbp6\"        \"Sncg\"          #> [153] \"Gzma\"          \"Grm2\"          \"Prph\"          \"Rsph1\"         #> [157] \"Sox8\"          \"Fam234a\"       \"Lims2\"         \"Aqp4\"          #> [161] \"Slc12a2\"       \"Cd74\"          \"Pdgfrb\"        \"Csf1r\"         #> [165] \"Cbln2\"         \"Frmd8\"         \"Gldc\"          \"Tcf7l2\"        #> [169] \"Bhlhe22\"       \"Kcnip2\"        \"Alas2\"         \"Gdf11\"         #> [173] \"Baiap2\"        \"Ifitm3\"        \"Phkg1\"         \"Nptx1\"         #> [177] \"Pde8a\"         \"Itih5\"         \"Homer2\"        \"Fam20c\"        #> [181] \"Cplx2\"         \"Myo5b\"         \"Snca\"          \"Col3a1\"        #> [185] \"Ecrg4\"         \"Map4k4\"        \"2010300C02Rik\" \"Ogfrl1\"        #> [189] \"Fn1\"           \"Efhd1\"         \"Ngef\"          \"Bok\"           #> [193] \"Tmem163\"       \"Lct\"           \"Cfh\"           \"Ptpn4\"         #> [197] \"Tnni1\"         \"Csrp1\"         \"Nfasc\"         \"Syt2\"          #> [201] \"Atp2b4\"        \"Rgs16\"         \"Ncf2\"          \"Cnih3\"         #> [205] \"Tmem63a\"       \"Cfap126\"       \"Meig1\"         \"Ccdc3\"         #> [209] \"Rgs5\"          \"Enkur\"         \"Myoc\"          \"Vim\"           #> [213] \"Prkcq\"         \"Gad2\"          \"Lcn2\"          \"Nr4a2\"         #> [217] \"Ermn\"          \"Fibcd1\"        \"Gsn\"           \"Grb14\"         #> [221] \"Notch1\"        \"Ube2l6\"        \"Gatm\"          \"Cd82\"          #> [225] \"Mdk\"           \"Lamp5\"         \"Itpka\"         \"Chgb\"          #> [229] \"Mal\"           \"Pdyn\"          \"Nkx2-2\"        \"Edn3\"          #> [233] \"Car2\"          \"Col9a3\"        \"Chrna4\"        \"Gss\"           #> [237] \"Slc7a11\"       \"Tm4sf1\"        \"Kcnab1\"        \"Shox2\"         #> [241] \"Serpini1\"      \"Tspan2\"        \"S100a11\"       \"Vcam1\"         #> [245] \"Lef1\"          \"Npy2r\"         \"F3\"            \"Calb1\"         #> [249] \"Epha7\"         \"Slc44a1\"       \"1110017D15Rik\" \"Tpm2\"          #> [253] \"Slc6a9\"        \"Laptm5\"        \"Sema3c\"        \"Hpca\"          #> [257] \"Padi2\"         \"Slc4a2\"        \"Gabrd\"         \"Rgs12\"         #> [261] \"Slc30a3\"       \"Emilin1\"       \"1700001C02Rik\" \"Gabra4\"        #> [265] \"Pdgfra\"        \"Epha5\"         \"Tesc\"          \"Pitpnm2\"       #> [269] \"Mmp17\"         \"Cit\"           \"Foxp2\"         \"Arpc1b\"        #> [273] \"Col1a2\"        \"Eln\"           \"Pcolce\"        \"Tsc22d4\"       #> [277] \"Cald1\"         \"Ccdc136\"       \"Npy\"           \"Slc13a4\"       #> [281] \"Gkn3\"          \"Slc6a13\"       \"Mgp\"           \"Lmo3\"          #> [285] \"Slco1c1\"       \"Cpne9\"         \"Itpr2\"         \"Slc6a11\"       #> [289] \"Vamp1\"         \"Cd9\"           \"Pglyrp1\"       \"Slc17a6\"       #> [293] \"Sipa1l3\"       \"Sh3gl3\"        \"Plekhb1\"       \"Nupr1\"         #> [297] \"Dkk3\"          \"Cox6a2\"        \"Dkkl1\"         \"Fgfr2\"         #> [301] \"Crym\"          \"Slc38a5\"       \"Flna\"          \"Bgn\"           #> [305] \"Col4a1\"        \"Plat\"          \"Nr3c2\"         \"Cbln1\"         #> [309] \"Gab1\"          \"Pllp\"          \"Necab2\"        \"Dbndd1\"        #> [313] \"Agt\"           \"Cryab\"         \"Tagln\"         \"Mcam\"          #> [317] \"Olfm2\"         \"Icam5\"         \"Anxa2\"         \"Rora\"          #> [321] \"Calml4\"        \"Htr3a\"         \"Paqr5\"         \"Rasgrf1\"       #> [325] \"Zic1\"          \"Mobp\"          \"Hhatl\"         \"Trf\"           #> [329] \"Cpne4\"         \"Cdhr4\"         \"Cd59a\"         \"Gng11\"         #> [333] \"Chrm1\"         \"Prr5l\"         \"Ugt8a\"         \"Rims3\"         #> [337] \"Sgpp2\"         \"Camkv\"         \"Sox10\"         \"Micall1\"       #> [341] \"Tie1\"          \"Fa2h\"          \"Ucp2\"          \"Vav3\"          #> [345] \"Ccp110\"        \"Gria2\"         \"Rasl10a\"       \"Foxj1\"         #> [349] \"Trim59\"        \"Dynlrb2\"       \"Gjc1\"          \"Neurod1\"       #> [353] \"Ttyh2\"         \"Cpne7\"         \"Nrip3\"         \"Tbr1\"          #> [357] \"Lcat\"          \"Tmem98\"        \"Myo1d\"         \"Prdm8\"         #> [361] \"Tgfbi\"         \"Kcnc2\"         \"Thrsp\"         \"Isg15\"         #> [365] \"Acta2\"         \"H2-Q4\"         \"Dock4\"         \"Myrf\"          #> [369] \"Lmo1\"          \"Igfbp7\"        \"P2ry12\"        \"Pcdh8\"         #> [373] \"Lgi4\"          \"Fxyd1\"         \"Fxyd7\"         \"Mag\"           #> [377] \"Zcchc12\"       \"Anln\"          \"Wnt4\"          \"C1ql2\"         #> [381] \"Unc93b1\"       \"Tspan15\"       \"Ppp1r14a\"      \"Clic4\"         #> [385] \"Galnt6\"        \"Ccn3\"          \"Rims2\"         \"Zmat4\"         #> [389] \"Cldn11\"        \"Ccdc33\"        \"Slc32a1\"       \"Tgm2\"          #> [393] \"Vstm2l\"        \"Neurod6\"       \"Crygn\"         \"Enpp6\"         #> [397] \"Neurod2\"       \"Satb2\"         \"Pcp4l1\"        \"Txnip\"         #> [401] \"Egr1\"          \"Otud7b\"        \"Car14\"         \"Rgs4\"          #> [405] \"Dock10\"        \"Lpar1\"         \"Trps1\"         \"Ptpn3\"         #> [409] \"Lefty1\"        \"Zfhx3\"         \"St6galnac5\"    \"Ak5\"           #> [413] \"Hrh3\"          \"Nexn\"          \"Adgrl4\"        \"Rlbp1\"         #> [417] \"Igfbp2\"        \"Wfs1\"          \"Cplx3\"         \"Orai2\"         #> [421] \"Olig2\"         \"Gpr37\"         \"Plcb4\"         \"Nxph4\"         #> [425] \"Ndufa4l2\"      \"Cacng5\"        \"Plekhg1\"       \"Cmtm5\"         #> [429] \"Gpr161\"        \"Rfx3\"          \"Igsf21\"        \"Ramp3\"         #> [433] \"Arhgap12\"      \"Nkx6-2\"        \"Ninj2\"         \"Cldn5\"         #> [437] \"Htr2c\"         \"Hspb8\"         \"Fmod\"          \"Prelp\"         #> [441] \"Mpped1\"        \"Rapgef5\"       \"Vwa1\"          \"Stab1\"         #> [445] \"Arl15\"         \"Reln\"          \"Mustn1\"        \"Pbxip1\"        #> [449] \"Dnali1\"        \"Id1\"           \"Lrrtm3\"        \"Tmem212\"       #> [453] \"Epop\"          \"Gjc2\"          \"1190005I06Rik\" \"Ctla2a\"        #> [457] \"Cnr1\"          \"Gpr4\"          \"Sowaha\"        \"Tent5c\"        #> [461] \"Serpinb1a\"     \"S1pr5\"         \"Penk\"          \"Cdc42ep2\"      #> [465] \"Slitrk6\"       \"Hpcal4\"        \"Olig1\"         \"Rprml\"         #> [469] \"Stxbp6\"        \"Hs3st2\"        \"Rbp1\"          \"Ppm1e\"         #> [473] \"Sox18\"         \"Kctd4\"         \"Nxph3\"         \"Vat1l\"         #> [477] \"Cd24a\"         \"Odf3b\"         \"Gjb1\"          \"Selplg\"        #> [481] \"Bcl11b\"        \"Lhfp\"          \"Ranbp3l\"       \"Msx1\"          #> [485] \"Zdhhc22\"       \"Phldb1\"        \"Ctxn1\"         \"Tprn\"          #> [489] \"Vstm2a\"        \"Ndnf\"          \"Pdp1\"          \"Scn3b\"         #> [493] \"Cdc42ep1\"      \"Gal3st1\"       \"Rasd1\"         \"Spink8\"        #> [497] \"Opalin\"        \"Gja4\"          \"Synpo2\"        \"Pcdh20\"        #> [501] \"Adra1b\"        \"Fam131a\"       \"Tmem125\"       \"Mb21d2\"        #> [505] \"Lingo3\"        \"Ncald\"         \"Siglech\"       \"Rgs14\"         #> [509] \"Gm14964\"       \"Gpr17\"         \"Cx3cr1\"        \"Ezr\"           #> [513] \"Adarb2\"        \"Cpne8\"         \"Plekhg3\"       \"Lamb2\"         #> [517] \"Creb5\"         \"Cntn2\"         \"Aldh1a1\"       \"Phgdh\"         #> [521] \"Tnfaip6\"       \"Camk2d\"        \"Shisa6\"        \"Cthrc1\"        #> [525] \"Tmem119\"       \"Hmgb2\"         \"Tmem158\"       \"Dsp\"           #> [529] \"Lrtm2\"         \"Gabra5\"        \"Tns1\"          \"Nell1\"         #> [533] \"Slain1\"        \"Prr18\"         \"S100a8\"        \"S100a9\"        #> [537] \"Col8a2\"        \"Synpr\"         \"Sertm1\"        \"Adgrf5\"        #> [541] \"Capg\"          \"Gjc3\"          \"Fcer1g\"        \"Pde1a\"         #> [545] \"Tafa1\"         \"Ddn\"           \"Hopx\"          \"Ptk2b\"         #> [549] \"Rgs3\"          \"Kcng2\"         \"Ntng1\"         \"H2-Q7\"         #> [553] \"Ifitm2\"        \"Plaat3\"        \"Plekhh1\"       \"Myl4\"          #> [557] \"H2-K1\"         \"Dpp6\"          \"Tmem91\"        \"Cyp2d22\"       #> [561] \"Ttr\"           \"Suclg2\"        \"Patj\"          \"Btbd3\"         #> [565] \"Unc13c\"        \"Syt9\"          \"Shisal1\"       \"Grm4\"          #> [569] \"Sox11\"         \"Slc22a8\"       \"Slc24a3\"       \"Klk8\"          #> [573] \"Ipcef1\"        \"Tnnt1\"         \"Hhip\"          \"Spag8\"         #> [577] \"Fxyd6\"         \"Ppp1r3c\"       \"Cbln4\"         \"Nnat\"          #> [581] \"Myl9\"          \"Vxn\"           \"Lgals1\"        \"Gpr88\"         #> [585] \"Ctxn3\"         \"Lyz2\"          \"Tmem100\"       \"Wfdc17\"        #> [589] \"Ahnak\"         \"Hba-a2\"        \"Hba-a1\"        \"Ccdc153\"       #> [593] \"Ccnd1\"         \"Serpinh1\"      \"Gad1\"          \"Arhgef10\"      #> [597] \"2410004P03Rik\" \"Nt5dc2\"        \"Cebpd\"         \"Sod3\"          #> [601] \"H2-D1\"         \"C4b\"           \"Tmem88b\"       \"Hbb-bt\"        #> [605] \"Rhog\"          \"Rprm\"          \"Ly6a\"          \"Mog\"           #> [609] \"Trbc2\"         \"Igkc\"          \"Smim1\"         \"Hs3st4\"        #> [613] \"Evi2a\"         \"Prkcg\"         \"Ly6c1\"         \"Gbp4\"          #> [617] \"Wipf3\"         \"BC039966\"      \"Gm13889\"       \"Plcxd2\"        #> [621] \"Mia\"           \"Pou3f1\"        \"Lrrc10b\"       \"Apol11b\"       #> [625] \"Gpr62\"         \"Shisa8\"        \"Gm2115\"        \"Kctd12\"        #> [629] \"1700047M11Rik\" \"Lhfpl3\"        \"C030029H02Rik\" \"Gm19935\"       #> [633] \"9630013A20Rik\" \"2900040C04Rik\" featIDs(g, subset = nr_cells < 100) #>  [1] \"Col1a1\"        \"Inmt\"          \"Cp\"            \"Nid1\"          #>  [5] \"Vipr2\"         \"Aldh1a2\"       \"Lbp\"           \"Myh11\"         #>  [9] \"Dcn\"           \"Slc17a8\"       \"Ascl1\"         \"Aebp1\"         #> [13] \"Fbln5\"         \"Akr1c18\"       \"Efcab6\"        \"Clic6\"         #> [17] \"Sncg\"          \"Gzma\"          \"Prph\"          \"Rsph1\"         #> [21] \"Cd74\"          \"Col3a1\"        \"Ncf2\"          \"Cfap126\"       #> [25] \"Meig1\"         \"Enkur\"         \"Myoc\"          \"Lcn2\"          #> [29] \"Edn3\"          \"1110017D15Rik\" \"Tpm2\"          \"Emilin1\"       #> [33] \"1700001C02Rik\" \"Col1a2\"        \"Eln\"           \"Pcolce\"        #> [37] \"Slc13a4\"       \"Gkn3\"          \"Slc6a13\"       \"Nupr1\"         #> [41] \"Slc38a5\"       \"Tagln\"         \"Calml4\"        \"Htr3a\"         #> [45] \"Paqr5\"         \"Cdhr4\"         \"Tie1\"          \"Foxj1\"         #> [49] \"Dynlrb2\"       \"Gjc1\"          \"Tgfbi\"         \"H2-Q4\"         #> [53] \"Ccdc33\"        \"Tgm2\"          \"Crygn\"         \"Nexn\"          #> [57] \"Nxph4\"         \"Fmod\"          \"Stab1\"         \"Mustn1\"        #> [61] \"Dnali1\"        \"Tmem212\"       \"Gpr4\"          \"Tent5c\"        #> [65] \"Slitrk6\"       \"Odf3b\"         \"Ranbp3l\"       \"Msx1\"          #> [69] \"Ndnf\"          \"Gja4\"          \"Gm14964\"       \"Dsp\"           #> [73] \"S100a8\"        \"S100a9\"        \"Col8a2\"        \"Capg\"          #> [77] \"H2-Q7\"         \"Hhip\"          \"Spag8\"         \"Ctxn3\"         #> [81] \"Wfdc17\"        \"Ccdc153\"       \"2410004P03Rik\" \"Igkc\"          #> [85] \"Gbp4\"          \"BC039966\"      \"Mia\"           \"Apol11b\"       #> [89] \"Shisa8\"        \"C030029H02Rik\" \"Gm19935\"       \"9630013A20Rik\" #> [93] \"2900040C04Rik\"  gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\") featIDs(gpoints) #>   [1] \"Mlc1\"      \"Gprc5b\"    \"Gfap\"      \"Ednrb\"     \"Sox9\"      \"Aqp4\"      #>   [7] \"Gjc3\"      \"Sox8\"      \"Ntsr2\"     \"Adcyap1r1\" \"Smo\"       \"Gpr161\"    #>  [13] \"C1qb\"      \"Olig1\"     \"C1qa\"      \"Lmtk2\"     \"Pth1r\"     \"Ephb6\"     #>  [19] \"Gpr26\"     \"Gabbr1\"    \"Adra2a\"    \"Gabbr2\"    \"Timp4\"     \"Abcc9\"     #>  [25] \"Csf1r\"     \"Ntrk2\"     \"Adgrg1\"    \"Ntrk3\"     \"Ddr1\"      \"Erbb4\"     #>  [31] \"Selplg\"    \"Cspg5\"     \"Dlk1\"      \"Gpr37l1\"   \"Fzd1\"      \"Fgfr3\"     #>  [37] \"Slc25a18\"  \"Igf1r\"     \"Adgrl1\"    \"S1pr1\"     \"Ryk\"       \"Grm5\"      #>  [43] \"Eomes\"     \"Axl\"       \"Efemp1\"    \"Adgrb3\"    \"Sstr4\"     \"Fn1\"       #>  [49] \"Adora1\"    \"Erbb2\"     \"Gper1\"     \"Gramd3\"    \"Mertk\"     \"Slc32a1\"   #>  [55] \"Adgra1\"    \"Adgrl2\"    \"Ptgfr\"     \"Fzd2\"      \"Aldh1l1\"   \"Adgrg6\"    #>  [61] \"Egfr\"      \"Gpr162\"    \"Lpar4\"     \"Kit\"       \"Ptgdr\"     \"Gad1\"      #>  [67] \"Lgr4\"      \"Tyro3\"     \"Atp13a5\"   \"Ddr2\"      \"Rspo3\"     \"Arhgap29\"  #>  [73] \"Ackr3\"     \"Gpr146\"    \"Fzd7\"      \"Slc47a1\"   \"Insr\"      \"Ptger3\"    #>  [79] \"Bdkrb1\"    \"Traf4\"     \"Celsr2\"    \"Fzd4\"      \"Fgfr2\"     \"Cx3cr1\"    #>  [85] \"Anxa11\"    \"Adgrb1\"    \"Lpar1\"     \"Gpr17\"     \"Gpr173\"    \"Ror1\"      #>  [91] \"Cxcl12\"    \"Kiss1r\"    \"Epha4\"     \"Gpr182\"    \"Man1a\"     \"Gpr4\"      #>  [97] \"P2ry14\"    \"Hcar1\"     \"Ephb1\"     \"Adrb1\"     \"Grm3\"      \"P2ry1\"     #> [103] \"Nrp2\"      \"Ptk7\"      \"Slco1a4\"   \"Tmem108\"   \"Hrh3\"      \"Insrr\"     #> [109] \"Cmklr1\"    \"Opn3\"      \"Adra1b\"    \"Gpr62\"     \"Npy1r\"     \"Nrp1\"      #> [115] \"Fzd6\"      \"S1pr5\"     \"Pdgfrb\"    \"Flt1\"      \"Chrm3\"     \"Agtr1a\"    #> [121] \"Adgrl4\"    \"Ephb3\"     \"Lpar6\"     \"Epha6\"     \"Fzd5\"      \"Emcn\"      #> [127] \"Cldn5\"     \"Sstr1\"     \"Fzd3\"      \"P2ry12\"    \"Adgrl3\"    \"Sema4d\"    #> [133] \"Adgrf5\"    \"Gpr160\"    \"Mrgpre\"    \"Amigo2\"    \"Adgra3\"    \"P2yr13\"    #> [139] \"Epha3\"     \"Adgre1\"    \"P2ry6\"     \"Cx3cl1\"    \"Epha10\"    \"Tacr1\"     #> [145] \"Peg10\"     \"Ednra\"     \"Plxnb3\"    \"Flt4\"      \"Slc17a7\"   \"Drd2\"      #> [151] \"Tjap1\"     \"Fzd8\"      \"Cd300c2\"   \"Htr4\"      \"Gpr52\"     \"Tek\"       #> [157] \"S1pr2\"     \"Kdr\"       \"Ror2\"      \"Kcnj8\"     \"Hrh1\"      \"Celsr1\"    #> [163] \"Gpr153\"    \"S1pr3\"     \"Adgra2\"    \"Fgfrl1\"    \"Tie1\"      \"Slc15a3\"   #> [169] \"Ccr10\"     \"Pdgfra\"    \"Lhcgr\"     \"Mrgprf\"    \"Ascl1\"     \"Baiap2\"    #> [175] \"Gpr85\"     \"Gpr22\"     \"Gcgr\"      \"Grm1\"      \"Ptafr\"     \"Calcrl\"    #> [181] \"Gpr34\"     \"Cenpe\"     \"Adora2b\"   \"Adrb2\"     \"Ccr2\"      \"Alk\"       #> [187] \"Tacr3\"     \"Chrm5\"     \"Erbb3\"     \"Ccr9\"      \"Gpr21\"     \"Epha7\"     #> [193] \"Adra2b\"    \"Pcdh15\"    \"Blank-104\" \"Adora2a\"   \"Drd1\"      \"Blank-57\"  #> [199] \"Grm7\"      \"Htr1b\"     \"Fzd9\"      \"Grm4\"      \"Blank-152\" \"Aplnr\"     #> [205] \"Gpr176\"    \"F2r\"       \"Vmn1r43\"   \"Gpr156\"    \"Gpr55\"     \"Blank-155\" #> [211] \"Bdkrb2\"    \"C5ar2\"     \"Gpbar1\"    \"Adgrv1\"    \"Gprc5c\"    \"Lmod1\"     #> [217] \"Gpr135\"    \"Rxfp3\"     \"Tbxa2r\"    \"Fzd10\"     \"Ret\"       \"Blank-80\"  #> [223] \"Epha8\"     \"Gpr75\"     \"Ackr1\"     \"Adgrg4\"    \"Chrm1\"     \"Epha1\"     #> [229] \"Vmn2r1\"    \"Syt4\"      \"Tas2r135\"  \"Ccr1\"      \"Lpar2\"     \"Myh11\"     #> [235] \"Gipr\"      \"Musk\"      \"Gpr183\"    \"Cnr1\"      \"C3ar1\"     \"S1pr4\"     #> [241] \"Grm2\"      \"C5ar1\"     \"Ephb2\"     \"Fpr1\"      \"Rho\"       \"Gpr27\"     #> [247] \"Adra1d\"    \"Gpr157\"    \"Adgrg2\"    \"Blank-45\"  \"Gpr20\"     \"Casr\"      #> [253] \"Avpr2\"     \"Mc5r\"      \"Sctr\"      \"Epha5\"     \"Gpr158\"    \"Cxcr4\"     #> [259] \"Vipr1\"     \"Gpr6\"      \"Blank-148\" \"Celsr3\"    \"Uts2r\"     \"Hrh2\"      #> [265] \"Htr6\"      \"Slc17a6\"   \"Gpr1\"      \"Glp2r\"     \"Ppp1r3g\"   \"V1ra8\"     #> [271] \"Trhr\"      \"Sstr3\"     \"Gpr63\"     \"Htr1a\"     \"F2rl3\"     \"Pln\"       #> [277] \"Grin2b\"    \"Gpr37\"     \"Chrm4\"     \"Lgr6\"      \"Gpr61\"     \"Taar7e\"    #> [283] \"Mas1\"      \"Npy2r\"     \"Ptger2\"    \"P2ry2\"     \"Oprm1\"     \"Prokr2\"    #> [289] \"Adra1a\"    \"Gpr45\"     \"Mc4r\"      \"Blank-128\" \"Sstr2\"     \"Flt3\"      #> [295] \"Htr5a\"     \"Ghsr\"      \"Galr1\"     \"Blank-95\"  \"Gpr83\"     \"Crhr1\"     #> [301] \"Brs3\"      \"Drd5\"      \"Gpr139\"    \"Taar6\"     \"Htr5b\"     \"Vmn1r40\"   #> [307] \"Rrh\"       \"Blank-83\"  \"Crhr2\"     \"Blank-161\" \"Vmn1r50\"   \"Tas1r3\"    #> [313] \"Taar2\"     \"P2ry4\"     \"Mchr1\"     \"Tas1r1\"    \"Blank-69\"  \"Htr7\"      #> [319] \"Hcrtr2\"    \"Htr2a\"     \"Cysltr2\"   \"Vmn1r46\"   \"Grpr\"      \"Adgrf2\"    #> [325] \"Blank-127\" \"Opn5\"      \"Taar3\"     \"Oxtr\"      \"Cckbr\"     \"Nmbr\"      #> [331] \"Ptger4\"    \"Blank-145\" \"Gpr101\"    \"Slc17a8\"   \"Adgrf4\"    \"Epha2\"     #> [337] \"Blank-139\""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatLocsObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 spatLocsObj Class — spatLocsObj-class","title":"S4 spatLocsObj Class — spatLocsObj-class","text":"Framework store spatial location information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatLocsObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 spatLocsObj Class — spatLocsObj-class","text":"spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatLocsObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 spatLocsObj Class — spatLocsObj-class","text":"name name spatLocsObj coordinates data.table spatial coordinates/locations spat_unit spatial unit tag provenance origin aggregated information (applicable)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatLocsObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 spatLocsObj Class — spatLocsObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"spatLocsObj\") #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatQueryGiottoPolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","title":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","text":"Recursively select polygons based list spatial filters. Results returned new polygon-based spatial unit selection information recorded associated cell metadata. final item provided param filters layer information queried.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatQueryGiottoPolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","text":"","code":"spatQueryGiottoPolygons(   gobject,   filters,   name = \"query_polys\",   feat_type = NULL,   clip = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatQueryGiottoPolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","text":"gobject Giotto object filters list characters. Named list IDs query spatial filters names designate spatial unit use character values either '' vector cell_IDs use. name (optional) character. NULL, new spatial unit name generated results feat_type (optional) May changed future. Determines feature type metadata hierarchical selection information stored. clip boolean. Default = FALSE. Whether final round querying return polygons clipped polygons used select . TRUE, value must provided name param generate new spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatQueryGiottoPolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","text":"giottoPolygon","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatially shift an object — spatShift","title":"Spatially shift an object — spatShift","text":"Shift spatial locations object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatially shift an object — spatShift","text":"","code":"# S4 method for class 'giotto' spatShift(   x,   dx = 0,   dy = 0,   spat_unit = \":all:\",   feat_type = \":all:\",   images = \":all:\" )  # S4 method for class 'SpatExtent' spatShift(x, dx = 0, dy = 0)  # S4 method for class 'spatLocsObj' spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)  # S4 method for class 'data.frame' spatShift(   x,   dx = 0,   dy = 0,   dz = 0,   copy_obj = TRUE,   geom = c(\"sdimx\", \"sdimy\", \"sdimz\"),   ... )  # S4 method for class 'spatialNetworkObj' spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)  # S4 method for class 'giottoPolygon' spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for class 'giottoPoints' spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for class 'giottoLargeImage' spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for class 'giottoImage' spatShift(x, dx = 0, dy = 0, ...)  # S4 method for class 'giottoAffineImage' spatShift(x, dx = 0, dy = 0, ...)  # S4 method for class 'affine2d' spatShift(x, dx = 0, dy = 0, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatially shift an object — spatShift","text":"x object dx numeric. shift x axis dy numeric. shift y axis spat_unit character vector. spatial units affect feat_type character vector. feature types affect images character vector. Images affect. dz numeric. shift z axis copy_obj Default = TRUE ... additional params pass methods geom character. Named vector colnames x, y, (z) coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatially shift an object — spatShift","text":"object shifted spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spatially shift an object — spatShift","text":"giotto object, \"::\" token can passed spat_unit, feat_type, images arguments affect available items.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Spatially shift an object — spatShift","text":"spatShift(spatialNetworkObj): Shift locations spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatially shift an object — spatShift","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  spatShift(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial unit information — spatUnit-generic","title":"Spatial unit information — spatUnit-generic","text":"access set spat_unit slot S4 subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial unit information — spatUnit-generic","text":"","code":"# S4 method for class 'ANY' spatUnit(x)  # S4 method for class 'list' spatUnit(x)  # S4 method for class 'spatData' spatUnit(x)  # S4 method for class 'giottoPolygon' spatUnit(x)  # S4 method for class 'spatData' spatUnit(x) <- value  # S4 method for class 'giottoPolygon' spatUnit(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial unit information — spatUnit-generic","text":"x Giotto S4 class subobject spatial unit value value set spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial unit information — spatUnit-generic","text":"spat_unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Spatial unit information — spatUnit-generic","text":"spatUnit(): Get spatial unit information spatUnit(spatData): Get spatial unit information spatUnit(giottoPolygon): Get spatial unit information spatUnit(spatData) <- value: Set spatial unit information spatUnit(giottoPolygon) <- value: Set giottoPolygon spat_unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial unit information — spatUnit-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"featMetaObj\")  spatUnit(g) #> [1] \"aggregate\""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto object spatial values — spatValues","title":"Giotto object spatial values — spatValues","text":"Retrieve specific values giotto object specific spat_unit feat_type. Values returned data.table features requested cell_ID column. function may updated future search additional sets information. see currently available slot checks, see details.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto object spatial values — spatValues","text":"","code":"spatValues(   gobject,   spat_unit = NULL,   feat_type = NULL,   feats,   expression_values = NULL,   spat_loc_name = NULL,   spat_enr_name = NULL,   poly_info = NULL,   dim_reduction_to_use = NULL,   dim_reduction_name = NULL,   verbose = NULL,   debug = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto object spatial values — spatValues","text":"gobject giotto object spat_unit character. spatial unit check feat_type character. feature type check feats character vector. One features values find within giotto object expression_values character. (optional) Name expression information use spat_loc_name character. (optional) Name spatial locations information use spat_enr_name character. (optional) Name spatial enrichments use poly_info character. (optional) Name polygons use dim_reduction_to_use character. (optional) type dimension reduction use dim_reduction_name character. (optional) Name dimension reduction use verbose verbosity debug logical. (default = FALSE) See details.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto object spatial values — spatValues","text":"data.table cell_ID column whichever feats requested","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Giotto object spatial values — spatValues","text":"[search] spatValues searches set available information within giotto object matches feats. current search order cell expression cell metadata spatial locations spatial enrichment dimension reduction polygon info specific name one types information provided via param expression_values, spat_enr_name, etc, search performed type data.[debug] function uses Giotto's accessor functions can usually throw errors whenever specific set data features within set exist. function muffles errors, sends error data found getters fail. setting debug = TRUE, can see errors returned failed getter printed messages easier debugging.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto object spatial values — spatValues","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  # expression spatValues(g, spat_unit = \"aggregate\", feats = c(\"Mlc1\", \"Gfap\")) #> Getting values from [aggregate][rna][raw] expression #>                                      cell_ID  Mlc1  Gfap #>                                       <char> <num> <num> #>   1: 240649020551054330404932383065726870513     0     2 #>   2: 274176126496863898679934791272921588227     0     0 #>   3: 323754550002953984063006506310071917306     0     2 #>   4:  87260224659312905497866017323180367450     0     1 #>   5:  17817477728742691260808256980746537959     0     0 #>  ---                                                     #> 458:   6380671372744430258754116433861320161     2     2 #> 459:  75286702783716447443887872812098770697     1     2 #> 460:   9677424102111816817518421117250891895     3     1 #> 461:  17685062374745280598492217386845129350     0     3 #> 462:  32422253415776258079819139802733069941     0     4 spatValues(g,     spat_unit = \"aggregate\", feats = c(\"Mlc1\", \"Gfap\"),     expression_values = \"normalized\" ) #> Getting values from [aggregate][rna][normalized] expression #>                                      cell_ID     Mlc1      Gfap #>                                       <char>    <num>     <num> #>   1: 240649020551054330404932383065726870513 0.000000 10.481367 #>   2: 274176126496863898679934791272921588227 0.000000  0.000000 #>   3: 323754550002953984063006506310071917306 0.000000  7.901442 #>   4:  87260224659312905497866017323180367450 0.000000  5.886051 #>   5:  17817477728742691260808256980746537959 0.000000  0.000000 #>  ---                                                            #> 458:   6380671372744430258754116433861320161 6.701726  6.701726 #> 459:  75286702783716447443887872812098770697 5.644422  6.629928 #> 460:   9677424102111816817518421117250891895 7.878817  6.306062 #> 461:  17685062374745280598492217386845129350 0.000000 11.065993 #> 462:  32422253415776258079819139802733069941 0.000000 10.041155  # spatial enrichment spatValues(g, spat_unit = \"aggregate\", feats = c(\"1\", \"3\")) #> Getting values from [aggregate][rna][cluster_metagene] spatial enrichment #>                                      cell_ID         1         3 #>                                       <char>     <num>     <num> #>   1: 240649020551054330404932383065726870513 1.0148370 0.3160792 #>   2: 274176126496863898679934791272921588227 3.2074150 0.6728505 #>   3: 323754550002953984063006506310071917306 3.9536614 0.0000000 #>   4:  87260224659312905497866017323180367450 4.0936217 0.1962017 #>   5:  17817477728742691260808256980746537959 0.9789911 1.9563931 #>  ---                                                             #> 458:   6380671372744430258754116433861320161 2.2465293 0.1905173 #> 459:  75286702783716447443887872812098770697 1.3827322 0.0000000 #> 460:   9677424102111816817518421117250891895 3.6843575 0.0000000 #> 461:  17685062374745280598492217386845129350 1.0010248 0.0000000 #> 462:  32422253415776258079819139802733069941 2.3449006 0.0000000  # polygon info spatValues(g, spat_unit = \"aggregate\", feats = c(\"agg_n\", \"valid\")) #> Getting values from [aggregate] polygon info #>                                      cell_ID agg_n valid #>                                       <char> <int> <int> #>   1: 100210519278873141813371229408401071444     2     1 #>   2: 101161259912191124732236989250178928032     2     1 #>   3: 101488859781016188084173008420811094152     2     1 #>   4: 101523780333017320796881555775415156847     2     1 #>   5: 102184699197574201819246996094734116255     2     1 #>  ---                                                     #> 458:   9677424102111816817518421117250891895     2     1 #> 459:  97068595823890802071024838798130036179     2     1 #> 460:  97411078642927912684859796714759494710     2     1 #> 461:   9816437869021910185567097363182418837     2     1 #> 462:  98561957902191275233320065611022298397     2     1  # cell meta spatValues(g, spat_unit = \"aggregate\", feats = c(\"nr_feats\")) #> Getting values from [aggregate][rna] cell metadata #>                                      cell_ID nr_feats #>                                       <char>    <int> #>   1: 240649020551054330404932383065726870513        5 #>   2: 274176126496863898679934791272921588227       27 #>   3: 323754550002953984063006506310071917306       23 #>   4:  87260224659312905497866017323180367450       37 #>   5:  17817477728742691260808256980746537959       18 #>  ---                                                  #> 458:   6380671372744430258754116433861320161       54 #> 459:  75286702783716447443887872812098770697       45 #> 460:   9677424102111816817518421117250891895       30 #> 461:  17685062374745280598492217386845129350        5 #> 462:  32422253415776258079819139802733069941       12"},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"Convert spatialNetworkObj non-directed igraph representation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"","code":"spat_net_to_igraph(spatialNetworkObj, attr = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"spatialNetworkObj spatialNetworkObj attr columns include edge attributes.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"igraph","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"","code":"sn <- GiottoData::loadSubObjectMini(\"spatialNetworkObj\") # only name attribute g <- spat_net_to_igraph(sn)  # view other column info besides to and from cols head(sn[], 1) #>                                       from #>                                     <char> #> 1: 100210519278873141813371229408401071444 #>                                         to sdimx_begin sdimy_begin sdimx_end #>                                     <char>       <num>       <num>     <num> #> 1: 216701996099683814512199402223708471323    6637.881   -5140.465   6612.68 #>    sdimy_end distance     weight #>        <num>    <num>      <num> #> 1: -5145.746 25.74799 0.03883798  # include distance and weight col info g <- spat_net_to_igraph(sn, attr = c(\"distance\", \"weight\"))"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"Utility function convert SpatialExperiment object Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"","code":"spatialExperimentToGiotto(   spe,   python_path,   nn_network = NULL,   sp_network = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"spe Input SpatialExperiment object convert Giotto object. python_path Specify path python. nn_network Specify name nearest neighbour network(s) input SpatialExperiment object. Default NULL use existing networks. sp_network Specify name spatial network(s) input SpatialExperiment object. Default NULL use existing networks. can vector multiple network names. verbose boolean value specifying progress messages displayed . Default TRUE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"","code":"if (FALSE) { # \\dontrun{ library(SpatialExperiment) example(read10xVisium, echo = FALSE) spatialExperimentToGiotto(spe) } # }"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 spatialGridObj Class — spatialGridObj-class","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"Framework store spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"S4 object defines spatial grid. structure grid stored data.table within gridDT slot defined start stop spatial locations along spatial axes. data.table also includes names cell grid names spatial axis locations make cell. Grids can annotated spatial feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"name name spatialGridObj method method used generate spatial grid parameters additional method-specific parameters used spatial grid generation gridDT data.table holding spatial grid information spat_unit spatial unit feat_type feature type provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatialGridObj\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 spatialNetworkObj Class — spatialNetworkObj-class","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"Framework store spatial network information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"generic access operators work data within networkDT slot (filtered).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"name name spatialNetworkObj method method used generate spatial network parameters additional method-specific parameters used spatial network generation outputObj network geometry object networkDT data.table network connections, distances, weightings networkDT_before_filter unfiltered data.table  network connections, distances, weightings cellShapeObj network cell shape information crossSectionObjects crossSectionObjects spat_unit spatial unit tag provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatialNetworkObj\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial binary operations — spatial_binary_ops","title":"Spatial binary operations — spatial_binary_ops","text":"Perform geometric binary operations Giotto spatial classes (giottoPolygon, giottoPoints spatLocsObj) underlying representations (terra SpatVector right now.)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial binary operations — spatial_binary_ops","text":"","code":"# S4 methods for giottoPolygon, giottoPoints, spatLocsObj, SpatVector #  # S4 method for class 'spatialClasses,spatialClasses' erase(x, y, ...)  # S4 method for class 'giottoSpatial' snap(x, y = NULL, tolerance, ...)  # S4 method for class 'spatialClasses,spatialClasses' symdif(x, y, ...)  # S4 method for class 'spatialClasses,spatialClasses' union(x, y)  # S4 method for class 'spatialClasses,spatialClasses' intersect(x, y)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial binary operations — spatial_binary_ops","text":"x spatial object 1 y spatial object 2 (can missing NULL) ... additional args pass tolerance numeric. Snapping tolerance (distance geometries)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial binary operations — spatial_binary_ops","text":"class x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial binary operations — spatial_binary_ops","text":"","code":"gpoly1 <- GiottoData::loadSubObjectMini(\"giottoPolygon\") epoly <- as.polygons(ext(c(6600, 6800, -5000, -4800))) gpoly2 <- spatShift(gpoly1, dx = 20)  plot(gpoly1)  plot(union(gpoly1, gpoly2))  plot(erase(gpoly1, epoly))   plot(union(gpoly1, epoly))   plot(symdif(gpoly1, epoly))   plot(intersect(gpoly1, epoly))   if (FALSE) {     # takes a long time so don't run in checks     plot(snap(gpoly1, tolerance = 0.2)) }"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert SpatialData to Giotto — spatialdataToGiotto","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"Converts saved SpatialData object Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"","code":"spatialdataToGiotto(   spatialdata_path = NULL,   n_key_added = NULL,   spatial_n_key_added = NULL,   delaunay_spat_net = TRUE,   spat_unit = NULL,   feat_type = NULL,   python_path = NULL,   env_name = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"spatialdata_path path SpatialData object n_key_added equivalent \"key_added\" argument scanpy.pp.neighbors(). multiple spatial networks anndata object, list key_added terms may provided. converting anndata object giottoToAnnData, .txt file may provided, generated function, .e. {spat_unit}_{feat_type}_nn_network_keys_added.txt \"spatial\". becomes name nearest network gobject. spatial_n_key_added equivalent \"key_added\" argument squidpy.gr.spatial_neighbors. multiple spatial networks anndata object, list key_added terms may provided. converting anndata object giottoToAnnData, .txt file may provided, generated function, .e. {spat_unit}_{feat_type}_spatial_network_keys_added.txt n_key_added. delaunay_spat_net binary parameter spatial network. TRUE, spatial network delaunay network. spat_unit desired spatial unit conversion, default NULL feat_type desired feature type conversion, default NULL python_path path python executable within conda/miniconda environment env_name name environment containing python_path executable","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"Function beta. Converts structured SpatialData file Giotto object. returned Giotto Object take default insructions exception python path, may customized. See changeGiottoInstructions modify instructions creation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":null,"dir":"Reference","previous_headings":"","what":"Spin an object — spin","title":"Spin an object — spin","text":"Spin (rotate) object spatially (usually limited xy rotations)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spin an object — spin","text":"","code":"# S4 method for class 'giotto' spin(x, angle, x0 = NULL, y0 = NULL, spat_unit = \":all:\", feat_type = \":all:\")  # S4 method for class 'giottoPolygon' spin(x, angle, x0 = NULL, y0 = NULL)  # S4 method for class 'giottoPoints' spin(x, angle, x0 = NULL, y0 = NULL)  # S4 method for class 'spatLocsObj' spin(   x,   angle = NULL,   x0 = NULL,   y0 = NULL,   z0 = NULL,   xy_angle = NULL,   zy_angle = NULL,   xz_angle = NULL )  # S4 method for class 'data.frame' spin(   x,   angle = NULL,   x0 = NULL,   y0 = NULL,   z0 = NULL,   xy_angle = NULL,   zy_angle = NULL,   xz_angle = NULL,   geom = c(\"sdimx\", \"sdimy\", \"sdimz\") )  # S4 method for class 'giottoLargeImage' spin(x, angle = NULL, x0 = NULL, y0 = NULL, ...)  # S4 method for class 'giottoAffineImage' spin(x, angle = NULL, x0 = NULL, y0 = NULL, ...)  # S4 method for class 'affine2d' spin(x, angle = NULL, x0 = NULL, y0 = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spin an object — spin","text":"x object angle numeric. Angle rotation degrees x0 numeric. x-coordinate center rotation. Defaults center x val given. y0 numeric. y-coordinate center rotation. Defaults center y val given. spat_unit character vector. spatial units affect feat_type character vector. feature types affect (giottoPoints ). z0 spatLocsObj specific. Numeric. z-coordinate center rotation. Depending z data present, defaults either 0 center z val given. xy_angle spatLocsObj specific. xy plane rotation degrees. Overrides angle param zy_angle spatLocsObj specific. zy plane rotation xz_angle spatLocsObj specific. xz plane rotation geom character. Named vector colnames x, y, (z) coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\") ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spin an object — spin","text":"spun object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spin an object — spin","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  spin(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a Giotto Object — splitGiotto","title":"Split a Giotto Object — splitGiotto","text":"Split Giotto object based cell metadata column list multiple Giotto objects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a Giotto Object — splitGiotto","text":"","code":"splitGiotto(gobject, by, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a Giotto Object — splitGiotto","text":"gobject giotto object split cell metadata column split object spat_unit character. Controls spatial unit pull splitting information . However, spatial units always affected split. feat_type character. Split affects feature type(s). Default \"rna\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a Giotto Object — splitGiotto","text":"list giotto objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split a Giotto Object — splitGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" splitGiotto(g, \"leiden_clus\") #> $leiden_clus_2 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 122 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_5 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 84 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_1 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 162 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_3 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 108 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_6 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 45 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_7 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 10 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_4 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 93 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"standardise_flex — standardise_flex","title":"standardise_flex — standardise_flex","text":"standardizes matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"standardise_flex — standardise_flex","text":"","code":"standardise_flex(x, center = TRUE, scale = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"standardise_flex — standardise_flex","text":"x matrix center center data scale scale data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"standardise_flex — standardise_flex","text":"standardized matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"standardise_flex — standardise_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  standardise_flex(m)"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":null,"dir":"Reference","previous_headings":"","what":"stitchFieldCoordinates — stitchFieldCoordinates","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"Helper function stitch field coordinates together form one complete picture","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"","code":"stitchFieldCoordinates(   location_file,   offset_file,   cumulate_offset_x = FALSE,   cumulate_offset_y = FALSE,   field_col = \"Field of View\",   X_coord_col = \"X\",   Y_coord_col = \"Y\",   reverse_final_x = FALSE,   reverse_final_y = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"location_file location dataframe X Y coordinates offset_file dataframe describes offset field (see details) cumulate_offset_x (boolean) x-axis offset values need cumulated? cumulate_offset_y (boolean) y-axis offset values need cumulated? field_col column indicates field within location_file X_coord_col column indicates x coordinates Y_coord_col column indicates x coordinates reverse_final_x (boolean) final x coordinates need reversed? reverse_final_y (boolean) final y coordinates need reversed?","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"Updated location dataframe new X ['X_final'] Y ['Y_final'] coordinates","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"Stitching fields: cell locations: least 3 columns: field, X, Y create offset file: offset file 3 columns: field, x_offset, y_offset create new cell location file stitching original cell locations stitchFieldCoordinates provide new cell location file createGiottoObject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"Function stitch together multiple field view (FOV) images single final image. Images loaded Giotto giottoLargeImage stitched based set FOV positions single final giottoLargeImage.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"","code":"stitchGiottoLargeImage(   largeImage_list = NULL,   gobject_list = NULL,   largeImage_nameList = NULL,   FOV_positions = NULL,   FOV_xcol = NULL,   FOV_ycol = NULL,   FOV_inverty = FALSE,   method = c(\"mosaic\", \"merge\"),   round_positions = FALSE,   filename = NULL,   dataType = NULL,   fileType = NULL,   dryRun = TRUE,   overwrite = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"largeImage_list list giottoLargeImage objects gobject_list list gobjects containing giottoLargeImages largeImage_nameList list names giottoLargeImages within gobjects FOV_positions dataframe FOV positions. Values () directly added current image mapping FOV_xcol column name FOV position x values FOV_ycol column name FOV position y values FOV_inverty make FOV y position values negative method method stitching images (mosaic: average overlapping area values, merge:values get priority order images given) round_positions boolean. Round image positions. May necessary run. filename file name write stitched image . Defaults \"save_dir/stitch.tif\" save_dir param found first gobject's Giotto instructions dataType (optional) values dataType \"INT1U\", \"INT2U\", \"INT2S\", \"INT4U\", \"INT4S\", \"FLT4S\", \"FLT8S\". first three letters indicate whether dataType integer (whole numbers) real number (decimal numbers), fourth character indicates number bytes used (allowing large numbers /precision), \"S\" \"U\" indicate whether values signed (negative positive) unsigned (positive values ). fileType (optional) image format (e.g. .tif) given, defaults format given filename dryRun boolean. Plot placeholder bounding rectangles FOV images stitched without actually proceeding full image stitching saving process. overwrite boolean. Overwrite filename save image already exists. Defaults TRUE verbose boolean. verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"largeGiottoImage object pointer stitched image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"function time consuming. Setting save location filename parameter also highly recommended file size likely large. function creates single stitched image multiple FOV tiles saves image disk works. finished, pointer new image loaded giottoLargeImage object. Note: Dry runs default dryRun param must set FALSE proceed final stitching operation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"dry-runs-are-default","dir":"Reference","previous_headings":"","what":"Dry runs are default","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"ensure disk space time wasted, function defaults previewing stitching operation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"fov-positions","dir":"Reference","previous_headings":"","what":"FOV positions","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"final image stitched together multiple FOV tiles. FOV_positions parameter accepts table x y values FOV tile placed performing stitch. columns x y values determined FOV_xcol FOV_ycol params respectively. FOV tiles full resolution starting position either lower left upper left image touch origin depending value FOV_inverty param. FOV image translated according x y shift values.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"fov-invert-y","dir":"Reference","previous_headings":"","what":"FOV invert y","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"Many imaging systems may treat origin according image convention (0,0) upper left image. odds coordinate convention Giotto uses internally coordinate (0,0) lower left. FOV_inverty defaults FALSE, set TRUE, FOV tile images start upper left touching (0,0) y values given FOV_positions FOV_ycol treated negative y shift values.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"datatype","dir":"Reference","previous_headings":"","what":"dataType","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"multiple datatypes defining range intensity values images can saved . Setting value dataType para optional Giotto attempts determine compatible data type save image automatically.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  stitchGiottoLargeImage(largeImage_list = list(g_image))  #> NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":null,"dir":"Reference","previous_headings":"","what":"stitchTileCoordinates — stitchTileCoordinates","title":"stitchTileCoordinates — stitchTileCoordinates","text":"Helper function stitch tile coordinates together form one complete picture","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"stitchTileCoordinates — stitchTileCoordinates","text":"","code":"stitchTileCoordinates(location_file, Xtilespan, Ytilespan)"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"stitchTileCoordinates — stitchTileCoordinates","text":"location_file location dataframe X Y coordinates Xtilespan numerical value specifying width tile Ytilespan numerical value specifying height tile","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"stitchTileCoordinates — stitchTileCoordinates","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"stitchTileCoordinates — stitchTileCoordinates","text":"","code":"location_file <- data.table::data.table(     field = rep(c(1, 2), 5),     X.X = rnorm(10), Y.Y = rnorm(10), XtileIndex = seq_len(10),     YtileIndex = seq_len(10) )  stitchTileCoordinates(location_file, Xtilespan = 0.5, Ytilespan = 0.5) #>     field         X.X        Y.Y XtileIndex YtileIndex     Xcoord      Ycoord #>     <num>       <num>      <num>      <int>      <int>      <num>       <num> #>  1:     1  1.18770051 -0.4300296          1          1  1.1877005 -0.43002963 #>  2:     2  0.01308331  0.7811606          2          2  0.5130833  1.28116058 #>  3:     1  0.64365001  0.3784188          3          3  1.6436500  1.37841880 #>  4:     2 -2.48768926 -1.0124020          4          4 -0.9876893  0.48759798 #>  5:     1  0.93101913 -2.0656557          5          5  2.9310191 -0.06565571 #>  6:     2 -1.89955741  1.0928168          6          6  0.6004426  3.59281676 #>  7:     1  1.21015863 -1.7202851          7          7  4.2101586  1.27971492 #>  8:     2 -1.46457418 -0.3058085          8          8  2.0354258  3.19419149 #>  9:     1  0.75557357 -0.3731366          9          9  4.7555736  3.62686344 #> 10:     2  0.42274803  0.4004511         10         10  4.9227480  4.90045106"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"subsetGiotto — subsetGiotto","title":"subsetGiotto — subsetGiotto","text":"Subsets Giotto object including previous analyses. subsetting subcellular information without editing aggregate information, use subsetGiottoLocsSubcellular","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"subsetGiotto — subsetGiotto","text":"","code":"subsetGiotto(   gobject,   spat_unit = \":all:\",   feat_type = \"rna\",   cell_ids = NULL,   feat_ids = NULL,   poly_info = spat_unit,   all_spat_units = NULL,   all_feat_types = NULL,   spat_unit_fsub = \":all:\",   feat_type_ssub = \":all:\",   verbose = FALSE,   toplevel_params = 2 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"subsetGiotto — subsetGiotto","text":"gobject giotto object spat_unit, feat_type character vector. (default = '::') One spatial units feature types subset. Accepts '::' token subset across available. cell_ids character. cell IDs keep feat_ids character. feature IDs keep poly_info character. polygon info(s) subset present. (defaults spat_unit) all_spat_units deprecated. use spat_unit_fsub = '::' all_feat_types deprecated. use feat_type_ssub = '::' spat_unit_fsub character vector. (default = '::') limit feat_id subsets spat_units feat_type_ssub character vector. (default = '::') limit cell_id subsets feat_types verbose verbose toplevel_params parameters extract","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"subsetGiotto — subsetGiotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"subsetGiotto — subsetGiotto","text":"Subsets Giotto object specific spatial unit feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"subsetGiotto — subsetGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  subsetGiotto(g, cell_ids = c(\"AACTCGATGGCGCAGT-1\", \"GGCTGGCTAGCTTAAA-1\")) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 2 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset by spatial locations — subsetGiottoLocs","title":"Subset by spatial locations — subsetGiottoLocs","text":"Subsets Giotto object spatially defining set cropping bounds. information subset preferred spatial locations. spat_loc_name given, first available set spatial locations spat_unit picked. spatial locations available, polygon information subset. Spatial IDs surviving crop applied rest Giotto object using subsetGiotto.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset by spatial locations — subsetGiottoLocs","text":"","code":"subsetGiottoLocs(   gobject,   spat_unit = NULL,   feat_type = NULL,   feat_type_ssub = \":all:\",   spat_loc_name = NULL,   x_max = NULL,   x_min = NULL,   y_max = NULL,   y_min = NULL,   z_max = NULL,   z_min = NULL,   poly_info = NULL,   return_gobject = TRUE,   verbose = FALSE,   toplevel_params = 5 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset by spatial locations — subsetGiottoLocs","text":"gobject giotto object spat_unit spatial unit subset feat_type (optional) feat type use return_gobject = TRUE combined data.table output desired. feat_type_ssub feat types across apply spatial subset spat_loc_name name spatial locations use within spat_unit x_max, x_min, y_max, y_min, z_max, z_min minimum maximum x, y, z coordinates subset poly_info character. polygon information subset (considered separately spat_units subset) return_gobject return Giotto object verbose verbose toplevel_params parameters extract","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset by spatial locations — subsetGiottoLocs","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Subset by spatial locations — subsetGiottoLocs","text":"return_gobject = FALSE, filtered combined metadata data.table returned","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset by spatial locations — subsetGiottoLocs","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  subsetGiottoLocs(g, x_max = 4000, y_max = -1000) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 175 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsMulti.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — subsetGiottoLocsMulti","title":"deprecated — subsetGiottoLocsMulti","text":"deprecated","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsMulti.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — subsetGiottoLocsMulti","text":"","code":"subsetGiottoLocsMulti(   gobject,   spat_unit = \":all:\",   feat_type = NULL,   feat_type_ssub = \":all:\",   spat_loc_name = NULL,   x_max = NULL,   x_min = NULL,   y_max = NULL,   y_min = NULL,   z_max = NULL,   z_min = NULL,   poly_info = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsMulti.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — subsetGiottoLocsMulti","text":"gobject giotto object spat_unit spatial unit subset feat_type (optional) feat type use return_gobject = TRUE combined data.table output desired. feat_type_ssub feat types across apply spatial subset spat_loc_name name spatial locations use within spat_unit x_max, x_min, y_max, y_min, z_max, z_min minimum maximum x, y, z coordinates subset poly_info named list character vectors. names correspond spat_unit character vectors polygons associated spat units return_gobject return Giotto object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsMulti.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — subsetGiottoLocsMulti","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"Subsets Giotto object based spatial coordinates. subset function intended poly_info feat_types matching aggregated information.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"","code":"subsetGiottoLocsSubcellular(   gobject,   poly_info = NULL,   feat_type = NULL,   x_min = NULL,   x_max = NULL,   y_min = NULL,   y_max = NULL,   z_max = NULL,   z_min = NULL,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"gobject giotto object poly_info character. polygons spatially subset feat_type character. feature info spatially subset x_max, x_min, y_max, y_min, z_max, z_min minimum maximum x, y, z coordinates subset verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"separate subsetGiottoLocs spat_units attached aggregated information removed using cell_ids-based approach order ensure paired information removed together. Polygons points information without associated aggregated values issue can directly spatially subset.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset part of an object with [ — subset_bracket","title":"Subset part of an object with [ — subset_bracket","text":"Extract values Giotto classes. Providing empty brackets : x[] usually extract main contained data representation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset part of an object with [ — subset_bracket","text":"","code":"# S4 method for class 'gdtData,gIndex,gIndex,missing' x[i, j]  # S4 method for class 'gdtData,logical,missing,missing' x[i, j]  # S4 method for class 'gdtData,character,missing,missing' x[i, j]  # S4 method for class 'gdtData,missing,numeric,missing' x[i, j]  # S4 method for class 'gdtData,missing,logical,missing' x[i, j]  # S4 method for class 'coordDataDT,ANY,ANY,missing' x[i, j]  # S4 method for class 'coordDataDT,missing,ANY,missing' x[i, j]  # S4 method for class 'coordDataDT,missing,character,missing' x[i, j]  # S4 method for class 'coordDataDT,ANY,missing,missing' x[i, j]  # S4 method for class 'coordDataDT,missing,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,gIndex,missing,missing' x[i, j]  # S4 method for class 'metaData,missing,ANY,missing' x[i, j]  # S4 method for class 'metaData,missing,character,missing' x[i, j]  # S4 method for class 'metaData,ANY,missing,missing' x[i, j]  # S4 method for class 'metaData,missing,missing,missing' x[i, j]  # S4 method for class 'dimObj,ANY,ANY,missing' x[i, j]  # S4 method for class 'dimObj,missing,missing,missing' x[i, j]  # S4 method for class 'exprData,missing,ANY,missing' x[i, j]  # S4 method for class 'exprData,ANY,missing,missing' x[i, j]  # S4 method for class 'exprData,ANY,ANY,missing' x[i, j]  # S4 method for class 'exprData,missing,missing,missing' x[i, j]  # S4 method for class 'spatNetData,missing,missing,missing' x[i, j]  # S4 method for class 'nnData,missing,missing,missing' x[i, j]  # S4 method for class 'enrData,missing,missing,missing' x[i, j]  # S4 method for class 'enrData,ANY,missing,missing' x[i, j]  # S4 method for class 'enrData,missing,ANY,missing' x[i, j]  # S4 method for class 'enrData,missing,character,missing' x[i, j]  # S4 method for class 'spatGridData,missing,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,missing,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,gIndex,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,character,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,missing,gIndex,missing' x[i, j]  # S4 method for class 'giottoPolygon,missing,missing,missing' x[i, j]  # S4 method for class 'giottoPolygon,gIndex,missing,missing' x[i, j]  # S4 method for class 'giottoPolygon,character,missing,missing' x[i, j]  # S4 method for class 'giottoPolygon,missing,gIndex,missing' x[i, j]  # S4 method for class 'terraVectData,gIndex,gIndex,missing' x[i, j]  # S4 method for class 'giottoLargeImage,missing,missing,missing' x[i, j]  # S4 method for class 'giottoImage,missing,missing,missing' x[i, j]  # S4 method for class 'affine2d,missing,missing,missing' x[i, j]"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset part of an object with [ — subset_bracket","text":"x Giotto S4 object subset information , j indices specifying elements extract. Indices numeric character vectors, empty","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset part of an object with [ — subset_bracket","text":"x unless brackets empty case, main internal representation returned.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"-methods","dir":"Reference","previous_headings":"","what":"`[` methods","title":"Subset part of an object with [ — subset_bracket","text":"Return coordinates slot data.table giotto S4 Select rows () cols (j) giotto S4 metaDT slot Return metaDT slot data.table giotto S4 Return coordinates slot matrix giotto S4 dimObj Select rows () cols (j) giotto S4 exprMat slot Return exprMat slot Matrix object giotto S4 Return spatNetData slot network data.table object giotto S4 Return nnData slot igraph object giotto S4 Return enrData slot enrichment data.table object giotto S4 Return spatGridData slot data.table object giotto S4 Return giottoPoints spatVector slot Return giottoPolygon spatVector slot","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset part of an object with [ — subset_bracket","text":"","code":"gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  # extract contained `SpatVector` gpoints[] #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3  # subset by feature gpoints[c(\"Mlc1\", \"Gfap\")] #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 5464, 3  (geometries, attributes) #>  extent      : 6400.037, 6899.441, -5149.827, -4700.029  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                   Gfap        0            3 #>                   Gfap        0            4 #>   # subset by feature and colname gpoints[\"Mlc1\", c(\"feat_ID\", \"feat_ID_uniq\")] #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 488, 2  (geometries, attributes) #>  extent      : 6400.037, 6899.308, -5149.827, -4703.377  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :    Mlc1            1 #>                   Mlc1           55 #>                   Mlc1          127 #>   # subset by index gpoints[seq(20)] #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 20, 3  (geometries, attributes) #>  extent      : 6400.037, 6400.745, -5096.167, -4770.126  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset part of an object with $ — subset_dollar","title":"Subset part of an object with $ — subset_dollar","text":"Subset values Giotto Class using $ operator.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset part of an object with $ — subset_dollar","text":"","code":"# S4 method for class 'giotto' x$name  # S4 method for class 'coordDataDT' x$name  # S4 method for class 'spatEnrObj' x$name  # S4 method for class 'dimObj' x$name  # S4 method for class 'metaData' x$name  # S4 method for class 'terraVectData' x$name  # S4 method for class 'affine2d' x$name"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset part of an object with $ — subset_dollar","text":"x Giotto S4 object extract columns name literal character string (possibly backtick quoted). normally matched colnames.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset part of an object with $ — subset_dollar","text":"vector values requested column","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Subset part of an object with $ — subset_dollar","text":"$: Subset giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"-methods","dir":"Reference","previous_headings":"","what":"`$` methods","title":"Subset part of an object with $ — subset_dollar","text":"Select colname giotto S4 data.table coordinates slot. Select colname giotto S4 spatEnrObj Select entries misc slot giotto S4 dimObj. Select colname giotto S4 data.table metaDT slot. Select colname giotto S4 spatVector slot. Select piecewise transform values affine2d","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset part of an object with $ — subset_dollar","text":"","code":"enr <- GiottoData::loadSubObjectMini(\"spatEnrObj\")  enr$cell_ID #>   [1] \"240649020551054330404932383065726870513\" #>   [2] \"274176126496863898679934791272921588227\" #>   [3] \"323754550002953984063006506310071917306\" #>   [4] \"87260224659312905497866017323180367450\"  #>   [5] \"17817477728742691260808256980746537959\"  #>   [6] \"182132384503107798660396708280285136358\" #>   [7] \"316289522368890354495930310222776908199\" #>   [8] \"318995879282318989627235045690211636294\" #>   [9] \"104570855383158731814075192607294301741\" #>  [10] \"115370283894795045523368609208878185314\" #>  [11] \"123860671559578247432410194986927758864\" #>  [12] \"126981423897188762239468136959275655616\" #>  [13] \"134398773695365619188678200952912609063\" #>  [14] \"15242486364109501724975900940581726845\"  #>  [15] \"152684748256642370929802439227360458069\" #>  [16] \"153751792203577791006158581642177087065\" #>  [17] \"16326589507615554063401897357427439030\"  #>  [18] \"165786478473465185470745991122188406667\" #>  [19] \"167710327060928309829388429279250508392\" #>  [20] \"172181421897607556322673704318102678295\" #>  [21] \"176844289786228093052039491926955764947\" #>  [22] \"182235958169292445695483205478317795477\" #>  [23] \"183227745956657225549068107012033843521\" #>  [24] \"186988931894710833920932112634285943415\" #>  [25] \"190687643154627893064711601675234362640\" #>  [26] \"20548793658722995878220914240286086757\"  #>  [27] \"206702762285684421190019779213421380201\" #>  [28] \"216701996099683814512199402223708471323\" #>  [29] \"21934936165997373583174173761929761438\"  #>  [30] \"230344318208995342827768566280706457626\" #>  [31] \"251905496166492083168644493421091558216\" #>  [32] \"262996653580953175020435707363716649390\" #>  [33] \"27666206735695437393204421885258583706\"  #>  [34] \"286906689872367261752702769926754066848\" #>  [35] \"288822108801800165318171357739905375883\" #>  [36] \"301054712356664458042996323827909441002\" #>  [37] \"304842190541754537761816256358565562302\" #>  [38] \"318439340668767417720582355350205310941\" #>  [39] \"335295524680090725199231409883288198017\" #>  [40] \"35118346554513854436644695033199584696\"  #>  [41] \"41054036480225512911591384807281320971\"  #>  [42] \"43731708947199618294982749003938483862\"  #>  [43] \"48024672048124996997588408479044670509\"  #>  [44] \"51348907619842676963078202479438175138\"  #>  [45] \"67532821514617092397935003422482443295\"  #>  [46] \"77151711298730578178892667721058396928\"  #>  [47] \"77782228870577724567477221255169934206\"  #>  [48] \"8777587181320516093160667806451882030\"   #>  [49] \"95838678880751873613229512065975406368\"  #>  [50] \"95947958963963707263153541936375959179\"  #>  [51] \"9668748337336721830701975018211142813\"   #>  [52] \"97411078642927912684859796714759494710\"  #>  [53] \"101161259912191124732236989250178928032\" #>  [54] \"110615983935499449765434338770904504245\" #>  [55] \"110858042010405247711695373195937122852\" #>  [56] \"110900719814678261966908552089216814729\" #>  [57] \"12925323527075390484710711277617599454\"  #>  [58] \"137348923180371322628727011975895485209\" #>  [59] \"138859376429590720661963324654447571708\" #>  [60] \"140543565961583233746802451796981444137\" #>  [61] \"143386081176260440019925196855300710659\" #>  [62] \"143408196806895889016075556052288734233\" #>  [63] \"145421744145915784890159499930205641713\" #>  [64] \"148336156782096202859532636956126767457\" #>  [65] \"150082699777048696177232440639953146354\" #>  [66] \"15247055772869406897093633424720409278\"  #>  [67] \"15834776842182822801451197571763335013\"  #>  [68] \"170833460535439412738579124041592991444\" #>  [69] \"173780780834031059819946658163431921979\" #>  [70] \"174306823762889142173283452439684229948\" #>  [71] \"175540604452034099044348476236813150837\" #>  [72] \"177757177666889772027017950398587309639\" #>  [73] \"17868848607867654301368031294266874310\"  #>  [74] \"180947508370750255585892730777436680945\" #>  [75] \"187952627468949069447188707715308813657\" #>  [76] \"1900302715660571356090444774019116326\"   #>  [77] \"203192161403397797138670022274582721699\" #>  [78] \"206016050634629330546630679047044021073\" #>  [79] \"214394514156259228118188949454902817376\" #>  [80] \"221669638772738575000116137509912039310\" #>  [81] \"224458376429228506642398057779371677646\" #>  [82] \"226912346807310637711937183879196326571\" #>  [83] \"227232155811404089141823608874580791245\" #>  [84] \"236677629222667262221261861475728542818\" #>  [85] \"244015124549889909957742476033146111487\" #>  [86] \"244247765904337326625465691380839405459\" #>  [87] \"244448312826260498647079278647004353269\" #>  [88] \"244840145612854293464477850603474951260\" #>  [89] \"262797098003740683881650619022037793005\" #>  [90] \"265185306239991354232232246957204545228\" #>  [91] \"266413162898429280572455841453688616870\" #>  [92] \"275784684664527332374777211328350223506\" #>  [93] \"277057315125198906319398446608128392905\" #>  [94] \"291975341311453330406711526698967834209\" #>  [95] \"295193149306421749943849825086053455411\" #>  [96] \"30222355550742125173065032035537805062\"  #>  [97] \"304560432600831995659079356647103974886\" #>  [98] \"30571638947438619177947320407779261750\"  #>  [99] \"306415949245581212081161219410047325001\" #> [100] \"311565496674213535805029947713320284697\" #> [101] \"314397389362641167108869069386457433770\" #> [102] \"3188909098022617910378369321966273882\"   #> [103] \"322879686187630160969459793861944841206\" #> [104] \"330850389163886577071114668277958486114\" #> [105] \"334199301045926627171760429217123408914\" #> [106] \"339814056401091912617621500767389941735\" #> [107] \"36648998424868029072860674954666559763\"  #> [108] \"39033692777509843205319060807429911979\"  #> [109] \"3942785923272820952395109293003259310\"   #> [110] \"47275912178029130797780898068213599096\"  #> [111] \"56815638009315000170441964570512336625\"  #> [112] \"57203625626451579261315887898923502046\"  #> [113] \"62669443199671326763841071380380779477\"  #> [114] \"64228015236811922665804882776457047292\"  #> [115] \"68418314542386876178693610244900595267\"  #> [116] \"70219882915166469874938407731799217344\"  #> [117] \"75660428514717127988983246148828583482\"  #> [118] \"75682347267697870039469591993208007445\"  #> [119] \"87903363874776475366779322866396664731\"  #> [120] \"88743795534206169429467675642537392511\"  #> [121] \"9538866320245722231901445225545432644\"   #> [122] \"96091484747656303270745913028146994621\"  #> [123] \"116860147088450350976374609398998546737\" #> [124] \"133061403473432310288273623600023558748\" #> [125] \"137154375879163008723188861204335796821\" #> [126] \"185903314401459366597627436588666236388\" #> [127] \"217996462208701069168232210617040322639\" #> [128] \"226667648171626631993624597360362535576\" #> [129] \"254829253202043893331055483138743800247\" #> [130] \"271967915636064836314881508293335292245\" #> [131] \"273673567134859598195435250950149370161\" #> [132] \"305306955532868686456926844192964831687\" #> [133] \"307030440204593378842812081935039092344\" #> [134] \"311587331826654155209560142756469108973\" #> [135] \"44197902970141946871502798467323259089\"  #> [136] \"44721220002773982161418195292536576043\"  #> [137] \"65855854848879329159292019718060662708\"  #> [138] \"76322781861215450124167009829890606622\"  #> [139] \"11065258297873257226330942251431244138\"  #> [140] \"118071411587380747913796380721014165557\" #> [141] \"123540785709544435621019288242840920053\" #> [142] \"130428604684362047522418850101908720496\" #> [143] \"134509424346276649608483685115101376571\" #> [144] \"136341171141277731884608634279863298546\" #> [145] \"137356600627014280700323828086313714576\" #> [146] \"151798130004305208790801168757831384604\" #> [147] \"162684318525520950869468479178769741207\" #> [148] \"164424478098970510930576318421517316799\" #> [149] \"166456955228473064319115194076209471689\" #> [150] \"168376325588102040437463621554621047372\" #> [151] \"179297712006471333306826676970515917851\" #> [152] \"19311588976622944909682910864587104989\"  #> [153] \"204611834270911643022584999768859598082\" #> [154] \"212501669348639182111017279862555064555\" #> [155] \"222047855782557501653245982274520432658\" #> [156] \"231212643322278795528005770495251497705\" #> [157] \"233229703476821612486041386363745481186\" #> [158] \"23470744401352443589618734383441183930\"  #> [159] \"234988593327199604253479621078255555503\" #> [160] 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[179] \"334356931858742201981142004419227940530\" #> [180] \"42056064196611141769700924475836317519\"  #> [181] \"59141517931138845718061638546803837463\"  #> [182] \"77541886028463256801311974652160917274\"  #> [183] \"79668971589879493465166271739355011800\"  #> [184] \"90740652120142025598838838824737408007\"  #> [185] \"93766399603521973873598911761678204002\"  #> [186] \"94915957193797412218079317943892351685\"  #> [187] \"101488859781016188084173008420811094152\" #> [188] \"102184699197574201819246996094734116255\" #> [189] \"107393799088150693125543893285009932508\" #> [190] \"111687473021757662663527126267334037424\" #> [191] \"112201175467804501210529603201546927780\" #> [192] \"115235047525370533075441381313256765131\" #> [193] \"119102272531447353986749088457842353881\" #> [194] \"121108122402850896937802185181656711412\" #> [195] \"122906612256038341059239630042273244949\" #> [196] \"126809950897128716226739975254707226975\" #> [197] 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'giotto,gIndex,missing,missing' x[i, j, ..., drop = TRUE]  # S4 method for class 'giotto,missing,gIndex,missing' x[i, j, ..., drop = TRUE]  # S4 method for class 'giotto,gIndex,gIndex,missing' x[i, j, ..., drop = TRUE]  # S4 method for class 'giotto,missing,missing,missing' x[i, j, ..., drop = TRUE]  # S4 method for class 'giotto' subset(   x,   subset,   feat_ids = NULL,   cell_ids = NULL,   spat_unit = NULL,   feat_type = NULL,   negate = FALSE,   quote = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset a giotto object — subset_giotto","text":"x giotto object ... additional params pass spatValues used subset param drop used subset Logical expression evaluated expression values feat_ids, character vector. Feature IDs subset object . cell_ids, j character vector. Cell/spatial IDs subset object . spat_unit character. Controls spatial unit pull subsetting information using cell_ids/j subset params. However, spatial units always affected subset. feat_type character. Subset affects feature type(s). Default \"rna\" negate logical. TRUE IDs subset selected quote logical. TRUE, subset param quoted substitute(). Set FALSE calling function, although may recommended since NSE output can unexpected used interactively.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset a giotto object — subset_giotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Subset a giotto object — subset_giotto","text":"x[: Subset giotto objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset a giotto object — subset_giotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  # `[` examples g[1:5] #> Warning: [cell] subset poly: no overlap between poly_IDs and cell_ids to keep #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 5, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used g[, 2:10] #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 9 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used g[1:5, 2:10] #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 5, 9 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used g[c(TRUE, FALSE), ] #> Warning: [cell] subset poly: no overlap between poly_IDs and cell_ids to keep #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 317, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used  # subset() examples subset(g, nr_feats > 300) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 218 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used subset(g, nr_feats > 300,     cell_ids = c(\"GAATCGCCGGACACGG-1\", \"GAGGGCATCGCGTATC-1\") ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 1 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used subset(g, Gfap + Gna12 > 10) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 97 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset giotto subobjects — subset_giotto_subobjects","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"Subset giotto object [[ disassemble list Giotto S4 subobjects. drop FALSE, selected subobjects reassembled new giotto object. Note indexing within [[ filters subobjects attributes. may remove unexpected information. specifically splitting giotto object spatial unit /feature type keeping expected information, use sliceGiotto()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"","code":"# S4 method for class 'giotto,missing,missing' x[[spat_unit = NULL, feat_type = NULL, drop = TRUE, ...]]  # S4 method for class 'giotto,character,missing' x[[i, spat_unit = NULL, feat_type = NULL, drop = TRUE, ...]]  # S4 method for class 'giotto,missing,character' x[[j, spat_unit = NULL, feat_type = NULL, drop = TRUE, ...]]  # S4 method for class 'giotto,character,character' x[[i, j, spat_unit = NULL, feat_type = NULL, drop = TRUE, ...]]"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"x giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type use (e.g. \"rna\", \"protein\") drop logical. Default = TRUE ... additional arguments character. Indicates slot name j character. Indicates subobject name","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"giotto subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" force(g) #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used  # return as lists of subobjects with drop = TRUE (default) g[[, \"raw\"]] #> [[1]] #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"z0\" #> provenance: z0  #> dimensions: 498 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6405.067 -4780.499  40951783403982682273285375368232495429 #> 2: 6426.020 -4972.519 240649020551054330404932383065726870513 #> 3: 6428.456 -4799.158 274176126496863898679934791272921588227 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6402.438 -5146.726 #> [2,] 6899.203 -4700.157 #>  #>  #> [[2]] #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"z1\" #> provenance: z1  #> dimensions: 504 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6404.014 -4779.625  40951783403982682273285375368232495429 #> 2: 6408.296 -4970.794  17685062374745280598492217386845129350 #> 3: 6401.148 -4991.061 223553142498364321238189328942498473503 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.148 -5147.193 #> [2,] 6899.323 -4700.410 #>  #>  #> [[3]] #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>  #>  #> [[4]] #> An object of class exprObj : \"raw\" #> spat_unit : \"z0\" #> feat_type : \"rna\" #> provenance: z0  #>  #> contains: #> 337 x 498 sparse Matrix of class \"dgCMatrix\" #>                                          #> Mlc1   . . . . . . . .  . . . . . ...... #> Gprc5b . . 1 . 1 . . .  1 . 2 . . ...... #> Gfap   . . . 1 1 . . . 27 . . . . ...... #>  #>  ........suppressing 485 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  40951783403982682273285375368232495429 #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306  #>  #> [[5]] #> An object of class exprObj : \"raw\" #> spat_unit : \"z1\" #> feat_type : \"rna\" #> provenance: z1  #>  #> contains: #> 337 x 504 sparse Matrix of class \"dgCMatrix\" #>                                          #> Mlc1   . . . . . . . . . . .  1 . ...... #> Gprc5b . . . . . . . 2 . . .  1 . ...... #> Gfap   . 3 . 2 . 1 4 . . . . 18 . ...... #>  #>  ........suppressing 491 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  40951783403982682273285375368232495429 #>  17685062374745280598492217386845129350 #>  223553142498364321238189328942498473503 #>  240649020551054330404932383065726870513  #>  #> [[6]] #> An object of class exprObj : \"raw\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                          #> Mlc1   . . . . . .  1 . . 1 . . . ...... #> Gprc5b . 1 . 3 . .  2 . 4 2 . 1 . ...... #> Gfap   2 . 2 1 . . 45 . 1 1 . . . ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>  g[[\"expression\", spat_unit = \"aggregate\"]] #> [[1]] #> An object of class exprObj : \"raw\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                          #> Mlc1   . . . . . .  1 . . 1 . . . ...... #> Gprc5b . 1 . 3 . .  2 . 4 2 . 1 . ...... #> Gfap   2 . 2 1 . . 45 . 1 1 . . . ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>  #> [[2]] #> An object of class exprObj : \"normalized\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                                                                           #> Mlc1    .       .        .        .        . .  5.291601 . .        5.821597 . .        . #> Gprc5b  .       6.398031 .        7.454658 . .  6.273066 . 7.680054 6.808785 . 5.082989 . #> Gfap   10.48137 .        7.901442 5.886051 . . 10.746982 . 5.701006 5.821597 . .        . #>               #> Mlc1   ...... #> Gprc5b ...... #> Gfap   ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>  #> [[3]] #> An object of class exprObj : \"scaled\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #>   Provenance: z0 z1 #> 337 x 462 dense matrix of class \"dgeMatrix\" #>  #>                  [,1]       [,2]       [,3]       [,4]       [,5]       [,6] #> Mlc1      -0.51096453 -0.4718074 -0.3859440 -0.4383384 -0.3827836 -0.3152653 #> Gprc5b    -0.97549417  1.6804631 -0.5746594  1.2850731 -0.5794505 -0.4583322 #> Gfap       5.46807822 -0.7367558  1.3902670  0.5804327 -0.6152080 -0.4843442 #> Ednrb      9.34063752  3.7384966  2.5412669  1.5736461  2.8570134 -0.2823656 #> Sox9      -0.59906517 -0.5143258  2.4318798 -0.4671338 -0.4200826 -0.3423988 #> Aqp4      -0.64987710 -0.5388482  2.0705344  1.0223253  1.9919249 -0.3580479 #> Gjc3       0.02982685  5.0161718 -0.1662473 -0.2615829 -0.1538300 -0.1487112 #> Sox8      -0.47826316  3.5325216  2.5366322 -0.4276501 -0.3689389 -0.3051939 #> Ntsr2      6.06580557  2.6068464  1.7367543  1.1330202 -0.6019376 -0.4746906 #> Adcyap1r1 -2.17060870  0.8282834  0.8492637 -0.9807865 -1.0854235 -0.8264062 #>                [,7]       [,8]       [,9]      [,10] #> Mlc1       1.546533 -0.3614888 -0.5076115  2.5761153 #> Gprc5b     1.235844 -0.5485629  1.6600474  2.0842933 #> Gfap       1.944454 -0.5825762  0.6870865  1.1388811 #> Ednrb      1.705886 -0.3184691 -0.4650954  3.3799076 #> Sox9       1.888188 -0.3969684 -0.5426758  2.2576086 #> Aqp4       2.116905 -0.4174313  1.7014365  2.5684989 #> Gjc3       4.531175 -0.1437027 -0.2923745 -0.2723587 #> Sox8       1.695510 -0.3483194 -0.4945962  2.8035269 #> Ntsr2      1.406620 -0.5699532  1.7102932  2.7162251 #> Adcyap1r1 -1.160557 -1.0298563  0.3757894  0.7075043 #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>  #> [[4]] #> An object of class exprObj : \"pearson\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #>   Provenance: z0 z1 #> 337 x 462 dense matrix of class \"dgeMatrix\" #>  #>                 [,1]       [,2]       [,3]       [,4]       [,5]       [,6] #> Mlc1      -0.1671233 -0.4887705 -0.4090814 -0.5848627 -0.3515289 -0.3681237 #> Gprc5b    -0.2390668  0.7264405 -0.5847568  2.7313611 -0.5026041 -0.5262978 #> Gfap       4.1820021 -1.2576333  0.8204327 -0.8491028 -0.9074561 -0.9499730 #> Ednrb      6.2681837  8.3133382  2.2399348  1.2854419  2.7238921 -0.3428383 #> Sox9      -0.1862585 -0.5445941  3.9225159 -0.6515799 -0.3917326 -0.4102193 #> Aqp4      -0.2836816 -0.8280158  2.1766489  0.0105117  1.0752709 -0.6242357 #> Gjc3      -0.1409193  4.4308083 -0.3450090 -0.4933833 -0.2964520 -0.3104520 #> Sox8      -0.1577216  6.0278079  2.2000617 -0.5520553 -0.3317706 -0.3474348 #> Ntsr2      5.2211595 12.2321831  2.5314771  1.9147811 -0.7517658 -0.7870865 #> Adcyap1r1 -0.3682081 -0.1508472  0.2046257 -1.2808439 -0.7730688 -0.8093776 #>                 [,7]       [,8]       [,9]      [,10] #> Mlc1       0.6581840 -0.4139145 -0.6241861  1.0672640 #> Gprc5b     0.8940330 -0.5916531  3.5614736  1.4696046 #> Gfap      21.4941853 -1.0670577 -0.9900047 -0.8977729 #> Ednrb      0.8099276 -0.3854930 -0.5814107  3.0206482 #> Sox9       2.9072540 -0.4612263 -0.6953491  0.8272268 #> Aqp4       6.8660546 -0.7016483  1.7534888  1.9205849 #> Gjc3      12.4888269 -0.3490872 -0.5265923 -0.5046983 #> Sox8       0.7812349 -0.3906598 -0.5891883  1.2004721 #> Ntsr2      2.2943725 -0.8844258  6.0655865  8.7636477 #> Adcyap1r1 -1.5740789 -0.9094310 -0.6471715 -0.5594111 #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>   # return as a subset giotto object with drop = FALSE g[[, \"raw\", drop = FALSE]] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #>  #>  #> Use objHistory() to see steps and params used g[[spat_unit = \"aggregate\", drop = FALSE]] #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 462 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : aggregate  #> [AGGREGATE INFO] #> expression ----------------------- #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"t_flex — t_flex","title":"t_flex — t_flex","text":"t_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"t_flex — t_flex","text":"","code":"t_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"t_flex — t_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"t_flex — t_flex","text":"matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"t_flex — t_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  t_flex(m) #>              [,1]       [,2]       [,3]        [,4]       [,5]        [,6] #>  [1,]  1.13475968 -0.1236010  0.8402388  0.09488557 -0.3051016  2.61356953 #>  [2,]  1.23346046 -0.7598318  1.2102308 -0.79255887 -1.0285583  0.53468162 #>  [3,] -0.07576892  0.5285784  0.6529490  1.65551988  0.8628259  1.48753032 #>  [4,] -2.09101499  0.6828611  1.2112902  0.95150212 -2.6957950 -0.90818349 #>  [5,]  0.47029282 -0.3990772 -0.2482703 -0.07380394 -1.9934812 -1.42041042 #>  [6,]  0.50937786 -0.5727822 -1.8640852  0.09639107 -0.5443541  1.48551609 #>  [7,] -2.18684352  0.1086828  0.7365619  0.09315147  0.0132255 -1.04726906 #>  [8,] -1.31266853 -0.7109888  0.2669893  0.53664180  0.2404480  0.01366106 #>  [9,]  1.59534811  0.6553744  0.1503795 -0.59067813  0.6122497  0.37854906 #> [10,]  2.50702432 -0.2506748 -0.6089946 -0.88808468 -0.6624071  0.73643913 #>             [,7]       [,8]        [,9]       [,10] #>  [1,]  0.4033562  2.4011713  1.49373183 -0.07131230 #>  [2,] -0.2549574 -1.3450848  0.25582422 -1.24728794 #>  [3,] -0.7928009 -0.4488620 -1.00887476 -1.68556568 #>  [4,] -3.0512252  0.7783738  2.81270232 -0.73703947 #>  [5,]  1.2947209 -1.1102363  0.08404357 -0.09540202 #>  [6,] -0.3448927 -0.2134763  1.15903245 -0.45740931 #>  [7,] -0.7027522 -0.2350337  0.82302884  1.67890702 #>  [8,] -0.5580017 -0.4879339  0.87933344  0.87836272 #>  [9,] -0.7803218 -0.9206261  0.67446169 -1.17164534 #> [10,]  0.6153136 -1.5068803 -1.14078881 -0.48878187"},{"path":"https://drieslab.github.io/GiottoClass/reference/terraVectData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic class for terra SpatVector-based objects — terraVectData-class","title":"Basic class for terra SpatVector-based objects — terraVectData-class","text":"Classes inherit class contain spatVector slot meant hold work terra SpatVector objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/terraVectData-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basic class for terra SpatVector-based objects — terraVectData-class","text":"object spatVector slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":null,"dir":"Reference","previous_headings":"","what":"Tessellated grid of polygons — tessellate","title":"Tessellated grid of polygons — tessellate","text":"Generates tessellated grid polygons within provided spatial extent","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tessellated grid of polygons — tessellate","text":"","code":"tessellate(   extent,   shape = c(\"hexagon\", \"square\"),   shape_size = NULL,   gap = 0,   radius = NULL,   id_prefix = \"ID_\",   name = \"grid\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tessellated grid of polygons — tessellate","text":"extent SpatExtent anything else SpatExtent can extracted created shape Shape tessellation grid. Available options \"hexagon\" \"square\". shape_size numeric. Size shape tessellate. (x-axis width hexagons, side length squares) gap numeric. Shrink polygons add gap tessellated polygons radius deprecated. numeric. Radius size tessellation grid. id_prefix character. prefix add poly_ID names generated name name giottoPolygons grid make","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tessellated grid of polygons — tessellate","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tessellated grid of polygons — tessellate","text":"function generates tessellated grid spatial locations based input spatial locations. shape tessellation grid can either hexagonal square. shape_size parameter determines size grid cells bin size.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tessellated grid of polygons — tessellate","text":"","code":"# Create an extent across which to generate tessellated polygons e <- ext(0, 100, 0, 100) # produce hexagons with a diameter of 10 x <- tessellate(extent = e, shape = \"hexagon\", shape_size = 10) #> 104 polygons generated plot(x)   # same size grid, but now with a gap x <- tessellate(extent = e, shape = \"hexagon\", shape_size = 10, gap = 1) #> 104 polygons generated plot(x)   # square grid with a gap x <- tessellate(extent = e, shape = \"square\", shape_size = 10, gap = 1) #> 100 polygons generated plot(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":null,"dir":"Reference","previous_headings":"","what":"Transpose — transpose","title":"Transpose — transpose","text":"Spatially transpose object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transpose — transpose","text":"","code":"# S4 method for class 'giotto' t(x)  # S4 method for class 'spatLocsObj' t(x)  # S4 method for class 'spatialNetworkObj' t(x)  # S4 method for class 'giottoPoints' t(x)  # S4 method for class 'giottoPolygon' t(x)  # S4 method for class 'giottoLargeImage' t(x)  # S4 method for class 'giottoAffineImage' t(x)  # S4 method for class 'affine2d' t(x)  # S3 method for class 'spatLocsObj' t(x)  # S3 method for class 'spatialNetworkObj' t(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transpose — transpose","text":"x object transposed","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transpose — transpose","text":"transposed object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transpose — transpose","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  plot(t(sl))"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"updateGiottoImage — updateGiottoImage","title":"updateGiottoImage — updateGiottoImage","text":"Updates spatial positioning sizing giotto image largeImage attached giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"updateGiottoImage — updateGiottoImage","text":"","code":"updateGiottoImage(   gobject = NULL,   image_name = NULL,   largeImage_name = NULL,   xmax_adj = 0,   xmin_adj = 0,   ymax_adj = 0,   ymin_adj = 0,   x_shift = 0,   y_shift = 0,   scale_factor = NULL,   scale_x = 1,   scale_y = 1,   order = c(\"first_adj\", \"first_scale\"),   xmax_set = NULL,   xmin_set = NULL,   ymax_set = NULL,   ymin_set = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"updateGiottoImage — updateGiottoImage","text":"gobject gobject containing desired image object image_name name giotto image object largeImage_name name giotto largeImage object xmax_adj, xmin_adj, ymax_adj, ymin_adj adjust image boundaries increasing maximum decreasing minimum bounds respectively xy bounds x_shift, y_shift shift entire image along xy axes scale_factor set scale_x scale_y params time scale_x, scale_y independently scale x y axis image mapping coordinate origin order order operations fine adjustments (adjustment shift parameters) scaling xmin_set, xmax_set, ymin_set, ymax_set directly set xy image boundaries. Overrides minmax values spatial anchor. return_gobject return giotto object TRUE, giotto image object FALSE verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"updateGiottoImage — updateGiottoImage","text":"giotto object updated giotto image object return_gobject = FALSE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"updateGiottoImage — updateGiottoImage","text":"function works image objects associated Giotto.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"updateGiottoImage — updateGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  updateGiottoImage(g, largeImage_name = \"image\") #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":null,"dir":"Reference","previous_headings":"","what":"updateGiottoImageMG — updateGiottoImageMG","title":"updateGiottoImageMG — updateGiottoImageMG","text":"Updates boundaries giotto image object attached giotto object gobject image_name params given. Alternatively can directly accept return image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"updateGiottoImageMG — updateGiottoImageMG","text":"","code":"updateGiottoImageMG(   gobject = NULL,   image_name = NULL,   giottoImage = NULL,   xmax_adj = 0,   xmin_adj = 0,   ymax_adj = 0,   ymin_adj = 0,   x_shift = 0,   y_shift = 0,   scale_factor = NULL,   scale_x = 1,   scale_y = 1,   order = c(\"first_adj\", \"first_scale\"),   xmin_set = NULL,   xmax_set = NULL,   ymin_set = NULL,   ymax_set = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"updateGiottoImageMG — updateGiottoImageMG","text":"gobject giotto object containing giotto image object image_name name giotto image object giottoImage image object directly update xmax_adj, xmin_adj, ymax_adj, ymin_adj adjust image boundaries increasing maximum decreasing minimum bounds respectively xy bounds x_shift, y_shift shift entire image along xy axes scale_factor set scale_x scale_y params time scale_x, scale_y independently scale x y axis image mapping coordinate origin order order operations fine adjustments (adjustment shift parameters) scaling xmin_set set image xmin boundary. Applied adjustments xmax_set set image xmax boundary. Applied adjustments ymin_set set image ymin boundary. Applied adjustments ymax_set set image ymax boundary. Applied adjustments return_gobject return giotto object TRUE, giotto image object FALSE verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"updateGiottoImageMG — updateGiottoImageMG","text":"giotto object updated giotto image object return_gobject = FALSe","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"updateGiottoImageMG — updateGiottoImageMG","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- convertGiottoLargeImageToMG(g,     largeImage_name = \"image\",     return_gobject = FALSE )  updateGiottoImageMG(g, giottoImage = g_image) #> giottoImage argument is given and will take priority #>  #>  return_gobject set to FALSE #> Error in updateGiottoImageMG(g, giottoImage = g_image): object 'g_image' not found"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"updateGiottoLargeImage — updateGiottoLargeImage","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"Updates boundaries giotto largeImage object attached giotto object gobject largeImage_name params given. Alternatively can directly accept return largeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"","code":"updateGiottoLargeImage(   gobject = NULL,   largeImage_name = NULL,   giottoLargeImage = NULL,   xmax_adj = 0,   xmin_adj = 0,   ymax_adj = 0,   ymin_adj = 0,   x_shift = 0,   y_shift = 0,   scale_factor = NULL,   scale_x = 1,   scale_y = 1,   order = c(\"first_adj\", \"first_scale\"),   xmin_set = NULL,   xmax_set = NULL,   ymin_set = NULL,   ymax_set = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"gobject giotto object containing giotto largeImage object largeImage_name name giotto largeImage object giottoLargeImage largeImage object directly update xmax_adj, xmin_adj, ymax_adj, ymin_adj adjust image boundaries increasing maximum decreasing minimum bounds respectively xy bounds x_shift, y_shift shift entire image along xy axes scale_factor set scale_x scale_y params time scale_x, scale_y independently scale x y axis image mapping coordinate origin order order operations fine adjustments (adjustment shift parameters) scaling xmin_set, xmax_set, ymin_set, ymax_set directly set xy image boundaries. Overrides minmax values spatial anchor. return_gobject return giotto object TRUE, giotto largeImage object FALSE verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"giotto object updated giotto largeImage object return_gobject = FALSE","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  updateGiottoLargeImage(g, largeImage_name = \"image\") #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":null,"dir":"Reference","previous_headings":"","what":"Update giotto object — updateGiottoObject","title":"Update giotto object — updateGiottoObject","text":"Updates giotto object changes structure backwards compatibility earlier versions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update giotto object — updateGiottoObject","text":"","code":"updateGiottoObject(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update giotto object — updateGiottoObject","text":"gobject giotto object update","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update giotto object — updateGiottoObject","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update giotto object — updateGiottoObject","text":"Supported updates: 3.2.0 update adding multiomics slot master branch suite - TODO","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update giotto object — updateGiottoObject","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  g <- updateGiottoObject(g)"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":null,"dir":"Reference","previous_headings":"","what":"Update giotto points object — updateGiottoPointsObject","title":"Update giotto points object — updateGiottoPointsObject","text":"Update giotto points object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update giotto points object — updateGiottoPointsObject","text":"","code":"updateGiottoPointsObject(gpoints)"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update giotto points object — updateGiottoPointsObject","text":"gpoints giotto points object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update giotto points object — updateGiottoPointsObject","text":"GiottoPointsObject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update giotto points object — updateGiottoPointsObject","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  updateGiottoPointsObject(g) #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":null,"dir":"Reference","previous_headings":"","what":"Update giotto polygon object — updateGiottoPolygonObject","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"Update giotto polygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"","code":"updateGiottoPolygonObject(gpoly)"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"gpoly giotto polygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"GiottoPolygonObject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  updateGiottoPolygonObject(g) #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    : rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Update giotto parameters — update_giotto_params","title":"Update giotto parameters — update_giotto_params","text":"Update giotto parameters","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update giotto parameters — update_giotto_params","text":"","code":"update_giotto_params(   gobject,   description = \"_test\",   return_gobject = TRUE,   toplevel = 2 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update giotto parameters — update_giotto_params","text":"gobject giotto object description description function run return_gobject logical. Whether giotto object returned toplevel expected relative stackframe call recorded made. negative, param recording skipped","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update giotto parameters — update_giotto_params","text":"giotto object list parameters","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update giotto parameters — update_giotto_params","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  update_giotto_params(g, toplevel = 1) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap giotto terra pointer information — wrap","title":"Wrap giotto terra pointer information — wrap","text":"Extension wrap methods terra Giotto's terra-based S4 objects. Allows pointer information packaged memory can passed connection (e.g. nodes computer cluster)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap giotto terra pointer information — wrap","text":"","code":"# S4 method for class 'giottoPolygon' wrap(x)  # S4 method for class 'giotto' wrap(x)  # S4 method for class 'giottoPoints' wrap(x)  # S4 method for class 'packedGiottoPolygon' vect(x)  # S4 method for class 'packedGiottoPoints' vect(x)  # S4 method for class 'packedGiotto' vect(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap giotto terra pointer information — wrap","text":"x giottoPolygon giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrap giotto terra pointer information — wrap","text":"wrapped giottoPolygon giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Wrap giotto terra pointer information — wrap","text":"wrap(giottoPolygon): Wrap giottoPolygon wrap(giotto): Wrap giotto wrap(giottoPoints): Wrap giottoPoints vect(packedGiottoPolygon): Unwrap giottoPolygon vect(packedGiottoPoints): Unwrap giottoPolygon vect(packedGiotto): Unwrap giotto","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrap giotto terra pointer information — wrap","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  wrap(g) #> [1] \"This is a packedGiottoPoints object. Use 'GiottoClass::vect()' to unpack it\""},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"writeGiottoLargeImage — writeGiottoLargeImage","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"Write full resolution image file. Filetype extension included filename argument. careful write time disk space needed image large.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"","code":"writeGiottoLargeImage(   giottoLargeImage = NULL,   gobject = NULL,   largeImage_name = NULL,   filename = NULL,   dataType = NULL,   max_intensity = NULL,   overwrite = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"giottoLargeImage giottoLargeImage object gobject giotto object largeImage_name name giottoLargeImage filename file name path write image dataType (optional) values dataType \"INT1U\", \"INT2U\", \"INT2S\", \"INT4U\", \"INT4S\", \"FLT4S\", \"FLT8S\". first three letters indicate whether dataType integer (whole numbers) real number (decimal numbers), fourth character indicates number bytes used (allowing large numbers /precision), \"S\" \"U\" indicate whether values signed (negative positive) unsigned (positive values ). max_intensity (optional) image max intensity value dataType can automatically determined overwrite Overwrite filename already existing verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"image local file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  writeGiottoLargeImage(     gobject = g, largeImage_name = \"image\",     filename = paste0(\"tempfile()\", \".png\") ) #> Writing image to disk as INT1U"},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":null,"dir":"Reference","previous_headings":"","what":"Zoom a Giotto spatial object — zoom","title":"Zoom a Giotto spatial object — zoom","text":"Works like terra::zoom(). Zoom plot providing new extent, default done clicking twice existing plot. passing SpatExtent without drawing, pre-existing plot needed.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Zoom a Giotto spatial object — zoom","text":"","code":"# S4 method for class 'giottoLargeImage' zoom(x, e = terra::draw(), ...)  # S4 method for class 'giottoPolygon' zoom(x, e = terra::draw(), ...)  # S4 method for class 'giottoPoints' zoom(x, e = terra::draw(), ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Zoom a Giotto spatial object — zoom","text":"x giotto image, giottoPolygon, giottoPoints object e SpatExtent ... additional parameters pass plot()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Zoom a Giotto spatial object — zoom","text":"SpatExtent (invisibly)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Zoom a Giotto spatial object — zoom","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" gimg <- getGiottoImage(g, image_type = \"largeImage\") gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\") e <- ext(6400, 6800, -4860, -4750) # arbitrary  # With extent passed zoom(gimg, e)  zoom(gpoly, e)  zoom(gpoints, e)"},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-4-0","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.4.0 (2024/10/27)","text":"stop exporting deprecated internal accessors terra requirement raised 1.7.41 minCircle()","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-4-0","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.4.0 (2024/10/27)","text":"fix dimnames() subobjects fix joinGiottoObject() gobjects poly point data #233 fix joinGiottoObject() gobjects image intensity overlaps features fix subsetting error due expression matrix drop numeric one cell left shift_vertical_step shift_horizontal_step args createGiottoPolygonsFromMask() numeric now shift steps based dims image instead just numerical value provided. fix feature metadata mixedsorted join fix non-inclusive subsetting minmax values supplied subsetGiottoLocs() fix giottoAffineImage loading saved","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-4-0","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.4.0 (2024/10/27)","text":"python packages install pip now settable installGiottoEnvironment() #224 giotto initialize() slot checking behavior can toggled now using 'giotto.init' 'giotto.check_valid' options. #946 rbutleriii setGiotto() now initializes performs checks items added list input provided. instructions() args now call createGiottoInstructions(). can also supply named args. instructions(gobject, param) instructions(gobject, param)<- now work giottoInstructions objects convenience. [, [[, $, $<-, subset() giotto see ?GiottoClass::subset_giotto subset spatIDs() featIDs() objName(), spatUnit(), featType() generics now return NA_character_ instead erroring used unsupported classes. ext() ext<-() can now used get set extent affine2d rownames(), colnames(), dimnames() giotto spatValues() can get values multiple spatial units. createGiottoPolygonsFromMask() now works anything terra::rast() can read createGiottoLargeImage() now works anything terra::rast() can read","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-4-0","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.4.0 (2024/10/27)","text":"sliceGiotto() pulling specific spatial units feature types independent giotto objects splitGiotto() splitting Giotto object list Giotto objects based cell metadata column .list() method giotto dump data list subobjects XY() XY<-() accessing setting coordinate values subobjects matrix terra convHull(), minRect(), minCircle() Giotto spatial vector classes area() SpatVector giottoPolygon","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-3-5","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.3.5 (2024/08/28)","text":"set_giotto_python_path() now also initialize python env set default print python env active, otherwise nothing python env already initialized. deprecated readGiottoInstructions(), showGiottoInstructions(), changeGiottoInstructions(), replaceGiottoInstructions() favor instructions() generic","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-5","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.5 (2024/08/28)","text":"intensity images now automatically scale estimated highest value giottoPolygon plot() default max_poly raised 1e6 giottoInstructions longer lose class specific params replaced ometif_to_tif() now checks imagecodecs package well anndataToGiotto() giottoToAnndata now check anndata package well. fix joinGiottoObjects() \"z_stack\" join method fix error documentation #214 shaojunyu fix error installGiottoEnvironment() #1006 13954380607","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-5","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.5 (2024/08/28)","text":"print() method giottoInstructions rbind() spatLocsObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-4","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.4 (2024/08/04)","text":"hotfix anndata matrix support #216 wwang-chcn","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-3","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.3 (2024/07/29)","text":"fix flipping issue giottoAffineImage certain affine transforms","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-3","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.3 (2024/07/29)","text":"missing method affine() instantiates affine2d object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-3-2","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.3.2 (2024/07/26)","text":"python environment installation relates default settings .condarc may changed. giottoImage name slot now requires character accept NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-2","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.2 (2024/07/26)","text":"loadGiotto() longer errors similarly named spat_units feat_types (e.g. “cell” “new_cell” previously throw error) fix giottoToSpatialExperiment() fix giottoToSeuratV5 cosmx mini dataset #989 guillermoturiel fix issue prints createGiottoCosMxObject() #960 GBeattie","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-2","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.2 (2024/07/26)","text":"verbose param createNearestNetwork() checkGiottoEnvironment() addition full filepaths, also now supports name environment installation directory installGiottoEnvironment(), removeGiottoEnvironment() now conda param setting path conda executable envname param specifying environment name installGiottoEnvironment() now confirm param skipping path input checks t() giotto now affects images well.","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-3-2","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.3.2 (2024/07/26)","text":"affine() giottoPolygon, giottoPoints, spatLocsObj, giotto shear() giottoPoints, giottoPolygon, spatLocsObj, affine2d affine2d class accumulating linear transforms used affine() initialize(), [, $, show(), plot(), methods affine2d spin(), rescale, spatShift(), affine(), flip(), shear() t() methods affine2d giottoAffineImage class just--time affine transformed images initialize(), method giottoLargeImage initialize(), ext(), crop(), rescale(), spatShift(), plot(), methods giottoAffineImage rescale() method giottoImage spin(), shear(), affine(), flip(), t() methods giottoAffineImage giottoLargeImage (converts giottoAffineImage) () conversion giottoLargeImage giottoAffineImage .get_centroid_xy() internal getting numeric centroid xy values object responds ext() .bound_poly() internal generating dummy polygon extent object responds ext() .aff_shift_2d(), .aff_shift_2d<-(), .aff_linear_2d, .aff_linear_2d()<- internals accessing manipulating affine matrices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-1","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.1 (2024/05/21)","text":"allow passing additional params setGiotto() ... spatShift() can now perform z shifts start spatLocsObj z information fix bug joinGiottoObjects() v0.3.0 looks now non-existent @largeImages slot fix bug .update_image_slot() v0.3.0 NULL @largeImages slot result error fix bugs spatShift() rescale() methods giotto setting default spat_unit feat_type","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-1","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.1 (2024/05/21)","text":"joinGiottoObjects() extent detection xshift defaults now depend ext() gobject instead images (available) joinGiottoObjects() now dry_run param previewing datasets spatially located join","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-3-1","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.3.1 (2024/05/21)","text":"() conversion giottoLargeImage array .matrix() method spatLocsObj()","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-3-0","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.3.0 (2024/05/13)","text":"deprecation reconnect_image_object(), reconnect_giottoImage_MG() reconnect_giottoLargeImage() internals favor simpler reconnect() generic giotto @largeImage slot removed. images now exist @images slot. backwards compatibility S3 spatialNetworkObj removed finding specific spatialNetworkObj getSpatialNetwork() now upgraded error instead returning NULL line accessors. backwards compatibility bare data.table spatial coordinates information removed","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-0","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.0 (2024/05/13)","text":"fix plot() params passing giottoPolygon type = \"centroid\" fix ext() output giottoImage spatShift() rescale() now also affect gobject attached images #945 rbutleriii","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-0","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.0 (2024/05/13)","text":"use faster terra::rasterize() terra::plot() instead scattermore::scattermoreplot() giottoPoints plot() method plot() giottoPoints method now plots density dens = TRUE show_max param density() hist() plot image object’s max_window setting .identify_background_range_polygons() now finds polygons larger threshold percentage overall extent SpatVector input. ext() can now used giotto objects #945 rbutleriii ext()<- can now used giottoImage conversion giottoLargeImage giottoImage (giottoImage sampled) crop() works spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-3-0","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.3.0 (2024/05/13)","text":"new spatValues() get specific values giotto object data.table format new ometif_to_tif convert .ome.tif .tif new terra::density() terra::hist() wrappers giottoLargeImage","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-2-3","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.2.3 (2024/03/12)","text":"fix saveGiotto overwrite = TRUE #870 rbutlerii fix plot() method param passing giottoLargeImage. Ensure access terra params","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-2-3","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.2.3 (2024/03/12)","text":"createGiottoPoints data.frame method can now select columns use x_colname, y_colname, feat_ID_colname params giotto now responds spatial manipulation generics: t(), flip(), rescale(), spatShift(), spin() spatUnit() featType() now vectorized internal get_spatial_locations_list() get_spatial_network_list() accessors now accept “::” token get available, ignoring spat_unit","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-2-2","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.2.2 (2024/03/01)","text":"fix createGiottoPolygonsFromMask() IDs applied sync mask values fix createGiottoPolygon() character method dispatch raster inputs remove unused fix_multipart param createGiottoPolygonsFromMask() fix giottoPolygon ID caching rbind()","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-2-2","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.2.2 (2024/03/01)","text":"createGiottoPolygonsFromMask() now ID_fmt param finer control automatic poly_ID generation .flip_spatvect() internal flipping SpatVector across arbitrary x y vals","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-2-1","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.2.1 (2024/02/28)","text":"giotto slot versions supercedes OS_platform. Used tracking GiottoClass version.","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-2-1","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.2.1 (2024/02/28)","text":"fix subsetGiotto unused argument fix giotto object saving image intensities overlaps data present. fix exprObj show() small matrices fix giotto calculateOverlap() method working image intensities data.","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-2-1","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.2.1 (2024/02/28)","text":"createNetwork() hub function creation Giotto NN spatial networks directly matrices. Mainly developers advanced users. edge_distances() calculating euclidean distances numeric m x n matrix (nodes) data.table cols define node connections.","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-2-1","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.2.1 (2024/02/28)","text":"addCellMetadata() addFeatMetadata() now support merging names provided vector factor data metadata cell_ID/feat_ID.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-1-3","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.1.3 (2024/01/12)","text":"fix unexpected sorting addCellMetadata() addFeatMetadata() #853 rbutleriii","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-1-3","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.1.3 (2024/01/12)","text":"init_gobject param loadGiotto() control whether object initialization also performed load vignette image tools","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-1-3","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.1.3 (2024/01/12)","text":"ID sorts now use gtools::mixedsort() #853 rbutleriii subobjects respond colnames, rownames, dimnames plot() show() now handle 3D spatLocsObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"added-0-1-2","dir":"Changelog","previous_headings":"","what":"Added","title":"GiottoClass 0.1.2 (2024/01/02)","text":"Added: max_window colors slots giottoLargeImage. Use GiottoClass:::.update_giotto_image() update outdated objects. Added: .bitdepth() internal function detect image bitdepth sampled values Added: re-export getMonochromeColors() GiottoUtils Added: giottoPolygon, giottoLargeImage method calculateOverlap() Added: vignette working spatial classes Added: output param .spatraster_sample_values(). Can now return sampled data.frame, array, magick, EBImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-1-2","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.1.2 (2024/01/02)","text":"param fixes raster calculateOverlap() workflows","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-1-1","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"GiottoClass 0.1.1 (2023/12/16)","text":"Removed: getRainbowColors() GiottoUtils Removed: get_prev_fname() get_args() GiottoUtils Removed: aggregateStacksPolygonsOLD()","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"added-0-1-1","dir":"Changelog","previous_headings":"","what":"Added","title":"GiottoClass 0.1.1 (2023/12/16)","text":"Added: .gstop() GiottoClass specific errors Added: plot() method dimObj Added: ncol() nrow() methods dimObj Added: dimObj additional info now accessible using $ $<- Added: spatEnrObj cols now accessible using $ $<- Added: evaluate_input() exported wrapper evaluate functions Added: .polygons() data.frame method correctly formatted data.tables (replaces internal dt_to_spatvector_polygon()) Added: .polygons() data.frame method correctly formatted data.tables (replaces internal dt_to_spatvector_points()) Added: autocompletes $ spatLocsObj, spatEnrObj, dimObj, cellMetaObj, featMetaObj, giottoPolygon, giottoPoints Added: toplevel_params param subsetGiottoLocs() Added: spin, spatShift, rescale methods data.frame","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"changes-0-1-1","dir":"Changelog","previous_headings":"","what":"Changes","title":"GiottoClass 0.1.1 (2023/12/16)","text":"Fixed: Provenance now accidentally created list addSpatialCentroidLocations() Changed: giottoPolygon plot() now automatically switches centroid plotting 1e4 polys Changed: Package internal functions now . prefix","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-1-0","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"GiottoClass 0.1.0 (2023/11/29)","text":"Giotto subsetting rework","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"added-0-1-0","dir":"Changelog","previous_headings":"","what":"Added","title":"GiottoClass 0.1.0 (2023/11/29)","text":"Added: terraVectData virtual parent class giottoPolygon giottoPoints classes Added: $ $<- methods terraVectData Added: ext<-() method giottoPolygon, giottoPoints Added: crop() method giottoLargeImage, giottoPoints Added: [ subsetting giottoPoints giottoPolygon numerical, logical, character (ID) Added: .sf() .stars() converters giottoPoints giottoPolygon Added: setGiotto() generic Added: gap param tessellate() introduces variable gap polygons tessellated Added: triGrid() Added: orthoGrid() Added: DelayedMatrixStats suggests Added: calculateOverlap() overlapToMatrix() generic functions feature image overlap aggregations","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"changes-0-1-0","dir":"Changelog","previous_headings":"","what":"Changes","title":"GiottoClass 0.1.0 (2023/11/29)","text":"Improved: performance gefToGiotto() Updated: spatIDs() featIDs() methods giottoPolygon giottoPoints allow returning non-unique IDs Added: check plot() giottoPolygon giottoPoints objects contain geometries Added: warning crop() giottoLargeImage, giottoPolygon, giottoPoints objects cropped extent include information Changed: Conversion createGiottoPoints() generic function Deprecate: radius param favor shape_size tessellate() Fixed: python .install_github_link_pip() param Fixed: python create_AnnData() added globals.R","code":""}]
+[{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2024 GiottoClass authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/articles/image_tools.html","id":"overview","dir":"Articles","previous_headings":"Giotto Image Tools","what":"1. Overview","title":"Giotto image tools","text":"Giotto uses giottoLargeImage represent images raster information. S4 class built based terra SpatRaster. older class called giottoImage based magick package also exists, currently phased . Ideally, giottoLargeImages also renamed giottoImage afterwards, simplifying naming scheme. object structure giottoLargeImage","code":"giottoLargeImage \\- name                (object name) \\- raster_object       (terra raster object) \\- extent              (current spatial extent) \\- overall_extent      (spatial extent of original image - experimental) \\- scale_factor        (pixels per coordinate unit - experimental) \\- resolution          (coordinate units covered per pixel) \\- max_intensity       (approximate maximum intensity value) \\- min_intensity       (approximate minimum intensity value) \\- max_window          (value to set as maximum intensity in color scaling) \\- colors              (vector of color mappings provided as hex codes) \\- is_int              (whether values are integers) \\- file_path           (filepath to the image) \\- OS_platform         (operating system)"},{"path":"https://drieslab.github.io/GiottoClass/articles/image_tools.html","id":"sampling","dir":"Articles","previous_headings":"Giotto Image Tools","what":"2. Sampling","title":"Giotto image tools","text":"Spatial images often extremely large files. high detail (resolution), large spatial region captured, precision recorded values (bitdepth) often results files 10s gigabytes. makes full size images difficult work . One way get around perform regular sampling image, touching values original image needed generate downscaled representation. implemented terra spatSample(). plotting, Giotto optimizes speed sampling striking balance terra::crop() terra::spatSample() try prevent sampling unnecessary regions, also avoid large crop operations fullsize image, can costly. done plot_auto_largeImage_resample() giottoLargeImages can also resampled image formats (magick EBImage) addition data.table array using GiottoClass:::.spatraster_sample_values() two functions experimental exported using common function names future.","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/image_tools.html","id":"color-scaling","dir":"Articles","previous_headings":"Giotto Image Tools","what":"3 Color scaling","title":"Giotto image tools","text":"distGiottoImage() can used look values present within giottoLargeImage. often case values recorded within image map full set values allowed bitdepth. Giotto plots images guessing bitdepth based estimated maximum value detected. mapping may always optimal.   Since values beyond 70, try setting max_window 70 color mapping better represents available information.  colormap use image can also edited. default greyscale image monochrome black white. color scales can supplied. monochrome colorscales: getMonochromeColors()","code":"library(GiottoClass) gimg <- GiottoData::loadSubObjectMini(\"giottoLargeImage\", idx = 2) gimg <- GiottoClass:::.update_giotto_image(gimg) # update older images that are missing slots  plot(gimg) distGiottoImage(giottoLargeImage = gimg) gimg@max_window <- 70 plot(gimg) # plot(gimg, max_intensity = 150) # can be used without setting the slot gimg@colors <- getMonochromeColors(\"green\") plot(gimg) viridis_colors <- hcl.colors(256, palette = \"viridis\") plot(gimg, col = viridis_colors) # can be used without setting the slot"},{"path":"https://drieslab.github.io/GiottoClass/articles/image_tools.html","id":"todos","dir":"Articles","previous_headings":"Giotto Image Tools > 3 Color scaling","what":"TODOs:","title":"Giotto image tools","text":"provide accessors slots make ggplot-based plotting also obey settings","code":"sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.5 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        ##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    ##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           ## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] GiottoClass_0.4.1 ##  ## loaded via a namespace (and not attached): ##  [1] sass_0.4.9                  SparseArray_1.4.8           ##  [3] gtools_3.9.5                lattice_0.22-6              ##  [5] digest_0.6.37               magrittr_2.0.3              ##  [7] evaluate_1.0.1              grid_4.4.1                  ##  [9] fastmap_1.2.0               jsonlite_1.8.9              ## [11] Matrix_1.7-0                backports_1.5.0             ## [13] GenomeInfoDb_1.40.1         GiottoData_0.2.15           ## [15] httr_1.4.7                  SingleCellExperiment_1.26.0 ## [17] UCSC.utils_1.0.0            codetools_0.2-20            ## [19] textshaping_0.4.0           jquerylib_0.1.4             ## [21] abind_1.4-8                 cli_3.6.3                   ## [23] rlang_1.1.4                 crayon_1.5.3                ## [25] XVector_0.44.0              Biobase_2.64.0              ## [27] cachem_1.1.0                DelayedArray_0.30.1         ## [29] yaml_2.3.10                 S4Arrays_1.4.1              ## [31] tools_4.4.1                 GiottoUtils_0.2.0           ## [33] checkmate_2.3.2             SpatialExperiment_1.14.0    ## [35] GenomeInfoDbData_1.2.12     SummarizedExperiment_1.34.0 ## [37] BiocGenerics_0.50.0         R6_2.5.1                    ## [39] magick_2.8.5                matrixStats_1.4.1           ## [41] stats4_4.4.1                lifecycle_1.0.4             ## [43] zlibbioc_1.50.0             S4Vectors_0.42.1            ## [45] fs_1.6.4                    htmlwidgets_1.6.4           ## [47] IRanges_2.38.1              ragg_1.3.3                  ## [49] desc_1.4.3                  pkgdown_2.1.1               ## [51] terra_1.7-83                bslib_0.8.0                 ## [53] data.table_1.16.2           Rcpp_1.0.13                 ## [55] systemfonts_1.1.0           highr_0.11                  ## [57] xfun_0.48                   GenomicRanges_1.56.2        ## [59] MatrixGenerics_1.16.0       knitr_1.48                  ## [61] rjson_0.2.23                htmltools_0.5.8.1           ## [63] rmarkdown_2.28              compiler_4.4.1"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"spatial-unit-and-feature-type","dir":"Articles","previous_headings":"","what":"Spatial unit and feature type","title":"Overview","text":"","code":"library(GiottoClass)  vizmini <- GiottoData::loadGiottoMini(\"vizgen\") ## 1. read Giotto object ## 2. read Giotto feature information ## 3. read Giotto spatial information ## 3.1 read Giotto spatial shape information ## 3.2 read Giotto spatial centroid information ## 3.3 read Giotto spatial overlap information ## 4. read Giotto image information ## checking default envname 'giotto_env' ## a system default python environment was found ## Using python path: ##  \"/usr/share/miniconda/envs/giotto_env/bin/python\" vizmini ## An object of class giotto  ## >Active spat_unit:  z0  ## >Active feat_type:  rna  ## dimensions    : 337, 498 (features, cells) ## [SUBCELLULAR INFO] ## polygons      : z0 z1 aggregate  ## features      : rna  ## [AGGREGATE INFO] ## expression ----------------------- ##   [z0][rna] raw ##   [z1][rna] raw ##   [aggregate][rna] raw normalized scaled pearson ## spatial locations ---------------- ##   [z0] raw ##   [z1] raw ##   [aggregate] raw ## spatial networks ----------------- ##   [aggregate] Delaunay_network kNN_network ## spatial enrichments -------------- ##   [aggregate][rna] cluster_metagene ## dim reduction -------------------- ##   [aggregate][rna] pca umap tsne ## nearest neighbor networks -------- ##   [aggregate][rna] sNN.pca ## attached images ------------------ ## images      : 4 items... ##  ##  ## Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"show-and-list-functions","dir":"Articles","previous_headings":"","what":"Show and list functions","title":"Overview","text":"Show list functions also provided determining information exists within slots nesting. show functions print preview data within slot, return information","code":"showGiottoSpatLocs(vizmini) ## ├──Spatial unit \"z0\" ## │  └──S4 spatLocsObj \"raw\" coordinates:   (498 rows) ## │        An object of class spatLocsObj  ## │        provenance: z0 ## │            ------------------------ ## │              sdimx     sdimy                                 cell_ID ## │              <num>     <num>                                  <char> ## │        1: 6405.067 -4780.499  40951783403982682273285375368232495429 ## │        2: 6426.020 -4972.519 240649020551054330404932383065726870513 ## │        3: 6428.456 -4799.158 274176126496863898679934791272921588227 ## │        4: 6408.155 -4816.583 323754550002953984063006506310071917306 ## │         ## │        ranges: ## │                sdimx     sdimy ## │        [1,] 6402.438 -5146.726 ## │        [2,] 6899.203 -4700.157 ## │         ## │         ## │      ## ├──Spatial unit \"z1\" ## │  └──S4 spatLocsObj \"raw\" coordinates:   (504 rows) ## │        An object of class spatLocsObj  ## │        provenance: z1 ## │            ------------------------ ## │              sdimx     sdimy                                 cell_ID ## │              <num>     <num>                                  <char> ## │        1: 6404.014 -4779.625  40951783403982682273285375368232495429 ## │        2: 6408.296 -4970.794  17685062374745280598492217386845129350 ## │        3: 6401.148 -4991.061 223553142498364321238189328942498473503 ## │        4: 6430.153 -4971.251 240649020551054330404932383065726870513 ## │         ## │        ranges: ## │                sdimx     sdimy ## │        [1,] 6401.148 -5147.193 ## │        [2,] 6899.323 -4700.410 ## │         ## │         ## │      ## └──Spatial unit \"aggregate\" ##    └──S4 spatLocsObj \"raw\" coordinates:   (462 rows) ##          An object of class spatLocsObj  ##          provenance: z0 z1 ##              ------------------------ ##                sdimx     sdimy                                 cell_ID ##                <num>     <num>                                  <char> ##          1: 6637.881 -5140.465 100210519278873141813371229408401071444 ##          2: 6471.978 -4883.541 101161259912191124732236989250178928032 ##          3: 6801.610 -4968.685 101488859781016188084173008420811094152 ##          4: 6789.055 -5105.338 101523780333017320796881555775415156847 ##           ##          ranges: ##                  sdimx     sdimy ##          [1,] 6401.412 -5146.747 ##          [2,] 6899.108 -4700.326 ##           ##           ## list_expression(vizmini) ##    spat_unit feat_type       name ##       <char>    <char>     <char> ## 1:        z0       rna        raw ## 2:        z1       rna        raw ## 3: aggregate       rna        raw ## 4: aggregate       rna normalized ## 5: aggregate       rna     scaled ## 6: aggregate       rna    pearson # Find specific spat_unit objects # list_expression(vizmini, spat_unit = \"z0\") ##    spat_unit feat_type   name ##       <char>    <char> <char> ## 1:        z0       rna    raw list_expression_names(vizmini, spat_unit = \"z1\", feat_type = \"rna\") ## [1] \"raw\""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"provenance","dir":"Articles","previous_headings":"","what":"Provenance","title":"Overview","text":"Going , sometimes different sources information can used aggregating particular spatial unit. easily shown subcellular datasets Vizgen MERSCOPE platform provide feature polygon information multiple confocal planes within tissue. aggregated information produced drawn different z-planes combinations thereof. Giotto tracks provenance information set aggregated data.","code":"expr_mat <- getExpression(vizmini, spat_unit = \"aggregate\") prov(expr_mat) ## [1] \"z0\" \"z1\""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"giotto-subobjects","dir":"Articles","previous_headings":"","what":"Giotto subobjects","title":"Overview","text":"Giotto 3.0 update introduced S4 subobjects used within giotto object processing. subobjects provide formalized definitions information formatting needed giotto object slots order functional. objects standalone extensible commonly used spatial manipulation plotting methods implemented . addition, subobjects carry several pieces metadata additional slots alongside main information (e.g. also slots spat_unit feat_type alongside exprDT slot exprObj S4). makes nesting information retained taken giotto object nesting information need supplied anymore interacting setter functions. getter functions now output param defaults extracting information giotto object S4 subobject. extracting information modified returned giotto object, preferred information extracted S4 tagged information lost, convenient work S4’s main data slot [ [<- generics.","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"constructors","dir":"Articles","previous_headings":"","what":"Constructors","title":"Overview","text":"directly creating subobject, constructor functions can used. constructors createExprObj() createCellMetaObj() createFeatMetaObj() createDimObj() createNearestNetObj() createSpatLocsObj() createSpatNetObj() createSpatEnrObj() createSpatialGrid() createGiottoPoints() createGiottoPolygonsFromDfr() createGiottoPolygonsFromMask() createGiottoImage() createGiottoLargeImage() non numeric integer columns spatial location input column position(s): 3 first non-numeric column considered cell ID test consistency expression matrix. non numeric columns removed","code":"coords <- data.table::data.table(     sdimx = c(1, 2, 3),     sdimy = c(1, 2, 3),     cell_ID = c(\"A\", \"B\", \"C\") )  st <- createSpatLocsObj(     name = \"test\",     spat_unit = \"cell\",     coordinates = coords,     provenance = \"cell\" ) ## There are non numeric or integer columns for the spatial location ##  input at column position(s): 3 ##  The first non-numeric column will be considered as a cell ID ##  to test for consistency with the expression matrix ##  Other non numeric columns will be removed print(st) ## An object of class spatLocsObj : \"test\" ## spat_unit : \"cell\" ## provenance: cell  ## dimensions: 3 3  ## preview   : ##    sdimx sdimy cell_ID ##    <num> <num>  <char> ## 1:     1     1       A ## 2:     2     2       B ## 3:     3     3       C ##  ## ranges: ##      sdimx sdimy ## [1,]     1     1 ## [2,]     3     3"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"readers","dir":"Articles","previous_headings":"","what":"Readers","title":"Overview","text":"Alternatively, read functions can used take named nested lists raw data input convert lists subobjects directly usable setter functions. readers readPolygonData() readFeatData() readExprData() readCellMetadata() readFeatMetadata() readSpatLocsData() readSpatNetData() readSpatEnrichData() readDimReducData() readNearestNetData() non numeric integer columns spatial location input column position(s): 3. first non-numeric column considered cell ID test consistency expression matrix. non numeric columns removed non numeric integer columns spatial location input column position(s): 3. first non-numeric column considered cell ID test consistency expression matrix. non numeric columns removed","code":"st2 <- readSpatLocsData(list(cell2 = list(     test1 = coords,     test2 = coords ))) ## list depth of 2 ##  ## List item [1]: ##  spat_unit: cell2 ##  name: test1 ## There are non numeric or integer columns for the spatial location ##  input at column position(s): 3 ##  The first non-numeric column will be considered as a cell ID ##  to test for consistency with the expression matrix ##  Other non numeric columns will be removed ##  ## List item [2]: ##  spat_unit: cell2 ##  name: test2 ## There are non numeric or integer columns for the spatial location ##  input at column position(s): 3 ##  The first non-numeric column will be considered as a cell ID ##  to test for consistency with the expression matrix ##  Other non numeric columns will be removed print(st2) ## [[1]] ## An object of class spatLocsObj : \"test1\" ## spat_unit : \"cell2\" ## provenance: cell2  ## dimensions: 3 3  ## preview   : ##    sdimx sdimy cell_ID ##    <num> <num>  <char> ## 1:     1     1       A ## 2:     2     2       B ## 3:     3     3       C ##  ## ranges: ##      sdimx sdimy ## [1,]     1     1 ## [2,]     3     3 ##  ##  ## [[2]] ## An object of class spatLocsObj : \"test2\" ## spat_unit : \"cell2\" ## provenance: cell2  ## dimensions: 3 3  ## preview   : ##    sdimx sdimy cell_ID ##    <num> <num>  <char> ## 1:     1     1       A ## 2:     2     2       B ## 3:     3     3       C ##  ## ranges: ##      sdimx sdimy ## [1,]     1     1 ## [2,]     3     3"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"giotto-accessors","dir":"Articles","previous_headings":"","what":"Giotto Accessors","title":"Overview","text":"Giotto provides getter setter functions manually accessing information contained within giotto object. Note setters require data provided compatible S4 subobjects lists thereof. External data can read appropriate formats using reader functions. getter functions return S4 subobjects default. getters getExpression() getCellMetadata() getFeatMetadata() getSpatialLocations() getDimReduction() getNearestNetwork() getSpatialNetwork() getPolygonInfo() getFeatureInfo() getSpatialEnrichment() getGiottoImage() setters setExpression() setCellMetadata() setFeatureMetadata() setSpatialLocations() setDimReduction() setNearestNetwork() setSpatialNetwork() setPolygonInfo() setFeatureInfo() setSpatialEnrichment() setGiottoImage()","code":"expval <- getExpression(vizmini) print(expval) ## An object of class exprObj : \"raw\" ## spat_unit : \"z0\" ## feat_type : \"rna\" ## provenance: z0  ##  ## contains: ## 337 x 498 sparse Matrix of class \"dgCMatrix\" ##                                          ## Mlc1   . . . . . . . .  . . . . . ...... ## Gprc5b . . 1 . 1 . . .  1 . 2 . . ...... ## Gfap   . . . 1 1 . . . 27 . . . . ...... ##  ##  ........suppressing 485 columns and 331 rows in show(); maybe adjust options(max.print=, width=) ##                                            ## Adgrf4    . . . . . . . . . . . . . ...... ## Epha2     . . . . . . . . . . . . . ...... ## Blank-139 . . . . . . . . . . . . . ...... ##  ##  First four colnames: ##  40951783403982682273285375368232495429 ##  240649020551054330404932383065726870513 ##  274176126496863898679934791272921588227 ##  323754550002953984063006506310071917306"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"get-and-set-s4-spat_unit-feat_type-provenance","dir":"Articles","previous_headings":"","what":"Get and set S4 spat_unit, feat_type, provenance","title":"Overview","text":"spatUnit(), featType(), prov() replacement functions tagged spatial unit, feature type, provenance information respectively.","code":"# spat_unit spatUnit(expval) <- \"new_spat\" spatUnit(expval) ## [1] \"new_spat\" # feat_type featType(expval) <- \"new_feat\" featType(expval) ## [1] \"new_feat\" # provenance prov(expval) <- \"cell\" prov(expval) ## [1] \"cell\""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"setting-an-s4-subobject","dir":"Articles","previous_headings":"","what":"Setting an S4 subobject","title":"Overview","text":"spat_unit, feat_type, name params longer need given setting S4 subobject tagged information giottoObject. However, input given set function parameters prioritized tagged information tagged information updated.","code":"# set exprObj to tagged nesting location vizmini <- setExpression(vizmini, expval) ## Setting expression [new_spat][new_feat] raw list_expression(vizmini) ##    spat_unit feat_type       name ##       <char>    <char>     <char> ## 1:        z0       rna        raw ## 2:        z1       rna        raw ## 3: aggregate       rna        raw ## 4: aggregate       rna normalized ## 5: aggregate       rna     scaled ## 6: aggregate       rna    pearson ## 7:  new_spat  new_feat        raw"},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"working-with-s4-subobjects","dir":"Articles","previous_headings":"","what":"Working with S4 subobjects","title":"Overview","text":"Giotto’s S4 subobjects wrap one main data object. empty [] []<- operators defined shorthand directly accessing slot contains data. example, spatLocsObj: class(spatLocsObj[]) equivalent class(spatLocsObj@coordinates) way, S4 subobjects can used contexts wrapped objects .","code":"st <- getSpatialLocations(vizmini) class(st) ## [1] \"spatLocsObj\" ## attr(,\"package\") ## [1] \"GiottoClass\" # With empty brackets class(st[]) ## [1] \"data.table\" \"data.frame\""},{"path":"https://drieslab.github.io/GiottoClass/articles/overview.html","id":"setting-information","dir":"Articles","previous_headings":"Working with S4 subobjects","what":"Setting information","title":"Overview","text":"","code":"print(st) ## An object of class spatLocsObj : \"raw\" ## spat_unit : \"z0\" ## provenance: z0  ## dimensions: 498 3  ## preview   : ##       sdimx     sdimy                                 cell_ID ##       <num>     <num>                                  <char> ## 1: 6405.067 -4780.499  40951783403982682273285375368232495429 ## 2: 6426.020 -4972.519 240649020551054330404932383065726870513 ## 3: 6428.456 -4799.158 274176126496863898679934791272921588227 ##  ## ranges: ##         sdimx     sdimy ## [1,] 6402.438 -5146.726 ## [2,] 6899.203 -4700.157 st[] <- coords print(st) ## An object of class spatLocsObj : \"raw\" ## spat_unit : \"z0\" ## provenance: z0  ## dimensions: 3 3  ## preview   : ##    sdimx sdimy cell_ID ##    <num> <num>  <char> ## 1:     1     1       A ## 2:     2     2       B ## 3:     3     3       C ##  ## ranges: ##      sdimx sdimy ## [1,]     1     1 ## [2,]     3     3 sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.5 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        ##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    ##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           ## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] GiottoClass_0.4.1 ##  ## loaded via a namespace (and not attached): ##  [1] rappdirs_0.3.3              sass_0.4.9                  ##  [3] SparseArray_1.4.8           gtools_3.9.5                ##  [5] lattice_0.22-6              digest_0.6.37               ##  [7] magrittr_2.0.3              evaluate_1.0.1              ##  [9] grid_4.4.1                  fastmap_1.2.0               ## [11] jsonlite_1.8.9              Matrix_1.7-0                ## [13] backports_1.5.0             GenomeInfoDb_1.40.1         ## [15] GiottoData_0.2.15           httr_1.4.7                  ## [17] SingleCellExperiment_1.26.0 UCSC.utils_1.0.0            ## [19] codetools_0.2-20            textshaping_0.4.0           ## [21] jquerylib_0.1.4             abind_1.4-8                 ## [23] cli_3.6.3                   rlang_1.1.4                 ## [25] crayon_1.5.3                XVector_0.44.0              ## [27] Biobase_2.64.0              withr_3.0.1                 ## [29] cachem_1.1.0                DelayedArray_0.30.1         ## [31] yaml_2.3.10                 S4Arrays_1.4.1              ## [33] tools_4.4.1                 GiottoUtils_0.2.0           ## [35] checkmate_2.3.2             SpatialExperiment_1.14.0    ## [37] GenomeInfoDbData_1.2.12     SummarizedExperiment_1.34.0 ## [39] BiocGenerics_0.50.0         reticulate_1.39.0           ## [41] png_0.1-8                   R6_2.5.1                    ## [43] magick_2.8.5                matrixStats_1.4.1           ## [45] stats4_4.4.1                lifecycle_1.0.4             ## [47] zlibbioc_1.50.0             S4Vectors_0.42.1            ## [49] fs_1.6.4                    htmlwidgets_1.6.4           ## [51] IRanges_2.38.1              ragg_1.3.3                  ## [53] pkgconfig_2.0.3             desc_1.4.3                  ## [55] pkgdown_2.1.1               terra_1.7-83                ## [57] bslib_0.8.0                 glue_1.8.0                  ## [59] data.table_1.16.2           Rcpp_1.0.13                 ## [61] systemfonts_1.1.0           xfun_0.48                   ## [63] GenomicRanges_1.56.2        MatrixGenerics_1.16.0       ## [65] knitr_1.48                  rjson_0.2.23                ## [67] igraph_2.1.1                htmltools_0.5.8.1           ## [69] rmarkdown_2.28              compiler_4.4.1"},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"overview","dir":"Articles","previous_headings":"","what":"1. Overview","title":"Giotto spatial geometry classes","text":"GiottoClass represents spatial polygons points respectively S4 classes giottoPolygon giottoPoints. objects built top terra SpatVectors order represent spatial biology. also respond many terra’s generics, enhancements. objects spatVector slot contains main information. common slot inherited VIRTUAL terraVectData class, however naming may subject change data representations added. structures classes : note unique_ID_cache slots used get around memory usage incurred frequently accessing SpatVectors attributes. caches updated modifications object. automatically performed using [] subsetting.","code":"terraVectData \\- spatVector  giottoPolygon \\- spatVector           (spatial polygons SpatVector) \\- spatVectorCentroids  (centroids points SpatVector) \\- overlaps             (list of overlapped features info) \\- name                 (object name/spat_unit) \\- unique_ID_cache      (cache of polygon IDs)  giottoPoints \\- spatVector           (spatial points SpatVector) \\- networks             (feature network) \\- feat_type            (object name/feat_type) \\- unique_ID_cache      (cache of feature IDs)"},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"polygon-object-creation","dir":"Articles","previous_headings":"","what":"2.1 Polygon object creation","title":"Giotto spatial geometry classes","text":"createGiottoPolygon() accepts number inputs, including filepaths spatial files .wkt, .shp, .GeoJSON mask image files common formats .tif .png. reading files, passed respective methods SpatVector SpatRaster (mask image). data.frame-like inputs also allowed long formatted similarly terra’s matrix representation polygon geometries, least following columns. geom: integer identifier polygon part: integer identifier part polygon, case multi polygon x: numeric x coordinate polygon vertex y: numeric y coordinate polygon vertex hole: integer identifier hole within polygon poly_ID: standard Giotto identifier polygon. Akin cell_ID Additional columns can included attributes, set poly_IDs required. de-novo generation simple polygon arrays, see documentation polyStamp() tessellate()","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"points-object-creation","dir":"Articles","previous_headings":"","what":"2.2 Points object creation","title":"Giotto spatial geometry classes","text":"relatively fewer input methods giottoPoints since currently tend provided flat files opposed spatial-specific formats. createGiottoPoints() works data.frame-like inputs least columns x-coordinate, y-coordinate, ID information. first two detected numeric columns expected x y respectively. first character column assumed feat_IDs. terra SpatVector inputs also accepted. helpful parameter split_keyword accepts list regex keywords pull matched features separate giottoPoints objects. useful situations multiple feature modalities /QC targets provided together interfere analyzed together. (see examples createGiottoPoints() documentation)","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"subsetting","dir":"Articles","previous_headings":"","what":"3. Subsetting","title":"Giotto spatial geometry classes","text":"giottoPoints giottoPolygons can subset either logical vectors ID.      $ extraction can used pull attributes objects vectors","code":"library(GiottoClass) gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  # full objects print(gpoly) ## An object of class giottoPolygon ## spat_unit : \"aggregate\" ## Spatial Information: ##  class       : SpatVector  ##  geometry    : polygons  ##  dimensions  : 462, 4  (geometries, attributes) ##  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       :                   poly_ID stack agg_n valid ##  type        :                     <chr> <chr> <int> <int> ##  values      : 100210519278873141813371~    NA     2     1 ##                101161259912191124732236~    NA     2     1 ##                101488859781016188084173~    NA     2     1 ##  centroids   : calculated ##  overlaps    : rna print(gpoints) ## An object of class giottoPoints ## feat_type : \"rna\" ## Feature Information: ##  class       : SpatVector  ##  geometry    : points  ##  dimensions  : 79761, 3  (geometries, attributes) ##  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       : feat_ID global_z feat_ID_uniq ##  type        :   <chr>    <int>        <int> ##  values      :    Mlc1        0            1 ##                 Gprc5b        0            2 ##                   Gfap        0            3 # subsets plot(gpoly) plot(gpoly[c(\"100210519278873141813371229408401071444\", \"101161259912191124732236989250178928032\", \"101488859781016188084173008420811094152\")]) print(gpoly[c(\"100210519278873141813371229408401071444\", \"101161259912191124732236989250178928032\", \"101488859781016188084173008420811094152\")]) ## An object of class giottoPolygon ## spat_unit : \"aggregate\" ## Spatial Information: ##  class       : SpatVector  ##  geometry    : polygons  ##  dimensions  : 3, 4  (geometries, attributes) ##  extent      : 6463.427, 6806.944, -5146.466, -4876.088  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       :                   poly_ID stack agg_n valid ##  type        :                     <chr> <chr> <int> <int> ##  values      : 100210519278873141813371~    NA     2     1 ##                101161259912191124732236~    NA     2     1 ##                101488859781016188084173~    NA     2     1 ##  centroids   : calculated ##  overlaps    : rna plot(gpoly[c(T,F)]) plot(gpoints) plot(gpoints[c(\"Fn1\")]) print(gpoints[c(\"Fn1\")]) ## An object of class giottoPoints ## feat_type : \"rna\" ## Feature Information: ##  class       : SpatVector  ##  geometry    : points  ##  dimensions  : 814, 3  (geometries, attributes) ##  extent      : 6400.663, 6884.093, -5149.767, -4711.758  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       : feat_ID global_z feat_ID_uniq ##  type        :   <chr>    <int>        <int> ##  values      :     Fn1        0          166 ##                    Fn1        0          181 ##                    Fn1        0          195 head(gpoly$poly_ID) ## [1] \"100210519278873141813371229408401071444\" ## [2] \"101161259912191124732236989250178928032\" ## [3] \"101488859781016188084173008420811094152\" ## [4] \"101523780333017320796881555775415156847\" ## [5] \"102184699197574201819246996094734116255\" ## [6] \"102893953956695364131894293580364005295\""},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"conversion-to-data-table","dir":"Articles","previous_headings":"","what":"4. Conversion to data.table","title":"Giotto spatial geometry classes","text":"GiottoClass set functions converting giottoPoints giottoPolygon objects spatial classes using .sf(), .sp(), .stars(), .terra(). terra-based giottoPoints giottoPolygon objects can also converted data.table geometry manipulation. method largely piggybacks terra’s .data.frame() adds support geom = \"XY\" polygon geometry. tables can either re-ingested using createGiottoPolygon() createGiottoPoints() converted SpatVector using .polygons() .points()","code":"gpoly_dt <- data.table::as.data.table(gpoly, geom = \"XY\") gpoints_dt <- data.table::as.data.table(gpoints, geom = \"XY\")  print(gpoly_dt) ## Key: <geom> ##         geom  part        x         y  hole ##        <int> <num>    <num>     <num> <num> ##     1:     1     1 6642.257 -5136.674     0 ##     2:     1     1 6642.711 -5137.020     0 ##     3:     1     1 6643.050 -5137.462     0 ##     4:     1     1 6643.310 -5137.956     0 ##     5:     1     1 6643.484 -5138.518     0 ##    ---                                      ## 35971:   462     1 6788.764 -4942.998     0 ## 35972:   462     1 6788.905 -4942.999     0 ## 35973:   462     1 6789.575 -4942.999     0 ## 35974:   462     1 6789.576 -4943.000     0 ## 35975:   462     1 6789.695 -4943.000     0 ##                                        poly_ID  stack agg_n valid ##                                         <char> <char> <int> <int> ##     1: 100210519278873141813371229408401071444   <NA>     2     1 ##     2: 100210519278873141813371229408401071444   <NA>     2     1 ##     3: 100210519278873141813371229408401071444   <NA>     2     1 ##     4: 100210519278873141813371229408401071444   <NA>     2     1 ##     5: 100210519278873141813371229408401071444   <NA>     2     1 ##    ---                                                            ## 35971:  98561957902191275233320065611022298397   <NA>     2     1 ## 35972:  98561957902191275233320065611022298397   <NA>     2     1 ## 35973:  98561957902191275233320065611022298397   <NA>     2     1 ## 35974:  98561957902191275233320065611022298397   <NA>     2     1 ## 35975:  98561957902191275233320065611022298397   <NA>     2     1 print(gpoints_dt) ##          feat_ID global_z feat_ID_uniq        x         y ##           <char>    <int>        <int>    <num>     <num> ##     1:      Mlc1        0            1 6400.037 -4966.651 ##     2:    Gprc5b        0            2 6400.041 -4965.377 ##     3:      Gfap        0            3 6400.078 -5081.453 ##     4:      Gfap        0            4 6400.084 -5038.288 ##     5:     Ednrb        0            5 6400.172 -4816.516 ##    ---                                                    ## 79757:    Adgra1        1        80339 6900.010 -4773.595 ## 79758:     Cspg5        1        80340 6900.023 -4772.980 ## 79759: Adcyap1r1        1        80341 6900.024 -5007.432 ## 79760:   Slc17a7        1        80342 6900.026 -4924.840 ## 79761:     Cldn5        1        80343 6900.030 -4746.916 print(as.polygons(gpoly_dt)) ##  class       : SpatVector  ##  geometry    : polygons  ##  dimensions  : 462, 4  (geometries, attributes) ##  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       :                   poly_ID stack agg_n valid ##  type        :                     <chr> <chr> <int> <int> ##  values      : 100210519278873141813371~    NA     2     1 ##                101161259912191124732236~    NA     2     1 ##                101488859781016188084173~    NA     2     1 # gpoints currently still requires addition of geom, part, and hole cols gpoints_dt[, geom := 1:.N] gpoints_dt[, part := 1] gpoints_dt[, hole := 0] print(as.points(gpoints_dt)) ##  class       : SpatVector  ##  geometry    : points  ##  dimensions  : 79761, 3  (geometries, attributes) ##  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       : feat_ID global_z feat_ID_uniq ##  type        :   <chr>    <int>        <int> ##  values      :    Mlc1        0            1 ##                 Gprc5b        0            2 ##                   Gfap        0            3"},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"centroids","dir":"Articles","previous_headings":"","what":"5. Centroids","title":"Giotto spatial geometry classes","text":"Centroids information carried giottoPolygon objects spatVectorCentroids slot. centroids() generic terra pulls slot information already exists. Otherwise, calculates returns set centroids polygons SpatVector points. append_gpolygon param makes giottoPolygon centroids info appended returned instead.","code":""},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"overlaps","dir":"Articles","previous_headings":"","what":"6.1 Overlaps","title":"Giotto spatial geometry classes","text":"Overlaps sets features overlapped polygons. calculateOverlaps() generic function performs overlapping polygons points polygons raster (intensity) data. Overlaps stored list giottoPolygon overlaps slot, separated modalities. list can retrieved using overlaps(). case overlapped points geometries, list items points SpatVector objects. poly_ID column tracks polygon overlapping point feature designated feat_ID feat_ID_uniq. NA values mean feature overlapped. overlaps intensities, results stored data.tables nested list called intensity main overlaps list.","code":"gpoly@overlaps <- NULL # reset overlaps info gpoly <- calculateOverlap(gpoly, gpoints, verbose = FALSE)  gimg <- GiottoData::loadSubObjectMini(\"giottoLargeImage\") gpoly <- calculateOverlap(gpoly, gimg, verbose = FALSE, progress = FALSE) print(gpoly@overlaps$rna) ##  class       : SpatVector  ##  geometry    : points  ##  dimensions  : 79761, 3  (geometries, attributes) ##  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) ##  coord. ref. :   ##  names       : poly_ID feat_ID feat_ID_uniq ##  type        :   <chr>   <chr>        <int> ##  values      :      NA    Mlc1            1 ##                     NA  Gprc5b            2 ##                     NA    Gfap            3 print(gpoly@overlaps$intensity) ## $dapi_z0 ##                                          poly_ID mini_dataset_dapi_z0 ##                                           <char>                <num> ##       1: 100210519278873141813371229408401071444                    8 ##       2: 100210519278873141813371229408401071444                    8 ##       3: 100210519278873141813371229408401071444                    8 ##       4: 100210519278873141813371229408401071444                    8 ##       5: 100210519278873141813371229408401071444                    8 ##      ---                                                              ## 3170620:  98561957902191275233320065611022298397                   58 ## 3170621:  98561957902191275233320065611022298397                   58 ## 3170622:  98561957902191275233320065611022298397                   88 ## 3170623:  98561957902191275233320065611022298397                   88 ## 3170624:  98561957902191275233320065611022298397                   88"},{"path":"https://drieslab.github.io/GiottoClass/articles/spatial_geometries.html","id":"overlaps-to-matrix","dir":"Articles","previous_headings":"","what":"6.2 Overlaps to matrix","title":"Giotto spatial geometry classes","text":"Overlap results can converted expression matrices using overlapToMatrix()","code":"# points, rna modality (default) rna_mat <- overlapToMatrix(gpoly) ## Warning: [overlapToMatrix] expected col_names and row_names ##  not provided together. Points aggregation Matrix output ##  may be missing some cols and rows where no detections ##  were found. print(rna_mat[1:3,1:3]) ## 3 x 3 sparse Matrix of class \"dgCMatrix\" ##       100210519278873141813371229408401071444 ## Abcc9                                       . ## Ackr1                                       . ## Ackr3                                       . ##       101161259912191124732236989250178928032 ## Abcc9                                       . ## Ackr1                                       . ## Ackr3                                       . ##       101488859781016188084173008420811094152 ## Abcc9                                       . ## Ackr1                                       . ## Ackr3                                       2 # intensity, dapi_z0 intens_mat <- overlapToMatrix(gpoly, type = \"intensity\", feat_info = \"dapi_z0\") print(intens_mat[1, 1:3, drop = FALSE]) ## 1 x 3 Matrix of class \"dgeMatrix\" ##                      100210519278873141813371229408401071444 ## mini_dataset_dapi_z0                                   80200 ##                      101161259912191124732236989250178928032 ## mini_dataset_dapi_z0                                  369434 ##                      101488859781016188084173008420811094152 ## mini_dataset_dapi_z0                                  220020 sessionInfo() ## R version 4.4.1 (2024-06-14) ## Platform: x86_64-pc-linux-gnu ## Running under: Ubuntu 22.04.5 LTS ##  ## Matrix products: default ## BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3  ## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0 ##  ## locale: ##  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        ##  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8    ##  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           ## [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C    ##  ## time zone: UTC ## tzcode source: system (glibc) ##  ## attached base packages: ## [1] stats     graphics  grDevices utils     datasets  methods   base      ##  ## other attached packages: ## [1] GiottoClass_0.4.1 ##  ## loaded via a namespace (and not attached): ##  [1] tidyselect_1.2.1            dplyr_1.1.4                 ##  [3] fastmap_1.2.0               SingleCellExperiment_1.26.0 ##  [5] digest_0.6.37               lifecycle_1.0.4             ##  [7] sf_1.0-18                   terra_1.7-83                ##  [9] magrittr_2.0.3              exactextractr_0.10.0        ## [11] compiler_4.4.1              rlang_1.1.4                 ## [13] sass_0.4.9                  tools_4.4.1                 ## [15] utf8_1.2.4                  yaml_2.3.10                 ## [17] data.table_1.16.2           knitr_1.48                  ## [19] S4Arrays_1.4.1              htmlwidgets_1.6.4           ## [21] sp_2.1-4                    classInt_0.4-10             ## [23] DelayedArray_0.30.1         KernSmooth_2.23-24          ## [25] abind_1.4-8                 BiocGenerics_0.50.0         ## [27] desc_1.4.3                  grid_4.4.1                  ## [29] stats4_4.4.1                fansi_1.0.6                 ## [31] e1071_1.7-16                colorspace_2.1-1            ## [33] ggplot2_3.5.1               scales_1.3.0                ## [35] gtools_3.9.5                SummarizedExperiment_1.34.0 ## [37] cli_3.6.3                   rmarkdown_2.28              ## [39] crayon_1.5.3                ragg_1.3.3                  ## [41] generics_0.1.3              httr_1.4.7                  ## [43] rjson_0.2.23                DBI_1.2.3                   ## [45] cachem_1.1.0                proxy_0.4-27                ## [47] zlibbioc_1.50.0             XVector_0.44.0              ## [49] matrixStats_1.4.1           vctrs_0.6.5                 ## [51] Matrix_1.7-0                jsonlite_1.8.9              ## [53] GiottoData_0.2.15           IRanges_2.38.1              ## [55] S4Vectors_0.42.1            scattermore_1.2             ## [57] systemfonts_1.1.0           magick_2.8.5                ## [59] GiottoUtils_0.2.0           jquerylib_0.1.4             ## [61] units_0.8-5                 glue_1.8.0                  ## [63] pkgdown_2.1.1               codetools_0.2-20            ## [65] gtable_0.3.6                GenomeInfoDb_1.40.1         ## [67] raster_3.6-30               GenomicRanges_1.56.2        ## [69] UCSC.utils_1.0.0            munsell_0.5.1               ## [71] tibble_3.2.1                pillar_1.9.0                ## [73] htmltools_0.5.8.1           GenomeInfoDbData_1.2.12     ## [75] R6_2.5.1                    textshaping_0.4.0           ## [77] evaluate_1.0.1              lattice_0.22-6              ## [79] Biobase_2.64.0              highr_0.11                  ## [81] backports_1.5.0             SpatialExperiment_1.14.0    ## [83] bslib_0.8.0                 class_7.3-22                ## [85] Rcpp_1.0.13                 SparseArray_1.4.8           ## [87] checkmate_2.3.2             xfun_0.48                   ## [89] fs_1.6.4                    MatrixGenerics_1.16.0       ## [91] pkgconfig_2.0.3"},{"path":"https://drieslab.github.io/GiottoClass/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Ruben Dries. Author, maintainer. Jiaji George Chen. Author. Guo-Cheng Yuan. Author. Matthew O'Brien. Author. Joselyn C. Chávez-Fuentes. Author. Edward Ruiz. Author.","code":""},{"path":"https://drieslab.github.io/GiottoClass/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Dries R, George Chen J, Yuan G, O'Brien M, Chávez-Fuentes J, Ruiz E (2024). GiottoClass: Giotto Suite object definitions framework. R package version 0.4.1, https://drieslab.github.io/GiottoClass/.","code":"@Manual{,   title = {GiottoClass: Giotto Suite object definitions and framework},   author = {Ruben Dries and Jiaji {George Chen} and Guo-Cheng Yuan and Matthew O'Brien and Joselyn C. Chávez-Fuentes and Edward Ruiz},   year = {2024},   note = {R package version 0.4.1},   url = {https://drieslab.github.io/GiottoClass/}, }"},{"path":"https://drieslab.github.io/GiottoClass/index.html","id":"giottoclass-","dir":"","previous_headings":"","what":"Giotto Suite object definitions and framework","title":"Giotto Suite object definitions and framework","text":"package contains Giotto object subobject class definitions frameworks. Functionalities relating data ingestion, basic object creation, data access within Giotto object, generics defined Giotto classes found . Applications framework convenience functions loading specific technologies found base Giotto package.","code":""},{"path":"https://drieslab.github.io/GiottoClass/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Giotto Suite object definitions and framework","text":"can install GiottoClass like:","code":"library(devtools) install_github('drieslab/GiottoClass')"},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4dimObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Dimension reductions — S3toS4dimObj","title":"Dimension reductions — S3toS4dimObj","text":"Convert S3 dimObj S4","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4dimObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dimension reductions — S3toS4dimObj","text":"","code":"S3toS4dimObj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4dimObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dimension reductions — S3toS4dimObj","text":"object S3 dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4dimObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dimension reductions — S3toS4dimObj","text":"S4 dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatGridObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatially Binned Data — S3toS4spatGridObj","title":"Spatially Binned Data — S3toS4spatGridObj","text":"convert S3 spatialGridObj S4","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatGridObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatially Binned Data — S3toS4spatGridObj","text":"","code":"S3toS4spatialGridObj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatGridObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatially Binned Data — S3toS4spatGridObj","text":"object S3 spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatGridObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatially Binned Data — S3toS4spatGridObj","text":"S4 spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial coordinates — XY","title":"Spatial coordinates — XY","text":"Directly get set xy(z) coordinates spatial subobjects (currently spatLocsObj, giottoPoints, giottoPolygon). coordinate values retrieved set matrix.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial coordinates — XY","text":"","code":"# S4 method for class 'spatLocsObj' XY(x, ...)  # S4 method for class 'spatLocsObj,matrix' XY(x) <- value  # S4 method for class 'giottoPoints' XY(x, ...)  # S4 method for class 'giottoPoints,ANY' XY(x, ...) <- value  # S4 method for class 'giottoPolygon' XY(x, ...)  # S4 method for class 'giottoPolygon,ANY' XY(x, ...) <- value  # S4 method for class 'SpatVector' XY(x, include_geom = FALSE, ...)  # S4 method for class 'SpatVector,matrix' XY(x, ...) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial coordinates — XY","text":"x object ... additional args pass value matrix. xy(z) coordinates set include_geom logical. Whether geom, part, hole terra geometry matrix included.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial coordinates — XY","text":"XY() returns matrix. XY<-() returns class x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/XY.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial coordinates — XY","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  m1 <- XY(sl) plot(sl)  XY(sl) <- m1 + 1000 plot(sl)   m2 <- XY(gpoints) plot(gpoints)  XY(gpoints) <- m2 * 2 + 1000 plot(gpoints)   m3 <- XY(gpoly) plot(gpoly)  XY(gpoly) <- m3 / 2 plot(gpoly)   XY(gpoly[1:10]) # vertices from first 10 polys #>               x         y #>   [1,] 3321.128 -2568.337 #>   [2,] 3321.356 -2568.510 #>   [3,] 3321.525 -2568.731 #>   [4,] 3321.655 -2568.978 #>   [5,] 3321.742 -2569.259 #>   [6,] 3321.794 -2569.596 #>   [7,] 3321.792 -2569.987 #>   [8,] 3321.844 -2570.324 #>   [9,] 3321.902 -2570.663 #>  [10,] 3321.831 -2571.014 #>  [11,] 3321.711 -2571.295 #>  [12,] 3321.740 -2571.389 #>  [13,] 3321.849 -2571.754 #>  [14,] 3321.902 -2572.157 #>  [15,] 3321.792 -2572.625 #>  [16,] 3321.576 -2572.893 #>  [17,] 3321.316 -2573.096 #>  [18,] 3321.015 -2573.233 #>  [19,] 3320.662 -2573.220 #>  [20,] 3320.302 -2573.113 #>  [21,] 3320.001 -2572.997 #>  [22,] 3319.680 -2572.845 #>  [23,] 3319.302 -2572.735 #>  [24,] 3318.940 -2572.772 #>  [25,] 3318.635 -2572.911 #>  [26,] 3318.329 -2572.893 #>  [27,] 3318.060 -2572.677 #>  [28,] 3317.865 -2572.481 #>  [29,] 3317.723 -2572.444 #>  [30,] 3317.379 -2572.356 #>  [31,] 3317.141 -2572.247 #>  [32,] 3316.922 -2572.078 #>  [33,] 3316.693 -2571.904 #>  [34,] 3316.528 -2571.777 #>  [35,] 3316.282 -2571.653 #>  [36,] 3316.034 -2571.461 #>  [37,] 3315.792 -2571.220 #>  [38,] 3315.648 -2570.908 #>  [39,] 3315.574 -2570.556 #>  [40,] 3315.628 -2570.146 #>  [41,] 3315.628 -2569.846 #>  [42,] 3315.680 -2569.540 #>  [43,] 3315.791 -2569.269 #>  [44,] 3315.950 -2569.001 #>  [45,] 3316.137 -2568.817 #>  [46,] 3316.189 -2568.764 #>  [47,] 3316.263 -2568.480 #>  [48,] 3316.222 -2568.074 #>  [49,] 3316.223 -2567.650 #>  [50,] 3316.522 -2567.598 #>  [51,] 3316.881 -2567.653 #>  [52,] 3317.256 -2567.754 #>  [53,] 3317.634 -2567.862 #>  [54,] 3317.995 -2567.863 #>  [55,] 3318.404 -2567.809 #>  [56,] 3318.538 -2567.777 #>  [57,] 3318.599 -2567.753 #>  [58,] 3318.634 -2567.753 #>  [59,] 3318.811 -2567.710 #>  [60,] 3319.109 -2567.599 #>  [61,] 3319.353 -2567.327 #>  [62,] 3319.517 -2567.056 #>  [63,] 3319.802 -2566.959 #>  [64,] 3320.100 -2567.152 #>  [65,] 3320.279 -2567.403 #>  [66,] 3320.443 -2567.705 #>  [67,] 3320.679 -2567.946 #>  [68,] 3320.929 -2568.141 #>  [69,] 3320.989 -2568.233 #>  [70,] 3321.128 -2568.337 #>  [71,] 3237.913 -2438.411 #>  [72,] 3238.208 -2438.540 #>  [73,] 3238.503 -2438.725 #>  [74,] 3238.739 -2438.961 #>  [75,] 3238.902 -2439.197 #>  [76,] 3239.070 -2439.493 #>  [77,] 3239.184 -2439.842 #>  [78,] 3239.284 -2440.183 #>  [79,] 3239.231 -2440.717 #>  [80,] 3239.190 -2441.019 #>  [81,] 3239.176 -2441.185 #>  [82,] 3239.104 -2441.356 #>  [83,] 3239.070 -2441.465 #>  [84,] 3238.996 -2441.610 #>  [85,] 3238.855 -2441.941 #>  [86,] 3238.642 -2442.267 #>  [87,] 3238.610 -2442.336 #>  [88,] 3238.474 -2442.643 #>  [89,] 3238.316 -2442.966 #>  [90,] 3238.113 -2443.211 #>  [91,] 3237.981 -2443.510 #>  [92,] 3237.798 -2443.795 #>  [93,] 3237.616 -2444.089 #>  [94,] 3237.484 -2444.381 #>  [95,] 3237.285 -2444.639 #>  [96,] 3237.062 -2444.862 #>  [97,] 3237.031 -2444.887 #>  [98,] 3237.018 -2444.906 #>  [99,] 3236.755 -2445.124 #> [100,] 3236.421 -2445.346 #> [101,] 3236.013 -2445.474 #> [102,] 3235.935 -2445.490 #> [103,] 3235.881 -2445.508 #> [104,] 3235.781 -2445.522 #> [105,] 3235.592 -2445.561 #> [106,] 3235.537 -2445.554 #> [107,] 3235.492 -2445.561 #> [108,] 3235.165 -2445.513 #> [109,] 3235.114 -2445.507 #> [110,] 3235.108 -2445.505 #> [111,] 3235.093 -2445.502 #> [112,] 3234.745 -2445.398 #> [113,] 3234.450 -2445.231 #> [114,] 3234.157 -2445.071 #> [115,] 3233.922 -2444.900 #> [116,] 3233.708 -2444.639 #> [117,] 3233.604 -2444.314 #> [118,] 3233.513 -2444.023 #> [119,] 3233.493 -2443.982 #> [120,] 3233.234 -2443.673 #> [121,] 3232.758 -2443.616 #> [122,] 3232.317 -2443.728 #> [123,] 3231.971 -2443.905 #> [124,] 3231.713 -2443.721 #> [125,] 3231.878 -2443.390 #> [126,] 3231.876 -2442.860 #> [127,] 3232.082 -2442.543 #> [128,] 3232.507 -2442.472 #> [129,] 3233.042 -2442.472 #> [130,] 3233.444 -2442.420 #> [131,] 3233.604 -2442.259 #> [132,] 3233.684 -2441.916 #> [133,] 3233.712 -2441.460 #> [134,] 3233.766 -2441.058 #> [135,] 3233.820 -2440.884 #> [136,] 3233.820 -2440.665 #> [137,] 3233.898 -2440.244 #> [138,] 3233.981 -2439.774 #> [139,] 3234.143 -2439.398 #> [140,] 3234.362 -2439.078 #> [141,] 3234.618 -2438.817 #> [142,] 3234.938 -2438.610 #> [143,] 3235.281 -2438.420 #> [144,] 3235.728 -2438.360 #> [145,] 3236.143 -2438.210 #> [146,] 3236.572 -2438.155 #> [147,] 3236.991 -2438.044 #> [148,] 3237.393 -2438.148 #> [149,] 3237.730 -2438.336 #> [150,] 3237.825 -2438.386 #> [151,] 3237.913 -2438.411 #> [152,] 3402.663 -2485.171 #> [153,] 3402.779 -2485.447 #> [154,] 3402.983 -2485.644 #> [155,] 3403.289 -2485.755 #> [156,] 3403.472 -2485.921 #> [157,] 3403.294 -2486.144 #> [158,] 3402.906 -2486.140 #> [159,] 3402.795 -2486.185 #> [160,] 3402.672 -2486.251 #> [161,] 3402.654 -2486.241 #> [162,] 3402.626 -2486.252 #> [163,] 3402.239 -2486.253 #> [164,] 3401.955 -2486.143 #> [165,] 3401.730 -2485.983 #> [166,] 3401.482 -2485.940 #> [167,] 3401.271 -2485.984 #> [168,] 3401.010 -2486.036 #> [169,] 3400.748 -2486.091 #> [170,] 3400.691 -2486.090 #> [171,] 3400.498 -2486.200 #> [172,] 3400.223 -2486.306 #> [173,] 3399.889 -2486.291 #> [174,] 3399.499 -2486.271 #> [175,] 3399.257 -2486.418 #> [176,] 3398.942 -2486.468 #> [177,] 3398.709 -2486.355 #> [178,] 3398.601 -2486.074 #> [179,] 3398.790 -2485.902 #> [180,] 3399.067 -2485.810 #> [181,] 3399.400 -2485.719 #> [182,] 3399.627 -2485.809 #> [183,] 3399.789 -2485.606 #> [184,] 3399.741 -2485.552 #> [185,] 3399.615 -2485.425 #> [186,] 3399.614 -2485.424 #> [187,] 3399.411 -2485.223 #> [188,] 3399.405 -2485.219 #> [189,] 3399.249 -2485.114 #> [190,] 3398.995 -2485.008 #> [191,] 3398.786 -2484.920 #> [192,] 3398.602 -2484.792 #> [193,] 3398.496 -2484.617 #> [194,] 3398.438 -2484.350 #> [195,] 3398.496 -2484.137 #> [196,] 3398.645 -2483.935 #> [197,] 3398.764 -2483.761 #> [198,] 3398.927 -2483.597 #> [199,] 3399.102 -2483.477 #> [200,] 3399.256 -2483.323 #> [201,] 3399.369 -2483.210 #> [202,] 3399.409 -2483.111 #> [203,] 3399.550 -2482.874 #> [204,] 3399.678 -2482.628 #> [205,] 3399.893 -2482.416 #> [206,] 3400.066 -2482.243 #> [207,] 3400.289 -2482.087 #> [208,] 3400.633 -2482.030 #> [209,] 3400.684 -2482.052 #> [210,] 3400.796 -2482.030 #> [211,] 3401.111 -2482.030 #> [212,] 3401.372 -2482.044 #> [213,] 3401.582 -2482.144 #> [214,] 3401.842 -2482.247 #> [215,] 3402.052 -2482.357 #> [216,] 3402.172 -2482.516 #> [217,] 3402.251 -2482.651 #> [218,] 3402.286 -2482.679 #> [219,] 3402.394 -2482.950 #> [220,] 3402.403 -2482.975 #> [221,] 3402.495 -2483.164 #> [222,] 3402.495 -2483.210 #> [223,] 3402.499 -2483.220 #> [224,] 3402.496 -2483.234 #> [225,] 3402.497 -2483.389 #> [226,] 3402.428 -2483.552 #> [227,] 3402.391 -2483.888 #> [228,] 3402.432 -2484.165 #> [229,] 3402.442 -2484.215 #> [230,] 3402.551 -2484.417 #> [231,] 3402.556 -2484.444 #> [232,] 3402.588 -2484.504 #> [233,] 3402.595 -2484.624 #> [234,] 3402.607 -2484.682 #> [235,] 3402.607 -2484.837 #> [236,] 3402.663 -2485.171 #> [237,] 3395.458 -2551.178 #> [238,] 3395.699 -2551.123 #> [239,] 3395.996 -2551.123 #> [240,] 3396.184 -2551.216 #> [241,] 3396.317 -2551.347 #> [242,] 3396.368 -2551.590 #> [243,] 3396.309 -2551.806 #> [244,] 3396.202 -2551.945 #> [245,] 3396.044 -2552.036 #> [246,] 3396.044 -2552.230 #> [247,] 3396.044 -2552.461 #> [248,] 3396.025 -2552.549 #> [249,] 3395.992 -2552.751 #> [250,] 3395.933 -2552.915 #> [251,] 3395.867 -2553.087 #> [252,] 3395.778 -2553.236 #> [253,] 3395.664 -2553.345 #> [254,] 3395.548 -2553.460 #> [255,] 3395.368 -2553.510 #> [256,] 3395.139 -2553.546 #> [257,] 3395.125 -2553.560 #> [258,] 3395.082 -2553.577 #> [259,] 3395.012 -2553.618 #> [260,] 3394.931 -2553.641 #> [261,] 3395.010 -2553.877 #> [262,] 3395.122 -2554.007 #> [263,] 3395.236 -2554.204 #> [264,] 3395.338 -2554.380 #> [265,] 3395.435 -2554.627 #> [266,] 3395.452 -2554.858 #> [267,] 3395.340 -2555.025 #> [268,] 3395.112 -2555.082 #> [269,] 3394.872 -2555.130 #> [270,] 3394.633 -2555.074 #> [271,] 3394.439 -2554.963 #> [272,] 3394.258 -2554.860 #> [273,] 3394.069 -2554.778 #> [274,] 3393.882 -2554.647 #> [275,] 3393.750 -2554.515 #> [276,] 3393.617 -2554.325 #> [277,] 3393.552 -2554.137 #> [278,] 3393.504 -2554.054 #> [279,] 3393.494 -2554.050 #> [280,] 3393.483 -2554.018 #> [281,] 3393.439 -2553.940 #> [282,] 3393.336 -2553.769 #> [283,] 3393.224 -2553.562 #> [284,] 3393.172 -2553.340 #> [285,] 3393.135 -2553.159 #> [286,] 3393.087 -2553.037 #> [287,] 3393.066 -2552.869 #> [288,] 3393.063 -2552.856 #> [289,] 3393.061 -2552.847 #> [290,] 3393.010 -2552.682 #> [291,] 3392.995 -2552.547 #> [292,] 3392.957 -2552.382 #> [293,] 3392.912 -2552.272 #> [294,] 3392.859 -2552.197 #> [295,] 3392.952 -2552.043 #> [296,] 3393.009 -2551.882 #> [297,] 3393.063 -2551.667 #> [298,] 3393.141 -2551.543 #> [299,] 3393.230 -2551.356 #> [300,] 3393.333 -2551.237 #> [301,] 3393.389 -2551.181 #> [302,] 3393.390 -2551.181 #> [303,] 3393.477 -2551.093 #> [304,] 3393.552 -2551.018 #> [305,] 3393.661 -2550.906 #> [306,] 3393.668 -2550.904 #> [307,] 3393.692 -2550.879 #> [308,] 3393.882 -2550.797 #> [309,] 3393.917 -2550.790 #> [310,] 3393.983 -2550.743 #> [311,] 3394.192 -2550.704 #> [312,] 3394.371 -2550.691 #> [313,] 3394.603 -2550.691 #> [314,] 3394.782 -2550.748 #> [315,] 3394.960 -2550.799 #> [316,] 3395.072 -2550.911 #> [317,] 3395.213 -2551.001 #> [318,] 3395.335 -2551.122 #> [319,] 3395.418 -2551.170 #> [320,] 3395.458 -2551.178 #> [321,] 3405.306 -2439.104 #> [322,] 3405.702 -2439.289 #> [323,] 3406.003 -2439.585 #> [324,] 3406.140 -2439.997 #> [325,] 3406.005 -2440.572 #> [326,] 3405.909 -2440.595 #> [327,] 3405.955 -2440.751 #> [328,] 3405.955 -2441.196 #> [329,] 3405.884 -2441.656 #> [330,] 3405.742 -2441.970 #> [331,] 3405.575 -2442.280 #> [332,] 3405.469 -2442.617 #> [333,] 3405.384 -2442.883 #> [334,] 3405.417 -2442.996 #> [335,] 3405.200 -2443.372 #> [336,] 3404.986 -2443.696 #> [337,] 3404.814 -2443.808 #> [338,] 3404.632 -2443.991 #> [339,] 3404.343 -2444.169 #> [340,] 3404.065 -2444.342 #> [341,] 3403.780 -2444.456 #> [342,] 3403.442 -2444.563 #> [343,] 3403.045 -2444.658 #> [344,] 3402.759 -2444.783 #> [345,] 3402.480 -2444.942 #> [346,] 3402.342 -2444.922 #> [347,] 3402.335 -2444.940 #> [348,] 3401.967 -2444.996 #> [349,] 3401.681 -2444.725 #> [350,] 3401.518 -2444.359 #> [351,] 3401.745 -2444.115 #> [352,] 3401.713 -2443.940 #> [353,] 3401.624 -2443.603 #> [354,] 3401.624 -2443.157 #> [355,] 3401.677 -2442.774 #> [356,] 3401.757 -2442.516 #> [357,] 3401.679 -2442.308 #> [358,] 3401.733 -2441.790 #> [359,] 3401.937 -2441.444 #> [360,] 3402.161 -2441.101 #> [361,] 3402.425 -2440.794 #> [362,] 3402.560 -2440.387 #> [363,] 3402.704 -2439.966 #> [364,] 3402.734 -2439.930 #> [365,] 3402.744 -2439.826 #> [366,] 3402.865 -2439.486 #> [367,] 3402.973 -2439.145 #> [368,] 3402.972 -2438.784 #> [369,] 3402.920 -2438.415 #> [370,] 3402.866 -2438.023 #> [371,] 3402.921 -2437.627 #> [372,] 3403.025 -2437.320 #> [373,] 3403.191 -2437.051 #> [374,] 3403.259 -2436.984 #> [375,] 3403.321 -2436.868 #> [376,] 3403.676 -2436.672 #> [377,] 3404.003 -2436.671 #> [378,] 3404.151 -2436.637 #> [379,] 3404.544 -2436.616 #> [380,] 3404.821 -2436.781 #> [381,] 3404.925 -2437.079 #> [382,] 3405.038 -2437.418 #> [383,] 3405.145 -2437.755 #> [384,] 3405.145 -2438.203 #> [385,] 3405.090 -2438.600 #> [386,] 3405.092 -2438.940 #> [387,] 3405.131 -2439.058 #> [388,] 3405.306 -2439.104 #> [389,] 3410.722 -2520.655 #> [390,] 3410.774 -2520.453 #> [391,] 3410.885 -2520.293 #> [392,] 3411.039 -2520.140 #> [393,] 3411.268 -2520.127 #> [394,] 3411.548 -2520.127 #> [395,] 3411.774 -2520.186 #> [396,] 3411.970 -2520.232 #> [397,] 3412.121 -2520.388 #> [398,] 3412.235 -2520.501 #> [399,] 3412.240 -2520.503 #> [400,] 3412.404 -2520.610 #> [401,] 3412.583 -2520.726 #> [402,] 3412.781 -2520.773 #> [403,] 3412.942 -2520.882 #> [404,] 3413.053 -2520.995 #> [405,] 3413.200 -2521.143 #> [406,] 3413.269 -2521.296 #> [407,] 3413.324 -2521.502 #> [408,] 3413.324 -2521.769 #> [409,] 3413.324 -2522.030 #> [410,] 3413.276 -2522.176 #> [411,] 3413.272 -2522.403 #> [412,] 3413.184 -2522.588 #> [413,] 3413.112 -2522.781 #> [414,] 3413.003 -2522.943 #> [415,] 3412.893 -2523.104 #> [416,] 3412.835 -2523.269 #> [417,] 3412.728 -2523.473 #> [418,] 3412.639 -2523.619 #> [419,] 3412.540 -2523.779 #> [420,] 3412.403 -2523.916 #> [421,] 3412.287 -2524.032 #> [422,] 3412.136 -2524.183 #> [423,] 3412.026 -2524.294 #> [424,] 3411.823 -2524.350 #> [425,] 3411.556 -2524.349 #> [426,] 3411.371 -2524.298 #> [427,] 3411.278 -2524.236 #> [428,] 3411.062 -2524.188 #> [429,] 3411.057 -2524.186 #> [430,] 3410.941 -2524.189 #> [431,] 3410.863 -2524.135 #> [432,] 3410.680 -2524.185 #> [433,] 3410.565 -2524.368 #> [434,] 3410.424 -2524.484 #> [435,] 3410.203 -2524.512 #> [436,] 3410.076 -2524.404 #> [437,] 3409.962 -2524.233 #> [438,] 3409.861 -2524.064 #> [439,] 3409.747 -2523.862 #> [440,] 3409.750 -2523.607 #> [441,] 3409.798 -2523.381 #> [442,] 3409.857 -2523.154 #> [443,] 3409.911 -2522.937 #> [444,] 3409.931 -2522.854 #> [445,] 3409.929 -2522.846 #> [446,] 3409.912 -2522.639 #> [447,] 3409.911 -2522.379 #> [448,] 3409.964 -2522.171 #> [449,] 3410.019 -2521.961 #> [450,] 3410.074 -2521.753 #> [451,] 3410.156 -2521.629 #> [452,] 3410.180 -2521.533 #> [453,] 3410.220 -2521.475 #> [454,] 3410.238 -2521.425 #> [455,] 3410.349 -2521.233 #> [456,] 3410.458 -2521.081 #> [457,] 3410.563 -2520.939 #> [458,] 3410.675 -2520.828 #> [459,] 3410.685 -2520.817 #> [460,] 3410.722 -2520.655 #> [461,] 3354.402 -2544.060 #> [462,] 3354.294 -2544.061 #> [463,] 3354.217 -2544.001 #> [464,] 3354.099 -2544.006 #> [465,] 3353.980 -2544.006 #> [466,] 3353.864 -2544.006 #> [467,] 3353.805 -2543.948 #> [468,] 3353.805 -2543.865 #> [469,] 3353.806 -2543.743 #> [470,] 3353.855 -2543.684 #> [471,] 3353.860 -2543.563 #> [472,] 3353.878 -2543.500 #> [473,] 3353.912 -2543.381 #> [474,] 3353.912 -2543.296 #> [475,] 3353.969 -2543.196 #> [476,] 3353.967 -2543.081 #> [477,] 3354.026 -2543.011 #> [478,] 3354.022 -2542.894 #> [479,] 3354.021 -2542.810 #> [480,] 3354.076 -2542.710 #> [481,] 3354.086 -2542.642 #> [482,] 3354.100 -2542.605 #> [483,] 3354.074 -2542.546 #> [484,] 3353.973 -2542.145 #> [485,] 3353.752 -2541.790 #> [486,] 3353.644 -2541.417 #> [487,] 3353.757 -2540.995 #> [488,] 3353.981 -2540.755 #> [489,] 3354.401 -2540.756 #> [490,] 3354.788 -2540.844 #> [491,] 3354.734 -2541.318 #> [492,] 3354.788 -2541.787 #> [493,] 3354.845 -2542.269 #> [494,] 3355.134 -2542.543 #> [495,] 3355.545 -2542.642 #> [496,] 3355.906 -2542.442 #> [497,] 3356.103 -2542.141 #> [498,] 3356.287 -2541.784 #> [499,] 3356.398 -2541.361 #> [500,] 3356.398 -2540.838 #> [501,] 3356.469 -2540.423 #> [502,] 3356.667 -2540.060 #> [503,] 3356.920 -2539.843 #> [504,] 3357.287 -2539.679 #> [505,] 3357.694 -2539.517 #> [506,] 3358.117 -2539.464 #> [507,] 3358.528 -2539.352 #> [508,] 3359.003 -2539.404 #> [509,] 3359.308 -2539.614 #> [510,] 3359.614 -2539.815 #> [511,] 3359.979 -2539.960 #> [512,] 3360.397 -2540.107 #> [513,] 3360.815 -2540.216 #> [514,] 3360.944 -2540.561 #> [515,] 3360.832 -2541.182 #> [516,] 3360.672 -2541.520 #> [517,] 3360.232 -2541.576 #> [518,] 3359.810 -2541.725 #> [519,] 3359.759 -2542.167 #> [520,] 3359.541 -2542.499 #> [521,] 3359.376 -2542.863 #> [522,] 3359.072 -2543.034 #> [523,] 3358.708 -2543.083 #> [524,] 3358.403 -2542.873 #> [525,] 3358.183 -2542.600 #> [526,] 3357.951 -2542.305 #> [527,] 3357.589 -2542.440 #> [528,] 3357.270 -2542.653 #> [529,] 3356.999 -2542.924 #> [530,] 3356.723 -2543.146 #> [531,] 3356.359 -2543.346 #> [532,] 3356.106 -2543.599 #> [533,] 3355.855 -2543.851 #> [534,] 3355.548 -2544.105 #> [535,] 3355.273 -2544.332 #> [536,] 3354.833 -2544.278 #> [537,] 3354.513 -2544.060 #> [538,] 3354.513 -2544.060 #> [539,] 3354.402 -2544.060 #> [540,] 3449.139 -2505.144 #> [541,] 3449.139 -2505.540 #> [542,] 3449.139 -2505.935 #> [543,] 3449.139 -2506.330 #> [544,] 3449.139 -2506.726 #> [545,] 3449.139 -2507.121 #> [546,] 3449.086 -2507.520 #> [547,] 3448.979 -2507.790 #> [548,] 3448.816 -2508.055 #> [549,] 3448.688 -2508.290 #> [550,] 3448.556 -2508.462 #> [551,] 3448.468 -2508.613 #> [552,] 3448.326 -2508.869 #> [553,] 3448.218 -2509.086 #> [554,] 3448.055 -2509.342 #> [555,] 3447.894 -2509.517 #> [556,] 3447.679 -2509.680 #> [557,] 3447.457 -2509.791 #> [558,] 3447.201 -2509.899 #> [559,] 3447.167 -2509.908 #> [560,] 3447.139 -2509.943 #> [561,] 3447.087 -2510.281 #> [562,] 3447.082 -2510.569 #> [563,] 3446.976 -2510.817 #> [564,] 3446.699 -2510.705 #> [565,] 3446.568 -2510.457 #> [566,] 3446.430 -2510.220 #> [567,] 3446.156 -2510.061 #> [568,] 3445.890 -2509.955 #> [569,] 3445.631 -2509.787 #> [570,] 3445.568 -2509.742 #> [571,] 3445.429 -2509.676 #> [572,] 3445.228 -2509.556 #> [573,] 3445.028 -2509.357 #> [574,] 3444.865 -2509.193 #> [575,] 3444.724 -2508.939 #> [576,] 3444.647 -2508.688 #> [577,] 3444.646 -2508.317 #> [578,] 3444.599 -2507.955 #> [579,] 3444.537 -2507.696 #> [580,] 3444.428 -2507.412 #> [581,] 3444.430 -2507.069 #> [582,] 3444.486 -2506.757 #> [583,] 3444.539 -2506.487 #> [584,] 3444.684 -2506.242 #> [585,] 3444.752 -2505.947 #> [586,] 3444.876 -2505.722 #> [587,] 3445.029 -2505.514 #> [588,] 3445.230 -2505.313 #> [589,] 3445.405 -2505.138 #> [590,] 3445.582 -2504.960 #> [591,] 3445.782 -2504.760 #> [592,] 3445.992 -2504.653 #> [593,] 3446.214 -2504.484 #> [594,] 3446.451 -2504.384 #> [595,] 3446.710 -2504.272 #> [596,] 3447.026 -2504.217 #> [597,] 3447.118 -2504.201 #> [598,] 3447.373 -2504.110 #> [599,] 3447.719 -2504.014 #> [600,] 3447.897 -2504.014 #> [601,] 3448.058 -2504.274 #> [602,] 3448.273 -2504.435 #> [603,] 3448.494 -2504.604 #> [604,] 3448.706 -2504.814 #> [605,] 3448.973 -2504.919 #> [606,] 3448.984 -2504.934 #> [607,] 3448.986 -2504.934 #> [608,] 3448.986 -2504.936 #> [609,] 3449.139 -2505.144 #> [610,] 3277.795 -2513.815 #> [611,] 3278.047 -2513.923 #> [612,] 3278.234 -2514.048 #> [613,] 3278.439 -2514.194 #> [614,] 3278.630 -2514.385 #> [615,] 3278.771 -2514.584 #> [616,] 3278.872 -2514.829 #> [617,] 3278.872 -2515.188 #> [618,] 3278.818 -2515.529 #> [619,] 3278.696 -2515.721 #> [620,] 3278.500 -2515.870 #> [621,] 3278.276 -2516.038 #> [622,] 3278.000 -2516.091 #> [623,] 3277.643 -2516.091 #> [624,] 3277.337 -2516.036 #> [625,] 3277.088 -2515.927 #> [626,] 3276.893 -2515.791 #> [627,] 3276.704 -2515.603 #> [628,] 3276.536 -2515.440 #> [629,] 3276.379 -2515.223 #> [630,] 3276.313 -2515.197 #> [631,] 3276.293 -2515.204 #> [632,] 3276.044 -2515.224 #> [633,] 3275.791 -2515.281 #> [634,] 3275.539 -2515.223 #> [635,] 3275.299 -2515.175 #> [636,] 3275.137 -2515.061 #> [637,] 3274.976 -2514.900 #> [638,] 3274.810 -2514.737 #> [639,] 3274.702 -2514.575 #> [640,] 3274.592 -2514.361 #> [641,] 3274.532 -2514.127 #> [642,] 3274.487 -2513.877 #> [643,] 3274.487 -2513.571 #> [644,] 3274.487 -2513.266 #> [645,] 3274.541 -2513.014 #> [646,] 3274.595 -2512.757 #> [647,] 3274.648 -2512.518 #> [648,] 3274.758 -2512.313 #> [649,] 3274.843 -2512.118 #> [650,] 3274.905 -2511.978 #> [651,] 3274.920 -2511.897 #> [652,] 3275.030 -2511.652 #> [653,] 3275.174 -2511.496 #> [654,] 3275.226 -2511.459 #> [655,] 3275.295 -2511.331 #> [656,] 3275.405 -2511.169 #> [657,] 3275.544 -2510.980 #> [658,] 3275.678 -2510.791 #> [659,] 3275.830 -2510.638 #> [660,] 3275.973 -2510.497 #> [661,] 3276.164 -2510.357 #> [662,] 3276.372 -2510.262 #> [663,] 3276.420 -2510.259 #> [664,] 3276.436 -2510.247 #> [665,] 3276.703 -2510.138 #> [666,] 3276.987 -2510.198 #> [667,] 3277.240 -2510.305 #> [668,] 3277.380 -2510.495 #> [669,] 3277.522 -2510.686 #> [670,] 3277.625 -2510.935 #> [671,] 3277.737 -2511.180 #> [672,] 3277.738 -2511.535 #> [673,] 3277.794 -2511.816 #> [674,] 3277.792 -2512.093 #> [675,] 3277.793 -2512.399 #> [676,] 3277.846 -2512.650 #> [677,] 3277.846 -2512.954 #> [678,] 3277.792 -2513.208 #> [679,] 3277.733 -2513.460 #> [680,] 3277.731 -2513.715 #> [681,] 3277.731 -2513.721 #> [682,] 3277.795 -2513.815 #> [683,] 3410.037 -2453.522 #> [684,] 3409.858 -2453.624 #> [685,] 3409.686 -2453.790 #> [686,] 3409.405 -2453.733 #> [687,] 3409.129 -2453.692 #> [688,] 3408.849 -2453.629 #> [689,] 3408.629 -2453.522 #> [690,] 3408.411 -2453.415 #> [691,] 3408.178 -2453.306 #> [692,] 3407.952 -2453.191 #> [693,] 3407.765 -2453.092 #> [694,] 3407.602 -2452.925 #> [695,] 3407.396 -2452.771 #> [696,] 3407.395 -2451.343 #> [697,] 3407.602 -2451.241 #> [698,] 3407.600 -2451.035 #> [699,] 3407.462 -2450.781 #> [700,] 3407.548 -2450.596 #> [701,] 3407.702 -2450.389 #> [702,] 3407.879 -2450.260 #> [703,] 3407.916 -2450.174 #> [704,] 3408.083 -2450.007 #> [705,] 3408.249 -2449.841 #> [706,] 3408.423 -2449.722 #> [707,] 3408.629 -2449.565 #> [708,] 3408.813 -2449.466 #> [709,] 3409.040 -2449.322 #> [710,] 3409.074 -2449.304 #> [711,] 3409.076 -2449.303 #> [712,] 3409.327 -2449.141 #> [713,] 3409.544 -2449.027 #> [714,] 3409.815 -2448.919 #> [715,] 3410.085 -2448.867 #> [716,] 3410.332 -2448.759 #> [717,] 3410.640 -2448.704 #> [718,] 3410.946 -2448.650 #> [719,] 3411.251 -2448.709 #> [720,] 3411.549 -2448.757 #> [721,] 3411.765 -2448.866 #> [722,] 3411.981 -2449.031 #> [723,] 3412.090 -2449.252 #> [724,] 3412.238 -2449.507 #> [725,] 3412.415 -2449.680 #> [726,] 3412.579 -2449.846 #> [727,] 3412.736 -2450.055 #> [728,] 3412.899 -2450.272 #> [729,] 3413.009 -2450.489 #> [730,] 3412.917 -2450.708 #> [731,] 3412.735 -2450.938 #> [732,] 3412.739 -2451.296 #> [733,] 3412.706 -2451.602 #> [734,] 3412.526 -2451.790 #> [735,] 3412.358 -2451.956 #> [736,] 3412.077 -2452.001 #> [737,] 3411.990 -2452.065 #> [738,] 3411.866 -2452.175 #> [739,] 3411.657 -2452.330 #> [740,] 3411.473 -2452.514 #> [741,] 3411.328 -2452.713 #> [742,] 3411.176 -2452.923 #> [743,] 3411.008 -2453.141 #> [744,] 3410.791 -2453.251 #> [745,] 3410.433 -2453.245 #> [746,] 3410.200 -2453.411 #> [747,] 3410.146 -2453.438 #> [748,] 3410.037 -2453.522"},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Active feature type — activeFeatType-generic","title":"Active feature type — activeFeatType-generic","text":"Retrieve set active feature type. value default feature type giotto object uses.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Active feature type — activeFeatType-generic","text":"","code":"# S4 method for class 'giotto' activeFeatType(gobject)  # S4 method for class 'giotto,character' activeFeatType(gobject) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Active feature type — activeFeatType-generic","text":"gobject giotto object value feat_type set default","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Active feature type — activeFeatType-generic","text":"active feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeFeatType-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Active feature type — activeFeatType-generic","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" activeFeatType(g) #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Active spatial unit — activeSpatUnit-generic","title":"Active spatial unit — activeSpatUnit-generic","text":"Retrieve set active spatial unit. value default spatial unit giotto object uses.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Active spatial unit — activeSpatUnit-generic","text":"","code":"# S4 method for class 'giotto' activeSpatUnit(gobject)  # S4 method for class 'giotto,character' activeSpatUnit(gobject) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Active spatial unit — activeSpatUnit-generic","text":"gobject giotto object value spat_unit set default","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Active spatial unit — activeSpatUnit-generic","text":"active spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/activeSpatUnit-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Active spatial unit — activeSpatUnit-generic","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" activeSpatUnit(g) #> [1] \"cell\""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Add cell metadata — addCellMetadata","title":"Add cell metadata — addCellMetadata","text":"Adds cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add cell metadata — addCellMetadata","text":"","code":"addCellMetadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   new_metadata,   vector_name = NULL,   by_column = FALSE,   column_cell_ID = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add cell metadata — addCellMetadata","text":"gobject giotto object spat_unit spatial unit feat_type feature type new_metadata new cell metadata use (data.table, data.frame, vector, factor, ...) vector_name (optional) custom name new metadata column single vector factor provided by_column merge metadata based cell_ID column pDataDT (default = FALSE) column_cell_ID column name new metadata use by_column = TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add cell metadata — addCellMetadata","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add cell metadata — addCellMetadata","text":"can add additional cell metadata several manners: 1. Provide data.frame-like object, vector, factor cell annotations order cell_ID column pDataDT(gobject). bit risky recommended. 2. Provide data.frame-like object cell annotations specify column contains cell IDs, cell IDs need match cell_ID column pDataDT(gobject) 3. Provide vector factor named cell IDs correspond . names matched cell_ID column pDataDT(gobject).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add cell metadata — addCellMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  m <- pDataDT(g) m <- m[, c(\"cell_ID\", \"leiden_clus\")] m$cell_type <- paste0(\"cell_type_\", m$leiden_clus) m <- m[, c(\"cell_ID\", \"cell_type\")]  g <- addCellMetadata(     g,     new_metadata = m,     by_column = TRUE,     column_cell_ID = \"cell_ID\" )  pDataDT(g) #>                 cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                  <char>     <int>    <int>      <num>      <num>       <num> #>   1: AACTCGATGGCGCAGT-1         1      265   41.79811  1057.9308           2 #>   2: GGCTGGCTAGCTTAAA-1         1      279   44.00631  1064.7493           5 #>   3: GACGCCTGTTGCAGGG-1         1      219   34.54259   964.9294           2 #>   4: GAGGGCATCGCGTATC-1         1      294   46.37224  1142.7664           2 #>   5: TCAACACATTGGGTAA-1         1      261   41.16719  1063.3517           2 #>  ---                                                                         #> 620: GGTAGTGCTCGCACCA-1         1      179   28.23344   768.4749           5 #> 621: AAGCTCGTGCCAAGTC-1         1      195   30.75710   756.0675           5 #> 622: TATTCAATTCTAATCC-1         1      247   38.95899   921.8264           5 #> 623: TTCAAAGTCTCTAGCC-1         1      384   60.56782   916.5929           6 #> 624: TTGAATATGGACTTTC-1         1      380   59.93691   912.3051           6 #>      custom_leiden   cell_type #>              <num>      <char> #>   1:             4 cell_type_2 #>   2:             3 cell_type_5 #>   3:             3 cell_type_2 #>   4:             3 cell_type_2 #>   5:             3 cell_type_2 #>  ---                           #> 620:             4 cell_type_5 #> 621:             4 cell_type_5 #> 622:             4 cell_type_5 #> 623:             7 cell_type_6 #> 624:             4 cell_type_6"},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Add feature metadata — addFeatMetadata","title":"Add feature metadata — addFeatMetadata","text":"Adds feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add feature metadata — addFeatMetadata","text":"","code":"addFeatMetadata(   gobject,   feat_type = NULL,   spat_unit = NULL,   new_metadata,   vector_name = NULL,   by_column = FALSE,   column_feat_ID = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add feature metadata — addFeatMetadata","text":"gobject giotto object feat_type feature type spat_unit spatial unit new_metadata new metadata use) vector_name (optional) custom name provide single vector by_column merge metadata based feat_ID column fDataDT column_feat_ID column name new metadata use by_column = TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add feature metadata — addFeatMetadata","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add feature metadata — addFeatMetadata","text":"can add additional feature metadata several manners: 1. Provide data.table data.frame feature annotations order feat_ID column fDataDT(gobject) bit risky recommended. 2. Provide data.table data.frame feature annotations specify column contains feature IDs, feature IDs need match feat_ID column fDataDT(gobject) 3. Provide vector factor named feature IDs correspond . names matched feat_ID column fDataDT(gobject).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addFeatMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add feature metadata — addFeatMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  m <- fDataDT(g) m <- m[, \"feat_ID\"] m$new_feat_ID <- paste0(\"gene_\", m$feat_ID)  g <- addFeatMetadata(     g,     new_metadata = m,     by_column = TRUE,     column_feat_ID = \"feat_ID\" )  fDataDT(g) #>            feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det #>             <char>    <int>      <num>      <num>     <num>         <num> #>   1:         Gna12      502  80.448718  1987.1333 3.1845085      3.958433 #>   2:         Ccnd2      357  57.211538  1254.4730 2.0103734      3.513930 #>   3:        Btbd17      252  40.384615   781.9747 1.2531645      3.103074 #>   4:          Sox9      309  49.519231  1019.7255 1.6341755      3.300083 #>   5:          Sez6      504  80.769231  2177.4740 3.4895416      4.320385 #>  ---                                                                      #> 630:        Lhfpl3      235  37.660256   732.3595 1.1736530      3.116423 #> 631: C030029H02Rik       72  11.538462   203.0811 0.3254506      2.820572 #> 632:       Gm19935       57   9.134615   172.1079 0.2758139      3.019436 #> 633: 9630013A20Rik       52   8.333333   157.2602 0.2520196      3.024235 #> 634: 2900040C04Rik       61   9.775641   179.7015 0.2879831      2.945926 #>         hvf        new_feat_ID #>      <char>             <char> #>   1:     no         gene_Gna12 #>   2:     no         gene_Ccnd2 #>   3:     no        gene_Btbd17 #>   4:     no          gene_Sox9 #>   5:     no          gene_Sez6 #>  ---                           #> 630:     no        gene_Lhfpl3 #> 631:     no gene_C030029H02Rik #> 632:     no       gene_Gm19935 #> 633:     no gene_9630013A20Rik #> 634:     no gene_2900040C04Rik"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"addGiottoImage — addGiottoImage","title":"addGiottoImage — addGiottoImage","text":"Adds lists giottoImages giottoLargeImages gobjects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addGiottoImage — addGiottoImage","text":"","code":"addGiottoImage(   gobject = NULL,   images = NULL,   largeImages = NULL,   spat_loc_name = NULL,   scale_factor = NULL,   negative_y = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addGiottoImage — addGiottoImage","text":"gobject gobject add images objects images list giotto images add largeImages deprecated spat_loc_name provide spatial location slot Giotto align giottoImages. Defaults first one scale_factor provide scale image pixel dimensions relative spatial coordinates. negative_y Map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addGiottoImage — addGiottoImage","text":"updated Giotto object access list images","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addGiottoImage — addGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  addGiottoImage(g, largeImages = list(g_image)) #> Warning: The `largeImages` argument of `addGiottoImage()` is deprecated as of #> GiottoClass 0.3.0. #> ℹ Please use the `images` argument instead. #> ℹ All images should be supplied to `images` instead #> ℹ Names of images may not overlap #>  #> alignment has already been used, will be overwritten #> > image 'alignment' already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":null,"dir":"Reference","previous_headings":"","what":"addGiottoImageMG — addGiottoImageMG","title":"addGiottoImageMG — addGiottoImageMG","text":"Adds giotto image objects giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addGiottoImageMG — addGiottoImageMG","text":"","code":"addGiottoImageMG(   gobject,   images,   spat_unit = NULL,   spat_loc_name = NULL,   scale_factor = NULL,   negative_y = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addGiottoImageMG — addGiottoImageMG","text":"gobject giotto object images list giotto image objects, see createGiottoImage spat_unit spatial unit spat_loc_name provide spatial location slot Giotto align images. Defaults first one scale_factor provide scale image pixel dimensions relative spatial coordinates. negative_y Map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addGiottoImageMG — addGiottoImageMG","text":"updated Giotto object access list images","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoImageMG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addGiottoImageMG — addGiottoImageMG","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  addGiottoImageMG(g, images = list(g_image)) #> Warning: image [1] is not a giotto image object #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"addGiottoLargeImage — addGiottoLargeImage","title":"addGiottoLargeImage — addGiottoLargeImage","text":"Add giotto image objects giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addGiottoLargeImage — addGiottoLargeImage","text":"","code":"addGiottoLargeImage(   gobject = NULL,   largeImages = NULL,   spat_loc_name = NULL,   scale_factor = NULL,   negative_y = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addGiottoLargeImage — addGiottoLargeImage","text":"gobject giotto object largeImages list giottoLargeImage objects spat_loc_name provide spatial location slot Giotto align images. (optional) scale_factor provide scale image pixel dimensions relative spatial coordinates. negative_y map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left. verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addGiottoLargeImage — addGiottoLargeImage","text":"updated Giotto object access list images","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addGiottoLargeImage — addGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  addGiottoLargeImage(g, largeImages = list(g_image)) #>  #> alignment has already been used, will be overwritten #> > image 'alignment' already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Add subcellular giotto points object to giotto object — addGiottoPoints","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"Adds Giotto points existing Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"","code":"addGiottoPoints(gobject, gpoints)  addGiottoPoints3D(gobject, coords, feat_type = \"rna\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"gobject giotto object gpoints list giotto point objects, see createGiottoPoints coords data.frame spatVector least xyz coordinates feature ids. feat_type character. feat_type must previously exist Giotto object. Default = \"rna\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add subcellular giotto points object to giotto object — addGiottoPoints","text":"","code":"x_points <- GiottoData::loadSubObjectMini(\"giottoPoints\") x_expression <- matrix(seq_len(337 * 2), nrow = 337) rownames(x_expression) <- unique(x_points$feat_ID) g <- createGiottoObject(expression = x_expression) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed  g <- addGiottoPoints(gobject = g, gpoints = list(x_points))"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Add giotto polygons to giotto object — addGiottoPolygons","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"Adds Giotto polygon existing Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"","code":"addGiottoPolygons(gobject, gpolygons)"},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"gobject giotto object gpolygons list giotto polygon objects, see createGiottoPolygonsFromMask createGiottoPolygonsFromDfr","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addGiottoPolygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add giotto polygons to giotto object — addGiottoPolygons","text":"","code":"x <- GiottoData::loadSubObjectMini(\"giottoPolygon\") g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  g <- addGiottoPolygons(gobject = g, gpolygons = list(x))"},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":null,"dir":"Reference","previous_headings":"","what":"addNetworkLayout — addNetworkLayout","title":"addNetworkLayout — addNetworkLayout","text":"Add network layout selected nearest neighbor network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addNetworkLayout — addNetworkLayout","text":"","code":"addNetworkLayout(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_network_to_use = \"sNN\",   network_name = \"sNN.pca\",   layout_type = c(\"drl\"),   options_list = NULL,   layout_name = \"layout\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addNetworkLayout — addNetworkLayout","text":"gobject giotto object spat_unit spatial unit feat_type feature type nn_network_to_use kNN sNN network_name name NN network used layout_type layout algorithm use options_list list options selected layout layout_name name layout return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addNetworkLayout — addNetworkLayout","text":"giotto object updated layout selected NN network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"addNetworkLayout — addNetworkLayout","text":"function creates layout coordinates based provided kNN sNN. Currently force-directed graph layout \"drl\", see layout_with_drl, implemented. provides alternative tSNE UMAP based visualizations.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addNetworkLayout.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addNetworkLayout — addNetworkLayout","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  addNetworkLayout(g) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":null,"dir":"Reference","previous_headings":"","what":"addSpatialCentroidLocations — addSpatialCentroidLocations","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"Calculates centroid locations polygons within one selected layers","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"","code":"addSpatialCentroidLocations(   gobject,   poly_info = \"cell\",   feat_type = NULL,   spat_loc_name = \"raw\",   provenance = poly_info,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"gobject giotto object poly_info polygon information feat_type feature type spat_loc_name name give created spatial locations provenance (optional) provenance assign generated spatLocsObj. provided, provenance default poly_info return_gobject return giotto object (default: TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"return_gobject = TRUE giotto object containing calculated polygon centroids returned. return_gobject = FALSE generated polygon centroids returned spatLocObj.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addSpatialCentroidLocations — addSpatialCentroidLocations","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  addSpatialCentroidLocations(g, poly_info = \"aggregate\") #> Start centroid calculation for polygon information #>  layer: aggregate #> > spatial locations for polygon information layer \" aggregate \" and name \" raw #>  \" already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":null,"dir":"Reference","previous_headings":"","what":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"Calculates centroid locations polygons within one selected layer","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"","code":"addSpatialCentroidLocationsLayer(   gobject,   poly_info = \"cell\",   feat_type = NULL,   provenance = poly_info,   spat_loc_name = \"raw\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"gobject giotto object poly_info polygon information feat_type feature type provenance (optional) provenance assign generated spatLocsObj. provided, provenance default poly_info spat_loc_name name give created spatial locations return_gobject return giotto object (default: TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"return_gobject = TRUE giotto object containing calculated polygon centroids returned. return_gobject = FALSE generated polygon centroids returned spatLocsObj.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/addSpatialCentroidLocationsLayer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"addSpatialCentroidLocationsLayer — addSpatialCentroidLocationsLayer","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  addSpatialCentroidLocationsLayer(g, poly_info = \"aggregate\") #> > spatial locations for polygon information layer \" aggregate \" and name \" raw #>  \" already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":null,"dir":"Reference","previous_headings":"","what":"Add alpha channel to image array — add_img_array_alpha","title":"Add alpha channel to image array — add_img_array_alpha","text":"Add alpha channel image array","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add alpha channel to image array — add_img_array_alpha","text":"","code":"add_img_array_alpha(x, alpha)"},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add alpha channel to image array — add_img_array_alpha","text":"x image array use alpha global alpha value use. Numeric. Scales 0 1, 0 fully transparent 1 fully visible","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add alpha channel to image array — add_img_array_alpha","text":"image array 4th channel transparency","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Add alpha channel to image array — add_img_array_alpha","text":"Add 4th alpha channel 3 channel RGB image arrays","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/add_img_array_alpha.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add alpha channel to image array — add_img_array_alpha","text":"","code":"x <- matrix(rnorm(4), nrow = 2)  add_img_array_alpha(x, alpha = 0.1) #> , , 1 #>  #>            [,1]       [,2] #> [1,] -0.8289657 -0.8621887 #> [2,] -0.8413987  0.6702333 #>  #> , , 2 #>  #>            [,1]       [,2] #> [1,] -0.8289657 -0.8621887 #> [2,] -0.8413987  0.6702333 #>  #> , , 3 #>  #>            [,1]       [,2] #> [1,] -0.8289657 -0.8621887 #> [2,] -0.8413987  0.6702333 #>  #> , , 4 #>  #>      [,1] [,2] #> [1,]  0.1  0.1 #> [2,]  0.1  0.1 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":null,"dir":"Reference","previous_headings":"","what":"Affine transformations — affine","title":"Affine transformations — affine","text":"Apply affine transformation matrix spatial object. Currently works 2D transforms.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Affine transformations — affine","text":"","code":"# S4 method for class 'giotto,matrix' affine(   x,   y,   inv = FALSE,   spat_unit = \":all:\",   feat_type = \":all:\",   images = \":all:\",   ... )  # S4 method for class 'missing,missing' affine(x)  # S4 method for class 'ANY,missing' affine(x)  # S4 method for class 'ANY,affine2d' affine(x, y, ...)  # S4 method for class 'SpatVector,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'giottoPoints,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'giottoPolygon,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'spatLocsObj,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'giottoLargeImage,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'giottoAffineImage,matrix' affine(x, y, inv = FALSE, ...)  # S4 method for class 'affine2d,matrix' affine(x, y, inv = FALSE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Affine transformations — affine","text":"x object affine transform matrix y matrix coercible matrix (affine2d). matrix either 2 3 columns (linear affine). inv logical. Whether inverse affine transform applied. spat_unit character vector. spatial units affect. :: token affect can used. feat_type character vector. feature types affect. :: token affect can used. images character vector. Images affect. :: token affect can used. ... additional args pass (none implemented)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Affine transformations — affine","text":"affine transformed object affine2d matrix passed x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/affine.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Affine transformations — affine","text":"","code":"m <- diag(rep(1, 3)) trans_m <- matrix(c(1, 0, 0, 0, 1, 0, 200, 300, 1), nrow = 3) scale_m <- matrix(c(2, 0, 0, 0, 3, 0, 0, 0, 1), nrow = 3) aff_m <- matrix(c(2, 3, 0, 0.2, 3, 0, 100, 29, 1), nrow = 3)  gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\") gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  # creation of affine2d aff <- affine(m) aff <- spin(flip(shear(aff, fx = 0.2)), 45) plot(aff) # blue is start, red is end   # giottoPoints ############################################## plot(gpoints)  plot(affine(gpoints, trans_m))   # giottoPolygon ############################################# plot(gpoly)  plot(affine(gpoly, scale_m))  plot(affine(gpoly, aff)) # affine() with `affine2d`   # spatLocsObj ############################################### plot(affine(sl, m))  plot(affine(sl, trans_m))  plot(affine(sl, scale_m))  # this transformation can be inverted aff_sl <- affine(sl, aff_m) plot(aff_sl)  plot(affine(aff_sl, aff_m, inv = TRUE))"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacks — aggregateStacks","title":"aggregateStacks — aggregateStacks","text":"aggregate expression matrices different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacks — aggregateStacks","text":"","code":"aggregateStacks(   gobject,   spat_units,   feat_type,   values,   summarize_expression = \"sum\",   summarize_locations = \"mean\",   for_loop = FALSE,   for_loop_group_size = 100,   new_spat_unit = \"aggregate\",   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacks — aggregateStacks","text":"gobject giotto object spat_units spatial units aggregate feat_type feature type values values use summarize_expression method summarize expression information summarize_locations method summarize spatial location information for_loop aggregate polygons loop (default = FALSE) for_loop_group_size size polygon groups aggregate loop new_spat_unit new name aggregated spatial unit verbose verbosity","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacks — aggregateStacks","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"aggregateStacks — aggregateStacks","text":"Combines aggregateStacksExpression aggregateStacksLocations","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacks — aggregateStacks","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacks(g,     spat_units = c(\"z0\", \"z1\"), feat_type = \"rna\",     values = \"raw\" ) #> 1. Start aggregating expression data #> > raw already exists and will be replaced with new values #> > Cell metadata for spat_unit \" aggregate \" and feat_type \" rna \" already #>  exists and will be replaced with new metadata. #> Setting cell metadata [aggregate][rna] #> > Feat metadata for spat_unit \" aggregate \" and feat_type \" rna \" already #>  exists and will be replaced with new metadata. #> Setting feature metadata [aggregate][rna] #> 1. Aggregating expression data completed #> 2. Start aggregating Polygon data #> 2. Aggregating polygon data completed #> 3. Start aggregating centroid location data #> Start centroid calculation for polygon information #>  layer: aggregate #> > spatial locations for polygon information layer \" aggregate \" and name \" raw #>  \" already exists and will be replaced #> 3. Aggregating centroid location data completed #> 4. Start aggregating polygon overlap data #> 4. Aggregating polygon overlap data completed #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksExpression — aggregateStacksExpression","title":"aggregateStacksExpression — aggregateStacksExpression","text":"aggregate expression matrices different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksExpression — aggregateStacksExpression","text":"","code":"aggregateStacksExpression(   gobject,   spat_units,   feat_type,   values = \"raw\",   summarize = \"sum\",   new_spat_unit = \"aggregate\",   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksExpression — aggregateStacksExpression","text":"gobject giotto object spat_units spatial units aggregate feat_type feature type values values use summarize method summarize expression information new_spat_unit new name aggregated spatial unit verbose verbosity","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksExpression — aggregateStacksExpression","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksExpression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacksExpression — aggregateStacksExpression","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacksExpression(g, spat_units = c(\"z0\", \"z1\"), feat_type = \"rna\") #> > raw already exists and will be replaced with new values #> > Cell metadata for spat_unit \" aggregate \" and feat_type \" rna \" already #>  exists and will be replaced with new metadata. #> Setting cell metadata [aggregate][rna] #> > Feat metadata for spat_unit \" aggregate \" and feat_type \" rna \" already #>  exists and will be replaced with new metadata. #> Setting feature metadata [aggregate][rna] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksLocations — aggregateStacksLocations","title":"aggregateStacksLocations — aggregateStacksLocations","text":"aggregate expression matrices different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksLocations — aggregateStacksLocations","text":"","code":"aggregateStacksLocations(   gobject,   spat_units,   values = \"raw\",   summarize = \"mean\",   new_spat_unit = \"aggregate\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksLocations — aggregateStacksLocations","text":"gobject giotto object spat_units spatial units aggregate values values use summarize method summarize spatial location information new_spat_unit new name aggregated spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksLocations — aggregateStacksLocations","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksLocations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacksLocations — aggregateStacksLocations","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacksLocations(g, spat_units = c(\"z0\", \"z1\")) #> > raw already exists and will be replaced with new spatial #>  locations #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"aggregate polygons overlap information different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"","code":"aggregateStacksPolygonOverlaps(   gobject,   spat_units,   feat_type,   new_spat_unit = \"aggregate\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"gobject giotto object spat_units spatial units aggregate feat_type feature type used overlap calculations new_spat_unit new name aggregated spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonOverlaps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacksPolygonOverlaps — aggregateStacksPolygonOverlaps","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacksPolygonOverlaps(g,     spat_units = c(\"z0\", \"z1\"),     feat_type = \"rna\" ) #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksPolygons — aggregateStacksPolygons","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"aggregate polygons different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"","code":"aggregateStacksPolygons(   gobject,   spat_units,   new_spat_unit = \"aggregate\",   for_loop = FALSE,   for_loop_group_size = 100 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"gobject giotto object spat_units spatial units aggregate new_spat_unit new name aggregated spatial unit for_loop aggregate polygons loop (default = FALSE) for_loop_group_size size polygon groups aggregate loop","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"aggregateStacksPolygons — aggregateStacksPolygons","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  aggregateStacksPolygons(g, spat_units = c(\"z0\", \"z1\")) #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert anndata to Giotto — anndataToGiotto","title":"Convert anndata to Giotto — anndataToGiotto","text":"Converts spatial anndata (e.g. scanpy) .h5ad file Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert anndata to Giotto — anndataToGiotto","text":"","code":"anndataToGiotto(   anndata_path = NULL,   n_key_added = NULL,   spatial_n_key_added = NULL,   delaunay_spat_net = TRUE,   spat_unit = NULL,   feat_type = NULL,   h5_file = NULL,   python_path = NULL,   env_name = \"giotto_env\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert anndata to Giotto — anndataToGiotto","text":"anndata_path path .h5ad file n_key_added equivalent \"key_added\" argument scanpy.pp. neighbors(). multiple spatial networks anndata object, list key_added terms may provided. converting anndata object giottoToAnnData, .txt file may provided, generated function, .e. {spat_unit}_{feat_type}_nn_network_keys_added.txt. \"spatial\". becomes name nearest network gobject. spatial_n_key_added equivalent \"key_added\" argument squidpy.gr.spatial_neighbors. multiple spatial networks anndata object, list key_added terms may provided. converting anndata object giottoToAnnData, .txt file may provided, generated function, .e. {spat_unit}_{feat_type}_spatial_network_keys_added.txt n_key_added. delaunay_spat_net binary parameter spatial network. TRUE, spatial network delaunay network. spat_unit desired spatial unit use conversion, default NULL feat_type desired feature type use conversion, default NULL h5_file name create -disk HDF5 file python_path path python executable within conda/miniconda environment env_name name environment containing python_path executable","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert anndata to Giotto — anndataToGiotto","text":"Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/anndataToGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert anndata to Giotto — anndataToGiotto","text":"Function beta. Converts .h5ad file Giotto object. returned Giotto Object take default instructions exception python path, may customized. See changeGiottoInstructions modify instructions creation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Annotate Giotto object — annotateGiotto","title":"Annotate Giotto object — annotateGiotto","text":"Map user provided annotations/labels based another existing metadata column (usually clustering labels)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate Giotto object — annotateGiotto","text":"","code":"annotateGiotto(   gobject,   spat_unit = NULL,   feat_type = NULL,   annotation_vector = NULL,   cluster_column = NULL,   name = \"cell_types\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Annotate Giotto object — annotateGiotto","text":"gobject giotto object spat_unit spatial unit feat_type feature type annotation_vector named character vector. Vector names labels cluster column. Labels assign vector values. cluster_column character. Cell metaadata column map annotation values based . name new name annotation column","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Annotate Giotto object — annotateGiotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Annotate Giotto object — annotateGiotto","text":"need specify (cluster) column want annotate need provide annotation vector like : 1. identify cell type cluster 2. create vector cell types, e.g. cell_types =  c('T-cell', 'B-cell', 'Stromal') 3. provide original cluster names previous vector, e.g. names(cell_types) = c(2, 1, 3)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Annotate Giotto object — annotateGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  annotation <- c(     \"1\" = \"cell_type_1\",     \"2\" = \"cell_type_2\",     \"3\" = \"cell_type_3\",     \"4\" = \"cell_type_4\",     \"5\" = \"cell_type_5\",     \"6\" = \"cell_type_6\",     \"7\" = \"cell_type_7\",     \"8\" = \"cell_type_8\" )  g <- annotateGiotto(g,     annotation_vector = annotation,     cluster_column = \"leiden_clus\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"annotateSpatialGrid — annotateSpatialGrid","title":"annotateSpatialGrid — annotateSpatialGrid","text":"annotate spatial grid cell ID cell metadata (optional)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"annotateSpatialGrid — annotateSpatialGrid","text":"","code":"annotateSpatialGrid(   gobject,   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = \"raw\",   spatial_grid_name = \"spatial_grid\",   cluster_columns = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"annotateSpatialGrid — annotateSpatialGrid","text":"gobject Giotto object spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations spatial_grid_name name spatial grid, see showGiottoSpatGrids cluster_columns names cell metadata, see pDataDT","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"annotateSpatialGrid — annotateSpatialGrid","text":"annotated spatial grid data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"annotateSpatialGrid — annotateSpatialGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  annotateSpatialGrid(g) #>      sdimx sdimy            cell_ID gr_x_loc gr_y_loc    gr_loc #>      <int> <int>             <char>   <char>   <char>    <char> #>   1:  5477 -4125 AAAGGGATGTAGCAAG-1 gr_x_482 gr_y_264 gr_178007 #>   2:  5959 -2808 AAATGGCATGTCTTGT-1 gr_x_579 gr_y_528 gr_356304 #>   3:  4720 -5202 AAATGGTCAATGTGCC-1 gr_x_331  gr_y_49  gr_32731 #>   4:  5202 -5322 AAATTAACGGGTAGCT-1 gr_x_427  gr_y_25  gr_16627 #>   5:  4101 -4604 AACAACTGGTAGTTGC-1 gr_x_207 gr_y_169 gr_113607 #>  ---                                                            #> 620:  4996 -5442 TTGTAATCCGTACTCG-1 gr_x_386   gr_y_1    gr_386 #> 621:  6303 -2688 TTGTATCACACAGAAT-1 gr_x_648 gr_y_552 gr_372573 #> 622:  5202 -3885 TTGTCGTTCAGTTACC-1 gr_x_427 gr_y_312 gr_210352 #> 623:  5340 -3406 TTGTGGCCCTGACAGT-1 gr_x_455 gr_y_408 gr_275180 #> 624:  5615 -4125 TTGTTCAGTGTGCTAC-1 gr_x_510 gr_y_264 gr_178035"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"annotateSpatialNetwork — annotateSpatialNetwork","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"Annotate spatial network cell metadata information.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"","code":"annotateSpatialNetwork(   gobject,   spat_unit = NULL,   feat_type = NULL,   spatial_network_name = \"Delaunay_network\",   cluster_column,   create_full_network = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"gobject giotto object spat_unit spatial unit feat_type feature type spatial_network_name name spatial network use cluster_column name column use clusters create_full_network convert reduced full network representation","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"annotated network data.table format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateSpatialNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"annotateSpatialNetwork — annotateSpatialNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  annotateSpatialNetwork(g, cluster_column = \"leiden_clus\") #>                     from                 to sdimx_begin sdimy_begin sdimx_end #>                   <char>             <char>       <num>       <num>     <num> #>    1: AAAGGGATGTAGCAAG-1 TCAAACAACCGCGTCG-1        5477       -4125      5340 #>    2: AAAGGGATGTAGCAAG-1 ACGATCATACATAGAG-1        5477       -4125      5546 #>    3: AAAGGGATGTAGCAAG-1 TATGCTCCCTACTTAC-1        5477       -4125      5408 #>    4: AAAGGGATGTAGCAAG-1 TTGTTCAGTGTGCTAC-1        5477       -4125      5615 #>    5: AAAGGGATGTAGCAAG-1 ATCGACTCTTTCCGTT-1        5477       -4125      5408 #>   ---                                                                         #> 1766: TTCAAGCCGAGCTGAG-1 TTGTATCACACAGAAT-1        6372       -2808      6303 #> 1767: TTCGACGGGAAGGGCG-1 TTCGCACTCGCGTGCT-1        4239       -4125      4308 #> 1768: TTCTTAGTGGCTCAGA-1 TTGTGGCCCTGACAGT-1        5408       -3287      5340 #> 1769: TTCTTGTAACCTAATG-1 TTGGCTCGCATGAGAC-1        3620       -4005      3757 #> 1770: TTGCACGGAGCAGCAC-1 TTGTCGTTCAGTTACC-1        5271       -3766      5202 #>       sdimy_end distance      weight to_cell_type from_cell_type type_int #>           <num>    <num>       <num>       <char>         <char>   <char> #>    1:     -4125 137.0000 0.007299270            5              1   hetero #>    2:     -4244 137.5573 0.007269700            1              1     homo #>    3:     -4244 137.5573 0.007269700            1              1     homo #>    4:     -4125 138.0000 0.007246377            1              1     homo #>    5:     -4005 138.4233 0.007224219            1              1     homo #>   ---                                                                     #> 1766:     -2688 138.4233 0.007224219            2              2     homo #> 1767:     -4245 138.4233 0.007224219            3              3     homo #> 1768:     -3406 137.0584 0.007296161            5              5     homo #> 1769:     -4005 137.0000 0.007299270            1              1     homo #> 1770:     -3885 137.5573 0.007269700            1              3   hetero #>       from_to unified_int #>        <char>      <char> #>    1:     1-5        1--5 #>    2:     1-1        1--1 #>    3:     1-1        1--1 #>    4:     1-1        1--1 #>    5:     1-1        1--1 #>   ---                     #> 1766:     2-2        2--2 #> 1767:     3-3        3--3 #> 1768:     5-5        5--5 #> 1769:     1-1        1--1 #> 1770:     3-1        1--3"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":null,"dir":"Reference","previous_headings":"","what":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"annotate spatial locations 2D spatial grid information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"","code":"annotate_spatlocs_with_spatgrid_2D(spatloc, spatgrid)"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"spatloc spatial_locs slot giotto object spatgrid selected spatial_grid slot giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"annotated spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_2D.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"annotate_spatlocs_with_spatgrid_2D — annotate_spatlocs_with_spatgrid_2D","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5) g_spatloc <- getSpatialLocations(g, output = \"data.table\") g_spatgrid <- getSpatialGrid(g) #> The grid name was not specified, default to the first: \"spatial_grid\"  annotate_spatlocs_with_spatgrid_2D(     spatloc = g_spatloc,     spatgrid = g_spatgrid ) #>      sdimx sdimy            cell_ID gr_x_loc gr_y_loc    gr_loc #>      <int> <int>             <char>   <char>   <char>    <char> #>   1:  5477 -4125 AAAGGGATGTAGCAAG-1 gr_x_482 gr_y_264 gr_178007 #>   2:  5959 -2808 AAATGGCATGTCTTGT-1 gr_x_579 gr_y_528 gr_356304 #>   3:  4720 -5202 AAATGGTCAATGTGCC-1 gr_x_331  gr_y_49  gr_32731 #>   4:  5202 -5322 AAATTAACGGGTAGCT-1 gr_x_427  gr_y_25  gr_16627 #>   5:  4101 -4604 AACAACTGGTAGTTGC-1 gr_x_207 gr_y_169 gr_113607 #>  ---                                                            #> 620:  4996 -5442 TTGTAATCCGTACTCG-1 gr_x_386   gr_y_1    gr_386 #> 621:  6303 -2688 TTGTATCACACAGAAT-1 gr_x_648 gr_y_552 gr_372573 #> 622:  5202 -3885 TTGTCGTTCAGTTACC-1 gr_x_427 gr_y_312 gr_210352 #> 623:  5340 -3406 TTGTGGCCCTGACAGT-1 gr_x_455 gr_y_408 gr_275180 #> 624:  5615 -4125 TTGTTCAGTGTGCTAC-1 gr_x_510 gr_y_264 gr_178035"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":null,"dir":"Reference","previous_headings":"","what":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"annotate spatial locations 3D spatial grid information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"","code":"annotate_spatlocs_with_spatgrid_3D(spatloc, spatgrid)"},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"spatloc spatial_locs slot giotto object spatgrid selected spatial_grid slot giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"annotated spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotate_spatlocs_with_spatgrid_3D.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"annotate_spatlocs_with_spatgrid_3D — annotate_spatlocs_with_spatgrid_3D","text":"","code":"g <- GiottoData::loadGiottoMini(\"starmap\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_spatloc <- getSpatialLocations(g, output = \"data.table\") g_spatgrid <- getSpatialGrid(g) #> The grid name was not specified, default to the first: \"spatial_grid\"  annotate_spatlocs_with_spatgrid_3D(     spatloc = g_spatloc,     spatgrid = g_spatgrid ) #>       sdimx sdimy sdimz    cell_ID gr_x_loc gr_y_loc gr_z_loc gr_loc #>       <int> <int> <int>     <char>   <char>   <char>   <char> <char> #>    1:   270   212    19  cell_2944   gr_x_2   gr_y_2   gr_z_2  gr_83 #>    2:  1389  1215    54 cell_17523   gr_x_7   gr_y_7   gr_z_4 gr_277 #>    3:  1051   360    89 cell_30080   gr_x_6   gr_y_2   gr_z_5 gr_303 #>    4:   592   777    10   cell_941   gr_x_3   gr_y_5   gr_z_1  gr_39 #>    5:  1058   223    84 cell_28514   gr_x_6   gr_y_2   gr_z_5 gr_303 #>   ---                                                                #> 3901:   348  1383    78 cell_26011   gr_x_2   gr_y_8   gr_z_5 gr_353 #> 3902:   674  1080    89 cell_31539   gr_x_4   gr_y_6   gr_z_5 gr_337 #> 3903:   919   532    22  cell_4185   gr_x_5   gr_y_3   gr_z_2  gr_95 #> 3904:   947   885    23  cell_3851   gr_x_5   gr_y_5   gr_z_2 gr_113 #> 3905:   144   439    60 cell_21337   gr_x_1   gr_y_3   gr_z_4 gr_235"},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":null,"dir":"Reference","previous_headings":"","what":"Get the area of individual polygons — area","title":"Get the area of individual polygons — area","text":"Compute area covered polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get the area of individual polygons — area","text":"","code":"# S4 method for class 'giottoPolygon' area(x, ...)  # S4 method for class 'SpatVector' area(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get the area of individual polygons — area","text":"x giottoPolygon ... additional args pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get the area of individual polygons — area","text":"numeric vector spatial area","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/area.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get the area of individual polygons — area","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  # area of polygons area(gpoly) #>   [1] 115.382156 137.699592  56.258785  40.229395  97.002577  45.332848 #>   [7]  71.292382  88.371522  66.422317  79.931111 127.027294  95.667698 #>  [13]  68.893156  34.568123  44.002485  28.509585 108.275150  73.819729 #>  [19]  78.608663 145.048538  20.719544  28.778835  54.980361  57.290988 #>  [25]  61.593386  39.112532  52.105403  51.045881  81.704714 168.285559 #>  [31]  42.937577 141.422443 164.660053  88.381279  77.152979  43.167074 #>  [37]  44.652023  49.536357  74.097684  93.333373 108.649889   3.625382 #>  [43]  32.388099 116.489993  57.535530  92.338288  52.509047  41.150838 #>  [49]  47.593223  57.158546  70.455928  25.063070  57.779990  47.941342 #>  [55]  42.424001  53.835541  41.876606  55.195710 137.303108  69.164203 #>  [61]  41.795739  67.310060  44.371163  46.254949  19.546489  81.625242 #>  [67] 118.715161  82.471018  87.892114  69.612346 103.555573  88.695051 #>  [73]  93.962734  19.435281 105.202436 152.572181  47.933664 156.543998 #>  [79]  64.170943  63.638421  66.326260 106.778907 112.661813 112.902630 #>  [85]  53.136703  39.287410  44.853020  78.877723  56.053503  46.070249 #>  [91] 113.380182  25.782623 157.828400  65.594372 171.872443  27.492766 #>  [97]  52.454251  92.875400  40.546921  80.775562  17.990194  48.474324 #> [103]  13.770289 115.135690  24.315644  97.226983  68.116633 101.073033 #> [109]  15.995823  43.848299  94.734965  78.376501  74.425205 119.146342 #> [115]  82.297781 101.410965 121.705213  30.474723  17.119168 151.719441 #> [121]  43.829745 191.541382 126.260435  36.689881  69.020409  54.050307 #> [127] 185.517103 101.842157  56.174526 121.983821  62.215237 159.424280 #> [133] 132.573959  42.641755  39.443430  29.879557 247.246029 121.401552 #> [139]  25.106711  38.583762 105.001640  74.286747  35.445152 139.179936 #> [145]  46.361149  60.738068  91.896979 129.837339  22.904326  33.473557 #> [151] 130.753727  53.185364 149.418428 132.050815  12.792682  78.129115 #> [157]  70.328907  33.537418  90.686201  19.452148  32.440515  90.376179 #> [163] 219.310104 101.376410  81.311602  45.864517 122.496632  54.147531 #> [169]  27.897431 126.962657  52.160437  81.601298  87.474158 122.075417 #> [175]  38.124635  62.559769 200.075231  76.312474 107.187281 189.431723 #> [181]  61.075352  44.449498  23.821415  38.340378 111.967876  95.682535 #> [187]  40.150629 150.355333 158.018954  70.179077  43.838012  29.885799 #> [193] 129.266905 137.371563  87.088326 103.063248  57.474822  61.101909 #> [199]  33.657407  38.653428  57.924050 177.706024  15.250413  36.841646 #> [205]  48.513825  87.425664 132.978824  66.737607 157.029775  54.854626 #> [211] 132.416601  37.131024  90.288613  35.586162  59.038520  95.582097 #> [217]  32.162960 100.569991 116.654919  28.754218  60.072974 102.246471 #> [223]  81.471684  20.977006  64.997885  54.027689  17.416627  67.521147 #> [229]  69.259391  75.810748  95.765004  25.195225 100.951886  44.630761 #> [235] 160.643637 179.393657  97.423910 215.156341  58.553909  29.777089 #> [241]  58.746361 121.143932  55.699201  89.429782 160.979431 145.446617 #> [247]  93.233779  83.193754  35.647268 158.733011 116.032780 124.781295 #> [253] 117.895490  22.248638  56.941543  62.493490  95.618526 112.839798 #> [259]  61.189989 148.845224  74.224374  80.251044  39.901354  66.450440 #> [265]  75.327080  43.292625 147.586155  38.198580  81.429289  67.505694 #> [271]  69.769232 119.652217 105.853346 101.714301  30.890972  87.606791 #> [277]  65.124539  27.064328  38.120760  40.075655  62.308542  80.001513 #> [283] 103.832092 142.686465  24.557224  64.228162  41.272696  58.873217 #> [289]  72.104235   6.660052  96.070015 145.968844  90.020228  37.489668 #> [295] 129.927467 134.536297  36.758667  20.868081  35.585220  70.229709 #> [301] 105.964373  25.159487  61.289897  78.716248  74.899171  17.922789 #> [307]  76.998708  75.030590  27.077454  51.461024  66.444366  71.757876 #> [313]  24.097374  62.408624  84.651353  57.801908 141.544944  65.071704 #> [319]  29.312598 108.802794  55.070164 254.011504 108.318436  97.225920 #> [325]  76.222028 219.411328  46.441821  83.046394  28.717752  24.335424 #> [331]  55.846265  99.011556  20.737471  70.343241  75.132632  19.092044 #> [337]  58.283696  63.382027  74.342376 114.644585  30.219673  26.280021 #> [343] 170.236248  63.422589 116.251979  48.900846  90.521441  60.011770 #> [349]  75.488249  54.209468  37.091655  84.761878  31.721098  97.065126 #> [355]  47.004961  32.547595 139.575862  11.718641  91.200086  62.877798 #> [361]  92.867375   9.942683 111.628109  46.906968 126.742572 146.659695 #> [367] 121.516530 128.993617  49.814376 159.781874 105.119283  76.190982 #> [373]  64.170765  74.998533  60.373170  54.510092  74.993138  74.356919 #> [379] 141.118014  65.791923  72.891288 139.330262  54.700658  20.005007 #> [385]  94.911861  91.686109  94.647883 147.515935 122.057396  39.560030 #> [391]  92.092400 163.831117  61.586632 117.874102  40.784218  39.639844 #> [397]  30.144736  66.180669  11.170534  56.022100 120.455304 157.455917 #> [403]  99.923896 176.239903  53.023597  36.134329  71.485715 113.977649 #> [409]  54.369377  65.763036  38.420173  66.186141 108.683300  49.961911 #> [415]  55.405510 109.453060  17.935675  76.790187 123.710744  31.263041 #> [421]  75.685700  40.072969  55.842580  44.135987  36.906334  96.058841 #> [427] 112.879696  35.377052 209.891465  58.217434 156.125202  83.515929 #> [433]  51.581023  89.286940  78.399934 103.823589  86.643317  64.811750 #> [439] 141.296392  89.394817  53.750554  53.189547  54.276573 100.814926 #> [445]  66.101887 179.872754  26.422177  59.277010 141.781207  65.796310 #> [451]  45.170500  71.155894  48.213360 243.277797  24.620358  99.923534 #> [457]  72.348473  82.358683 137.263692 151.990487  46.179693  73.811876  # area of the convex hull area(convHull(sl)) #> [1] 199333.6 feature_hulls <- convHull(gpoints, by = \"feat_ID\") area(feature_hulls) #>   [1] 144798.7133 187046.0487 188143.6215 210427.1860 180407.1047 179525.7058 #>   [7] 185662.0149 208822.2997 197475.9826 157464.4008  65313.8619  40607.1830 #>  [13] 158307.8761 195539.8183  56624.3065  85995.6127  63041.4641 209879.3008 #>  [19] 176481.9921 192658.6919 169032.8309 116820.7911 195495.3261 101153.2271 #>  [25] 120653.8204 137286.5447  93245.5725 128522.5729 193111.8414  49353.5278 #>  [31] 180804.6322 128139.1086 153051.7259 206020.5245 145642.8480 152505.7430 #>  [37] 186224.4956  50800.2600 209040.3709 187270.9635 166411.3041 169683.5130 #>  [43]   1972.2428 205098.5718 182544.5109  64448.4509  28331.9230  42322.6394 #>  [49]   3610.8130   8799.0106  23195.2945   3214.9414  10412.5134  72053.1368 #>  [55] 120626.5302  60738.7859  48229.3741  30282.2113   8911.4632  71181.9991 #>  [61]  22419.9289  53298.6136  84628.9170 200054.0014 200119.6959 102787.5843 #>  [67]  63361.1134  75000.6474 176626.0357  99097.9212  53069.9237  40702.9997 #>  [73]  61487.3084 127273.3633  57111.5701 133841.2571 144324.4832 210716.6701 #>  [79] 132207.5176  86146.5232 164093.7710 135874.2413  70953.2062  89728.6380 #>  [85] 180253.5931 165995.3587 108063.6174 150159.6246  35185.9014 183489.9072 #>  [91] 211191.0325 197805.1203 189662.1234 192889.5422 132440.8011  53443.2281 #>  [97] 203189.7307 157742.8703 157844.6759  78470.3163  42891.5510  33821.5507 #> [103] 151184.7287 205357.6787 153044.4755 186157.1746 144661.6144  67245.9256 #> [109]  99891.9217 130342.7695  55284.9318 165055.3305 190797.7633 123425.4347 #> [115] 170244.0299 158858.8945  68438.8563 181164.1319 147125.4539 176707.4455 #> [121] 196670.1410 129951.9862  56130.7498 194884.0727 130921.8166   8993.5075 #> [127] 184007.4069 204508.4589 163390.4550 175138.2561  85618.0998 108852.5692 #> [133] 178291.7166   5948.7906 189553.4023  33288.5603 187546.3609 193721.1221 #> [139] 187099.2455 111544.1916 169824.2427 182629.6453 153842.1615 114206.2984 #> [145] 210911.4279 199411.5661 193496.9836  52124.3816 111671.8368 217143.9693 #> [151]  52638.6489  61229.5578 149112.6940 140657.9052  43442.4975  60706.2032 #> [157]  38551.4045   2329.5772 123530.9205  13703.5970 185190.5158 146101.2328 #> [163] 149941.5042  97188.3608 127516.2228 148946.6473 149625.0486 197629.5924 #> [169] 153144.4427 168436.2364 130075.8993 134149.9173  72193.2872  26787.0221 #> [175] 119519.3617 156183.6477 134593.0607 163399.9948 131526.4735  47804.8863 #> [181] 205492.3323 157232.1028 121197.4900 163845.3479  40083.6591  18312.2989 #> [187]  85655.4469 153123.9948 174196.8676 121804.4182  52461.4857 171899.3641 #> [193] 211979.5539 105152.9139 192142.5217 159105.8015 150004.0432 141338.8031 #> [199] 188608.9360 145140.7287 199286.2949 154735.2345  31732.1041  53209.3025 #> [205]   6561.2860 115700.7475  89303.6690 134584.2116 133917.3126  96030.7518 #> [211]  10813.7838 155653.7377  67531.9731  33505.7382  95789.7497 106343.2921 #> [217] 207077.8986 190364.0199  17068.4872 143526.0469 183880.8817 162583.8700 #> [223] 154264.8404 195784.6299  77803.8483  59291.6180 102642.3201 207911.3473 #> [229] 180587.5670  88490.0306 169056.4974 132544.9566 164847.8773  83523.8146 #> [235]  76820.7102  24476.6428  20017.6829 193958.7959 206867.3557 127181.7507 #> [241]  69722.6199 111911.0138  80652.9708  26613.0416 160175.1586  94516.3283 #> [247] 197760.0457 171974.4749 213712.1538 200998.7761 210189.2502 205158.0394 #> [253]  53200.8816  21555.2591 129052.4588  45379.0769 132356.6424 189415.9034 #> [259] 152804.3918  23989.4458  30160.6806 127681.6720 125866.3606 171379.6925 #> [265] 160560.9106 181577.2311 170110.4521  62959.7269 135522.6912  82161.7389 #> [271]  64709.6904 120428.2414  51760.3808  29019.6612  92957.8966  67643.3438 #> [277]  79745.5991 162345.8387 177205.7244  64956.2263  73614.0551 170299.4173 #> [283]  47351.9062  18947.1547 165440.5822 115384.7093 206734.0143 209733.3384 #> [289] 128636.3201 137608.9949  26458.9509 117258.2422  40426.2985 176406.4456 #> [295] 169647.3954 154982.2534  41851.6406 187780.5956  38591.3468 205377.0827 #> [301] 175768.2754  56946.4078 162984.3471 208281.3627 196120.1871 207955.2629 #> [307] 166788.0597  58235.4575 123962.0055 147825.7471 153163.2194  38223.7941 #> [313]  53137.2779  15907.0189    696.8923 120960.3162   5148.3261  14033.1056 #> [319]  63886.6932 120026.6378  88685.3133 163816.3287 128323.9647 206332.1977 #> [325] 173391.6733 185103.9587 170731.6459  94495.2530 188002.2522  68231.3765 #> [331]  93176.2753  93399.5022  71158.8974 115309.0944  95269.5287    731.8556 #> [337]  84537.1417"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a text representation of an object — as.character","title":"Create a text representation of an object — as.character","text":"Create text representation object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a text representation of an object — as.character","text":"","code":"# S4 method for class 'giottoImage' as.character(x, ...)  # S4 method for class 'giottoLargeImage' as.character(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a text representation of an object — as.character","text":"x object ... additional params pass (none implemented)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a text representation of an object — as.character","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.character.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a text representation of an object — as.character","text":"","code":"img <- GiottoData::loadSubObjectMini(\"giottoLargeImage\") as.character(img) #> [1] \"<giottoLargeImage> dapi_z0\""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to data.table — as.data.table","title":"Coerce to data.table — as.data.table","text":"Coerce data.table possible","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to data.table — as.data.table","text":"","code":"# S3 method for class 'SpatVector' as.data.table(   x,   keep.rownames = FALSE,   geom = NULL,   include_values = TRUE,   ... )  # S3 method for class 'giottoPolygon' as.data.table(x, ...)  # S3 method for class 'giottoPoints' as.data.table(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to data.table — as.data.table","text":"x object coerce keep.rownames argument ignored geom character NULL. NULL, either \"XY\", \"WKT\", \"HEX\", get geometry included coordinates point vertex, Well-Known-Text hexadecimal notation. include_values whether include attributes information geom 'XY' ... additional arguments pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to data.table — as.data.table","text":"data.table","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/as.data.table.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to data.table — as.data.table","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  data.table::as.data.table(g) #>                                      poly_ID  stack agg_n valid #>                                       <char> <char> <int> <int> #>   1: 100210519278873141813371229408401071444   <NA>     2     1 #>   2: 101161259912191124732236989250178928032   <NA>     2     1 #>   3: 101488859781016188084173008420811094152   <NA>     2     1 #>   4: 101523780333017320796881555775415156847   <NA>     2     1 #>   5: 102184699197574201819246996094734116255   <NA>     2     1 #>  ---                                                            #> 458:   9677424102111816817518421117250891895   <NA>     2     1 #> 459:  97068595823890802071024838798130036179   <NA>     2     1 #> 460:  97411078642927912684859796714759494710   <NA>     2     1 #> 461:   9816437869021910185567097363182418837   <NA>     2     1 #> 462:  98561957902191275233320065611022298397   <NA>     2     1"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to a list — as.list,giotto-method","title":"Coerce to a list — as.list,giotto-method","text":"Generic coerce list possible","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to a list — as.list,giotto-method","text":"","code":"# S4 method for class 'giotto' as.list(x, slots, spat_unit = NULL, feat_type = NULL, name = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to a list — as.list,giotto-method","text":"x object coerce slots character vector. data slots include list. See details spat_unit spatial unit (e.g. \"cell\") feat_type feature type use (e.g. \"rna\", \"protein\") name name elements select slot ... additional arguments","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to a list — as.list,giotto-method","text":"list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.list.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Coerce to a list — as.list,giotto-method","text":"Giotto method - slots argument currently accepts multiple : \"spatial_info\", \"spatial_locs\", \"spatial_network\", \"feat_info\", \"expression\", \"cell_metadata\", \"feat_metadata\", \"spatial_enrichment\", \"nn_network\", \"dimension_reduction\", \"multiomics\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to matrix — as.matrix","title":"Coerce to matrix — as.matrix","text":"Coerce matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to matrix — as.matrix","text":"","code":"# S4 method for class 'spatLocsObj' as.matrix(x, id_rownames = TRUE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to matrix — as.matrix","text":"x object coerce id_rownames logical. Retain spatial IDs rownames ... additional params pass (none implemented)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to matrix — as.matrix","text":"matrix","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/as.matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to matrix — as.matrix","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") m <- as.matrix(sl)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to SpatVector points — as.points","title":"Coerce to SpatVector points — as.points","text":"Coversion SpatVector points.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to SpatVector points — as.points","text":"","code":"# S4 method for class 'data.frame' as.points(x, include_values = TRUE, specific_values = NULL)  # S4 method for class 'spatLocsObj' as.points(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to SpatVector points — as.points","text":"x SpatRaster, SpatVector, SpatExtent, correctly formatted data.frame include_values logical. Whether include additional columns geometry information SpatVector attributes. Default TRUE. specific_values character. Specific subset columns include attributes include_values = TRUE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to SpatVector points — as.points","text":"SpatVector points","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/as.points.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to SpatVector points — as.points","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  as.points(slot(g, \"spatVector\")) #> Warning: [as.points] returning a copy #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Coerce to SpatVector polygons — as.polygons","title":"Coerce to SpatVector polygons — as.polygons","text":"Coversion SpatVector polygons.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Coerce to SpatVector polygons — as.polygons","text":"","code":"# S4 method for class 'data.frame' as.polygons(   x,   include_values = TRUE,   specific_values = NULL,   sort_geom = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Coerce to SpatVector polygons — as.polygons","text":"x SpatRaster, SpatVector, SpatExtent, correctly formatted data.frame include_values logical. Whether include additional columns geometry information SpatVector attributes. Default TRUE. specific_values character. Specific subset columns include attributes include_values = TRUE. sort_geom logical. Whether sort key data.table input 'geom', 'part', 'hole' columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Coerce to SpatVector polygons — as.polygons","text":"SpatVector polygons","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/as.polygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Coerce to SpatVector polygons — as.polygons","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  as.polygons(slot(g, \"spatVector\")) #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 480, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1"},{"path":"https://drieslab.github.io/GiottoClass/reference/buffer.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a buffer around vector geometries — buffer","title":"Create a buffer around vector geometries — buffer","text":"Calculate buffer around geometries SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/buffer.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a buffer around vector geometries — buffer","text":"","code":"# S4 method for class 'spatLocsObj' buffer(x, width, ..., settle = TRUE)  # S4 method for class 'giottoPoints' buffer(x, width, ..., settle = TRUE)  # S4 method for class 'giottoPolygon' buffer(x, width, ..., settle = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/buffer.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a buffer around vector geometries — buffer","text":"x SpatRaster SpatVector width numeric. Unit meter x longitude/latitude CRS, units coordinate reference system cases (typically also meter). value > 0 x SpatRaster. x SpatVector, argument vectorized, meaning can provide different value geometry x; can also use name variable x widths ... additional params pass settle logical. Settle borders polygons cutting touch based voronoi boundaries.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/buffer.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a buffer around vector geometries — buffer","text":"giottoPolygon buffer polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/buffer.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a buffer around vector geometries — buffer","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") slb <- buffer(sl, 30) plot(slb)"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateMetaTable — calculateMetaTable","title":"calculateMetaTable — calculateMetaTable","text":"calculates average gene expression one (combined) annotation columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateMetaTable — calculateMetaTable","text":"","code":"calculateMetaTable(   gobject,   spat_unit = NULL,   feat_type = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   metadata_cols = NULL,   selected_feats = NULL,   selected_genes = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateMetaTable — calculateMetaTable","text":"gobject giotto object spat_unit spatial unit feat_type feature type expression_values expression values use metadata_cols annotation columns found pDataDT(gobject) selected_feats subset features use selected_genes subset genes use (deprecated)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateMetaTable — calculateMetaTable","text":"data.table average expression values gene per (combined) annotation","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateMetaTable — calculateMetaTable","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateMetaTable(g, metadata_cols = \"leiden_clus\") #>       leiden_clus uniq_ID      variable      value #>             <num>   <num>        <fctr>      <num> #>    1:           2       2         Gna12 2.95192565 #>    2:           5       5         Gna12 4.41905517 #>    3:           1       1         Gna12 2.51999975 #>    4:           3       3         Gna12 2.60980838 #>    5:           6       6         Gna12 4.18561316 #>   ---                                              #> 4434:           1       1 2900040C04Rik 0.48747773 #> 4435:           3       3 2900040C04Rik 0.21256443 #> 4436:           6       6 2900040C04Rik 0.47596999 #> 4437:           7       7 2900040C04Rik 0.00000000 #> 4438:           4       4 2900040C04Rik 0.04874282"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateMetaTableCells — calculateMetaTableCells","title":"calculateMetaTableCells — calculateMetaTableCells","text":"calculates average metadata values one (combined) annotation columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateMetaTableCells — calculateMetaTableCells","text":"","code":"calculateMetaTableCells(   gobject,   spat_unit = NULL,   feat_type = NULL,   value_cols = NULL,   metadata_cols = NULL,   spat_enr_names = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateMetaTableCells — calculateMetaTableCells","text":"gobject giotto object spat_unit spatial unit feat_type feature type value_cols metadata enrichment value columns use metadata_cols annotation columns found pDataDT(gobject) spat_enr_names spatial enrichment results include","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateMetaTableCells — calculateMetaTableCells","text":"data.table average metadata values per (combined) annotation","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateMetaTableCells — calculateMetaTableCells","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateMetaTableCells(g,     metadata_cols = \"cell_ID\",     value_cols = \"leiden_clus\" ) #>                 cell_ID    variable value #>                  <char>      <fctr> <num> #>   1: AAAGGGATGTAGCAAG-1 leiden_clus     1 #>   2: AAATGGCATGTCTTGT-1 leiden_clus     2 #>   3: AAATGGTCAATGTGCC-1 leiden_clus     4 #>   4: AAATTAACGGGTAGCT-1 leiden_clus     4 #>   5: AACAACTGGTAGTTGC-1 leiden_clus     6 #>  ---                                      #> 620: TTGTAATCCGTACTCG-1 leiden_clus     4 #> 621: TTGTATCACACAGAAT-1 leiden_clus     2 #> 622: TTGTCGTTCAGTTACC-1 leiden_clus     1 #> 623: TTGTGGCCCTGACAGT-1 leiden_clus     5 #> 624: TTGTTCAGTGTGCTAC-1 leiden_clus     1"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate features overlapped by polygons — calculateOverlap","title":"Calculate features overlapped by polygons — calculateOverlap","text":"Calculate subcellular points/feature info image values overlapped polygon annotations. provides summary spatial data overlapped polygon can processed become expression matrix.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate features overlapped by polygons — calculateOverlap","text":"","code":"# S4 method for class 'giotto,missing' calculateOverlap(   x,   name_overlap = NULL,   spatial_info = NULL,   feat_info = NULL,   image_names = NULL,   poly_subset_ids = NULL,   return_gobject = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'giottoPolygon,giottoPoints' calculateOverlap(   x,   y,   name_overlap = NULL,   poly_subset_ids = NULL,   feat_subset_column = NULL,   feat_subset_ids = NULL,   count_info_column = NULL,   return_gpolygon = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'giottoPolygon,giottoLargeImage' calculateOverlap(   x,   y,   name_overlap = NULL,   poly_subset_ids = NULL,   return_gpolygon = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'giottoPolygon,SpatRaster' calculateOverlap(   x,   y,   name_overlap = NULL,   poly_subset_ids = NULL,   return_gpolygon = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'SpatVector,SpatRaster' calculateOverlap(x, y, poly_subset_ids = NULL, verbose = TRUE, ...)  # S4 method for class 'SpatVector,SpatVector' calculateOverlap(   x,   y,   poly_subset_ids = NULL,   feat_subset_column = NULL,   feat_subset_ids = NULL,   count_info_column = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate features overlapped by polygons — calculateOverlap","text":"x Object spatial annotations: giottoPolygon, SpatVector polygons. Can also giotto object name_overlap name overlap results (default feat_info parameter) spatial_info character. Name polygon information feat_info character. Name vector feature information overlap image_names character vector. Name(s) image feature information overlap poly_subset_ids character vector. (optional) Specific poly_IDs use return_gobject return giotto object (default: TRUE) verbose verbose ... additional params pass methods. y Object features overlap: giottoPoints, giottoLargeImage, SpatVector points SpatRaster feat_subset_column character. (optional) feature info attribute subset feature points performing overlap calculation. feat_subset_ids (optional) values matched feat_subset_column order subset feature points performing overlap calculation. count_info_column character. (optional) column count information. Useful cases one detection reported per point. return_gpolygon default = TRUE. Whether return entire giottoPolygon provided x, overlaps information appended bare terra SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate features overlapped by polygons — calculateOverlap","text":"Usually object class x, overlaps information appended. return_* logical params usually allow return lower-level representation results instead. SpatVector,SpatRaster method different returns data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Calculate features overlapped by polygons — calculateOverlap","text":"feat_subset_column, feat_subset_ids, count_info_column specific overlaps feature points info, provided overlapping image data. three params can also passed giotto method ... param working overlaps feature points info.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate features overlapped by polygons — calculateOverlap","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" gpoly <- getPolygonInfo(g,     polygon_name = \"aggregate\",     return_giottoPolygon = TRUE ) gpoints <- getFeatureInfo(g, return_giottoPoints = TRUE) gimg <- getGiottoImage(g, image_type = \"largeImage\")  slot(gpoly, \"overlaps\") <- NULL overlaps(gpoly) # Should now be NULL #> NULL  # detections from 2 z-layers are provided table(gpoints$global_z) #>  #>     0     1  #> 35889 43872   # calculate all transcripts overlapped out_all <- calculateOverlap(gpoly, gpoints) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information overlaps_all <- overlaps(out_all) overlaps_all$rna #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : poly_ID feat_ID feat_ID_uniq #>  type        :   <chr>   <chr>        <int> #>  values      :      NA    Mlc1            1 #>                     NA  Gprc5b            2 #>                     NA    Gfap            3  # calculate z1 only out_z1 <- calculateOverlap(gpoly, gpoints,     feat_subset_column = \"global_z\",     feat_subset_ids = c(1) ) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information overlaps_z1 <- overlaps(out_z1) overlaps_z1$rna #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 43872, 3  (geometries, attributes) #>  extent      : 6400.043, 6900.03, -5149.983, -4699.984  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : poly_ID feat_ID feat_ID_uniq #>  type        :   <chr>   <chr>        <int> #>  values      :      NA  Gabbr2        36198 #>                     NA    Gfap        36199 #>                     NA    Gfap        36200  # overlap image to get sum intensities per cell out_img <- calculateOverlap(gpoly, gimg) #> Start image extract #>    |                                                                               |                                                                      |   0%   |                                                                               |                                                                      |   1%   |                                                                               |=                                                                     |   1%   |                                                                               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|======================================================================|  99%   |                                                                               |======================================================================| 100% #> End image extract overlaps_img <- overlaps(out_img) overlaps_img$intensity #> $dapi_z0 #>                                          poly_ID mini_dataset_dapi_z0 #>                                           <char>                <num> #>       1: 100210519278873141813371229408401071444                   18 #>       2: 100210519278873141813371229408401071444                   18 #>       3: 100210519278873141813371229408401071444                   18 #>       4: 100210519278873141813371229408401071444                   18 #>       5: 100210519278873141813371229408401071444                   18 #>      ---                                                              #> 3170620:  98561957902191275233320065611022298397                   98 #> 3170621:  98561957902191275233320065611022298397                   98 #> 3170622:  98561957902191275233320065611022298397                   88 #> 3170623:  98561957902191275233320065611022298397                   88 #> 3170624:  98561957902191275233320065611022298397                   88 #>   # giotto method # calculate z0 overlaps and return as gobject out_g <- calculateOverlap(g,     feat_subset_column = \"global_z\",     feat_subset_ids = 0 ) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information overlaps(getPolygonInfo(out_g, return_giottoPolygon = TRUE)) #> $rna #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 35889, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : poly_ID feat_ID feat_ID_uniq #>  type        :   <chr>   <chr>        <int> #>  values      :      NA    Mlc1            1 #>                     NA  Gprc5b            2 #>                     NA    Gfap            3 #>   # note that z0 and z1 nrows match that from the table of global z values. # With points overlaps, all points are returned, but non-overlapped points # only have an `NA` value for the `poly_ID` column. Overlapped points will # have the `poly_ID` of their overlapping polygon."},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateOverlapParallel — calculateOverlapParallel","title":"calculateOverlapParallel — calculateOverlapParallel","text":"calculate overlap cellular structures (polygons) features (points)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateOverlapParallel — calculateOverlapParallel","text":"","code":"calculateOverlapParallel(   gobject,   name_overlap = NULL,   spatial_info = \"cell\",   feat_info = \"rna\",   poly_ID_names = \"all\",   polygon_group_size = 500,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateOverlapParallel — calculateOverlapParallel","text":"gobject giotto object name_overlap name overlap results (default feat_info parameter) spatial_info polygon information feat_info feature information poly_ID_names list poly_IDs use polygon_group_size number polygons process per parallelization group return_gobject return giotto object (default: TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateOverlapParallel — calculateOverlapParallel","text":"giotto object spatVector overlapping information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"calculateOverlapParallel — calculateOverlapParallel","text":"parallel follows future approach. means plan(multisession) work, since underlying terra objects internal C pointers. plan(multicore) also supported Rstudio users.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapParallel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateOverlapParallel — calculateOverlapParallel","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateOverlapParallel(g, spatial_info = \"z1\") #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"calculate overlap cellular structures (polygons) images (intensities)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"","code":"calculateOverlapPolygonImages(   gobject,   name_overlap = \"protein\",   spatial_info = \"cell\",   poly_ID_names = NULL,   image_names = NULL,   poly_subset = NULL,   return_gobject = TRUE,   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"gobject giotto object name_overlap name overlap results (default feat_info parameter) spatial_info polygon information poly_ID_names (optional) list poly_IDs use image_names names images raw data poly_subset numerical values subset polygon spatVector return_gobject return giotto object (default: TRUE) verbose verbose ... additional params exact_extract","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"giotto object data.table overlapping information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapPolygonImages.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateOverlapPolygonImages — calculateOverlapPolygonImages","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateOverlapPolygonImages(g,     spatial_info = \"z0\",     image_names = \"dapi_z0\" ) #> [1] \"0. create image list\" #> [1] \"1. start extraction\" #>    |                                                                               |                                                                      |   0%   |                                                                               |                                                                      |   1%   |                                                                               |=                                                                     |   1%   |                                                                               |=                                                                     |   2%   |                                                                               |==                                                                    |   2%   |                                                                               |==                                                                    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|======================================================================|  99%   |                                                                               |======================================================================| 100% #>                                         poly_ID value coverage_fraction #>                                          <char> <num>             <num> #>       1: 40951783403982682273285375368232495429     8      1.420465e-01 #>       2: 40951783403982682273285375368232495429     8      4.332028e-01 #>       3: 40951783403982682273285375368232495429     8      5.996065e-01 #>       4: 40951783403982682273285375368232495429     8      6.887537e-01 #>       5: 40951783403982682273285375368232495429     8      7.144262e-01 #>      ---                                                                #> 2846020:  9677424102111816817518421117250891895     8      3.764088e-01 #> 2846021:  9677424102111816817518421117250891895     8      5.001789e-01 #> 2846022:  9677424102111816817518421117250891895     8      4.812778e-01 #> 2846023:  9677424102111816817518421117250891895     8      1.656012e-01 #> 2846024:  9677424102111816817518421117250891895     8      1.540388e-05 #>                                         poly_ID dapi_z0 #>                                          <char>   <num> #>       1: 40951783403982682273285375368232495429       8 #>       2: 40951783403982682273285375368232495429       8 #>       3: 40951783403982682273285375368232495429       8 #>       4: 40951783403982682273285375368232495429       8 #>       5: 40951783403982682273285375368232495429       8 #>      ---                                                #> 2846020:  9677424102111816817518421117250891895       8 #> 2846021:  9677424102111816817518421117250891895       8 #> 2846022:  9677424102111816817518421117250891895       8 #> 2846023:  9677424102111816817518421117250891895       8 #> 2846024:  9677424102111816817518421117250891895       8 #> > \" z0 \" already exists and will be replaced #>  with new giotto polygon #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateOverlapRaster — calculateOverlapRaster","title":"calculateOverlapRaster — calculateOverlapRaster","text":"calculate overlap cellular structures (polygons) features (points).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateOverlapRaster — calculateOverlapRaster","text":"","code":"calculateOverlapRaster(   gobject,   name_overlap = NULL,   spatial_info = NULL,   poly_ID_names = NULL,   feat_info = NULL,   feat_subset_column = NULL,   feat_subset_ids = NULL,   count_info_column = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateOverlapRaster — calculateOverlapRaster","text":"gobject giotto object name_overlap name overlap results (default feat_info parameter) spatial_info character. name polygon information poly_ID_names (optional) list poly_IDs use feat_info character. name feature information feat_subset_column feature info column subset features feat_subset_ids ids within feature info column use subsetting count_info_column column count information (optional) return_gobject return giotto object (default: TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateOverlapRaster — calculateOverlapRaster","text":"giotto object spatVector overlapping information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"calculateOverlapRaster — calculateOverlapRaster","text":"Serial overlapping function.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapRaster.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateOverlapRaster — calculateOverlapRaster","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateOverlapRaster(g) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateOverlapSerial — calculateOverlapSerial","title":"calculateOverlapSerial — calculateOverlapSerial","text":"calculate overlap cellular structures (polygons) features (points)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateOverlapSerial — calculateOverlapSerial","text":"","code":"calculateOverlapSerial(   gobject,   name_overlap = NULL,   spatial_info = \"cell\",   feat_info = \"rna\",   poly_ID_names = \"all\",   polygon_group_size = 500,   return_gobject = TRUE,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateOverlapSerial — calculateOverlapSerial","text":"gobject giotto object name_overlap name overlap results (default feat_info parameter) spatial_info polygon information feat_info feature information poly_ID_names list poly_IDs use polygon_group_size number polygons process per group return_gobject return giotto object (default: TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateOverlapSerial — calculateOverlapSerial","text":"giotto object spatVector overlapping information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"calculateOverlapSerial — calculateOverlapSerial","text":"Serial overlapping function works groups polygons time. Number polygons per group defined polygon_group_size param","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateOverlapSerial.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateOverlapSerial — calculateOverlapSerial","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateOverlapSerial(g, spatial_info = \"z1\") #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":null,"dir":"Reference","previous_headings":"","what":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"calculates proportion table cell metadata column (e.g. cluster labels) spatial neighbors source cell. words calculates niche composition given annotation cell.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"","code":"calculateSpatCellMetadataProportions(   gobject,   spat_unit = NULL,   feat_type = NULL,   spat_network = NULL,   metadata_column = NULL,   name = \"proportion\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"gobject giotto object spat_unit spatial unit feat_type feature type spat_network spatial network metadata_column metadata column use name descriptive name calculated proportions return_gobject return giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"giotto object (default) enrichment object return_gobject = FALSE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculateSpatCellMetadataProportions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"calculateSpatCellMetadataProportions — calculateSpatCellMetadataProportions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  calculateSpatCellMetadataProportions(g,     spat_network = \"Delaunay_network\", metadata_column = \"leiden_clus\" ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS proportion #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/cellMetaObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 cellMetaObj — cellMetaObj-class","title":"S4 cellMetaObj — cellMetaObj-class","text":"Framework store cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cellMetaObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 cellMetaObj — cellMetaObj-class","text":"cellMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cellMetaObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 cellMetaObj — cellMetaObj-class","text":"metaDT metadata info col_desc (optional) character vector describing columns metadata spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') provenance origin data aggregated expression information (applicable)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cellMetaObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 cellMetaObj — cellMetaObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"cellMetaObj\") #> An object of class cellMetaObj  #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #> dimensions: 462 6  #>  #>                                    cell_ID nr_feats perc_feats total_expr #>                                     <char>    <int>      <num>      <num> #> 1: 240649020551054330404932383065726870513        5   1.483680   49.40986 #> 2: 274176126496863898679934791272921588227       27   8.011869  191.50684 #> 3: 323754550002953984063006506310071917306       23   6.824926  173.86955 #>    leiden_clus louvain_clus #>          <num>        <num> #> 1:           2            0 #> 2:           2            3 #> 3:           4            8"},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"centroids-generic — centroids-generic","title":"centroids-generic — centroids-generic","text":"Access centroids information polygon objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"centroids-generic — centroids-generic","text":"","code":"# S4 method for class 'giottoPolygon' centroids(x, append_gpolygon = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"centroids-generic — centroids-generic","text":"x object append_gpolygon whether append centroids results giottoPolygon instead returning bare SpatVector. Defaults FALSE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"centroids-generic — centroids-generic","text":"spatVectorCentroids spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"centroids-generic — centroids-generic","text":"giottoPolygon, centroids already exist, pulls spatVectorCentroids slot. Otherwise, generates spatVector slot de novo","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/centroids-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"centroids-generic — centroids-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  centroids(g) #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6401.412, 6899.108, -5146.747, -4700.326  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1"},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — changeGiottoInstructions","title":"deprecated — changeGiottoInstructions","text":"Function change one instructions giotto object. one item supplied params new_values, use vector values. call initialize giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — changeGiottoInstructions","text":"","code":"changeGiottoInstructions(   gobject,   params = NULL,   new_values = NULL,   return_gobject = TRUE,   init_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — changeGiottoInstructions","text":"gobject giotto object params parameter(s) change new_values new value(s) parameter(s) return_gobject (boolean, default = TRUE) return giotto object init_gobject (boolean, default = TRUE) initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — changeGiottoInstructions","text":"giotto object one changed instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeGiottoInstructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"deprecated — changeGiottoInstructions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  changeGiottoInstructions(     gobject = g, params = \"save_plot\",     new_values = TRUE ) #> Warning: `changeGiottoInstructions()` was deprecated in GiottoClass 0.3.5. #> ℹ Please use `instructions()` instead. #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":null,"dir":"Reference","previous_headings":"","what":"changeImageBg — changeImageBg","title":"changeImageBg — changeImageBg","text":"Function change background color magick image plot another color","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"changeImageBg — changeImageBg","text":"","code":"changeImageBg(   mg_object,   bg_color,   perc_range = 10,   new_color = \"#FFFFFF\",   new_name = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"changeImageBg — changeImageBg","text":"mg_object magick image giotto image object bg_color estimated current background color perc_range range around estimated background color include (percentage) new_color new background color new_name change name Giotto image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"changeImageBg — changeImageBg","text":"magick image giotto image object updated background color","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/changeImageBg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"changeImageBg — changeImageBg","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- convertGiottoLargeImageToMG(g,     largeImage_name = \"image\",     return_gobject = FALSE )  changeImageBg(mg_object = g_image, bg_color = \"white\") #> An object of class ' giottoImage ' with name  image  #>   #> Min and max values are:  #>  Max on x-axis:  6790.5  #>  Min on x-axis:  2000.5  #>  Max on y-axis:  -2380.75  #>  Min on y-axis:  -5730.25  #>   #> Boundary adjustment are:  #>  Max adjustment on x-axis:  0  #>  Min adjustment on x-axis:  0  #>  Max adjustment on y-axis:  0  #>  Min adjustment on y-axis:  0  #>   #> Boundaries are:  #>  Image x-axis max boundary:  6790.5  #>  Image x-axis min boundary:  2000.5  #>  Image y-axis max boundary:  -2380.75  #>  Image y-axis min boundary:  -5730.25  #>   #> Scale factor:  #> x y  #> 1 1  #>  #>  Resolution:  #> x y  #> 1 1  #>  #>  File Path:  #> NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Python Package Installation — checkPythonPackage","title":"Check Python Package Installation — checkPythonPackage","text":"checks python environment provided package, installs found.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Python Package Installation — checkPythonPackage","text":"","code":"checkPythonPackage(   package_name = NULL,   github_package_url = NULL,   env_to_use = \"giotto_env\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Python Package Installation — checkPythonPackage","text":"package_name name python package. See details. github_package_url URL linking github repository containing python package may installed pip, e.g. git+https://github.com/TencentAILabHealthcare/pysodb.git; see details. env_to_use name environment python package installed.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Python Package Installation — checkPythonPackage","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkPythonPackage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Check Python Package Installation — checkPythonPackage","text":"Parameter github_package_url takes precedent package_name, .e. provided, github URL installed. function provided one parameter, .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/check_py_for_scanpy.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Scanpy Installation — check_py_for_scanpy","title":"Check Scanpy Installation — check_py_for_scanpy","text":"checks current python environment scanpy 1.9.0","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/check_py_for_scanpy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Scanpy Installation — check_py_for_scanpy","text":"","code":"check_py_for_scanpy()"},{"path":"https://drieslab.github.io/GiottoClass/reference/check_py_for_scanpy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Scanpy Installation — check_py_for_scanpy","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate circle polygon vertices — circleVertices","title":"Generate circle polygon vertices — circleVertices","text":"Generates vertex coordinates circle around (0,0) given radius. Modified packcircles.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate circle polygon vertices — circleVertices","text":"","code":"circleVertices(radius, npoints = 25)"},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate circle polygon vertices — circleVertices","text":"radius radius circle drawn npoints number vertices generate","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate circle polygon vertices — circleVertices","text":"data.table circle vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/circleVertices.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate circle polygon vertices — circleVertices","text":"","code":"circleVertices(radius = 10) #>              x             y #>          <num>         <num> #>  1: 10.0000000  0.000000e+00 #>  2:  9.6858316  2.486899e+00 #>  3:  8.7630668  4.817537e+00 #>  4:  7.2896863  6.845471e+00 #>  5:  5.3582679  8.443279e+00 #>  6:  3.0901699  9.510565e+00 #>  7:  0.6279052  9.980267e+00 #>  8: -1.8738131  9.822873e+00 #>  9: -4.2577929  9.048271e+00 #> 10: -6.3742399  7.705132e+00 #> 11: -8.0901699  5.877853e+00 #> 12: -9.2977649  3.681246e+00 #> 13: -9.9211470  1.253332e+00 #> 14: -9.9211470 -1.253332e+00 #> 15: -9.2977649 -3.681246e+00 #> 16: -8.0901699 -5.877853e+00 #> 17: -6.3742399 -7.705132e+00 #> 18: -4.2577929 -9.048271e+00 #> 19: -1.8738131 -9.822873e+00 #> 20:  0.6279052 -9.980267e+00 #> 21:  3.0901699 -9.510565e+00 #> 22:  5.3582679 -8.443279e+00 #> 23:  7.2896863 -6.845471e+00 #> 24:  8.7630668 -4.817537e+00 #> 25:  9.6858316 -2.486899e+00 #> 26: 10.0000000 -2.449294e-15 #>              x             y"},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"colMeans_flex — colMeans_flex","title":"colMeans_flex — colMeans_flex","text":"colMeans_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"colMeans_flex — colMeans_flex","text":"","code":"colMeans_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"colMeans_flex — colMeans_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"colMeans_flex — colMeans_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colMeans_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"colMeans_flex — colMeans_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  colMeans_flex(m) #>  [1] -0.1115180 -0.2079954  0.2838068  0.3373178 -0.1238467 -0.2577087 #>  [7] -0.2453714  0.5362443 -0.4952991  0.2693857"},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"colSums_flex — colSums_flex","title":"colSums_flex — colSums_flex","text":"colSums_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"colSums_flex — colSums_flex","text":"","code":"colSums_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"colSums_flex — colSums_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"colSums_flex — colSums_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/colSums_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"colSums_flex — colSums_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  colSums_flex(m) #>  [1]   0.5626158   2.5194923 -10.1333315  -2.4267322   3.8784106  -1.9650656 #>  [7]  -2.8342559  -1.9619765   6.9062217  -2.2261136"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":null,"dir":"Reference","previous_headings":"","what":"combineCellData — combineCellData","title":"combineCellData — combineCellData","text":"combine cell data information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineCellData — combineCellData","text":"","code":"combineCellData(   gobject,   feat_type = \"rna\",   include_spat_locs = TRUE,   spat_loc_name = \"raw\",   include_poly_info = TRUE,   poly_info = \"cell\",   include_spat_enr = TRUE,   spat_enr_names = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineCellData — combineCellData","text":"gobject giotto object feat_type feature type include_spat_locs include information spatial locations spat_loc_name spatial location name include_poly_info include information polygon poly_info polygon information name include_spat_enr include information spatial enrichment spat_enr_names names spatial enrichment results include","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineCellData — combineCellData","text":"data.table combined spatial information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineCellData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineCellData — combineCellData","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineCellData(g, poly_info = \"aggregate\") #> $rna #> Key: <cell_ID> #>                                        cell_ID    sdimx     sdimy  geom  part #>                                         <char>    <num>     <num> <int> <num> #>     1: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>     2: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>     3: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>     4: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>     5: 100210519278873141813371229408401071444 6637.881 -5140.465     1     1 #>    ---                                                                        #> 35971:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #> 35972:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #> 35973:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #> 35974:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #> 35975:  98561957902191275233320065611022298397 6784.848 -4942.076   462     1 #>               x         y  hole  stack agg_n valid nr_feats perc_feats #>           <num>     <num> <num> <char> <int> <int>    <int>      <num> #>     1: 6642.257 -5136.674     0   <NA>     2     1       22    6.52819 #>     2: 6642.711 -5137.020     0   <NA>     2     1       22    6.52819 #>     3: 6643.050 -5137.462     0   <NA>     2     1       22    6.52819 #>     4: 6643.310 -5137.956     0   <NA>     2     1       22    6.52819 #>     5: 6643.484 -5138.518     0   <NA>     2     1       22    6.52819 #>    ---                                                                 #> 35971: 6788.764 -4942.998     0   <NA>     2     1       53   15.72700 #> 35972: 6788.905 -4942.999     0   <NA>     2     1       53   15.72700 #> 35973: 6789.575 -4942.999     0   <NA>     2     1       53   15.72700 #> 35974: 6789.576 -4943.000     0   <NA>     2     1       53   15.72700 #> 35975: 6789.695 -4943.000     0   <NA>     2     1       53   15.72700 #>        total_expr leiden_clus louvain_clus   feat #>             <num>       <num>        <num> <char> #>     1:   163.6923           4           15    rna #>     2:   163.6923           4           15    rna #>     3:   163.6923           4           15    rna #>     4:   163.6923           4           15    rna #>     5:   163.6923           4           15    rna #>    ---                                            #> 35971:   326.0539           1           26    rna #> 35972:   326.0539           1           26    rna #> 35973:   326.0539           1           26    rna #> 35974:   326.0539           1           26    rna #> 35975:   326.0539           1           26    rna #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":null,"dir":"Reference","previous_headings":"","what":"combineFeatureData — combineFeatureData","title":"combineFeatureData — combineFeatureData","text":"combine feature data information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineFeatureData — combineFeatureData","text":"","code":"combineFeatureData(   gobject,   feat_type = NULL,   spat_unit = NULL,   sel_feats = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineFeatureData — combineFeatureData","text":"gobject giotto object feat_type feature type spat_unit spatial unit sel_feats selected features (default: NULL selection)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineFeatureData — combineFeatureData","text":"data.table combined spatial feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineFeatureData — combineFeatureData","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineFeatureData(g, spat_unit = \"aggregate\", feat_type = \"rna\") #> $rna #> Key: <feat_ID> #>        feat_ID nr_cells perc_cells total_expr  mean_expr mean_expr_det hvg_orig #>         <char>    <int>      <num>      <num>      <num>         <num>   <char> #>     1:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     2:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     3:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     4:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     5:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>    ---                                                                          #> 79757:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 79758:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 79759:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 79760:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 79761:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #>              var    hvf  geom  part        x         y  hole global_z #>            <num> <char> <int> <num>    <num>     <num> <num>    <int> #>     1: 3.2630074    yes    52     1 6401.822 -5074.172     0        0 #>     2: 3.2630074    yes  1405     1 6434.212 -4994.575     0        0 #>     3: 3.2630074    yes  1524     1 6435.822 -4993.068     0        0 #>     4: 3.2630074    yes  1564     1 6436.190 -4993.599     0        0 #>     5: 3.2630074    yes  1568     1 6436.225 -4994.331     0        0 #>    ---                                                                #> 79757: 0.9765725     no 55606     1 6755.787 -4842.521     0        1 #> 79758: 0.9765725     no 64289     1 6788.817 -4766.861     0        1 #> 79759: 0.9765725     no 64391     1 6789.242 -4927.838     0        1 #> 79760: 0.9765725     no 65159     1 6792.122 -4894.507     0        1 #> 79761: 0.9765725     no 77586     1 6876.786 -5032.958     0        1 #>        feat_ID_uniq   feat spat_unit #>               <int> <char>    <char> #>     1:           52    rna aggregate #>     2:         1414    rna aggregate #>     3:         1534    rna aggregate #>     4:         1574    rna aggregate #>     5:         1578    rna aggregate #>    ---                               #> 79757:        56040    rna aggregate #> 79758:        64767    rna aggregate #> 79759:        64870    rna aggregate #> 79760:        65645    rna aggregate #> 79761:        78156    rna aggregate #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":null,"dir":"Reference","previous_headings":"","what":"combineFeatureOverlapData — combineFeatureOverlapData","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"combine feature data information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"","code":"combineFeatureOverlapData(   gobject,   feat_type = \"rna\",   sel_feats = NULL,   poly_info = \"cell\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"gobject giotto object feat_type feature type sel_feats selected features (default: NULL selection) poly_info polygon information name","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"data.table combined spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineFeatureOverlapData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineFeatureOverlapData — combineFeatureOverlapData","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineFeatureOverlapData(g, poly_info = \"aggregate\") #> $rna #> Key: <feat_ID> #>        feat_ID nr_cells perc_cells total_expr  mean_expr mean_expr_det hvg_orig #>         <char>    <int>      <num>      <num>      <num>         <num>   <char> #>     1:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     2:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     3:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     4:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>     5:   Abcc9       10   2.164502   71.39463 0.15453382      7.139463       no #>    ---                                                                          #> 32067:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 32068:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 32069:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 32070:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #> 32071:  Vmn2r1        7   1.515152   41.22525 0.08923213      5.889321       no #>              var    hvf  geom  part        x         y  hole #>            <num> <char> <int> <num>    <num>     <num> <num> #>     1: 3.2630074    yes   327     1 6434.212 -4994.575     0 #>     2: 3.2630074    yes   372     1 6435.822 -4993.068     0 #>     3: 3.2630074    yes   387     1 6436.190 -4993.599     0 #>     4: 3.2630074    yes   389     1 6436.225 -4994.331     0 #>     5: 3.2630074    yes  3476     1 6583.026 -5109.118     0 #>    ---                                                       #> 32067: 0.9765725     no 12671     1 6835.198 -4821.361     0 #> 32068: 0.9765725     no 13128     1 6850.250 -4791.958     0 #> 32069: 0.9765725     no 15407     1 6432.064 -5016.469     0 #> 32070: 0.9765725     no 21939     1 6742.455 -4972.980     0 #> 32071: 0.9765725     no 31289     1 6876.786 -5032.958     0 #>                                        poly_ID feat_ID_uniq stack poly_info #>                                         <char>        <int> <int>    <char> #>     1: 304842190541754537761816256358565562302         1414     1 aggregate #>     2: 304842190541754537761816256358565562302         1534     1 aggregate #>     3: 304842190541754537761816256358565562302         1574     1 aggregate #>     4: 304842190541754537761816256358565562302         1578     1 aggregate #>     5: 183227745956657225549068107012033843521         8860     1 aggregate #>    ---                                                                      #> 32067: 134146760472988945324695838070256730703        30405     1 aggregate #> 32068: 248026342734562151407765229569772513183        31685     1 aggregate #> 32069:  21934936165997373583174173761929761438        37793     2 aggregate #> 32070: 293490979527928845906184572736930005899        53817     2 aggregate #> 32071: 236938169420664432126575547704304293443        78156     2 aggregate #>          feat #>        <char> #>     1:    rna #>     2:    rna #>     3:    rna #>     4:    rna #>     5:    rna #>    ---        #> 32067:    rna #> 32068:    rna #> 32069:    rna #> 32070:    rna #> 32071:    rna #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"combineMetadata — combineMetadata","title":"combineMetadata — combineMetadata","text":"function combines cell metadata spatial locations enrichment results runSpatialEnrich.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineMetadata — combineMetadata","text":"","code":"combineMetadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = \"raw\",   spat_enr_names = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineMetadata — combineMetadata","text":"gobject Giotto object spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations include spat_enr_names names spatial enrichment results include verbose verbosity","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineMetadata — combineMetadata","text":"Extended cell metadata data.table format.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineMetadata — combineMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineMetadata(g) #> Key: <cell_ID> #>                 cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                  <char>     <int>    <int>      <num>      <num>       <num> #>   1: AAAGGGATGTAGCAAG-1         1      227   35.80442   995.1491           1 #>   2: AAATGGCATGTCTTGT-1         1      283   44.63722  1123.8751           2 #>   3: AAATGGTCAATGTGCC-1         1      248   39.11672  1027.6322           4 #>   4: AAATTAACGGGTAGCT-1         1      222   35.01577   974.3766           4 #>   5: AACAACTGGTAGTTGC-1         1      313   49.36909  1174.4881           6 #>  ---                                                                         #> 620: TTGTAATCCGTACTCG-1         1      315   49.68454  1184.0178           4 #> 621: TTGTATCACACAGAAT-1         1      240   37.85489   999.6419           2 #> 622: TTGTCGTTCAGTTACC-1         1      220   34.70032   994.6648           1 #> 623: TTGTGGCCCTGACAGT-1         1      204   32.17666   930.5489           5 #> 624: TTGTTCAGTGTGCTAC-1         1      237   37.38170  1034.8893           1 #>      custom_leiden sdimx sdimy #>              <num> <int> <int> #>   1:             1  5477 -4125 #>   2:             3  5959 -2808 #>   3:             2  4720 -5202 #>   4:             2  5202 -5322 #>   5:             2  4101 -4604 #>  ---                           #> 620:             2  4996 -5442 #> 621:             3  6303 -2688 #> 622:             1  5202 -3885 #> 623:             1  5340 -3406 #> 624:             1  5615 -4125"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"Combine cell metadata spatial cell information (e.g. polygon)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"","code":"combineSpatialCellMetadataInfo(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"gobject Giotto object spat_unit spatial unit feat_type feature type(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"list data.table(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"returned data.table following columns: sdimx: spatial feature location x-axis sdimy: spatial feature location y-axis cell_ID: unique cell ID feat: selected feature(s) columns part cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellMetadataInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"combineSpatialCellMetadataInfo — combineSpatialCellMetadataInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  combineSpatialCellMetadataInfo(g, spat_unit = \"aggregate\", feat_type = \"rna\") #> $rna #> Key: <cell_ID> #>                                      cell_ID  stack agg_n valid nr_feats #>                                       <char> <char> <int> <int>    <int> #>   1: 100210519278873141813371229408401071444   <NA>     2     1       22 #>   2: 101161259912191124732236989250178928032   <NA>     2     1       36 #>   3: 101488859781016188084173008420811094152   <NA>     2     1       35 #>   4: 101523780333017320796881555775415156847   <NA>     2     1       39 #>   5: 102184699197574201819246996094734116255   <NA>     2     1       44 #>  ---                                                                     #> 458:   9677424102111816817518421117250891895   <NA>     2     1       30 #> 459:  97068595823890802071024838798130036179   <NA>     2     1       46 #> 460:  97411078642927912684859796714759494710   <NA>     2     1       33 #> 461:   9816437869021910185567097363182418837   <NA>     2     1       31 #> 462:  98561957902191275233320065611022298397   <NA>     2     1       53 #>      perc_feats total_expr leiden_clus louvain_clus   feat #>           <num>      <num>       <num>        <num> <char> #>   1:   6.528190   163.6923           4           15    rna #>   2:  10.682493   228.7269           2           10    rna #>   3:  10.385757   242.0458           1           22    rna #>   4:  11.572700   262.3842           1           24    rna #>   5:  13.056380   291.5877           2            0    rna #>  ---                                                       #> 458:   8.902077   211.7179           2            3    rna #> 459:  13.649852   279.5605           2            5    rna #> 460:   9.792285   226.7092           4           15    rna #> 461:   9.198813   220.4129           3           13    rna #> 462:  15.727003   326.0539           1           26    rna #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine giottoPolygon geometries — combineToMultiPolygon","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"Combine multiple giottoPolygon geometries set multipolygons. Note attributes kept","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"","code":"combineToMultiPolygon(x, groups, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"x giottoPolygon groups data.frame columns 'poly_ID' 'group_ID' relates polygons now combined group_ID name (optional) name giottoPolygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineToMultiPolygon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"","code":"gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") groups <- data.table::data.table(     poly_ID = gpoly$poly_ID,     group_ID = sort(rep(LETTERS[seq_len(5)], length.out = nrow(gpoly)))     # make 5 groups )  multi_gp <- combineToMultiPolygon(gpoly, groups)  plot(multi_gp[\"A\"])"},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Compatible spatial network — compatible_spatial_network","title":"Compatible spatial network — compatible_spatial_network","text":"Function evaluate spatial network compatible provided expression matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compatible spatial network — compatible_spatial_network","text":"","code":"compatible_spatial_network(spatial_network, expression_matrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compatible spatial network — compatible_spatial_network","text":"spatial_network spatial network evaluate expression_matrix expression compare ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Compatible spatial network — compatible_spatial_network","text":"TRUE character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/compatible_spatial_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Compatible spatial network — compatible_spatial_network","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spat_net <- getSpatialNetwork(g, output = \"networkDT\") expr_m <- getExpression(g)  compatible_spatial_network(spat_net, expr_m) #> [1] TRUE"},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":null,"dir":"Reference","previous_headings":"","what":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"Get convex hull, minimal bounding rotated rectangle, minimal bounding circle Giotto spatial object terra SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"","code":"# S4 method for class 'spatLocsObj' convHull(x, by = \"\", ...)  # S4 method for class 'giottoSpatial' convHull(x, by = \"\", ...)  # S4 method for class 'spatLocsObj' minRect(x, by = \"\", ...)  # S4 method for class 'giottoSpatial' minRect(x, by = \"\", ...)  # S4 method for class 'spatLocsObj' minCircle(x, by = \"\", ...)  # S4 method for class 'giottoSpatial' minCircle(x, by = \"\", ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"x giotto image, giottoPolygon, giottoPoints, spatLocsObj, SpatVector character (variable name), get new geometry groups input geometries ... additional parameters pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convHull.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convex hull, minimal bounding rotated rectangle, and minimal bounding circle — convHull","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  h <- convHull(sl) plot(h)   r <- minRect(sl) plot(r)   circ <- minCircle(gpoints, by = \"feat_ID\") plot(circ, border = rainbow(100))"},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":null,"dir":"Reference","previous_headings":"","what":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"convert giottoLargeImage downsampling normal magick based giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"","code":"convertGiottoLargeImageToMG(   gobject = NULL,   largeImage_name = NULL,   giottoLargeImage = NULL,   mg_name = NULL,   spat_unit = NULL,   spat_loc_name = NULL,   crop_extent = NULL,   xmax_crop = NULL,   xmin_crop = NULL,   ymax_crop = NULL,   ymin_crop = NULL,   resample_size = 5e+05,   max_intensity = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"gobject gobject containing giottoLargeImage largeImage_name name giottoLargeImage giottoLargeImage alternative input param using giottoLargeImage object instead gobject largeImage_name params mg_name name assign converted magick image based giottoImage. Defaults name giottoLargeImage spat_unit spatial unit spat_loc_name gobject spatial location name map giottoImage (optional) crop_extent extent object focus specific region image xmax_crop assign crop boundary xmin_crop assign crop boundary ymax_crop assign crop boundary ymin_crop assign crop boundary resample_size maximum number pixels use resampling max_intensity value treat maximum intensity color scale return_gobject return giotto object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"giotto object return_gobject = TRUE updated giotto image object return_gobject = FALSE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convertGiottoLargeImageToMG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convertGiottoLargeImageToMG — convertGiottoLargeImageToMG","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  convertGiottoLargeImageToMG(g, largeImage_name = \"image\") #> image has already been used, will be overwritten #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":null,"dir":"Reference","previous_headings":"","what":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"converts magick image object data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"","code":"convert_mgImage_to_array_DT(mg_object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"mg_object magick image Giotto image object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"data.table image pixel information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_mgImage_to_array_DT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convert_mgImage_to_array_DT — convert_mgImage_to_array_DT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, name = \"image\") mgimg <- as(g_image, \"giottoImage\")  a <- convert_mgImage_to_array_DT(mgimg) force(a) #> Key: <x, y> #>            x     y       c.1       c.2       c.3     4     RGB #>        <int> <int>     <num>     <num>     <num> <num>  <char> #>     1:     1     1 0.5098039 0.5215686 0.5019608     1 #828580 #>     2:     1     2 0.5098039 0.5176471 0.5019608     1 #828480 #>     3:     1     3 0.5098039 0.5176471 0.5019608     1 #828480 #>     4:     1     4 0.5098039 0.5176471 0.4980392     1 #82847F #>     5:     1     5 0.5098039 0.5176471 0.4980392     1 #82847F #>    ---                                                         #> 41792:   172   239 0.3803922 0.3058824 0.4313725     1 #614E6E #> 41793:   172   240 0.4313725 0.3372549 0.4509804     1 #6E5673 #> 41794:   172   241 0.4196078 0.3215686 0.4392157     1 #6B5270 #> 41795:   172   242 0.4470588 0.3215686 0.4549020     1 #725274 #> 41796:   172   243 0.4392157 0.2941176 0.4470588     1 #704B72 force(a) #> Key: <x, y> #>            x     y       c.1       c.2       c.3     4     RGB #>        <int> <int>     <num>     <num>     <num> <num>  <char> #>     1:     1     1 0.5098039 0.5215686 0.5019608     1 #828580 #>     2:     1     2 0.5098039 0.5176471 0.5019608     1 #828480 #>     3:     1     3 0.5098039 0.5176471 0.5019608     1 #828480 #>     4:     1     4 0.5098039 0.5176471 0.4980392     1 #82847F #>     5:     1     5 0.5098039 0.5176471 0.4980392     1 #82847F #>    ---                                                         #> 41792:   172   239 0.3803922 0.3058824 0.4313725     1 #614E6E #> 41793:   172   240 0.4313725 0.3372549 0.4509804     1 #6E5673 #> 41794:   172   241 0.4196078 0.3215686 0.4392157     1 #6B5270 #> 41795:   172   242 0.4470588 0.3215686 0.4549020     1 #725274 #> 41796:   172   243 0.4392157 0.2941176 0.4470588     1 #704B72"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":null,"dir":"Reference","previous_headings":"","what":"convert_to_full_spatial_network — convert_to_full_spatial_network","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"Convert full spatial network, ie ensuring edges may currently represented \\(\\) -> \\(b\\) also reverse \\(b\\) -> \\(\\). entries made unique, interactions ranked distance, rank increases smaller larger distances. rank appended data.table rank_int column. Another rnk_src_trgt column added IDs \\(\\) \\(b\\) pasted together","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"","code":"convert_to_full_spatial_network(reduced_spatial_network_DT)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"reduced_spatial_network_DT reduced spatial network data.table format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_full_spatial_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convert_to_full_spatial_network — convert_to_full_spatial_network","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spat_net <- getSpatialNetwork(g, output = \"networkDT\")  spat_net_full <- convert_to_full_spatial_network(spat_net)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":null,"dir":"Reference","previous_headings":"","what":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"Convert reduced spatial network. Specifically, removes duplicated connections \\(\\) -> \\(b\\) interactions remain.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"","code":"convert_to_reduced_spatial_network(full_spatial_network_DT)"},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"full_spatial_network_DT full spatial network data.table format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/convert_to_reduced_spatial_network.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"convert_to_reduced_spatial_network — convert_to_reduced_spatial_network","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spat_net <- getSpatialNetwork(g, output = \"networkDT\") spat_net_full <- convert_to_full_spatial_network(spat_net)  convert_to_reduced_spatial_network(spat_net_full) #>                     from                 to sdimx_begin sdimy_begin sdimx_end #>                   <char>             <char>       <num>       <num>     <num> #>    1: AAAGGGATGTAGCAAG-1 TCAAACAACCGCGTCG-1        5477       -4125      5340 #>    2: AAAGGGATGTAGCAAG-1 ACGATCATACATAGAG-1        5477       -4125      5546 #>    3: AAAGGGATGTAGCAAG-1 TATGCTCCCTACTTAC-1        5477       -4125      5408 #>    4: AAAGGGATGTAGCAAG-1 TTGTTCAGTGTGCTAC-1        5477       -4125      5615 #>    5: AAAGGGATGTAGCAAG-1 ATCGACTCTTTCCGTT-1        5477       -4125      5408 #>   ---                                                                         #> 1766: TTCAAGCCGAGCTGAG-1 TTGTATCACACAGAAT-1        6372       -2808      6303 #> 1767: TTCGACGGGAAGGGCG-1 TTCGCACTCGCGTGCT-1        4239       -4125      4308 #> 1768: TTCTTAGTGGCTCAGA-1 TTGTGGCCCTGACAGT-1        5408       -3287      5340 #> 1769: TTCTTGTAACCTAATG-1 TTGGCTCGCATGAGAC-1        3620       -4005      3757 #> 1770: TTGCACGGAGCAGCAC-1 TTGTCGTTCAGTTACC-1        5271       -3766      5202 #>       sdimy_end distance      weight #>           <num>    <num>       <num> #>    1:     -4125 137.0000 0.007299270 #>    2:     -4244 137.5573 0.007269700 #>    3:     -4244 137.5573 0.007269700 #>    4:     -4125 138.0000 0.007246377 #>    5:     -4005 138.4233 0.007224219 #>   ---                                #> 1766:     -2688 138.4233 0.007224219 #> 1767:     -4245 138.4233 0.007224219 #> 1768:     -3406 137.0584 0.007296161 #> 1769:     -4005 137.0000 0.007299270 #> 1770:     -3885 137.5573 0.007269700"},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy an entire object — copy","title":"Copy an entire object — copy","text":"S4 generic Giotto's S4 subobjects return full copies certain subobjects usually return referenced information.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy an entire object — copy","text":"","code":"# S4 method for class 'coordDataDT' copy(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy an entire object — copy","text":"x Giotto S4 class subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Copy an entire object — copy","text":"giotto subobjects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Copy an entire object — copy","text":"copy(coordDataDT): Copy data.table-based spatial locations object.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/copy.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Copy an entire object — copy","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  copy(g) #> An object of class exprObj : \"normalized\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                                                                           #> Mlc1    .       .        .        .        . .  5.291601 . .        5.821597 . .        . #> Gprc5b  .       6.398031 .        7.454658 . .  6.273066 . 7.680054 6.808785 . 5.082989 . #> Gfap   10.48137 .        7.901442 5.886051 . . 10.746982 . 5.701006 5.821597 . .        . #>               #> Mlc1   ...... #> Gprc5b ...... #> Gfap   ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"cor_flex — cor_flex","title":"cor_flex — cor_flex","text":"cor_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"cor_flex — cor_flex","text":"","code":"cor_flex(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"cor_flex — cor_flex","text":"x data use ... arguments passed stats::cor()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"cor_flex — cor_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cor_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"cor_flex — cor_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  cor_flex(m) #>              [,1]        [,2]       [,3]        [,4]        [,5]        [,6] #>  [1,]  1.00000000  0.28099280 -0.6867656  0.42283126 -0.38987371 -0.07468685 #>  [2,]  0.28099280  1.00000000 -0.1659979 -0.51534964 -0.04087937 -0.59687113 #>  [3,] -0.68676564 -0.16599789  1.0000000 -0.48483005  0.23503091  0.37132983 #>  [4,]  0.42283126 -0.51534964 -0.4848301  1.00000000 -0.15473094  0.04134032 #>  [5,] -0.38987371 -0.04087937  0.2350309 -0.15473094  1.00000000  0.19145228 #>  [6,] -0.07468685 -0.59687113  0.3713298  0.04134032  0.19145228  1.00000000 #>  [7,]  0.17213620  0.19751817  0.1650136 -0.50007590 -0.30859664  0.18060348 #>  [8,]  0.11188918  0.05397874  0.4688130 -0.20095484  0.20343973  0.51007047 #>  [9,]  0.15068347 -0.65991342 -0.2022737  0.67766661 -0.15672350  0.39082372 #> [10,] -0.07803746 -0.34887195 -0.1485405  0.02694660 -0.47862493  0.34358459 #>              [,7]        [,8]        [,9]       [,10] #>  [1,]  0.17213620  0.11188918  0.15068347 -0.07803746 #>  [2,]  0.19751817  0.05397874 -0.65991342 -0.34887195 #>  [3,]  0.16501365  0.46881300 -0.20227374 -0.14854052 #>  [4,] -0.50007590 -0.20095484  0.67766661  0.02694660 #>  [5,] -0.30859664  0.20343973 -0.15672350 -0.47862493 #>  [6,]  0.18060348  0.51007047  0.39082372  0.34358459 #>  [7,]  1.00000000  0.08919887 -0.55902381  0.24693050 #>  [8,]  0.08919887  1.00000000  0.06649927 -0.36539126 #>  [9,] -0.55902381  0.06649927  1.00000000  0.22054868 #> [10,]  0.24693050 -0.36539126  0.22054868  1.00000000"},{"path":"https://drieslab.github.io/GiottoClass/reference/createBentoAdata.html","id":null,"dir":"Reference","previous_headings":"","what":"Create bento adata object from gobject — createBentoAdata","title":"Create bento adata object from gobject — createBentoAdata","text":"Create bento adata object gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createBentoAdata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create bento adata object from gobject — createBentoAdata","text":"","code":"createBentoAdata(gobject = NULL, env_to_use = \"giotto_env\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/createBentoAdata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create bento adata object from gobject — createBentoAdata","text":"gobject Giotto object env_to_use Python environment within bento installed. already installed, user prompted install bento-tools DEFAULT: \"giotto_env\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createBentoAdata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create bento adata object from gobject — createBentoAdata","text":"bento_adata bento adata object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 cellMetaObj — createCellMetaObj","title":"Create S4 cellMetaObj — createCellMetaObj","text":"Create S4 cellMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 cellMetaObj — createCellMetaObj","text":"","code":"createCellMetaObj(   metadata,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   col_desc = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 cellMetaObj — createCellMetaObj","text":"metadata metadata info spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') provenance origin data aggregated expression information (applicable) col_desc (optional) character vector describing columns metadata verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 cellMetaObj — createCellMetaObj","text":"cellMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createCellMetaObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 cellMetaObj — createCellMetaObj","text":"","code":"df <- data.frame(cell_ID = c(\"cell_1\", \"cell_2\", \"cell_3\"))  createCellMetaObj(metadata = df) #> An object of class cellMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #> dimensions: 3 1  #>  #>    cell_ID #>     <char> #> 1:  cell_1 #> 2:  cell_2 #> 3:  cell_3"},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 dimObj — createDimObj","title":"Create S4 dimObj — createDimObj","text":"Create S4 dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 dimObj — createDimObj","text":"","code":"createDimObj(   coordinates,   name = \"test\",   spat_unit = \"cell\",   feat_type = \"rna\",   method = NULL,   reduction = \"cells\",   provenance = NULL,   misc = NULL,   my_rownames = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 dimObj — createDimObj","text":"coordinates embedding coordinates name name dimObj spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') method method used generate dimension reduction reduction reduction columns (e.g. cells) rows (e.g. features) provenance origin data aggregated expression information (applicable) misc misc my_rownames (optional) needed, set coordinates rowname values ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 dimObj — createDimObj","text":"dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createDimObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 dimObj — createDimObj","text":"","code":"x <- matrix(c(2.81, 5.59, 10.54, 2.25, 5.12, 2.79), nrow = 3) rownames(x) <- c(\"cell_1\", \"cell_2\", \"cell_3\") colnames(x) <- c(\"Dim.1\", \"Dim.2\")  createDimObj(coordinates = x, name = \"pca\", method = \"pca\") #> An object of class dimObj : \"pca\" #> --| Contains dimension reduction generated with: pca  #> ----| for feat_type: rna  #> ----|     spat_unit: cell  #>  #>    2 dimensions for 3 data points #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 exprObj — createExprObj","title":"Create S4 exprObj — createExprObj","text":"Create S4 exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 exprObj — createExprObj","text":"","code":"createExprObj(   expression_data,   name = \"test\",   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL,   expression_matrix_class = c(\"dgCMatrix\", \"DelayedArray\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 exprObj — createExprObj","text":"expression_data expression data name name exprObj spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance origin data expression information (applicable) misc misc expression_matrix_class class expression matrix use (e.g. 'dgCMatrix', 'DelayedArray')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 exprObj — createExprObj","text":"exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createExprObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 exprObj — createExprObj","text":"","code":"x_expr <- readRDS(system.file(\"extdata/toy_matrix.RDS\",     package = \"GiottoClass\" ))  createExprObj(expression_data = x_expr) #> An object of class exprObj : \"test\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #>  #> contains: #> 10 x 10 sparse Matrix of class \"dgCMatrix\" #>                       #> a . . . . . . . . . . #> b . . . . 1 . . . . . #> c . . . . . . 1 . . . #> d . . . . . . . . . 1 #>  #>  ........suppressing 2 rows in show(); maybe adjust options(max.print=, width=) #>                       #> g 1 . . . . . . . . . #> h 1 . . . . . . . . 1 #> i . . . . . . . . . . #> j . . . 1 . 1 . . . . #>  #>  First four colnames: #>  A B C D"},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 featMetaObj — createFeatMetaObj","title":"Create S4 featMetaObj — createFeatMetaObj","text":"Create S4 featMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 featMetaObj — createFeatMetaObj","text":"","code":"createFeatMetaObj(   metadata,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   col_desc = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 featMetaObj — createFeatMetaObj","text":"metadata metadata info spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') provenance origin data aggregated expression information (applicable) col_desc (optional) character vector describing columns metadata verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 featMetaObj — createFeatMetaObj","text":"featMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createFeatMetaObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 featMetaObj — createFeatMetaObj","text":"","code":"x <- data.frame(     feat_ID = c(\"Mlc1\", \"Gprc5b\", \"Gfap\"),     nr_cells = c(80, 138, 151) )  createFeatMetaObj(metadata = x) #> An object of class featMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #>  #>    feat_ID nr_cells #>     <char>    <num> #> 1:    Mlc1       80 #> 2:  Gprc5b      138 #> 3:    Gfap      151"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"createGiottoImage — createGiottoImage","title":"createGiottoImage — createGiottoImage","text":"Creates giotto image can added Giotto object /used add image spatial plotting functions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createGiottoImage — createGiottoImage","text":"","code":"createGiottoImage(   gobject = NULL,   spat_unit = NULL,   spatial_locs = NULL,   spat_loc_name = NULL,   mg_object,   name = \"image\",   image_transformations = NULL,   negative_y = TRUE,   do_manual_adj = FALSE,   xmax_adj = 0,   xmin_adj = 0,   ymax_adj = 0,   ymin_adj = 0,   scale_factor = 1,   x_shift = NULL,   y_shift = NULL,   scale_x = NULL,   scale_y = NULL,   order = c(\"first_scale\", \"first_adj\"),   xmin_set = NULL,   xmax_set = NULL,   ymin_set = NULL,   ymax_set = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createGiottoImage — createGiottoImage","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") spatial_locs spatial locations (alternative gobject = NULL) spat_loc_name name spatial locations within gobject mg_object magick image object name name image image_transformations vector sequential image transformations negative_y Map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left. do_manual_adj (default = FALSE) flag use manual adj values instead automatic alignment given gobject spatlocs xmax_adj, xmin_adj, ymax_adj, ymin_adj adjustment maximum maximum x y-value align image scale_factor scaling image dimensions relative spatial coordinates x_shift, y_shift shift image along x y axes scale_x, scale_y independently scale image x y direction order perform scaling adjustments shifts first xmin_set, xmax_set, ymin_set, ymax_set values override image minmax spatial anchors adjustments verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createGiottoImage — createGiottoImage","text":"giottoImage object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createGiottoImage — createGiottoImage","text":"image_transformations: transformation options magick library [flip_x_axis] flip x-axis (image_flop) [flip_y_axis] flip y-axis (image_flip) Example: image_transformations = c(flip_x_axis, flip_y_axis); first flip x-axis y-axis","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createGiottoImage — createGiottoImage","text":"","code":"image_test <- system.file(\"extdata/toy_intensity.tif\",     package = \"GiottoClass\" )  createGiottoImage(mg_object = image_test) #> Warning: gobject or spatial locations are not provided  #> Arbitrary values will be given  #> An object of class ' giottoImage ' with name  image  #>   #> Min and max values are:  #>  Max on x-axis:  10  #>  Min on x-axis:  0  #>  Max on y-axis:  10  #>  Min on y-axis:  0  #>   #> Boundary adjustment are:  #>  Max adjustment on x-axis:  0  #>  Min adjustment on x-axis:  0  #>  Max adjustment on y-axis:  0  #>  Min adjustment on y-axis:  0  #>   #> Boundaries are:  #>  Image x-axis max boundary:  10  #>  Image x-axis min boundary:  0  #>  Image y-axis max boundary:  10  #>  Image y-axis min boundary:  0  #>   #> Scale factor:  #> x y  #> 1 1  #>  #>  Resolution:  #> x y  #> 1 1  #>  #>  File Path:  #> [1] \"/home/runner/work/_temp/Library/GiottoClass/extdata/toy_intensity.tif\""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"createGiottoLargeImage — createGiottoLargeImage","title":"createGiottoLargeImage — createGiottoLargeImage","text":"Creates large giotto image can added Giotto subcellular object. Generates deep copy SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createGiottoLargeImage — createGiottoLargeImage","text":"","code":"createGiottoLargeImage(   raster_object,   name = \"image\",   negative_y = TRUE,   extent = NULL,   use_rast_ext = FALSE,   image_transformations = NULL,   flip_vertical = FALSE,   flip_horizontal = FALSE,   xmax_bound = NULL,   xmin_bound = NULL,   ymax_bound = NULL,   ymin_bound = NULL,   scale_factor = 1,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createGiottoLargeImage — createGiottoLargeImage","text":"raster_object filepath image, terra SpatRaster , format openable via terra::rast() name name image negative_y Map image negative y spatial values TRUE. Meaning origin upper left instead lower left. extent SpatExtent object assign spatial extent. Takes priority unless use_rast_ext TRUE. use_rast_ext Use extent input raster object image_transformations vector sequential image transformations - construction flip_vertical flip raster vertical manner flip_horizontal flip raster horizontal manner xmax_bound, xmin_bound, ymax_bound, ymin_bound assign min max x y values image spatial placement scale_factor scaling image dimensions relative spatial coordinates verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createGiottoLargeImage — createGiottoLargeImage","text":"giottoLargeImage object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createGiottoLargeImage — createGiottoLargeImage","text":"","code":"image_test <- system.file(\"extdata/toy_intensity.tif\",     package = \"GiottoClass\" )  createGiottoLargeImage(raster_object = image_test) #> An object of class giottoLargeImage : \"image\" #> Image extent            : 0, 1091, -1107, 0 (xmin, xmax, ymin, ymax) #> Original image extent   : 0, 1091, -1107, 0 (xmin, xmax, ymin, ymax) #> Scale factor            : 1, 1 (x, y) #> Resolution              : 1, 1 (x, y) #> Layers                  : 1  #> Estimated max intensity : 168  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoClass/extdata/toy_intensity.tif'"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":null,"dir":"Reference","previous_headings":"","what":"createGiottoLargeImageList — createGiottoLargeImageList","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"Creates list large giotto images can added Giotto object. Generates deep copy SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"","code":"createGiottoLargeImageList(   raster_objects,   names = \"image\",   negative_y = TRUE,   extent = NULL,   use_rast_ext = FALSE,   image_transformations = NULL,   flip_vertical = FALSE,   flip_horizontal = FALSE,   xmax_bound = NULL,   xmin_bound = NULL,   ymax_bound = NULL,   ymin_bound = NULL,   scale_factor = 1,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"raster_objects vector image paths terra SpatRaster image objects names vector names images negative_y Map image negative y spatial values TRUE. Meaning origin upper left instead lower left. extent SpatExtent object assign spatial extent. Takes priority unless use_rast_ext TRUE. use_rast_ext Use extent input raster object image_transformations vector sequential image transformations - construction flip_vertical flip raster vertical manner flip_horizontal flip raster horizontal manner xmax_bound, xmin_bound, ymax_bound, ymin_bound assign min max x y values image spatial placement scale_factor scaling image dimensions relative spatial coordinates verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"list giottoLargeImage objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"See createGiottoLargeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoLargeImageList.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createGiottoLargeImageList — createGiottoLargeImageList","text":"","code":"image_test <- system.file(\"extdata/toy_intensity.tif\",     package = \"GiottoClass\" )  createGiottoLargeImageList(raster_objects = image_test) #> [[1]] #> An object of class giottoLargeImage : \"image\" #> Image extent            : 0, 1091, -1107, 0 (xmin, xmax, ymin, ymax) #> Original image extent   : 0, 1091, -1107, 0 (xmin, xmax, ymin, ymax) #> Scale factor            : 1, 1 (x, y) #> Resolution              : 1, 1 (x, y) #> Layers                  : 1  #> Estimated max intensity : 168  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoClass/extdata/toy_intensity.tif' #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a giotto object — createGiottoObject","title":"Create a giotto object — createGiottoObject","text":"Function create giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a giotto object — createGiottoObject","text":"","code":"createGiottoObject(   expression,   expression_feat = \"rna\",   spatial_locs = NULL,   spatial_info = NULL,   calc_poly_centroids = FALSE,   centroids_to_spatlocs = FALSE,   feat_info = NULL,   cell_metadata = NULL,   feat_metadata = NULL,   spatial_network = NULL,   spatial_grid = NULL,   spatial_grid_name = NULL,   spatial_enrichment = NULL,   dimension_reduction = NULL,   nn_network = NULL,   images = NULL,   largeImages = NULL,   offset_file = NULL,   instructions = NULL,   cores = determine_cores(),   raw_exprs = NULL,   expression_matrix_class = c(\"dgCMatrix\", \"DelayedArray\"),   h5_file = NULL,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a giotto object — createGiottoObject","text":"expression expression information expression_feat available features (e.g. rna, protein, ...) spatial_locs data.table data.frame coordinates cell centroids spatial_info list giotto polygon objects spatial information, see createGiottoPolygonsFromMask createGiottoPolygonsFromDfr calc_poly_centroids spatial_info provided, whether also calculate centroids centroids_to_spatlocs spatial_info provided, whether also convert centroids spatial locations feat_info list giotto point objects feature info, see createGiottoPoints cell_metadata cell annotation metadata feat_metadata feature annotation metadata unique feature spatial_network list spatial network(s) spatial_grid list spatial grid(s) spatial_grid_name list spatial grid name(s) spatial_enrichment list spatial enrichment score(s) spatial region dimension_reduction list dimension reduction(s) nn_network list nearest neighbor network(s) images list images largeImages deprecated offset_file file used stitch fields together (optional) instructions list instructions output result createGiottoInstructions cores many cores threads use read data paths provided raw_exprs deprecated, use expression expression_matrix_class class expression matrix use (e.g. 'dgCMatrix', 'DelayedArray') h5_file path h5 file verbose verbose building Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a giotto object — createGiottoObject","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a giotto object — createGiottoObject","text":"See http://giottosuite.com/articles/getting_started_gobject.html details [Requirements] create giotto object need provide least matrix genes row names cells column names. matrix can provided base matrix, sparse Matrix, data.frame, data.table path . include spatial information cells (regions) need provide matrix, data.table data.frame (path ) coordinates spatial dimensions. can 2D (x y) 3D (x, y, x). row order cell coordinates column order provided expression data. [Instructions] Additionally instruction file, generated manually createGiottoInstructions can provided instructions, default instruction file created Giotto object. [Multiple fields] case dataset consists multiple fields, like seqFISH+ example, offset file can provided stitch different fields together. stitchFieldCoordinates can used generate offset file. [Processed data] Processed count data, normalized data, can provided using one different expression slots (norm_expr, norm_scaled_expr, custom_expr). [Metadata] Cell gene metadata can provided using cell gene metadata slots. data can also added afterwards using addFeatMetadata addCellMetadata functions. [information] Additional information can provided appropriate slots: spatial networks spatial grids spatial enrichments dimensions reduction nearest neighbours networks images","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a giotto object — createGiottoObject","text":"","code":"expr_matrix <- readRDS(system.file(\"extdata/toy_matrix.RDS\",     package = \"GiottoClass\" ))  createGiottoObject(expression = expr_matrix) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 10, 10 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw #> spatial locations ---------------- #>   [cell] raw #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"Function create giotto object starting subcellular polygon (e.g. cell) points (e.g. transcripts) information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"","code":"createGiottoObjectSubcellular(   gpolygons = NULL,   polygon_mask_list_params = NULL,   polygon_dfr_list_params = NULL,   gpoints = NULL,   cell_metadata = NULL,   feat_metadata = NULL,   spatial_network = NULL,   spatial_network_name = NULL,   spatial_grid = NULL,   spatial_grid_name = NULL,   spatial_enrichment = NULL,   spatial_enrichment_name = NULL,   dimension_reduction = NULL,   nn_network = NULL,   images = NULL,   largeImages = NULL,   largeImages_list_params = NULL,   instructions = NULL,   cores = NA,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"gpolygons giotto polygons polygon_mask_list_params list parameters createGiottoPolygonsFromMask polygon_dfr_list_params list parameters createGiottoPolygonsFromDfr gpoints giotto points cell_metadata cell annotation metadata feat_metadata feature annotation metadata unique feature spatial_network list spatial network(s) spatial_network_name list spatial network name(s) spatial_grid list spatial grid(s) spatial_grid_name list spatial grid name(s) spatial_enrichment list spatial enrichment score(s) spatial region spatial_enrichment_name list spatial enrichment name(s) dimension_reduction list dimension reduction(s) nn_network list nearest neighbor network(s) images list images largeImages deprecated largeImages_list_params image params loading largeImages list instructions list instructions output result createGiottoInstructions cores many cores threads use read data paths provided verbose verbose building Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"two different ways create Giotto Object subcellular information: Starting polygons (spatial units e.g. cell) represented mask dataframe file giotto points (analyte coordinates e.g. transcripts) Starting polygons (spatial units e.g. cell) represented mask dataframe file raw intensity images (e.g. protein stains)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoObjectSubcellular.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a giotto object from subcellular data — createGiottoObjectSubcellular","text":"","code":"x_gpolygons <- GiottoData::loadSubObjectMini(\"giottoPolygon\") x_gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  createGiottoObjectSubcellular(     gpolygons = x_gpolygons,     gpoints = x_gpoints ) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> polygonlist is not a list #> [ cell ] Process polygon info... #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> Setting spatial locations [aggregate] raw #> pointslist is not a list #> [ rna ] Process point info... #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> An object of class giotto  #> [SUBCELLULAR INFO] #> polygons      : aggregate  #> features      : rna  #> [AGGREGATE INFO] #> spatial locations ---------------- #>   [aggregate] raw #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":null,"dir":"Reference","previous_headings":"","what":"Create giotto points object — createGiottoPoints","title":"Create giotto points object — createGiottoPoints","text":"Create giottoPoints object used represent subcellular point-type features. main values contained within spatVector slot, contain spatial point data also associated set attributes least feat_ID (name feature described) feat_ID_uniq (unique integer identifier specific point).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create giotto points object — createGiottoPoints","text":"","code":"# S4 method for class 'SpatVector' createGiottoPoints(   x,   feat_type = \"rna\",   verbose = TRUE,   split_keyword = NULL,   unique_IDs = NULL )  # S4 method for class 'data.frame' createGiottoPoints(   x,   x_colname = NULL,   y_colname = NULL,   feat_ID_colname = NULL,   feat_type = \"rna\",   verbose = TRUE,   split_keyword = NULL,   unique_IDs = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create giotto points object — createGiottoPoints","text":"x spatVector data.frame-like object points coordinate information (x, y, feat_ID) feat_type character. feature type. Provide one value using split_keyword param. set keywords split , additional feat_type provided order. verbose verbose split_keyword list character vectors keywords split giottoPoints object based feat_ID. Keywords grepl() matched feature IDs information. unique_IDs (optional) character vector unique IDs present within spatVector data. Provided cacheing purposes x_colname column name x-coordinates y_colname column name y-coordinates feat_ID_colname column name feature ids","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create giotto points object — createGiottoPoints","text":"giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create giotto points object — createGiottoPoints","text":"Using manual option can select names x, y, feat_ID columns compatible data.frame already names x, y, /feat_ID.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPoints.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create giotto points object — createGiottoPoints","text":"","code":"# data.frame input x <- data.frame(     ID = letters[seq_len(6)],     x = seq_len(6),     y = seq(6, 1) ) gpoints <- createGiottoPoints(x) #>   Selecting col \"ID\" as feat_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(gpoints,     raster = FALSE, # don't plot with rasterization or it will be hard to see     cex = 0.5 )   # with a split_keyword # Use this when values to read in contain multiple sets of information that # should be put into separate objects. gp_list <- createGiottoPoints(x,     feat_type = c(\"feat_a\", \"feat_b\"),     split_keyword = list(c(\"b\", \"c\")) ) #>   Selecting col \"ID\" as feat_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively force(gp_list) #> $feat_a #> An object of class giottoPoints #> feat_type : \"feat_a\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 4, 2  (geometries, attributes) #>  extent      : 1, 6, 1, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      d            4 #>                      e            5 #>  #>  #> $feat_b #> An object of class giottoPoints #> feat_type : \"feat_b\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 2, 2  (geometries, attributes) #>  extent      : 2, 3, 4, 5  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       b            2 #>                      c            3 #>  #>   # subsetting gpoints[c(1, 3)] # numerical #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 2, 2  (geometries, attributes) #>  extent      : 1, 3, 4, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      c            3 #>  gpoints[c(TRUE, FALSE, FALSE)] # logical #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 2, 2  (geometries, attributes) #>  extent      : 1, 4, 3, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      d            4 #>  gpoints[c(\"a\", \"f\")] # character subsetting is keyed on feat_ID attribute #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 2, 2  (geometries, attributes) #>  extent      : 1, 6, 1, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      f            6 #>  gpoints[] # drop to SpatVector #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 6, 2  (geometries, attributes) #>  extent      : 1, 6, 1, 6  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :       a            1 #>                      b            2 #>                      c            3"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Create giotto polygons object — createGiottoPolygon","title":"Create giotto polygons object — createGiottoPolygon","text":"Create giottoPolygon object used represent spatial annotations polygons. Inputs can structured data.frame object three columns correspond x/y vertices polygon ID additional columns set attributes, spatial file wkt, .shp, .GeoJSON, mask file (e.g. segmentation results).  character method file reading dispatch specific methods based kind data file .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create giotto polygons object — createGiottoPolygon","text":"","code":"# S4 method for class 'character' createGiottoPolygon(x, ...)  # S4 method for class 'SpatVector' createGiottoPolygon(x, name = \"cell\", calc_centroids = FALSE, verbose = TRUE)  # S4 method for class 'SpatRaster' createGiottoPolygon(   x,   name = \"cell\",   mask_method = c(\"guess\", \"single\", \"multiple\"),   remove_background_polygon = FALSE,   background_algo = c(\"range\"),   fill_holes = TRUE,   poly_IDs = NULL,   ID_fmt = \"cell_\",   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   remove_unvalid_polygons = TRUE,   calc_centroids = FALSE,   verbose = TRUE )  # S4 method for class 'data.frame' createGiottoPolygon(   x,   name = \"cell\",   calc_centroids = FALSE,   skip_eval_dfr = FALSE,   copy_dt = TRUE,   verbose = TRUE )  createGiottoPolygonsFromMask(   maskfile,   mask_method = c(\"guess\", \"single\", \"multiple\"),   name = \"cell\",   remove_background_polygon = FALSE,   background_algo = c(\"range\"),   fill_holes = TRUE,   poly_IDs = NULL,   ID_fmt = \"cell_\",   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   calc_centroids = FALSE,   remove_unvalid_polygons = TRUE,   verbose = FALSE )  createGiottoPolygonsFromDfr(   segmdfr,   name = \"cell\",   calc_centroids = FALSE,   verbose = TRUE,   skip_eval_dfr = FALSE,   copy_dt = TRUE )  createGiottoPolygonsFromGeoJSON(   GeoJSON,   name = \"cell\",   calc_centroids = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create giotto polygons object — createGiottoPolygon","text":"x input. Filepath .GeoJSON mask image file. Can also data.frame vertex 'x', 'y', 'poly_ID' information. ... additional params pass. character method, params pass SpatRaster SpatVector methods, depending whether x filepath maskfile spatial file (ex: wkt, shp, GeoJSON) respectively. name name giottoPolygon object created calc_centroids (default FALSE) calculate centroids polygons verbose verbose mask_method mask file defines individual segmentation annotations. See mask_method section remove_background_polygon try remove background polygon (default: FALSE) background_algo algorithm remove background polygon fill_holes fill holes within created polygons poly_IDs character vector. Default = NULL. Custom unique names polygon mask file. ID_fmt character. applied poly_IDs = NULL. Naming scheme poly_IDs. Default = \"cell_\". See ID_fmt section. flip_vertical flip mask figure vertical manner shift_vertical_step shift vertical (boolean numerical) flip_horizontal flip mask figure horizontal manner shift_horizontal_step shift horizontal (boolean numerical) remove_unvalid_polygons remove unvalid polygons (default: TRUE) skip_eval_dfr (default FALSE) skip evaluation provided dataframe copy_dt (default TRUE) segmdfr provided dt, determines whether copy made maskfile path mask file, terra SpatRaster, data class readable terra::rast() segmdfr data.frame-like object polygon coordinate information (x, y, poly_ID) x y vertex information polygon referenced poly_ID. See details columns selected coordinate ID information. GeoJSON path .GeoJSON file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create giotto polygons object — createGiottoPolygon","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create giotto polygons object — createGiottoPolygon","text":"determining column within tabular data intended provide polygon information, Giotto first checks column names 'x', 'y', 'poly_ID'. discovered, directly selected. discovered Giotto checks data type columns selects first 'character' type column 'poly_ID' first two 'numeric' columns 'x' 'y' respectively. also unsuccessful poly_ID defaults 3rd column. 'x' 'y' default 1st 2nd columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"mask-method","dir":"Reference","previous_headings":"","what":"mask_method","title":"Create giotto polygons object — createGiottoPolygon","text":"One \"single\", \"multiple\", \"guess\". \"single\" assumes provided mask image binary, polygon vs background distinct values. kind image, expected generated polygons single multipart polygon. \"single\" takes multipart polygon breaks apart individual singlepart polygons. initial simple numeric index 'nth' polygon found mask image applied ID (see ID_fmt section). \"multiple\" assumes provided mask image distinct intensity values specify IDs individual polygons. initial numeric ID applied intensity value pixels made annotation polygon mask image (see ID_fmt section). \"guess\" examines values image pick likely appropriate method \"single\" \"multiple\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"id-fmt","dir":"Reference","previous_headings":"","what":"ID_fmt","title":"Create giotto polygons object — createGiottoPolygon","text":"Defaults applying input prefix (using paste0()) numerical ID values detected  mask_method. (ie: ID_fmt = \"cell_\" produces cell_1, cell_2, cell_3, ...) \"%\" character detected input input treated sprintf() fmt param input instead. (ie: ID_fmt = \"cell_%03d\" produces cell_001, cell_002, cell_003, ...)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoPolygon.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create giotto polygons object — createGiottoPolygon","text":"","code":"# ------- create from a mask image ------- # m <- system.file(\"extdata/toy_mask_multi.tif\", package = \"GiottoClass\") plot(terra::rast(m), col = grDevices::hcl.colors(7))  gp <- createGiottoPolygon(     m,     flip_vertical = FALSE, flip_horizontal = FALSE,     shift_horizontal_step = FALSE, shift_vertical_step = FALSE,     ID_fmt = \"id_test_%03d\",     name = \"test\" ) plot(gp, col = grDevices::hcl.colors(7))   # ------- create from an shp file ------- # shp <- system.file(\"extdata/toy_poly.shp\", package = \"GiottoClass\") # vector inputs do not have params for flipping and shifting gp2 <- createGiottoPolygon(shp, name = \"test\") #> Selecting attribute \"poly_ID\" as poly_ID plot(gp2, col = grDevices::hcl.colors(7))   # ------- create from data.frame-like ------- # shp <- system.file(\"extdata/toy_poly.shp\", package = \"GiottoClass\") gpoly <- createGiottoPolygon(shp, name = \"test\") #> Selecting attribute \"poly_ID\" as poly_ID plot(gpoly)  gpoly_dt <- data.table::as.data.table(gpoly, geom = \"XY\") needed_cols_dt <- gpoly_dt[, .(geom, part, x, y, hole, poly_ID)] force(needed_cols_dt) #> Key: <geom> #>       geom  part        x        y  hole poly_ID #>      <int> <num>    <num>    <num> <num>  <char> #>   1:     1     1 7.000000 5.000000     0       a #>   2:     1     1 7.000000 5.000000     0       a #>   3:     1     1 6.937166 4.502620     0       a #>   4:     1     1 6.752613 4.036493     0       a #>   5:     1     1 6.457937 3.630906     0       a #>  ---                                             #> 183:     7     1 7.071654 9.688656     0       g #> 184:     7     1 7.457937 9.369094     0       g #> 185:     7     1 7.752613 8.963507     0       g #> 186:     7     1 7.937166 8.497380     0       g #> 187:     7     1 8.000000 8.000000     0       g  out <- createGiottoPolygon(needed_cols_dt,     name = \"test\" ) #>   Selecting col \"poly_ID\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(out)  mask_multi <- system.file(\"extdata/toy_mask_multi.tif\",     package = \"GiottoClass\" ) mask_single <- system.file(\"extdata/toy_mask_single.tif\",     package = \"GiottoClass\" ) plot(terra::rast(mask_multi), col = grDevices::hcl.colors(7))  plot(terra::rast(mask_single))   gpoly1 <- createGiottoPolygonsFromMask(     mask_multi,     flip_vertical = FALSE, flip_horizontal = FALSE,     shift_horizontal_step = FALSE, shift_vertical_step = FALSE,     ID_fmt = \"id_test_%03d\",     name = \"multi_test\" ) plot(gpoly1, col = grDevices::hcl.colors(7))   gpoly2 <- createGiottoPolygonsFromMask(     mask_single,     flip_vertical = FALSE, flip_horizontal = FALSE,     shift_horizontal_step = FALSE, shift_vertical_step = FALSE,     ID_fmt = \"id_test_%03d\",     name = \"single_test\" ) #>   Selecting col \"part\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(gpoly2, col = grDevices::hcl.colors(5))"},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":null,"dir":"Reference","previous_headings":"","what":"createMetafeats — createMetafeats","title":"createMetafeats — createMetafeats","text":"function creates average metafeat/metagene/module clusters.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createMetafeats — createMetafeats","text":"","code":"createMetafeats(   gobject,   spat_unit = NULL,   feat_type = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   feat_clusters,   stat = c(\"mean\", \"sum\", \"max\", \"min\"),   rescale_to = NULL,   name = paste0(\"metafeat_\", ifelse(is.function(stat), \"custom\", stat)),   return_gobject = TRUE,   verbose = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createMetafeats — createMetafeats","text":"gobject Giotto object spat_unit spatial unit feat_type feature type expression_values expression values use feat_clusters numerical vector features names stat statistical transformation calculate across cluster features per cell get metafeature value. Provided defaults \"mean\", 'sum', \"max\", \"min\". function  supplied instead, run via apply(MARGIN = 2) across expression matrix calculate  metafeature value. rescale_to numeric vector length 2. (optional) New maximum minimum rescale features calculating metafeature score using stat. Values first zeroed setting minimum value 0, rescaled. cases values across feature, rescale produces middle point range specified rescale_to name name metagene results return_gobject return giotto object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createMetafeats — createMetafeats","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createMetafeats — createMetafeats","text":"example 'gene_clusters' like : cluster_vector = c(1, 1, 2, 2) names(cluster_vector) = c('geneA', 'geneB', 'geneC', 'geneD')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createMetafeats — createMetafeats","text":"","code":"# load a dataset g <- GiottoData::loadGiottoMini(\"viz\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" # set a spat unit to use activeSpatUnit(g) <- \"aggregate\"  # define the metafeats # We do this by making a set of annotations. These annotations can be # made as either a vector or data.frame  # 1.1 annotation vector (numeric) feats_to_use <- featIDs(g)[seq_len(6)] clust_to_use1 <- c(1, 1, 1, 2, 2, 2) names(clust_to_use1) <- feats_to_use force(clust_to_use1) #>   Mlc1 Gprc5b   Gfap  Ednrb   Sox9   Aqp4  #>      1      1      1      2      2      2   g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use1,     name = \"metagene_1\" ) #> calculating metafeature: 1 #> calculating metafeature: 2  # 1.2 annotation vector (character) clust_to_use2 <- c(rep(\"sig_a\", 3), rep(\"sig_b\", 3)) names(clust_to_use2) <- feats_to_use force(clust_to_use2) #>    Mlc1  Gprc5b    Gfap   Ednrb    Sox9    Aqp4  #> \"sig_a\" \"sig_a\" \"sig_a\" \"sig_b\" \"sig_b\" \"sig_b\"   g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use2,     name = \"metagene_2\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 2.1 annotation data.frame (no weights) # Cols must be: # `clus` - which metafeature # `feat` - features to assign to this metafeature # `w` - (optional) weight to assign the feature before metafeature score #       calculation clust_to_use3 <- data.frame(     clus = c(rep(\"sig_a\", 3), rep(\"sig_b\", 3)),     feat = feats_to_use ) force(clust_to_use3) #>    clus   feat #> 1 sig_a   Mlc1 #> 2 sig_a Gprc5b #> 3 sig_a   Gfap #> 4 sig_b  Ednrb #> 5 sig_b   Sox9 #> 6 sig_b   Aqp4 g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use3,     name = \"metagene_3\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 2.1 annotation data.frame (weights) clust_to_use4 <- data.frame(     clus = c(rep(\"sig_a\", 3), rep(\"sig_b\", 3)),     feat = feats_to_use,     w = c(1, 1, 1, 2, 3, 4) ) force(clust_to_use4) #>    clus   feat w #> 1 sig_a   Mlc1 1 #> 2 sig_a Gprc5b 1 #> 3 sig_a   Gfap 1 #> 4 sig_b  Ednrb 2 #> 5 sig_b   Sox9 3 #> 6 sig_b   Aqp4 4 g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use4,     name = \"weighted_metagene\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 3. Other statistic transforms can be calculated # The default and what has been used so far is just finding the mean g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use4,     stat = \"sum\",     expression_values = \"raw\", # find summed raw expr for these feats     name = \"raw_sums\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 4. A custom stat function can also be supplied # These custom functions must be summary functions, as in, they must # produce only a single numeric output from many custom_stat <- function(x) {     if (max(x) == 0) {         return(0)     }     return(mean(x / max(x))) } g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use4,     stat = custom_stat,     expression_values = \"raw\",     name = \"raw_custom\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b  # 5. A rescale of the values to a specified numeric range can be applied # before the stat score calculation. g <- createMetafeats(     gobject = g,     feat_clusters = clust_to_use4,     stat = \"mean\",     expression_values = \"normalized\",     rescale_to = c(0, 1),     name = \"norm_scaled_mean_metafeat\" ) #> calculating metafeature: sig_a #> calculating metafeature: sig_b showGiottoSpatEnrichments(g) #> Spatial unit:  aggregate   #>  #> --> Feature type:  rna   #>  #> ----> Name  cluster_metagene :  #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #> 4: 4.093622 0.5886051 0.1962017 0.5886051     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #> 4:  87260224659312905497866017323180367450 #>  #> ----> Name  metagene_1 :  #>           1        2                                 cell_ID #>       <num>    <num>                                  <char> #> 1: 3.493789 3.160792 240649020551054330404932383065726870513 #> 2: 2.132677 2.795048 274176126496863898679934791272921588227 #> 3: 2.633814 7.570115 323754550002953984063006506310071917306 #> 4: 4.446903 3.924034  87260224659312905497866017323180367450 #>  #> ----> Name  metagene_2 :  #>       sig_a    sig_b                                 cell_ID #>       <num>    <num>                                  <char> #> 1: 3.493789 3.160792 240649020551054330404932383065726870513 #> 2: 2.132677 2.795048 274176126496863898679934791272921588227 #> 3: 2.633814 7.570115 323754550002953984063006506310071917306 #> 4: 4.446903 3.924034  87260224659312905497866017323180367450 #>  #> ----> Name  metagene_3 :  #>       sig_a    sig_b                                 cell_ID #>       <num>    <num>                                  <char> #> 1: 3.493789 3.160792 240649020551054330404932383065726870513 #> 2: 2.132677 2.795048 274176126496863898679934791272921588227 #> 3: 2.633814 7.570115 323754550002953984063006506310071917306 #> 4: 4.446903 3.924034  87260224659312905497866017323180367450 #>  #> ----> Name  weighted_metagene :  #>       sig_a     sig_b                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 3.493789  6.321584 240649020551054330404932383065726870513 #> 2: 2.132677  5.590096 274176126496863898679934791272921588227 #> 3: 2.633814 23.041672 323754550002953984063006506310071917306 #> 4: 4.446903 11.772102  87260224659312905497866017323180367450 #>  #> ----> Name  raw_sums :  #>    sig_a sig_b                                 cell_ID #>    <num> <num>                                  <char> #> 1:     2     2 240649020551054330404932383065726870513 #> 2:     1     8 274176126496863898679934791272921588227 #> 3:     2    16 323754550002953984063006506310071917306 #> 4:     4     6  87260224659312905497866017323180367450 #>  #> ----> Name  raw_custom :  #>        sig_a     sig_b                                 cell_ID #>        <num>     <num>                                  <char> #> 1: 0.3333333 0.3333333 240649020551054330404932383065726870513 #> 2: 0.3333333 0.3333333 274176126496863898679934791272921588227 #> 3: 0.3333333 0.6666667 323754550002953984063006506310071917306 #> 4: 0.4444444 0.5000000  87260224659312905497866017323180367450 #>  #> ----> Name  norm_scaled_mean_metafeat :  #>        sig_a     sig_b                                 cell_ID #>        <num>     <num>                                  <char> #> 1: 0.3009266 0.6666667 240649020551054330404932383065726870513 #> 2: 0.2139690 0.5895248 274176126496863898679934791272921588227 #> 3: 0.2268554 2.3591938 323754550002953984063006506310071917306 #> 4: 0.4182979 1.2189606  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 nnNetObj — createNearestNetObj","title":"Create S4 nnNetObj — createNearestNetObj","text":"Create S4 nnNetObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 nnNetObj — createNearestNetObj","text":"","code":"createNearestNetObj(   name = \"test\",   network,   nn_type = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 nnNetObj — createNearestNetObj","text":"name name nnNetObj network igraph object data.frame containing nearest neighbor information (see details) nn_type type nearest neighbor network spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 nnNetObj — createNearestNetObj","text":"nnNetObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create S4 nnNetObj — createNearestNetObj","text":"igraph dataframe-like inputs must include certain information. igraph, must , minimum vertex 'name' attributes 'distance' edge attribute. dataframe-like inputs must '', '', 'distance' columns","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 nnNetObj — createNearestNetObj","text":"","code":"x <- GiottoData::loadSubObjectMini(\"nnNetObj\")  createNearestNetObj(     network = slot(x, \"igraph\"), name = \"sNN\",     nn_type = \"sNN\" ) #> An object of class nnNetObj : \"sNN\" #> --| Contains nearest neighbor network generated with: sNN  #> ----| for feat_type: rna  #> ----|     spat_unit: cell  #> IGRAPH 859f76e DNW- 462 3021 --  #> + attr: name (v/c), weight (e/n), distance (e/n), shared (e/n), rank #> | (e/n) #> + edges from 859f76e (vertex names): #> [1] 240649020551054330404932383065726870513->335295524680090725199231409883288198017 #> [2] 240649020551054330404932383065726870513->77151711298730578178892667721058396928  #> [3] 240649020551054330404932383065726870513->322879686187630160969459793861944841206 #> [4] 240649020551054330404932383065726870513->31072896077757820678000109671990674373  #> [5] 240649020551054330404932383065726870513->102184699197574201819246996094734116255 #> [6] 240649020551054330404932383065726870513->17685062374745280598492217386845129350  #> + ... omitted several edges #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"createNearestNetwork — createNearestNetwork","title":"createNearestNetwork — createNearestNetwork","text":"create nearest neighbour (NN) network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createNearestNetwork — createNearestNetwork","text":"","code":"createNearestNetwork(   gobject,   spat_unit = NULL,   feat_type = NULL,   type = c(\"sNN\", \"kNN\"),   dim_reduction_to_use = \"pca\",   dim_reduction_name = NULL,   dimensions_to_use = seq_len(10),   feats_to_use = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   name = NULL,   return_gobject = TRUE,   k = 30,   minimum_shared = 5,   top_shared = 3,   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createNearestNetwork — createNearestNetwork","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") type sNN kNN dim_reduction_to_use dimension reduction method use dim_reduction_name name dimension reduction set use dimensions_to_use number dimensions use input feats_to_use dim_reduction_to_use = NULL, genes use expression_values expression values use name arbitrary name NN network. Defaults [type].[dim_reduction_to_use] return_gobject boolean: return giotto object (default = TRUE) k number k neighbors use minimum_shared minimum shared neighbors top_shared keep ... verbose verbose ... additional parameters kNN sNN functions dbscan","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createNearestNetwork — createNearestNetwork","text":"giotto object updated NN network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createNearestNetwork — createNearestNetwork","text":"function creates k-nearest neighbour (kNN) shared nearest neighbour (sNN) network based provided dimension reduction space. run directly gene expression matrix set dim_reduction_to_use = NULL. See also kNN sNN information networks created. Output kNN: : cell_ID source cell : cell_ID target cell distance: distance cells weight: \\(1/(1 + distance)\\) Output sNN: : cell_ID source cell : cell_ID target cell distance: distance cells weight: \\(1/(1 + distance)\\) shared: number shared neighbours rank: ranking pairwise cell neighbours sNN networks two additional parameters can set: minimum_shared: minimum number shared neighbours needed top_shared: keep number top shared neighbours, irrespective minimum_shared setting","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNearestNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createNearestNetwork — createNearestNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createNearestNetwork(g) #> > 'sNN.pca' already exists and will be replaced with #>  new nearest neighbor network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a network — createNetwork","title":"Create a network — createNetwork","text":"Create networks node values. hub function many different methods finding nearest neighbors. See details additional params important generating specific types networks.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a network — createNetwork","text":"","code":"createNetwork(   x,   type = c(\"sNN\", \"kNN\", \"delaunay\"),   method = c(\"dbscan\", \"geometry\", \"RTriangle\", \"deldir\"),   node_ids = NULL,   include_distance = TRUE,   include_weight = TRUE,   as.igraph = TRUE,   verbose = NULL,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a network — createNetwork","text":"x matrix. Data treat nodes. Examples include expression information, PCA matrix, spatial locations xy(z) coordinates. type type network create. Currently: \"sNN\", \"kNN\", \"delaunay\" method method used create type network requested. One \"dbscan\" sNN kNN \"geometry\", \"RTriangle\", \"deldir\" delaunay. node_ids character. Node ID values assign. NULL, integer indices used node IDs. include_distance logical. include edge distance attribute output include_weight logical. include edge weight attribute output .igraph logical. Whether return igraph. Otherwise returns data.table verbose verbose. Default = NULL (uses giotto verbosity option) ... additional params pass. See details section","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a network — createNetwork","text":"Either igraph .igraph = TRUE data.table otherwise.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a network — createNetwork","text":"Additional params described . Items parenthesis refer network types /methods params specific . [k] numeric. (sNN, kNN) number neighbors find. Default 30 [minimum_shared] numeric. (sNN) minimum shared neighbors allowed per edge [top_shared] numeric. (sNN) keep least many edges per node, kept edges top ranked terms number shared neighbors. [filter] logical. (kNN) whether filter unique edges apply minimum_k maximum_distance filters. set TRUE generating spatial kNN network. Default FALSE. [minimum_k] (delaunay, kNN) minimum nearest neighbours maximum_distance != NULL [maximum_distance] (delaunay, kNN) edge maximum euclidean distance allowed [Y] (RTriangle) TRUE prohibits insertion Steiner points mesh boundary. Default TRUE [j] (RTriangle) TRUE jettisons vertices part final triangulation output. Default TRUE [S] (RTriangle) Specifies maximum number added Steiner points. Default 0 [options] (geometry) default \"Pp\". See geometry::delaunayn [weight_fun] function calculate weights based distance include_weight = TRUE. Default \\(weight = 1 / (1 + distance)\\) \"kNN\" \"sNN\" types \\(weight = 1 / distance\\) delaunay type networks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a network — createNetwork","text":"","code":"pca <- GiottoData::loadSubObjectMini(\"dimObj\")[] sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")[]  # Delaunay via geometry::delaunayn() del_geom <- createNetwork(     x = as.matrix(sl[, .(sdimx, sdimy)]),     type = \"delaunay\",     method = \"geometry\",     include_weight = TRUE,     weight_fun = function(d) 1 / d,     as.igraph = FALSE,     node_ids = sl$cell_ID )  # Delaunay via RTriangle::triangulate() del_rt <- createNetwork(     x = as.matrix(sl[, .(sdimx, sdimy)]),     type = \"delaunay\",     method = \"RTriangle\",     include_weight = TRUE,     weight_fun = function(d) 1 / d,     as.igraph = FALSE,     node_ids = sl$cell_ID )  # Delaunay via deldir::deldir() del_dd <- createNetwork(     x = as.matrix(sl[, .(sdimx, sdimy)]),     type = \"delaunay\",     method = \"deldir\",     include_weight = TRUE,     weight_fun = function(d) 1 / d,     as.igraph = FALSE,     node_ids = sl$cell_ID )  # kNN spatial network kNN_spat <- createNetwork(     x = as.matrix(sl[, .(sdimx, sdimy)]),     type = \"kNN\",     method = \"dbscan\",     include_weight = TRUE,     weight_fun = function(d) 1 / d, # not the default     as.igraph = FALSE,     node_ids = sl$cell_ID,     k = 4L,     maximum_distance = NULL,     minimum_k = 0L )  # kNN NN network kNN <- createNetwork(     pca[, seq_len(10)],     type = \"kNN\",     method = \"dbscan\",     node_ids = rownames(pca),     as.igraph = TRUE )  # sNN NN network sNN <- createNetwork(     pca[, seq_len(10)],     type = \"sNN\",     method = \"dbscan\",     node_ids = rownames(pca),     as.igraph = TRUE )  # using defaults for sNN with index IDs to create igraph sNN_idx <- createNetwork(pca[, seq_len(10)])"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 spatEnrObj — createSpatEnrObj","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"Create S4 spatEnrObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"","code":"createSpatEnrObj(   enrichment_data,   name = \"test\",   spat_unit = \"cell\",   feat_type = \"rna\",   method = NULL,   provenance = NULL,   misc = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"enrichment_data spatial enrichment results, provided dataframe-like object name name S4 spatEnrObj spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') method method used generate spatial enrichment information provenance origin data aggregated expression information (applicable) misc misc additional information spatial enrichment generated verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"spatEnrObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatEnrObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 spatEnrObj — createSpatEnrObj","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatEnrObj\")  createSpatEnrObj(     enrichment_data = slot(x, \"enrichDT\"),     name = \"cluster_metagene\" ) #> There are non numeric or integer columns for the spatial #>  enrichment input at column position(s): 6 #>  The first non-numeric column will be considered as a cell ID to test for #>  consistency with the expression matrix. #>  Other non-numeric columns will be removed. #> An object of class spatEnrObj : \"cluster_metagene\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #>    ------------------------ #>  #> preview: #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #>  #> ...first 20 remaining colnames: #>  #>    #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 spatLocsObj — createSpatLocsObj","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"Create S4 spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"","code":"createSpatLocsObj(   coordinates,   name = \"test\",   spat_unit = \"cell\",   provenance = NULL,   misc = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"coordinates spatial coordinates name name spatLocsObj spat_unit spatial unit aggregated expression (e.g. 'cell') provenance origin data aggregated expression information (applicable) misc misc verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatLocsObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 spatLocsObj — createSpatLocsObj","text":"","code":"x <- data.frame(     cell_ID = c(\"cell_1\", \"cell_2\", \"cell_3\"),     sdimx = c(6637.881, 6471.978, 6801.610),     sdimy = c(-5140.465, -4883.541, -4968.685) )  createSpatLocsObj(coordinates = x, name = \"raw\") #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"cell\" #> dimensions: 3 3  #> preview   : #>       sdimx     sdimy cell_ID #>       <num>     <num>  <char> #> 1: 6637.881 -5140.465  cell_1 #> 2: 6471.978 -4883.541  cell_2 #> 3: 6801.610 -4968.685  cell_3 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6471.978 -5140.465 #> [2,] 6801.610 -4883.541 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 spatialNetworkObj — createSpatNetObj","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"Create S4 spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"","code":"createSpatNetObj(   network,   name = \"test\",   networkDT_before_filter = NULL,   method = NULL,   spat_unit = \"cell\",   provenance = NULL,   parameters = NULL,   outputObj = NULL,   cellShapeObj = NULL,   crossSectionObjects = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"network network data connections, distances, weightings name name spatialNetworkObj networkDT_before_filter (optional) unfiltered data.table  network connections, distances, weightings method method used generate spatial network spat_unit spatial unit tag provenance (optional) origin aggregated information (applicable) parameters (optional) additional method-specific parameters used spatial network generation outputObj (optional) network geometry object cellShapeObj (optional) network cell shape information crossSectionObjects (optional) crossSectionObjects misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatNetObj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 spatialNetworkObj — createSpatNetObj","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatialNetworkObj\")  createSpatNetObj(network = slot(x, \"networkDT\"), name = \"Delaunay_network\") #> An object of class spatialNetworkObj : \"Delaunay_network\" #> spat_unit : \"cell\" #>    1275 connections (filtered)"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"createSpatialDefaultGrid — createSpatialDefaultGrid","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"Create spatial grid using default method","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"","code":"createSpatialDefaultGrid(   gobject,   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = \"raw\",   sdimx_stepsize = NULL,   sdimy_stepsize = NULL,   sdimz_stepsize = NULL,   minimum_padding = 1,   name = NULL,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"gobject giotto object spat_unit spatial unit feat_type feature type spat_loc_name spatial location name sdimx_stepsize stepsize along x-axis sdimy_stepsize stepsize along y-axis sdimz_stepsize stepsize along z-axis minimum_padding minimum padding edges name name spatial grid (default = 'spatial_grid') return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"giotto object updated spatial grid slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"Creates spatial grid defined x, y (z) dimensions. dimension units based provided spatial location units.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDefaultGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createSpatialDefaultGrid — createSpatialDefaultGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialDefaultGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"Create spatial Delaunay network based cell centroid physical distances.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"","code":"createSpatialDelaunayNetwork(   gobject,   name = \"Delaunay_network\",   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = NULL,   method = c(\"deldir\", \"delaunayn_geometry\", \"RTriangle\"),   dimensions = \"all\",   maximum_distance = \"auto\",   minimum_k = 0,   options = \"Pp\",   Y = TRUE,   j = TRUE,   S = 0,   verbose = TRUE,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"gobject giotto object name name spatial network (default = 'delaunay_network') spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations method package use create Delaunay network dimensions spatial dimensions use. Use \"sdimx\" (spatial dimension x), \"sdimy\", \"sdimz\" respectively refer X (1st), Y (2nd) Z(3rd) dimension, see details. (default = ) maximum_distance distance cuttof Delaunay neighbors consider. \"auto\", \"upper whisker\" value distance vector neighbors used; see graphics::boxplot() documentation details.(default = \"auto\") minimum_k minimum number neighbours maximum_distance != NULL options (geometry) String containing extra control options underlying Qhull command; see Qhull documentation available options. (default = 'Pp', report precision problems) Y (RTriangle) TRUE prohibits insertion Steiner points mesh boundary. j (RTriangle) TRUE jettisons vertices part final triangulation output. S (RTriangle) Specifies maximum number added Steiner points. verbose verbose return_gobject logical. return giotto object (default = TRUE) output character. Object type return spatial network return_gobject = FALSE. (default: 'spatialNetworkObj') ... additional parameters","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"giotto object updated spatial network slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"Creates spatial Delaunay network explained delaunayn (default), deldir, triangulate.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialDelaunayNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a spatial Delaunay network — createSpatialDelaunayNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialDelaunayNetwork(g) #> Delaunay_network has already been used, will be overwritten #> > \" Delaunay_network \" already exists and will be replaced with new spatial #>  network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"Calculates centroid locations giotto polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"","code":"createSpatialFeaturesKNNnetwork(   gobject,   method = \"dbscan\",   feat_type = NULL,   name = \"knn_feats_network\",   k = 4,   maximum_distance = NULL,   minimum_k = 0,   add_feat_ids = FALSE,   verbose = TRUE,   return_gobject = TRUE,   toplevel_params = 2,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"gobject giotto object method kNN algorithm method feat_type feature type build feature network name name network k number neighbors maximum_distance maximum distance bewteen features minimum_k minimum number neighbors find add_feat_ids add feature id names (default = FALSE, increases object size) verbose verbose return_gobject return giotto object (default: TRUE) toplevel_params toplevel value pass updating giotto params ... additional parameters pass kNN","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"return_gobject = TRUE giotto object containing network returned. return_gobject = FALSE network returned datatable.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create kNN spatial feature network — createSpatialFeaturesKNNnetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialFeaturesKNNnetwork(g) #> Convert feature spatial info to matrix #> Create kNN network with dbscan #> Filter output for distance and minimum neighbours #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork_dbscan.html","id":null,"dir":"Reference","previous_headings":"","what":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","title":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","text":"create feature kNN spatial network using dbscan","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork_dbscan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","text":"","code":"createSpatialFeaturesKNNnetwork_dbscan(   gobject,   feat_type = NULL,   name = \"knn_feats_network\",   k = 4,   maximum_distance = NULL,   minimum_k = 0,   add_feat_ids = FALSE,   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork_dbscan.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","text":"gobject giotto object feat_type feature type name name assign generated feature network k number neighbors kNN find maximum_distance network maximum distance allowed minimum_k minimum neighbors allowed add_feat_ids boolean. whether add feature information verbose verbose ... additional parameters pass kNN","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialFeaturesKNNnetwork_dbscan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create kNN spatial feature network using dbscan — createSpatialFeaturesKNNnetwork_dbscan","text":"kNN spatial feature network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"createSpatialGrid — createSpatialGrid","title":"createSpatialGrid — createSpatialGrid","text":"Create spatial grid using default method","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createSpatialGrid — createSpatialGrid","text":"","code":"createSpatialGrid(   gobject,   spat_unit = NULL,   spat_loc_name = \"raw\",   name = NULL,   method = c(\"default\"),   sdimx_stepsize = NULL,   sdimy_stepsize = NULL,   sdimz_stepsize = NULL,   minimum_padding = 1,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createSpatialGrid — createSpatialGrid","text":"gobject giotto object spat_unit spatial unit spat_loc_name spatial location name name name spatial grid method method create spatial grid sdimx_stepsize stepsize along x-axis sdimy_stepsize stepsize along y-axis sdimz_stepsize stepsize along z-axis minimum_padding minimum padding edges return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createSpatialGrid — createSpatialGrid","text":"giotto object updated spatial grid slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"createSpatialGrid — createSpatialGrid","text":"Creates spatial grid defined x, y (z) dimensions. dimension units based provided spatial location units. default method: createSpatialDefaultGrid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createSpatialGrid — createSpatialGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"createSpatialKNNnetwork — createSpatialKNNnetwork","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"Create spatial knn network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"","code":"createSpatialKNNnetwork(   gobject,   method = \"dbscan\",   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = NULL,   dimensions = \"all\",   name = \"knn_network\",   k = 4,   maximum_distance = NULL,   minimum_k = 0,   verbose = FALSE,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"gobject giotto object method method create kNN network spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations dimensions spatial dimensions use (default = ) name name spatial network (default = 'spatial_network') k number nearest neighbors based physical distance maximum_distance distance cuttof nearest neighbors consider kNN network minimum_k minimum nearest neigbhours maximum_distance != NULL verbose verbose return_gobject boolean: return giotto object (default = TRUE) output character. Object type return spatial network return_gobject = FALSE. (default: 'spatialNetworkObj') ... additional arguments selected method function","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"giotto object updated spatial network slot dimensions:  default = '' takes possible dimensions. Alternatively can provide character vector specififies spatial dimensions use, e.g. c(\"sdimx', \"sdimy\") numerical vector, e.g. 2:3 maximum_distance:  create network based maximum distance , also need set k high value, e.g. k = 100","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialKNNnetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createSpatialKNNnetwork — createSpatialKNNnetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialKNNnetwork(g) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network knn_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Create spatial network — createSpatialNetwork","title":"Create spatial network — createSpatialNetwork","text":"Create spatial network based cell centroids. networks often used determining cell-cell connectivities spatial relationships. several types spatial networks multiple methods generate . Method-specific params labeled name method within parentheses descriptions.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create spatial network — createSpatialNetwork","text":"","code":"createSpatialNetwork(   gobject,   name = NULL,   spat_unit = NULL,   feat_type = NULL,   spat_loc_name = NULL,   dimensions = \"all\",   method = c(\"Delaunay\", \"kNN\"),   delaunay_method = c(\"deldir\", \"delaunayn_geometry\", \"RTriangle\"),   maximum_distance_delaunay = \"auto\",   options = \"Pp\",   Y = TRUE,   j = TRUE,   S = 0,   minimum_k = 0,   knn_method = \"dbscan\",   k = 4,   maximum_distance_knn = NULL,   verbose = FALSE,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create spatial network — createSpatialNetwork","text":"gobject giotto object name name spatial network (default = 'spatial_network') spat_unit spatial unit feat_type feature type spat_loc_name name spatial locations use dimensions spatial dimensions use (default = ) method method use create spatial network. (default = Delaunay) delaunay_method method use generate Delaunay network maximum_distance_delaunay distance cutoff nearest neighbors consider Delaunay network. \"auto\", \"upper whisker\" value distance vector neighbors used; see grDevices::boxplot.stats documentation details.(default = \"auto\") options (geometry) String containing extra control options underlying Qhull command; see Qhull documentation available options. (default = 'Pp', report precision problems) Y (RTriangle) TRUE prohibits insertion Steiner points mesh boundary. j (RTriangle) TRUE jettisons vertices part final triangulation output. S (RTriangle) Specifies maximum number added Steiner points. minimum_k minimum nearest neighbours maximum_distance != NULL knn_method method create kNN network k number nearest neighbors based physical distance maximum_distance_knn distance cutoff nearest neighbors consider kNN network verbose verbose return_gobject logical. return giotto object (default = TRUE) output character. Object type return spatial network return_gobject = FALSE. (default: 'spatialNetworkObj') ... Additional parameters selected function","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create spatial network — createSpatialNetwork","text":"giotto object updated spatial network slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create spatial network — createSpatialNetwork","text":"Creates spatial network connecting single-cells based physical distance . Delaunay method, neighbors decided Delaunay triangulation maximum distance criteria. kNN method, number neighbors can determined k, maximum distance cell without setting minimum k cell. **dimensions: ** default = '' takes possible dimensions. Alternatively can provide character vector specifies spatial dimensions use, e.g. c(\"sdimx', \"sdimy\") numerical vector, e.g. 2:3","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create spatial network — createSpatialNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialNetwork(g) #> Delaunay_network has already been used, will be overwritten #> > \" Delaunay_network \" already exists and will be replaced with new spatial #>  network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a spatial weight matrix — createSpatialWeightMatrix","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"Generate spatial weight matrix based strength spatial interactions nodes. Requires spatial networks first generated.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"","code":"createSpatialWeightMatrix(   gobject,   spat_unit = NULL,   spatial_network_to_use = \"kNN_network\",   method = c(\"distance\", \"adjacency\"),   wm_name = \"spat_weights\",   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"gobject giotto object spat_unit spatial unit spatial_network_to_use spatial network information use method type weighted matrix generate. See details wm_name name assign weight matrix values return_gobject (default = TRUE) whether return giotto object attached results bare weighted matrix verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"spatial weight matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"\"distance\" method calculated using 1/(1+distance) create inverse weighting based distance nodes. \"adjacency\" method binary matrix 1 signifying two nodes connected spatial network 0 indicating .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialWeightMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create a spatial weight matrix — createSpatialWeightMatrix","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  createSpatialWeightMatrix(g, spatial_network_to_use = \"spatial_network\") #> Attaching weight matrix to spatial_network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_KNNnetwork_dbscan.html","id":null,"dir":"Reference","previous_headings":"","what":"create_KNNnetwork_dbscan — create_KNNnetwork_dbscan","title":"create_KNNnetwork_dbscan — create_KNNnetwork_dbscan","text":"Create spatial knn network dbscan","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_KNNnetwork_dbscan.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_KNNnetwork_dbscan — create_KNNnetwork_dbscan","text":"","code":"create_KNNnetwork_dbscan(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   sdimz = \"sdimz\",   k = 4,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_KNNnetwork_dbscan.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_KNNnetwork_dbscan — create_KNNnetwork_dbscan","text":"spatial knn network dbscan","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":null,"dir":"Reference","previous_headings":"","what":"create_average_DT — create_average_DT","title":"create_average_DT — create_average_DT","text":"calculates average gene expression cell metadata factor (e.g. cluster)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_average_DT — create_average_DT","text":"","code":"create_average_DT(   gobject,   spat_unit = NULL,   feat_type = NULL,   meta_data_name,   expression_values = c(\"normalized\", \"scaled\", \"custom\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"create_average_DT — create_average_DT","text":"gobject giotto object spat_unit spatial unit feat_type feature type meta_data_name name metadata column use expression_values expression values use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_average_DT — create_average_DT","text":"data.table average gene expression values factor","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_DT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"create_average_DT — create_average_DT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  create_average_DT(g, meta_data_name = \"leiden_clus\") #>                cluster_2  cluster_5  cluster_1  cluster_3  cluster_6 cluster_7 #> Gna12         3.30737745 3.34082808 3.26309190 3.23263758 3.30171653 3.4313574 #> Ccnd2         1.94201357 2.05141093 2.18616953 2.02323861 1.91616817 2.3163818 #> Btbd17        1.18729607 1.29867174 1.21794661 1.43198694 1.25581641 0.7594994 #> Sox9          1.52919580 1.82629178 1.73707493 1.30671993 2.10794802 0.8765589 #> Sez6          3.45947190 3.30180445 3.77961671 3.45034173 3.07211639 3.7882936 #> Serpinf1      0.49689128 0.67245412 0.40614711 0.52461938 0.31016114 0.1371682 #> S100a6        2.42891377 2.33734168 2.42540182 2.09391026 2.41906585 1.8676702 #> Col1a1        0.22421466 0.10226721 0.10783051 0.29432743 0.15596186 0.3703106 #> Vwf           0.73980288 1.02125057 0.93244909 0.92739552 1.11699965 0.4919525 #> Esam          0.81955988 0.70087106 1.01971007 1.15689072 1.34596491 0.7461961 #> Npas1         0.33784649 0.56748473 0.53158683 0.63813928 0.44098006 0.7215881 #> Tiam1         2.04082965 1.80812107 1.72900493 2.00111715 1.35007867 1.2827112 #> Bcam          0.55274955 0.46173183 0.45044757 0.95543213 0.93821439 0.2666210 #> Hmgn2         2.06603581 2.04159933 1.99690865 1.76837367 1.84263924 2.1922319 #> Rab3b         1.77459139 1.75638043 1.64899950 1.56796461 1.60138382 1.6748753 #> Inmt          0.13863241 0.05262011 0.10527864 0.03996412 0.00000000 0.0000000 #> Ddr1          2.30055485 2.04984165 2.16648979 2.02195473 2.26367690 1.2358701 #> Homer3        1.26643552 1.15517582 1.11972968 1.01678407 0.71873936 1.6754294 #> Cp            0.22881160 0.39256404 0.21860348 0.25071201 0.00000000 0.2504086 #> Calb2         1.41862992 1.32679445 1.12525518 1.48135851 0.98242852 1.9040701 #> Man1a         1.17187286 1.31869487 1.24676725 1.17223778 0.97405462 2.2950651 #> Efnb3         3.00627172 3.13310020 2.69940050 2.74742453 3.06518311 3.0503625 #> Hlf           3.24839637 3.18753475 3.31310560 3.16226642 3.13612021 3.0091062 #> Gstm7         1.48500928 1.42703276 1.16225013 1.19766905 1.33959392 1.6747068 #> Cavin1        0.76178584 0.74779708 0.85791117 0.71491635 0.47148173 0.7352277 #> Sst           3.73684749 3.66376591 4.00841752 3.75201838 4.13871179 3.5194932 #> Hapln2        0.97869249 0.59951972 0.77294983 0.71085218 0.94971053 0.6425065 #> Hspb1         0.52971873 0.70520439 0.61274014 0.46869655 0.57186807 0.0000000 #> Ndrg1         3.13863431 2.61730487 3.02006093 2.98727188 3.46588636 1.8026284 #> Nid1          0.21553865 0.17652907 0.19669062 0.21101093 0.57025089 0.0000000 #> Kit           0.56833963 0.53109779 0.81175354 0.88306169 0.87098881 0.6870762 #> Pvalb         3.28835059 3.07327787 3.23604114 3.04990097 3.21770290 2.9380384 #> Tmbim1        2.37754522 2.08368796 1.92791556 1.88812870 1.74852239 1.1152814 #> Crip1         1.41009971 1.25450326 1.39849965 1.15120273 1.20854459 1.0925703 #> Tek           0.58846075 0.33380651 0.52905848 0.28965068 0.56496634 0.5935108 #> Elovl1        1.85542908 1.68257937 1.39440717 1.26707570 1.48335618 1.3114013 #> Cyba          1.03626710 1.15289251 0.86405628 1.23125127 0.63976179 1.2564585 #> Itih3         1.13630590 1.27197529 1.23250522 1.54389062 0.89307587 0.7474588 #> Cnp           6.03778097 5.82455446 5.72610313 5.77702510 6.08723395 5.0034797 #> Hap1          1.59121288 1.59382394 1.22734443 1.28449310 0.83700513 2.0214657 #> Clic1         1.00898108 0.61047121 0.60289933 0.76176127 0.55957882 0.6369316 #> Stx1a         2.43108017 2.42823381 2.88334873 2.45917900 2.37738140 2.2308187 #> Arpp19        4.42595642 4.35163328 4.80397850 3.89752350 4.45562164 3.9427566 #> Dio2          0.96343624 1.01739656 0.91295021 0.76877531 0.96959609 0.3908687 #> Id3           2.94529544 3.10331664 2.78821879 2.78836190 3.03403342 2.3991619 #> Crlf1         0.68633559 0.92119629 0.62912246 0.71898084 0.58334100 1.0250248 #> Ttc9b         4.29092470 4.57642934 4.57666226 4.01245305 4.26698811 4.2923582 #> Carhsp1       2.55785092 2.19549855 2.04605615 2.27045522 2.17840332 1.8752942 #> Cabp7         2.26141511 2.44514004 2.33171046 2.61207654 3.16472283 1.9179897 #> Fam163b       2.33735544 2.69302626 2.28224543 1.98406086 2.14181837 2.2600349 #> Rarres2       1.15314942 0.79457001 0.76443331 0.97133349 1.13558301 0.7671321 #> Syn2          4.48304876 4.69086545 4.68289652 4.49762071 4.61898034 4.2666136 #> Ick           1.33976866 1.21525841 1.35199145 0.94688793 0.97359053 0.6602028 #> Prox1         1.12087834 1.34728136 0.86501440 1.33385558 0.96045485 1.0248782 #> Adssl1        1.22683731 1.36701339 1.20495704 1.03050662 1.38292753 0.8528214 #> Vipr2         0.41622431 0.36140341 0.35658828 0.46596769 0.22133447 0.6305185 #> Gltp          2.15804351 1.84663313 2.04223111 1.76176658 2.14830600 1.9952998 #> Amotl1        1.59141088 1.52206874 1.67265575 1.88453192 1.80460555 1.5660657 #> Bcas1         3.64879117 3.22084650 3.42773536 3.41097031 3.13603555 2.8217151 #> Aldh1a2       0.12766617 0.06700689 0.09847394 0.30442144 0.00000000 0.3474831 #> Tppp3         2.60248409 2.12178859 2.28050208 2.27905129 2.24382333 2.2492398 #> Sirt2         4.50161397 4.42130053 4.35249062 4.42498751 4.26085093 4.2228421 #> Lpl           0.74898467 0.73794230 0.84582531 0.73030980 0.96083767 0.6531023 #> Cers2         2.35272710 2.57746727 2.31978260 2.28481964 2.52422789 3.1972147 #> Qdpr          5.23889427 4.77963136 4.90730301 4.97703997 5.36660249 4.9643569 #> Stk32c        2.43264753 2.31827006 2.27191999 2.16800239 2.11622851 1.1254119 #> Lbp           0.21986917 0.28440076 0.23720866 0.31418215 0.25051624 0.0000000 #> Hsd11b1       1.26986044 1.47931030 1.35631908 1.65409190 1.51951132 1.7326963 #> Vtn           2.72627600 2.74226687 2.48487479 2.41757776 2.62731419 1.6681123 #> Stac2         1.37615453 1.44983037 1.68280224 1.10862295 1.67586917 0.9597937 #> Plxdc1        1.22437375 1.44472440 1.42370524 1.50672610 1.12087763 0.8329171 #> Igfbp4        2.56466752 2.20266690 2.60079633 2.39337399 2.70624219 3.0103030 #> Dbndd2        2.48931976 2.38269055 2.34673722 2.41390483 2.46122731 2.5249243 #> Pltp          2.21518165 2.02049597 2.09493581 1.95665173 2.49435424 1.3305275 #> Slc12a4       0.98062041 0.87515793 0.89853208 0.65237371 0.98230366 0.9809346 #> Cadps2        1.66298140 1.79355599 1.70677869 1.60769029 1.55996625 1.4189812 #> Erbb3         0.41722543 0.37231331 0.41477667 0.49706419 0.60270594 0.9611556 #> Pmp22         1.47344250 1.44434883 1.32383976 1.40805034 1.14008930 1.1259126 #> Kcnab3        1.30572178 1.20773147 1.52367819 1.07447598 0.74673275 0.4728139 #> Myh11         0.19846986 0.24588139 0.22678101 0.26793807 0.10543429 0.4196490 #> Plod1         1.12228671 1.27754944 1.09295150 1.23896140 1.13073327 1.2264941 #> Etnppl        0.79577091 0.73976180 1.07222053 1.11998472 0.75859382 0.7478169 #> Arhgef25      3.32395185 3.23853885 3.39800246 3.38567462 2.97064593 3.5291598 #> Rcn3          0.41078586 0.24734435 0.67825434 0.56174438 0.25650623 0.5212264 #> Vip           0.83348717 0.73252192 0.69218987 0.83135659 0.52756790 0.5780129 #> Utrn          1.12996068 1.24445634 1.24669304 1.33442974 1.35301345 0.9244398 #> Grm1          1.67262407 1.55697786 1.67076335 2.15167949 1.61600199 1.3251047 #> Reep3         1.45149503 1.30521540 1.63704715 0.88291932 1.55062552 2.0238562 #> Fabp7         1.70844146 1.67648177 1.53028626 1.74460669 1.56617051 1.2506639 #> Dcn           0.47717856 0.33911219 0.31729641 0.46515059 0.30710267 0.6245136 #> Slc17a8       0.17280684 0.10455841 0.28782050 0.04330752 0.17635608 0.0000000 #> Dusp6         1.25874421 1.07733803 1.23134055 1.17891621 1.18342817 1.2890468 #> Kitl          1.41888612 1.55266742 1.57897181 1.31670195 1.02985082 1.0221684 #> Ccn2          0.64678980 1.03034906 0.93286268 0.51762328 1.18479178 0.6489568 #> Timp3         2.23409432 2.05459679 2.16335370 2.15665627 2.37840741 2.4935373 #> Ascl1         0.42848925 0.46801984 0.49010822 0.23662938 0.52055771 0.0000000 #> Unc5b         1.12443275 0.97559247 0.74116499 1.14892392 0.91670574 0.6871979 #> Vsir          1.00682289 0.86527542 0.84954259 0.77101413 1.46413962 0.4970584 #> Gamt          2.33360093 2.02585528 2.10745674 2.14681391 2.43994362 2.0382807 #> Ptprb         0.78607075 0.42205639 0.82417310 0.58637400 0.96141466 1.2463021 #> Csrp2         0.59065362 0.63314040 0.47274840 0.39455994 0.51584406 0.8911345 #> Adarb1        3.53550700 3.30058022 3.38098627 3.46216432 2.58062282 3.0655697 #> Rnf130        1.98574201 2.22208533 2.13350127 1.94480595 2.01370330 2.0420282 #> Nefh          2.05418571 2.14532273 2.08433434 2.32932866 1.89647811 2.7000541 #> Aebp1         0.47659104 0.35614418 0.44012339 0.36315284 0.27892980 0.0000000 #> Sept4         4.72125229 4.40519236 4.25235384 4.46364870 4.96708134 3.8270092 #> Gria1         4.12795684 4.34492850 4.29095060 4.17984545 4.00398837 4.2329121 #> Sypl          2.06287982 1.84444490 2.16063146 2.07372883 2.56105551 3.2220890 #> Arsg          1.27517546 1.23375248 0.99465993 1.03370270 1.58670989 0.2504086 #> Cacng4        1.53992884 1.49452708 1.76753612 1.58747283 1.01433516 1.1549710 #> Rab37         0.90145605 0.52665608 0.58522806 0.49870197 0.47213690 0.2564135 #> Itgb4         0.65964180 0.92831686 0.63561418 0.75968338 0.75914514 0.5053382 #> Aspa          1.87909375 1.45680189 1.53833872 1.72369905 1.46958193 2.5777761 #> Cygb          1.56224133 1.62942100 1.54136833 1.74061875 1.27509267 1.2047964 #> Rflnb         0.73297921 0.58146422 1.01514315 1.03543508 0.54574352 0.9564919 #> Doc2b         0.85036485 0.79605063 0.64340435 0.67876817 0.88942003 0.5897834 #> Gfap          3.12155168 3.24198121 3.03211737 2.75172258 3.35167866 3.7201425 #> Npas3         0.72428750 0.61893080 0.75975639 0.67456185 1.19424107 0.0000000 #> Serpina3n     1.23737941 1.38114731 1.07596381 1.15230991 0.81359560 1.8331696 #> Clmn          2.16643116 1.82939053 2.08910818 2.32066560 2.04461206 1.5499308 #> Prkch         0.47655716 0.50607402 0.56185862 0.61083942 0.73205288 0.6261503 #> Fbln5         0.27933271 0.16453232 0.30820530 0.23993262 0.27045984 0.0000000 #> Akr1c18       0.25486892 0.10717964 0.18107542 0.29201268 0.00000000 0.1371682 #> Gng4          0.93611513 0.72142584 0.89823297 0.87199592 0.72353001 1.9499755 #> Sema4d        2.03092581 1.86271608 1.89149412 1.77346033 1.74305382 1.3499372 #> Cxcl14        2.70461369 3.01340845 2.61703676 2.92785002 2.96684799 3.2410235 #> Hexb          3.00911612 3.37099821 3.18495493 3.30895148 3.64220022 2.5958016 #> Iqgap2        0.90895923 0.78908630 0.98281143 0.83299641 0.98028629 1.0300316 #> Crhbp         0.50371639 0.62988919 0.69393968 0.55015138 1.07634777 0.1371682 #> Rab3c         3.43988290 3.25891694 3.48259901 3.36089800 3.40901135 3.1297855 #> Thbs4         0.49765351 0.59669414 0.52533895 0.45375515 1.01070198 0.0000000 #> Serinc5       1.85389862 1.76190306 1.80870776 2.08593379 1.58414402 1.5293168 #> Erbin         2.45095864 1.96542277 2.62172379 2.34742867 2.29976160 2.4205313 #> Prkcd         2.57324385 2.61354668 2.38756697 2.87293417 2.13261309 2.2796092 #> Pdlim2        2.64100657 2.03304145 2.19677138 2.17522177 2.62607356 1.1154087 #> Ednrb         1.74214831 2.06030247 1.98828402 1.88385559 1.81672934 1.8173021 #> Cpne6         2.98364077 3.20817015 3.18107406 3.40839997 2.72992785 3.3275147 #> Sema5a        1.74619383 1.75016526 1.40190974 1.65337013 1.00666994 2.4115971 #> Matn2         1.02592291 1.31043133 1.24722461 1.06996228 1.28397813 1.0234107 #> Nptxr         3.98905107 4.10408925 4.54218333 4.02744883 3.77647703 4.0245328 #> Enpp2         4.43558458 4.31703048 4.29793558 4.11931597 4.59425832 3.7667837 #> Efcab6        0.31995630 0.44039143 0.53089320 0.32225920 0.43844731 0.8746874 #> Ppp1r1a       4.01406097 4.69827590 4.31408620 4.26538646 4.36988396 4.3554185 #> Litaf         1.76599530 1.58304036 1.59402701 1.46871417 1.80087344 1.7484272 #> Il1rap        1.83932810 1.47409370 1.46592131 1.65888997 1.58001808 1.2359937 #> Apod          5.11956478 5.00724135 4.93962837 4.96219926 5.42790752 3.9966022 #> Cpox          1.88485507 1.55457452 1.67161441 1.48853842 1.68145051 1.2664507 #> Grik1         0.55123294 0.54706355 0.40812361 0.55433660 0.31160914 1.1483943 #> Clic6         0.26628334 0.18558083 0.33574166 0.53274505 0.32058596 0.3474831 #> Nr4a1         0.64554738 0.73686764 0.99578525 0.71031972 0.25864240 0.2526861 #> Igfbp6        1.65030632 1.57194646 1.75294453 1.63411478 1.10892966 0.8347239 #> Sncg          0.40304031 0.28474379 0.38255750 0.38044514 0.42697491 0.0000000 #> Gzma          0.07190143 0.11410847 0.08815679 0.16416438 0.15574311 0.2504086 #> Grm2          0.96663539 0.96544707 1.11083722 0.84242663 0.70178515 0.6245136 #> Prph          0.17354909 0.25141501 0.14536617 0.34584096 0.00000000 0.3242240 #> Rsph1         0.27474608 0.16513017 0.23973773 0.20146095 0.31590239 0.6090279 #> Sox8          1.05032952 1.22311243 1.03490994 0.88191218 1.22329141 1.1165167 #> Fam234a       0.87158086 1.01867176 1.00146330 0.90913099 0.92536879 1.2068740 #> Lims2         1.27731649 1.25909487 1.00587185 1.06166966 1.35833723 1.0815706 #> Aqp4          2.67431922 2.75917648 2.54629507 2.82003279 2.84498269 2.9813845 #> Slc12a2       2.61481381 2.48155481 2.45199470 2.58709031 2.28611363 2.7799110 #> Cd74          0.16323129 0.28640037 0.16826600 0.26490651 0.08241013 0.0000000 #> Pdgfrb        0.53134815 0.69153085 0.59398354 0.55032243 0.82027150 0.2666210 #> Csf1r         2.66955319 2.53276487 2.42293815 2.23872947 2.61373883 2.8836846 #> Cbln2         0.85233400 0.44056965 0.53927191 0.76469578 0.74219937 0.1371682 #> Frmd8         1.46489626 1.19688364 1.45831748 1.18313898 1.21407728 1.1267537 #> Gldc          0.80769231 0.98218429 0.87414267 0.99385658 0.84366451 0.6635751 #> Tcf7l2        1.92964955 1.89001198 1.74476682 2.08429611 1.88492371 1.6457028 #> Bhlhe22       1.26730535 1.57124430 1.63385086 1.27426865 1.07416336 1.8132305 #> Kcnip2        2.25376431 2.23553466 2.76070190 2.34762087 2.53952800 3.1093760 #> Alas2         1.24029336 1.11196961 1.15905023 0.92345850 0.83743496 1.5693706 #> Gdf11         0.89456013 0.78694878 0.85317097 0.80486474 1.06354474 0.5940782 #> Baiap2        3.31778256 3.47637866 3.33135191 2.99228394 2.89563373 3.2529838 #> Ifitm3        1.66376351 1.90122708 1.56203622 1.98765479 2.12591695 1.2725191 #> Phkg1         0.85701198 0.92818993 0.80632925 0.91264376 1.24705822 0.0000000 #> Nptx1         3.44951987 3.60426494 3.51022093 3.32857508 3.53222106 3.4367115 #> Pde8a         0.95549842 0.97877848 0.91299388 1.06086870 1.00052882 0.0000000 #> Itih5         0.66908579 0.61358907 0.66298569 0.88788154 0.66934306 0.2564135 #> Homer2        1.96389655 2.22129055 1.81406114 1.84286080 2.66051456 1.6458791 #> Fam20c        2.02595270 2.06933668 1.66449848 1.96555317 1.41006144 2.5059174 #> Cplx2         4.84253940 5.22427279 4.94190933 4.76831409 4.92894758 5.1011530 #> Myo5b         1.08991437 1.30942463 1.27752362 1.23667112 1.09982000 1.0071975 #> Snca          4.62706705 4.73126980 4.85586143 4.61241596 4.60789463 5.0600640 #> Col3a1        0.10335846 0.09522224 0.14714881 0.21914560 0.13701240 0.0000000 #> Ecrg4         0.45018284 0.32103283 0.61516957 0.49927573 0.82417133 0.3875768 #> Map4k4        2.32223513 2.05759704 2.32236026 2.17313011 2.14955074 2.3387905 #> 2010300C02Rik 2.95949381 3.37786454 3.14329561 2.84124569 3.02035452 3.4352495 #> Ogfrl1        4.06706884 4.06803553 4.44373436 4.29416184 4.30641033 4.0158758 #> Fn1           1.10491890 0.98838442 1.10338559 0.92355011 1.00517314 0.6760625 #> Efhd1         1.68085370 1.43353602 1.55741521 1.35112243 1.69179593 0.8484207 #> Ngef          2.91242099 2.74592475 3.24004763 2.67797217 2.64117361 2.4591740 #> Bok           2.71366296 2.47116725 2.82089779 2.77238677 2.50119762 2.6689739 #> Tmem163       1.33074915 1.18819754 1.27391290 1.38626655 1.19782563 2.0900730 #> Lct           0.55087056 0.90609934 0.47985112 0.37742620 0.63297348 1.2735187 #> Cfh           0.88970003 0.91487359 0.72403399 0.65726992 0.53960703 1.0474544 #> Ptpn4         2.95295578 2.77964915 2.93667271 2.84916240 2.78932644 3.1403560 #> Tnni1         0.78849723 0.56909482 0.59023884 0.60013499 0.99522997 0.2824807 #> Csrp1         5.01572073 4.68519528 4.78446126 4.80670914 5.05684827 5.1119679 #> Nfasc         3.34835525 3.13436419 3.45235108 3.13689334 2.88211743 3.9146409 #> Syt2          0.66474670 0.55319344 0.69937910 0.56156080 0.27321902 0.2666210 #> Atp2b4        1.84269558 1.15386024 1.80429076 1.41293692 1.27377631 1.2427699 #> Rgs16         0.95357582 0.77241859 0.79247107 1.00855874 0.53107269 0.4951308 #> Ncf2          0.19577536 0.30744226 0.28517955 0.04401388 0.22083523 0.0000000 #> Cnih3         1.37787878 1.91073139 1.86309495 1.51923394 0.95664556 2.2298451 #> Tmem63a       1.59770579 1.66244580 1.57718404 1.76645489 1.62173987 0.8654414 #> Cfap126       0.22972328 0.20822942 0.17732501 0.33723331 0.34625506 0.0000000 #> Meig1         0.29109497 0.27586998 0.35000531 0.26306041 0.28185530 0.5090908 #> Ccdc3         0.78413847 0.73650858 0.63024330 0.68680921 0.59021747 1.1575822 #> Rgs5          2.02183992 2.33216198 2.25644205 2.17722922 2.79744251 2.4141827 #> Enkur         0.19258484 0.16684621 0.19068893 0.19143594 0.27889672 0.0000000 #> Myoc          0.58313508 0.62531156 0.54259460 0.46842173 0.37242729 0.2564135 #> Vim           1.63777758 1.87228319 1.50567183 1.96622246 1.92367017 1.2362695 #> Prkcq         0.57988915 0.51531037 0.72080768 0.76230445 0.99688914 0.6372650 #> Gad2          2.58905667 2.66586350 2.23435549 2.35198533 2.70805407 1.8277225 #> Lcn2          0.11001342 0.23756140 0.08109622 0.07181696 0.23086015 0.0000000 #> Nr4a2         1.22250797 0.88546766 1.12822732 0.84090078 1.14285461 1.1404969 #> Ermn          2.49706251 2.35035913 2.53116196 2.23101740 2.34756426 1.6429710 #> Fibcd1        1.06700564 1.12347821 1.12803125 1.14066428 1.31491645 2.0072588 #> Gsn           3.53057502 3.09333206 3.24377538 3.28817732 3.30329127 2.3946310 #> Grb14         3.42052836 3.36173213 2.77046062 3.08122822 3.00375570 2.9427657 #> Notch1        0.73795047 0.57299505 0.76784734 0.79697664 0.79244038 0.3703106 #> Ube2l6        0.79318618 0.71995881 0.73357527 0.72603253 0.68412857 0.7306790 #> Gatm          3.55985522 2.98305682 3.24247224 3.01039727 3.50364606 3.8087241 #> Cd82          1.49922529 1.58499533 1.36301618 1.50503499 1.30925932 1.4534073 #> Mdk           1.58694084 1.61605846 1.61063336 1.68377010 1.44990012 1.1585555 #> Lamp5         1.72564609 1.84724258 2.09268336 1.37732734 1.24490303 2.3696344 #> Itpka         3.38790169 3.77027935 3.64104099 3.56730816 3.20722970 3.6555564 #> Chgb          4.88863946 4.69165476 5.02117029 4.85742016 4.98184272 5.0368354 #> Mal           5.52489949 5.32136589 5.25246346 5.50360680 5.67157535 5.4366287 #> Pdyn          0.79158555 0.59079410 0.58304153 0.54279423 0.19734941 0.5758145 #> Nkx2-2        0.56734724 0.56550690 0.48407154 0.49525147 0.43224503 0.0000000 #> Edn3          0.13911894 0.05176152 0.10439934 0.24100412 0.17549881 0.0000000 #> Car2          4.79559426 4.66259955 4.63408113 4.92886903 4.97714175 5.0083894 #> Col9a3        0.73807814 0.71699776 0.55312249 0.70748193 0.83754395 1.2497755 #> Chrna4        1.65844964 1.85245203 1.94891048 1.54787324 1.42590930 1.1898229 #> Gss           1.23676224 0.97623337 1.16285378 1.02848915 1.06035712 0.2504086 #> Slc7a11       0.64926494 0.63902218 0.68024411 0.86961091 0.64560305 1.0871200 #> Tm4sf1        0.91410376 0.73984987 0.86342619 0.75260177 0.92873579 0.2666210 #> Kcnab1        2.77547276 2.98507524 2.92440955 2.70075041 2.18772552 3.4374489 #> Shox2         0.82458200 0.67605161 0.75661388 0.85502706 0.76525942 0.4929982 #> Serpini1      3.30040994 3.29933835 3.60183670 3.19300777 3.26845870 3.4041277 #> Tspan2        4.21697788 3.63807510 3.87527630 4.09312839 3.90853413 4.3763411 #> S100a11       0.55821875 0.46909211 0.50687831 0.66359584 0.74313723 0.0000000 #> Vcam1         0.90264419 1.11631737 0.91089476 0.85585352 1.14136059 1.0918987 #> Lef1          0.78796878 0.76062726 0.78915342 0.78366249 0.47511347 0.2564135 #> Npy2r         0.57723444 0.84627539 0.80665137 0.67953308 0.73797688 0.4196490 #> F3            1.17849759 1.49972532 1.29002259 1.29397785 1.59195340 0.0000000 #> Calb1         2.75161481 2.64565739 2.66071371 2.35304449 2.24703356 2.8503507 #> Epha7         2.07360225 1.93747690 2.12807952 2.16424935 1.78071038 2.7985356 #> Slc44a1       3.03127766 2.73384982 2.76202669 2.62223174 2.91734606 2.2830737 #> 1110017D15Rik 0.44254321 0.42104894 0.38350624 0.19568207 0.28069313 0.3703106 #> Tpm2          0.47347063 0.28035363 0.43004655 0.65260676 0.53526026 0.2564135 #> Slc6a9        1.76829554 1.79664252 1.68823316 1.74618441 2.14463735 1.3979006 #> Laptm5        1.75628277 1.68232228 1.38838393 1.44405341 1.98893577 2.1105590 #> Sema3c        0.79138634 0.46456785 0.85844214 0.52721566 0.30380740 0.6305185 #> Hpca          5.42154696 5.77634500 5.65291624 5.30758332 5.48050058 6.0249872 #> Padi2         1.47837486 1.10605178 1.07137082 0.92795207 1.38944203 0.4613923 #> Slc4a2        1.39994031 1.55371697 1.29468289 1.37431593 1.41444369 0.6038967 #> Gabrd         2.41994887 2.39963813 2.38924771 2.08800067 2.15819546 2.3539306 #> Rgs12         1.22645589 1.21384074 1.12066235 1.14204164 1.11072187 1.1780739 #> Slc30a3       1.89363523 1.69620000 1.88026617 1.62812203 1.71538297 1.7453630 #> Emilin1       0.15988581 0.06982516 0.02383032 0.08950430 0.19240122 0.0000000 #> 1700001C02Rik 0.18927101 0.05728738 0.07733503 0.01839425 0.15710555 0.0000000 #> Gabra4        2.60497866 2.43929779 2.57947094 2.71908436 2.31227760 2.8052710 #> Pdgfra        0.78804945 0.93572625 1.03361028 1.15029471 0.90386397 0.7194057 #> Epha5         2.38930589 2.35544274 2.31345803 1.94187464 2.14475995 2.2749732 #> Tesc          2.30027805 1.98764453 2.43810163 2.14169984 2.12836973 2.4553152 #> Pitpnm2       2.15711440 2.59388505 2.21222659 1.94021692 2.44767598 2.7039998 #> Mmp17         2.44647351 2.48596867 2.83821830 2.60643100 2.31549141 1.9436145 #> Cit           2.54506390 2.26660798 2.68180498 2.55911909 2.31233140 2.5188545 #> Foxp2         0.98678529 1.02917465 1.17179142 1.19784971 0.73538372 0.3436696 #> Arpc1b        1.62470466 1.29123387 1.73839998 1.34042337 1.61413436 1.7838762 #> Col1a2        0.68218467 0.49410901 0.33255629 0.40645615 0.51822386 0.0000000 #> Eln           0.09061027 0.12437313 0.18921346 0.15069912 0.28733407 0.0000000 #> Pcolce        0.40835217 0.17567545 0.31943003 0.44060403 0.47988101 0.0000000 #> Tsc22d4       4.68481739 4.87820011 4.58044772 4.72661026 4.51677143 4.2072991 #> Cald1         1.00831433 1.09999147 0.96943989 0.73670233 0.93050467 0.8055152 #> Ccdc136       3.19733978 2.90704090 2.90717882 3.07481517 2.32147603 2.3319452 #> Npy           2.70571597 2.42263758 2.73864823 2.31508768 2.82614785 1.9942862 #> Slc13a4       0.32992903 0.09337211 0.14992969 0.18884589 0.12359795 0.0000000 #> Gkn3          0.61270038 0.38462317 0.52145131 0.66694451 0.19017267 0.0000000 #> Slc6a13       0.33661496 0.22670062 0.23966019 0.37448920 0.20501486 0.0000000 #> Mgp           1.66148784 0.78793329 1.50269980 1.41650584 1.02778485 0.3436696 #> Lmo3          2.42932341 2.62194967 2.67226522 2.35574188 2.40708808 2.5245086 #> Slco1c1       1.54177117 2.06311666 2.01561258 1.99786085 1.87544335 2.5707408 #> Cpne9         1.35270330 0.85277249 1.42153976 1.27506722 1.41430820 0.8109540 #> Itpr2         0.68257703 0.50138653 0.75204281 0.89185105 0.91117434 0.3474831 #> Slc6a11       2.61604162 2.62012288 2.50593623 2.66856608 2.30484151 2.5784086 #> Vamp1         2.48963304 2.49782797 2.57893644 2.89025235 2.48330459 2.1890445 #> Cd9           3.11862023 3.00308144 2.84786535 2.72844377 2.86524077 2.3690098 #> Pglyrp1       0.88571095 0.96683044 0.80009758 0.93906298 1.21806059 0.5068221 #> Slc17a6       1.62291007 1.66658407 1.77797658 1.80386313 1.27191228 1.6023952 #> Sipa1l3       1.46441270 1.87109964 1.53637225 1.57753377 1.71206764 1.7216736 #> Sh3gl3        2.42227350 2.18739040 1.96729858 2.11239853 2.11841189 2.1834760 #> Plekhb1       5.26989022 5.08766180 5.33292848 5.29172376 5.43168172 5.4000485 #> Nupr1         0.34593129 0.60897633 0.28826812 0.43127770 0.34710384 0.0000000 #> Dkk3          3.43279965 3.25478191 3.65911228 3.12123621 3.00627044 3.6254150 #> Cox6a2        1.53223212 1.20097966 1.34653532 1.53161448 1.02634977 1.0002553 #> Dkkl1         0.84140367 0.69790200 1.07608973 0.75568738 0.97585842 0.0000000 #> Fgfr2         1.78640295 1.47183801 1.58647443 1.62810292 1.71937644 1.4072603 #> Crym          2.59338157 2.77401687 2.90799042 2.55813201 2.23842391 2.8514304 #> Slc38a5       0.21605026 0.17444448 0.20752276 0.34937317 0.55424647 0.0000000 #> Flna          1.09557690 1.29788690 1.28178968 1.09731220 0.93128353 0.8206811 #> Bgn           0.55339634 0.55505453 0.52065451 0.54507218 0.63729383 0.2564135 #> Col4a1        1.02425466 0.93547399 1.18324437 1.02022529 1.15861721 1.8394679 #> Plat          1.14540299 1.24250895 1.21317463 0.99302566 1.10865702 0.9816925 #> Nr3c2         1.74298171 1.99898592 1.65044180 1.59818056 1.15467732 2.5707193 #> Cbln1         0.50677361 0.56843914 0.49778664 0.67986802 0.53191317 0.7215881 #> Gab1          1.50292378 1.59756945 1.69453646 1.46556971 1.69383067 1.0986573 #> Pllp          3.22415451 3.21743067 3.01274890 3.03544285 2.74681104 2.5136211 #> Necab2        2.21168530 1.90715240 2.26504854 2.39376640 2.30668914 1.1476453 #> Dbndd1        1.15359092 1.34742373 1.27477861 1.35473435 1.17078218 0.7872716 #> Agt           2.58344953 2.65131727 2.23244375 2.66909410 2.54067049 2.9915034 #> Cryab         5.18551692 4.86790348 4.88570189 4.82335774 4.79686080 4.3052533 #> Tagln         0.33838878 0.37546179 0.46356002 0.56298326 0.21107501 0.0000000 #> Mcam          1.17115913 0.82098156 0.95253117 0.80677507 0.93344433 0.9827394 #> Olfm2         2.16938520 2.03888319 2.31740773 1.92146082 2.15946392 2.4801375 #> Icam5         2.81103374 2.98606878 2.87476056 2.66370075 3.01691101 3.2118431 #> Anxa2         0.57179514 0.34788829 0.50720952 0.70967632 0.45995659 0.6369316 #> Rora          2.72090769 3.14506075 2.91905783 2.85151295 2.69507749 1.8534747 #> Calml4        0.17812836 0.24026338 0.21439030 0.26489800 0.12279855 0.2564135 #> Htr3a         0.20623614 0.25779001 0.21562203 0.29249946 0.51795632 0.0000000 #> Paqr5         0.28548196 0.34937823 0.26226962 0.31439479 0.41305397 0.1371682 #> Rasgrf1       4.15342599 4.27961595 4.33009229 4.13530341 4.16508849 4.5934711 #> Zic1          1.47768397 1.44655695 1.39423152 1.80648344 1.34917327 2.0632232 #> Mobp          6.59632749 6.31520717 6.49676468 6.46728343 6.69364109 6.2946899 #> Hhatl         0.93681733 1.06462245 0.98033459 1.11457753 1.24083725 1.0382275 #> Trf           5.45009365 5.02241912 5.14522113 4.95783218 5.58619057 5.1389024 #> Cpne4         1.77621294 1.63315095 1.92080522 1.89454150 1.47925758 1.1136211 #> Cdhr4         0.10169997 0.12003410 0.12457179 0.06082551 0.00000000 0.0000000 #> Cd59a         1.09204790 1.27182310 1.17265850 0.83537412 0.89930350 1.3773815 #> Gng11         2.51158658 2.82844009 2.39374372 2.58329008 2.65677985 2.6251262 #> Chrm1         2.58901145 2.56080761 2.84557636 2.32416159 2.60370776 2.0795552 #> Prr5l         0.82610324 0.76269196 0.57957434 0.65938983 0.55913009 0.6862699 #> Ugt8a         2.78339796 2.44413871 2.53914210 2.46467594 2.32760436 0.9639957 #> Rims3         2.76819976 2.12361322 2.58159429 2.79867693 2.35592738 2.2271525 #> Sgpp2         0.93686313 0.51241116 0.76483544 0.87672988 1.07059811 0.9898886 #> Camkv         4.44530499 4.39151834 4.74003800 4.44649869 4.41698046 5.4369734 #> Sox10         1.87523360 1.68483776 1.86954113 1.71488287 1.81402802 1.9575917 #> Micall1       1.05263096 1.00082961 1.24536063 1.03367055 1.12657206 1.6637881 #> Tie1          0.34054619 0.32802029 0.30334945 0.33701117 0.32710426 0.2824807 #> Fa2h          2.70702598 2.15260925 2.41984825 2.42349903 2.22907359 1.7402922 #> Ucp2          0.79834906 0.75259766 1.12235205 1.13314304 1.32931986 1.5159634 #> Vav3          0.98378113 0.76786652 0.63515849 0.75285785 0.26584800 0.5328893 #> Ccp110        2.29732034 2.19807779 2.47177250 1.90358959 1.82606217 2.4110374 #> Gria2         4.59242525 4.64033571 4.81893386 4.40964277 4.66819325 5.2594264 #> Rasl10a       1.54192423 1.73460468 1.60630631 1.35696467 1.33128251 1.7335148 #> Foxj1         0.58587705 0.65336904 0.39514923 0.46595485 0.55686934 0.0000000 #> Trim59        0.87326383 1.06343482 1.05911906 0.80614020 1.19515684 0.7928307 #> Dynlrb2       0.26238060 0.21789545 0.17695090 0.13195426 0.24472416 0.0000000 #> Gjc1          0.25997653 0.40032750 0.38944777 0.32112771 0.39605926 0.9215004 #> Neurod1       0.67678261 0.81565899 0.80869242 0.72888077 0.64958901 0.9152128 #> Ttyh2         2.00867858 1.61856659 1.52483405 1.73481250 1.94563902 1.9251238 #> Cpne7         1.83558011 1.68264494 1.91383742 1.91205820 1.96437175 1.6219654 #> Nrip3         2.86404839 2.54543673 2.89416401 2.69424073 2.64936601 2.2236894 #> Tbr1          1.98502173 1.94914444 2.35409038 1.89777057 1.66296620 1.6540140 #> Lcat          1.48401002 1.79499129 1.41899153 1.42503144 1.49609368 1.4704056 #> Tmem98        0.84876609 0.78400162 0.76138953 0.85510839 1.28831323 0.6518838 #> Myo1d         0.62446089 0.40878407 0.64095163 0.47877072 0.52474848 0.6478262 #> Prdm8         1.04292224 1.27702526 1.13657692 0.83121952 0.77800741 1.6912317 #> Tgfbi         0.16242251 0.10086874 0.11706610 0.33153366 0.28952068 0.0000000 #> Kcnc2         2.85238527 2.59184448 2.80120583 2.81393417 1.82541417 3.5675709 #> Thrsp         1.66670187 2.09722949 1.64618163 2.02629276 1.75051207 2.3582313 #> Isg15         0.66931028 0.84537077 0.61051327 0.68058352 0.64991891 0.3935818 #> Acta2         0.57752461 0.54501809 0.56501864 0.64096745 0.69354224 0.0000000 #> H2-Q4         0.12644221 0.13312345 0.13251285 0.13326698 0.36279216 0.0000000 #> Dock4         2.29163340 2.21266447 2.43823628 1.83282468 1.96590270 2.4823942 #> Myrf          1.68052605 1.50964521 1.51786885 1.71116937 1.51161493 2.7020055 #> Lmo1          1.68561146 2.17490628 1.99279555 2.00818965 1.59998363 2.9855520 #> Igfbp7        1.77284339 1.99886593 1.93657362 2.05040476 2.33193718 1.0121604 #> P2ry12        1.37878842 1.24887876 1.19884558 1.45998888 1.78452703 1.7301314 #> Pcdh8         1.16073414 1.37681956 1.02213157 1.29615729 0.97496592 1.6198937 #> Lgi4          1.28584162 1.08700341 1.11107934 1.17937170 1.69896078 0.5068221 #> Fxyd1         3.14185573 3.03257244 3.09423916 3.31509575 3.39728196 3.1929004 #> Fxyd7         4.24985766 4.36743132 4.51523820 4.11282865 3.66635135 3.9561871 #> Mag           5.12500474 4.67191908 4.65072225 4.92307953 4.78339942 5.0692949 #> Zcchc12       1.52902191 1.75238761 1.50205089 1.30837531 1.18592398 2.1019134 #> Anln          1.06438290 1.22290140 1.02662252 0.75448601 1.21465958 0.6797875 #> Wnt4          1.07266316 1.11076790 1.04697232 1.19598207 0.44986225 0.8317029 #> C1ql2         0.63756061 0.83656585 0.55546037 0.74039217 0.42425309 1.4792838 #> Unc93b1       0.65399313 0.72501458 0.64464940 0.57091079 1.05917378 1.2411060 #> Tspan15       1.48416997 1.31211576 1.53793806 1.15584722 1.17124980 1.5972370 #> Ppp1r14a      3.34120410 2.99944064 2.85879699 2.91610667 3.11068072 3.0766945 #> Clic4         2.58666667 2.36671046 2.12576758 2.38873272 2.69836201 2.0664659 #> Galnt6        0.79259003 0.86166055 0.59304957 0.62816013 0.94087487 0.3242240 #> Ccn3          1.69445080 1.82519651 2.02261190 1.50804077 2.07883176 2.2958439 #> Rims2         2.29191029 2.32112167 2.29767291 2.16756388 1.45935355 1.7251028 #> Zmat4         1.55506361 1.57574686 1.53556433 1.42295301 1.05790010 1.4843569 #> Cldn11        5.12673269 4.91747338 4.91391632 4.85413605 4.93278681 5.2484757 #> Ccdc33        0.15646381 0.08911464 0.06165821 0.03512126 0.14687971 0.0000000 #> Slc32a1       1.59437851 1.52183497 1.70916749 1.78111100 1.95042305 1.1983679 #> Tgm2          0.39655722 0.24013140 0.25795652 0.33902515 0.57609405 0.0000000 #> Vstm2l        2.22098701 2.38136884 2.51948666 2.11308075 2.07506678 2.2089450 #> Neurod6       2.63428566 2.50013668 2.77025341 2.64586781 2.55916111 2.4965476 #> Crygn         0.16837963 0.15891147 0.11078299 0.02585192 0.25634860 0.0000000 #> Enpp6         0.61638331 0.76178677 0.88997335 0.67357231 0.41861134 0.2387173 #> Neurod2       2.39954962 2.38922135 2.53563564 2.49431276 1.92186944 2.1457090 #> Satb2         0.99178482 0.81658359 1.09482562 0.50963007 1.03455500 0.7250296 #> Pcp4l1        2.97992708 2.96077966 2.92023724 3.06136601 2.54141375 2.1498052 #> Txnip         0.81687069 0.55199932 0.77762053 0.82753556 1.02713336 0.4566015 #> Egr1          2.14886893 1.96359869 2.38581323 2.15333255 2.12058191 2.9450464 #> Otud7b        1.54728064 1.44846861 1.72710033 1.37022748 1.55159842 1.0621922 #> Car14         1.24424269 1.11343694 1.07236797 1.21006471 1.11457941 0.5862004 #> Rgs4          3.46613950 3.57801726 3.66691030 3.69097731 3.26991343 2.2863177 #> Dock10        1.28970847 1.57049487 1.14562505 1.29309427 1.52662939 1.1203111 #> Lpar1         2.09900245 1.58915403 1.77779593 2.03084932 1.87624640 1.6533343 #> Trps1         0.88635242 1.09999999 0.96537691 0.70914548 0.77885897 0.6262941 #> Ptpn3         2.03505854 1.71841934 2.02237954 2.18976046 1.75715473 1.6801179 #> Lefty1        0.53841045 0.66308465 0.78954952 0.70686947 0.71217809 0.8436765 #> Zfhx3         1.01463614 0.96580755 1.05374459 1.16390482 1.05445715 0.8927713 #> St6galnac5    2.16976535 2.53073593 2.28547222 2.07026295 2.41378148 2.3171005 #> Ak5           2.81209723 2.96793488 2.67339895 2.68978028 2.65212379 2.2315317 #> Hrh3          2.26063005 1.67483898 2.03100649 2.01218617 1.34537819 1.2703098 #> Nexn          0.56948760 0.48736435 0.47581899 0.49945862 0.27890296 0.2564135 #> Adgrl4        1.04985868 0.90483970 0.92898229 0.97800088 1.06809182 0.5068221 #> Rlbp1         0.77307162 1.09270069 0.79549368 0.85825563 0.41168285 0.7177937 #> Igfbp2        1.50043225 1.40823846 1.38463073 1.42376461 1.60911510 0.8100896 #> Wfs1          2.18927867 2.30295460 2.32184235 2.44810454 2.92937818 2.1068153 #> Cplx3         0.89687539 0.93155993 1.02811878 0.55739109 1.14881459 1.1910550 #> Orai2         1.69283039 2.08994082 1.92667785 1.68048975 1.55877682 1.6261425 #> Olig2         1.60203185 1.34909962 1.26060560 1.09819003 1.39070009 2.4657778 #> Gpr37         3.10942139 2.62248215 2.73938171 2.69477256 2.76208140 3.3843659 #> Plcb4         2.21541850 2.22112223 2.19114756 2.49093229 1.48135714 1.5824280 #> Nxph4         0.22263899 0.21444872 0.23321410 0.21511268 0.21381214 0.5123107 #> Ndufa4l2      0.76029564 0.59436411 0.42263532 0.59691739 0.75663938 0.2564135 #> Cacng5        0.75850207 1.10563582 0.59535977 0.80880499 0.67086059 0.4663389 #> Plekhg1       1.63237476 1.45942596 1.58926683 1.67521499 1.07618807 0.9779528 #> Cmtm5         3.59912609 3.09342087 3.27582574 3.38148577 3.24189183 4.0948043 #> Gpr161        0.61508999 0.70157514 0.60472709 0.51476430 0.53725598 1.3769960 #> Rfx3          1.19477919 1.18544260 0.89180005 1.05139857 0.66943743 0.8861989 #> Igsf21        1.68603070 1.22147136 1.83816298 1.36185664 1.39103066 1.7312896 #> Ramp3         2.10765261 2.07922426 1.91348009 2.04867784 2.03535612 1.8926492 #> Arhgap12      1.31951502 1.16740918 1.43679667 1.47682701 1.25994916 1.6957406 #> Nkx6-2        1.90055006 1.39579282 1.44117547 1.54679054 1.80681039 1.7592271 #> Ninj2         0.44872324 0.37088683 0.60350690 0.38235840 0.30128077 0.3758855 #> Cldn5         2.05797803 2.16118255 2.01543084 2.15157241 2.88085137 1.9432223 #> Htr2c         0.72402001 0.71674657 0.94921040 0.83540190 0.72370414 1.3014022 #> Hspb8         0.65264924 0.53639950 0.44501817 0.53386240 0.82568828 0.3703106 #> Fmod          0.16746162 0.12864624 0.12528572 0.18129535 0.13869958 0.0000000 #> Prelp         0.89738015 0.60641398 0.70944223 0.79762136 0.64964328 0.9521178 #> Mpped1        2.61638152 2.52593116 2.79221724 2.09534555 2.49422851 2.6844707 #> Rapgef5       1.96906516 2.42593863 2.26278751 1.91891904 1.81402583 1.9696632 #> Vwa1          1.13226660 1.31113787 1.04354593 1.31549050 1.40072163 2.2643882 #> Stab1         0.43845358 0.42299714 0.40552315 0.36719874 0.45872728 0.2504086 #> Arl15         1.26545235 1.28025241 1.37925059 1.28053546 0.71570803 1.4224155 #> Reln          0.86476575 0.83080429 1.00051023 0.96892689 0.77288492 0.1371682 #> Mustn1        0.26758770 0.09690683 0.16914040 0.12959606 0.00000000 0.0000000 #> Pbxip1        1.34938308 1.33038450 1.52504316 1.15143540 1.19436056 2.3029478 #> Dnali1        0.11444348 0.09526922 0.10768508 0.11466140 0.20920214 0.0000000 #> Id1           1.62154126 1.37257775 1.28516523 1.47026285 1.89182064 1.2202405 #> Lrrtm3        1.33048713 1.24589537 1.37982293 1.11962727 0.75626311 1.0594517 #> Tmem212       0.26257481 0.14465794 0.17697560 0.18815656 0.16627582 0.3741050 #> Epop          1.70575981 2.20123934 2.11031292 1.70178432 1.65954865 2.0015656 #> Gjc2          1.50615090 1.47433026 1.34343557 1.24223850 1.31123383 2.0603772 #> 1190005I06Rik 1.35043254 1.35570109 1.12952302 1.02266077 1.17287740 1.8616339 #> Ctla2a        1.24079344 0.98451329 1.06031270 1.13176646 0.99305478 0.3547843 #> Cnr1          1.99177163 2.19292993 2.33292360 2.01669127 2.45104316 2.1977566 #> Gpr4          0.32994338 0.38349617 0.51193651 0.56655929 0.48262546 0.5230345 #> Sowaha        2.11056381 2.81955510 2.20716759 2.34804256 2.87009279 2.6319992 #> Tent5c        0.51357553 0.52555080 0.38222326 0.34015465 0.31439325 0.3976548 #> Serpinb1a     1.16808584 0.95532207 0.97708237 1.03182567 1.20150453 0.5758145 #> S1pr5         1.28460786 0.98366694 0.86736555 0.86549324 0.81975136 0.7280132 #> Penk          1.28150874 1.48804379 1.37118419 1.07752180 1.50500529 1.8658537 #> Cdc42ep2      1.31112799 1.03877484 1.33480677 1.30032413 1.17369038 0.6871979 #> Slitrk6       0.42813022 0.21470071 0.48738984 0.42940442 0.22577354 0.0000000 #> Hpcal4        4.41959519 4.53852396 4.64722880 3.90770677 4.57671568 4.6085595 #> Olig1         4.59979138 4.17669248 4.25667919 4.33405253 4.42979786 2.9726222 #> Rprml         3.07675148 2.89096108 3.24192141 3.01097068 3.15841849 3.0885792 #> Stxbp6        1.68982961 1.67759145 1.49422978 1.59922746 1.34631155 1.6554338 #> Hs3st2        1.12198006 1.02177563 1.24062153 0.97789314 0.88637304 0.5769102 #> Rbp1          1.36164224 1.36587083 1.21432986 1.38511940 1.12779742 0.5328893 #> Ppm1e         3.14150738 3.06855235 3.37154134 3.05397217 3.21361904 3.4547617 #> Sox18         0.55977904 0.81528063 0.42582977 0.60139038 0.38481028 0.6037182 #> Kctd4         1.22576360 1.28181598 0.87460770 1.13942354 0.62521228 1.2614962 #> Nxph3         0.98709456 0.70831593 1.11105497 0.66187736 0.85333024 0.4936364 #> Vat1l         0.90595201 0.84805180 0.70829763 0.71705645 1.05167716 0.3474831 #> Cd24a         0.83585240 0.66717923 0.63308184 0.42952765 0.77319714 0.3935818 #> Odf3b         0.19472127 0.11610201 0.15056997 0.05604758 0.14914976 0.3703106 #> Gjb1          1.63349091 1.24850559 1.23920304 1.25310596 1.40097070 1.0983238 #> Selplg        1.46198870 0.95436411 1.26787210 1.27829013 1.58337965 0.8879271 #> Bcl11b        2.08720626 2.64724695 2.35003951 1.99581744 2.15090413 2.5578504 #> Lhfp          1.30109693 1.69313788 1.63660291 1.29043961 1.15576850 1.9859031 #> Ranbp3l       0.03242664 0.27743058 0.04010778 0.11302941 0.00000000 0.2824807 #> Msx1          0.27092155 0.36375093 0.21662745 0.36830708 0.12867615 0.2564135 #> Zdhhc22       1.89107607 1.70658932 1.55754351 1.79296320 1.68515227 1.1714144 #> Phldb1        2.72674466 2.28226498 2.33404266 2.08710097 2.45410574 2.9918993 #> Ctxn1         4.63620134 4.70894211 4.78510560 4.55425034 4.60291026 4.9102322 #> Tprn          1.75470671 1.39721522 1.28822863 1.36993821 1.31152137 1.3917156 #> Vstm2a        2.28073151 2.26633071 2.15393733 2.28636983 2.22163146 2.1500628 #> Ndnf          0.51310409 0.58195774 0.38392762 0.50161323 0.43649448 0.3875768 #> Pdp1          3.01037972 2.98742459 3.06598155 3.05666212 2.75897253 2.8148635 #> Scn3b         2.40820926 2.84722996 2.85438349 2.75251782 2.69454073 3.5098934 #> Cdc42ep1      1.25933372 1.34260246 0.99908397 1.00464598 1.27408659 0.7373906 #> Gal3st1       1.58753819 1.44401350 1.29638097 1.31334863 1.32980736 1.8481187 #> Rasd1         1.29763417 1.41015801 1.31560461 1.43060189 1.44304974 1.1781116 #> Spink8        1.27139206 1.48848462 1.41945551 1.55335746 1.84664197 1.9907929 #> Opalin        3.34713558 3.25712117 2.96589080 2.98397388 3.26812150 3.1494090 #> Gja4          0.12059199 0.22431300 0.18452209 0.26626134 0.32685198 0.0000000 #> Synpo2        1.30381698 1.05201536 1.04885488 1.25656357 1.22006726 1.5780861 #> Pcdh20        1.02000367 1.35575835 1.33769133 1.26211034 0.83403675 1.7809842 #> Adra1b        1.27403000 1.02719137 1.28061157 0.99103440 1.14741183 1.1441730 #> Fam131a       3.58531575 3.79288244 3.59295331 3.26990512 2.77153982 3.6632339 #> Tmem125       1.06154618 0.77941710 0.91822041 1.19434335 0.92088619 1.2462929 #> Mb21d2        1.88319470 1.57101132 1.53801536 1.78219219 1.39135704 1.3609037 #> Lingo3        1.08347499 1.27753513 1.01662036 1.12567323 0.70963331 1.2846233 #> Ncald         4.47619030 4.63623903 4.66581202 4.35115584 4.38541089 4.7700048 #> Siglech       0.82944635 0.65626474 0.78482842 0.55325551 1.51082291 1.0615638 #> Rgs14         1.49998504 1.67943201 1.31174597 1.36534501 1.12748511 1.3400020 #> Gm14964       0.50914628 0.24641944 0.35409220 0.44864513 0.24150887 0.0000000 #> Gpr17         0.95594366 0.75231028 0.93072472 0.95879073 1.21728945 0.6845804 #> Cx3cr1        1.02819592 1.13498291 0.84360013 1.02390163 1.29212364 0.7194057 #> Ezr           1.70220561 1.86477689 1.47255180 1.38241032 1.93366439 1.1799208 #> Adarb2        0.75636302 0.75530304 0.86623663 0.88371980 0.80480183 0.3976548 #> Cpne8         0.80722610 0.75749844 0.77400170 0.72723726 0.63598534 0.8251990 #> Plekhg3       0.93540440 0.69588822 0.70566064 0.88679433 0.85559176 1.0493189 #> Lamb2         0.89661890 1.11155264 0.88756112 1.02605030 1.13427781 1.4909428 #> Creb5         0.61650207 0.41841136 0.38959639 0.45888483 0.47775179 0.6407260 #> Cntn2         2.19769046 1.98853482 2.31129249 1.83212021 2.27929936 1.2398097 #> Aldh1a1       2.29817855 2.52563080 2.35379228 2.65641791 2.47922311 1.5909304 #> Phgdh         3.16186234 3.45444131 3.10165196 3.33673834 3.61300815 3.2276782 #> Tnfaip6       1.30991237 1.27427386 0.99731184 1.03838146 0.58299791 0.3775465 #> Camk2d        1.91013264 1.75440216 2.22769858 1.77491542 1.64604388 1.5496669 #> Shisa6        1.40168284 1.60698652 1.61333210 1.72421787 1.27669855 2.1950510 #> Cthrc1        0.75791455 0.78019177 0.73432917 0.85975193 0.59578985 0.5068221 #> Tmem119       1.01709217 0.81441820 0.77017322 1.08834503 1.01649421 1.1748484 #> Hmgb2         1.00275853 0.66241499 0.74258912 0.52707685 0.40160431 0.6541978 #> Tmem158       2.27830361 2.23153622 2.33674527 2.00456458 1.79358921 2.6565355 #> Dsp           0.32584473 0.34822123 0.15779537 0.13951865 0.04866590 0.8175892 #> Lrtm2         1.78561984 1.62725178 1.82437791 1.91200291 1.25072335 1.0239489 #> Gabra5        2.08271045 2.19042809 2.35036426 2.17363466 1.86402028 2.8035044 #> Tns1          0.86826741 0.57209402 0.76665670 0.99855609 0.51350110 0.6067047 #> Nell1         1.84269481 1.74220880 1.68494960 1.88827253 1.65591025 0.9011789 #> Slain1        2.82831747 2.25443731 2.49507274 2.66298154 2.19900915 2.3975510 #> Prr18         2.69529293 2.32592581 2.10526236 1.93626405 2.62882326 1.7417281 #> S100a8        0.39841914 0.31742352 0.40403127 0.53159406 0.58116865 0.3474831 #> S100a9        0.45259758 0.22712797 0.47389134 0.48781378 0.40056456 0.1371682 #> Col8a2        0.06717989 0.05587790 0.09922726 0.10487230 0.42155426 0.0000000 #> Synpr         2.06776280 2.30042058 2.13497232 2.36693755 2.13873900 1.8655386 #> Sertm1        1.35580865 1.46341900 1.25682736 1.08935281 1.13479998 2.0082069 #> Adgrf5        0.89756501 0.66877532 1.13318007 1.20908964 0.95886855 1.1535245 #> Capg          0.38903655 0.35245856 0.21153810 0.28855782 0.27376925 0.0000000 #> Gjc3          2.05012612 2.15068339 1.93199599 1.85360953 2.02416301 0.9383281 #> Fcer1g        1.31521853 1.40151280 1.16901605 1.22187509 1.33067651 2.1634638 #> Pde1a         2.60443179 2.51600334 3.10065238 2.33133041 2.97094728 2.2677380 #> Tafa1         1.43448588 1.38764327 1.53188164 0.93793749 0.83074187 1.2099745 #> Ddn           4.74116866 5.10769279 4.80497790 4.76725155 4.88958648 5.7241280 #> Hopx          2.84716359 2.93676383 2.80524269 2.57688789 3.64036484 2.4846092 #> Ptk2b         4.25083755 4.58330163 4.44088016 4.56974541 4.09386716 3.4133443 #> Rgs3          1.48949093 1.63216949 1.50739170 1.75153065 1.47722520 1.1313837 #> Kcng2         0.81096094 0.99894463 0.76329563 0.97884792 0.37033260 0.9943758 #> Ntng1         1.66959193 1.52111510 1.55641161 1.78292903 1.47126781 1.4775886 #> H2-Q7         0.07293258 0.07103938 0.11838827 0.19723209 0.14273118 0.0000000 #> Ifitm2        0.96906880 1.09064416 0.90269673 0.95391429 1.21353976 1.4021251 #> Plaat3        2.50487243 2.51184225 2.66509723 2.22563314 3.00090855 2.8468772 #> Plekhh1       1.74894875 1.68160253 1.50615974 1.50661273 1.58905469 1.2009855 #> Myl4          1.18020420 1.28964125 1.57277445 0.96930487 1.49492177 0.9777995 #> H2-K1         1.33428078 1.59535735 1.74512473 1.78442778 2.14500032 1.5905231 #> Dpp6          3.17192427 3.06393903 3.25492974 3.23346631 2.74675531 3.3143334 #> Tmem91        0.91325311 1.01976509 0.90439258 0.71761435 0.98623491 0.6407260 #> Cyp2d22       1.12801427 1.03854008 1.18972937 1.23368207 1.79398667 0.3935818 #> Ttr           6.19462776 6.26366576 6.08356036 6.07872249 6.84390319 5.7097158 #> Suclg2        0.71876825 1.05265778 0.79135694 0.56916264 0.62196847 1.2940937 #> Patj          0.94550036 0.73674309 0.75330778 0.87271454 0.90792393 1.0548719 #> Btbd3         3.23569186 3.66107529 3.30479961 3.62928422 2.70333505 4.1914698 #> Unc13c        1.12647624 0.85563289 0.83457482 0.82026022 0.60663106 1.3103061 #> Syt9          0.73252808 0.66269409 0.74731851 0.70257922 0.30197116 0.9660008 #> Shisal1       1.63781235 1.58658496 1.63079867 1.72592166 1.27391482 1.8356435 #> Grm4          0.82379382 0.55970502 0.91102293 0.77318015 0.76956595 0.9669871 #> Sox11         0.72569496 0.98116963 0.90692982 0.91801201 0.78341938 1.3880737 #> Slc22a8       0.62010027 0.65232266 0.44280445 0.57180855 0.71534210 0.7740998 #> Slc24a3       3.34455169 3.06058189 3.38792495 3.35547202 2.89063604 2.6629890 #> Klk8          1.14965101 1.48560121 1.13405184 1.37458564 1.32795052 1.4736128 #> Ipcef1        1.55486089 1.28809917 1.90560329 1.18308943 1.57157324 2.0242319 #> Tnnt1         1.85088086 1.54993758 1.34763068 1.57888624 0.78988791 1.3366398 #> Hhip          0.30280717 0.48120264 0.35418673 0.58559193 0.56028980 0.2666210 #> Spag8         0.07313899 0.11994541 0.07826858 0.07973453 0.24626610 0.0000000 #> Fxyd6         2.76320510 2.76118346 2.82867431 2.47509575 3.00110702 1.6754807 #> Ppp1r3c       1.24356108 1.19575277 1.30680502 1.07985846 0.81875439 0.2666210 #> Cbln4         0.65457753 0.56382202 0.54803959 0.66918493 0.58515336 0.3758855 #> Nnat          4.39845107 3.86182696 4.01859780 4.37346434 4.21748417 4.5339505 #> Myl9          1.26493377 1.38354292 1.03635801 1.13510805 1.44268258 0.6635751 #> Vxn           3.53117569 3.31903989 3.47201305 3.21175235 3.32323417 3.4741524 #> Lgals1        1.43037952 1.64432200 1.67221114 1.58771425 1.82899585 0.3436696 #> Gpr88         0.93007302 0.57660156 0.74518927 0.68161931 0.74959412 0.0000000 #> Ctxn3         0.36793834 0.44103903 0.31762107 0.54951397 0.33353101 0.0000000 #> Lyz2          0.64063495 0.29592774 0.40658358 0.50297824 0.68417195 0.3474831 #> Tmem100       0.72780347 0.76122785 0.83235817 0.73586833 0.72919557 0.8543052 #> Wfdc17        0.03592151 0.03125994 0.10073253 0.10269814 0.25262848 0.0000000 #> Ahnak         0.87442210 0.76469206 0.79734451 0.91531682 1.40794558 0.7167474 #> Hba-a2        6.31671961 6.30178206 6.17605155 6.06596014 6.26167421 6.2308667 #> Hba-a1        6.77230847 6.68048781 6.62388866 6.48718732 6.78048518 6.7279361 #> Ccdc153       0.36423938 0.18890700 0.24146879 0.32301029 0.36814199 0.0000000 #> Ccnd1         1.49172433 1.43781973 1.87903187 1.67180559 1.71349654 1.6711655 #> Serpinh1      0.77813139 1.16936908 0.77033088 0.75731999 0.68906297 0.2824807 #> Gad1          3.11135615 2.86412058 3.21870359 3.36647334 2.93370810 2.2695200 #> Arhgef10      1.30399703 1.11347707 1.43731120 1.03112802 0.99866752 1.5000659 #> 2410004P03Rik 0.14404681 0.17406545 0.08321509 0.08717661 0.17331548 0.0000000 #> Nt5dc2        0.71051009 0.77568089 0.64458904 0.80447504 0.71280335 1.2502371 #> Cebpd         0.91772180 1.20032716 0.86517644 0.93989122 1.13127334 1.5196409 #> Sod3          0.71522440 0.61108203 0.37187077 0.72537202 0.70488595 0.7834772 #> H2-D1         2.26112351 2.59192070 2.24441472 2.23564957 2.31971537 2.4143860 #> C4b           1.20912580 1.07666214 1.08784349 0.97983734 1.23896846 0.6141041 #> Tmem88b       3.07189636 2.53557020 2.75820730 2.74813759 2.36238987 1.9045927 #> Hbb-bt        5.73427869 5.85482772 5.61558173 5.57224388 5.69711546 6.0253158 #> Rhog          2.06081008 2.00638986 2.06360270 2.08136653 1.95855083 1.2839779 #> Rprm          1.75743433 1.72853508 1.58142372 1.53667923 1.82211970 1.8632513 #> Ly6a          2.45182370 2.27519555 2.34222985 2.60751217 2.75894028 2.0413342 #> Mog           3.85434500 3.66219244 3.74512123 3.72785284 4.14058242 2.8615374 #> Trbc2         1.20583296 1.28703415 1.50146442 1.22354779 1.38336445 0.6090279 #> Igkc          0.13555940 0.24448284 0.20547536 0.14835237 0.10338205 0.2504086 #> Smim1         1.09552768 0.96792008 1.05119351 1.16738202 1.91408576 1.7977655 #> Hs3st4        2.39012844 2.20126636 2.49203687 2.68146833 2.47900039 2.7906412 #> Evi2a         2.06586106 2.00947394 1.94122254 1.99571269 2.67085999 1.9128370 #> Prkcg         4.14188600 4.17863055 4.46934041 4.14347947 3.94561260 4.3279904 #> Ly6c1         2.47782910 2.71577070 2.59802701 2.53117760 2.70659596 2.7301925 #> Gbp4          0.14737745 0.05765225 0.07565243 0.32623728 0.05709014 0.2666210 #> Wipf3         2.55544936 2.96123354 2.99511897 3.11271141 2.75874347 3.3429219 #> BC039966      0.08464373 0.07695937 0.13722385 0.10447754 0.34869164 0.0000000 #> Gm13889       1.46735997 1.54319311 1.51447377 1.42448664 1.08310793 0.7766758 #> Plcxd2        1.64210575 1.30250470 1.60803209 1.32447479 0.56780985 0.4196490 #> Mia           0.26367437 0.31952226 0.25723706 0.29690062 0.26626194 0.0000000 #> Pou3f1        1.86305306 2.03310718 1.83260238 1.72681881 1.72651282 3.0430671 #> Lrrc10b       1.20742881 1.61461967 1.26439875 1.45805132 1.47514670 1.9429702 #> Apol11b       0.35929836 0.24092320 0.20236074 0.27629799 0.17705447 0.2564135 #> Gpr62         1.17578799 1.10082468 1.17761935 1.16650569 1.15881284 0.6983290 #> Shisa8        0.41727316 0.26971254 0.31966186 0.31993890 0.47023109 0.8756489 #> Gm2115        0.82234763 1.22818773 1.03188783 1.23356153 1.12760221 1.2121439 #> Kctd12        2.20413606 2.03580757 2.30484518 2.27816759 2.13535177 2.3238084 #> 1700047M11Rik 0.95685380 0.88367167 0.76632284 0.86813679 0.55009271 0.8187913 #> Lhfpl3        1.20532422 1.39255353 1.12989133 1.16122852 0.66136299 1.4522671 #> C030029H02Rik 0.37708569 0.39173442 0.28273725 0.26811175 0.29861244 0.3741050 #> Gm19935       0.35745016 0.29221866 0.23263621 0.21978974 0.42931808 0.0000000 #> 9630013A20Rik 0.17597264 0.29575033 0.28874834 0.26833691 0.09952757 0.0000000 #> 2900040C04Rik 0.32757163 0.28457067 0.32113707 0.17356740 0.32761432 0.0000000 #>                cluster_4 #> Gna12         2.60609824 #> Ccnd2         1.75449691 #> Btbd17        1.20395106 #> Sox9          1.65161246 #> Sez6          3.40864347 #> Serpinf1      0.61207785 #> S100a6        1.92737468 #> Col1a1        0.16085927 #> Vwf           0.77167716 #> Esam          0.85819635 #> Npas1         0.61792941 #> Tiam1         2.08517521 #> Bcam          0.78622815 #> Hmgn2         1.82635952 #> Rab3b         1.46259667 #> Inmt          0.12421173 #> Ddr1          1.94713727 #> Homer3        1.57341038 #> Cp            0.28275109 #> Calb2         1.44793211 #> Man1a         1.23827535 #> Efnb3         2.65042930 #> Hlf           3.09046018 #> Gstm7         1.46685037 #> Cavin1        0.70230817 #> Sst           3.66156380 #> Hapln2        0.76712800 #> Hspb1         0.66489715 #> Ndrg1         2.73408497 #> Nid1          0.04243022 #> Kit           0.77771411 #> Pvalb         3.09893154 #> Tmbim1        1.79891682 #> Crip1         1.57047760 #> Tek           0.62410035 #> Elovl1        1.46954470 #> Cyba          1.07571205 #> Itih3         0.95701386 #> Cnp           5.39410872 #> Hap1          1.61910843 #> Clic1         0.51866093 #> Stx1a         2.57695025 #> Arpp19        4.54109612 #> Dio2          0.79573740 #> Id3           2.79703382 #> Crlf1         1.15496768 #> Ttc9b         4.45687988 #> Carhsp1       1.57075592 #> Cabp7         2.48792771 #> Fam163b       2.60011746 #> Rarres2       0.60835906 #> Syn2          4.69831340 #> Ick           0.92748210 #> Prox1         1.02388754 #> Adssl1        0.83671153 #> Vipr2         0.32945893 #> Gltp          1.76140268 #> Amotl1        1.47332766 #> Bcas1         2.79866172 #> Aldh1a2       0.06307203 #> Tppp3         2.18130652 #> Sirt2         4.27459459 #> Lpl           1.07121408 #> Cers2         2.43882985 #> Qdpr          4.73326809 #> Stk32c        2.22177632 #> Lbp           0.19627608 #> Hsd11b1       1.52920468 #> Vtn           2.53775487 #> Stac2         1.29603399 #> Plxdc1        1.00394069 #> Igfbp4        2.18737537 #> Dbndd2        2.03506595 #> Pltp          2.01247707 #> Slc12a4       0.85628245 #> Cadps2        1.81067037 #> Erbb3         0.51423124 #> Pmp22         1.22235809 #> Kcnab3        1.11418182 #> Myh11         0.14259988 #> Plod1         1.01513955 #> Etnppl        0.77888619 #> Arhgef25      3.50954343 #> Rcn3          0.75698657 #> Vip           0.61427950 #> Utrn          1.01510328 #> Grm1          1.93235928 #> Reep3         1.57246606 #> Fabp7         1.74874429 #> Dcn           0.43218827 #> Slc17a8       0.11292223 #> Dusp6         1.53022592 #> Kitl          1.58339868 #> Ccn2          0.56396116 #> Timp3         2.12169068 #> Ascl1         0.42467991 #> Unc5b         0.88591120 #> Vsir          0.62922846 #> Gamt          1.93081585 #> Ptprb         0.95638887 #> Csrp2         0.61034920 #> Adarb1        3.34622701 #> Rnf130        1.79891419 #> Nefh          1.89682064 #> Aebp1         0.30265744 #> Sept4         4.18425152 #> Gria1         4.44084827 #> Sypl          2.28179773 #> Arsg          0.85763161 #> Cacng4        1.43833695 #> Rab37         0.52556290 #> Itgb4         0.52681245 #> Aspa          1.43052716 #> Cygb          2.20674896 #> Rflnb         0.86553427 #> Doc2b         0.59824740 #> Gfap          2.78027907 #> Npas3         0.82203709 #> Serpina3n     1.34144027 #> Clmn          2.33553604 #> Prkch         0.49976063 #> Fbln5         0.43630675 #> Akr1c18       0.10277605 #> Gng4          1.09385812 #> Sema4d        1.68305206 #> Cxcl14        3.03239260 #> Hexb          3.27353577 #> Iqgap2        1.20430675 #> Crhbp         0.49109958 #> Rab3c         3.27239312 #> Thbs4         0.61252956 #> Serinc5       1.99901133 #> Erbin         1.98244265 #> Prkcd         2.14637020 #> Pdlim2        2.33042211 #> Ednrb         1.59033225 #> Cpne6         3.56585260 #> Sema5a        1.87068636 #> Matn2         1.35789783 #> Nptxr         4.61099196 #> Enpp2         4.51135587 #> Efcab6        0.43987268 #> Ppp1r1a       4.59851094 #> Litaf         1.79792102 #> Il1rap        1.40773267 #> Apod          4.62594045 #> Cpox          1.27439556 #> Grik1         0.52200308 #> Clic6         0.42591897 #> Nr4a1         0.85403244 #> Igfbp6        1.55487402 #> Sncg          0.39717035 #> Gzma          0.01537066 #> Grm2          1.19803763 #> Prph          0.26203379 #> Rsph1         0.26057185 #> Sox8          1.07632871 #> Fam234a       0.93518603 #> Lims2         0.98938857 #> Aqp4          2.39931394 #> Slc12a2       2.10404227 #> Cd74          0.10955569 #> Pdgfrb        0.56980162 #> Csf1r         2.53418697 #> Cbln2         0.53026081 #> Frmd8         1.45107637 #> Gldc          0.81997077 #> Tcf7l2        1.78881915 #> Bhlhe22       1.69768308 #> Kcnip2        2.85003650 #> Alas2         0.98245807 #> Gdf11         0.85765670 #> Baiap2        3.57025234 #> Ifitm3        1.65475491 #> Phkg1         0.95307076 #> Nptx1         3.83192513 #> Pde8a         0.48703240 #> Itih5         1.08149119 #> Homer2        2.19581914 #> Fam20c        1.76695203 #> Cplx2         5.27754568 #> Myo5b         1.38504287 #> Snca          4.82591434 #> Col3a1        0.13151465 #> Ecrg4         0.59745978 #> Map4k4        2.08664581 #> 2010300C02Rik 3.16523944 #> Ogfrl1        4.14079304 #> Fn1           1.07906684 #> Efhd1         1.06229685 #> Ngef          2.75647904 #> Bok           2.78164079 #> Tmem163       1.34780537 #> Lct           0.85846186 #> Cfh           0.71937055 #> Ptpn4         3.05481348 #> Tnni1         0.63957991 #> Csrp1         4.62308151 #> Nfasc         3.34781941 #> Syt2          0.45448942 #> Atp2b4        1.76384060 #> Rgs16         0.82849384 #> Ncf2          0.09961637 #> Cnih3         1.78926516 #> Tmem63a       1.60914217 #> Cfap126       0.21236296 #> Meig1         0.43572822 #> Ccdc3         0.53051383 #> Rgs5          2.22307367 #> Enkur         0.16460524 #> Myoc          0.35233935 #> Vim           1.55448093 #> Prkcq         0.53553084 #> Gad2          2.50678278 #> Lcn2          0.12253289 #> Nr4a2         0.95915164 #> Ermn          2.25647105 #> Fibcd1        1.39882457 #> Gsn           3.05493280 #> Grb14         2.61113828 #> Notch1        0.58981274 #> Ube2l6        0.73267755 #> Gatm          3.15793713 #> Cd82          1.39403665 #> Mdk           1.53376080 #> Lamp5         1.81610150 #> Itpka         3.73740983 #> Chgb          4.89580590 #> Mal           5.04683942 #> Pdyn          0.83021815 #> Nkx2-2        0.38872638 #> Edn3          0.10673408 #> Car2          4.83859775 #> Col9a3        0.93330550 #> Chrna4        1.63380471 #> Gss           1.63093165 #> Slc7a11       0.85798499 #> Tm4sf1        0.89917395 #> Kcnab1        3.04226008 #> Shox2         0.74921670 #> Serpini1      2.94974436 #> Tspan2        3.66338603 #> S100a11       0.55417837 #> Vcam1         0.90587290 #> Lef1          0.82801917 #> Npy2r         1.04472256 #> F3            1.34499351 #> Calb1         3.10570843 #> Epha7         2.52694235 #> Slc44a1       2.59962787 #> 1110017D15Rik 0.25822164 #> Tpm2          0.37449563 #> Slc6a9        1.73057613 #> Laptm5        1.38439411 #> Sema3c        0.66432371 #> Hpca          5.92641822 #> Padi2         0.79418108 #> Slc4a2        1.22137346 #> Gabrd         2.14254530 #> Rgs12         1.37988885 #> Slc30a3       1.95904506 #> Emilin1       0.27462874 #> 1700001C02Rik 0.08247050 #> Gabra4        2.73396239 #> Pdgfra        0.91472515 #> Epha5         2.46494758 #> Tesc          2.63279774 #> Pitpnm2       2.26748973 #> Mmp17         2.76300035 #> Cit           2.09743659 #> Foxp2         1.05428719 #> Arpc1b        1.56174316 #> Col1a2        0.27025654 #> Eln           0.23647582 #> Pcolce        0.29688338 #> Tsc22d4       4.38214380 #> Cald1         1.05283005 #> Ccdc136       3.18618838 #> Npy           2.51459626 #> Slc13a4       0.11711368 #> Gkn3          0.32377812 #> Slc6a13       0.34682235 #> Mgp           1.36713519 #> Lmo3          2.63058172 #> Slco1c1       1.79393540 #> Cpne9         1.15978487 #> Itpr2         0.70815555 #> Slc6a11       2.31871251 #> Vamp1         2.87882461 #> Cd9           2.77532732 #> Pglyrp1       0.83805061 #> Slc17a6       1.74404575 #> Sipa1l3       1.97744447 #> Sh3gl3        2.10938506 #> Plekhb1       5.03052367 #> Nupr1         0.35617664 #> Dkk3          3.32926588 #> Cox6a2        1.13090877 #> Dkkl1         0.54054309 #> Fgfr2         1.71329354 #> Crym          2.53876400 #> Slc38a5       0.52886519 #> Flna          0.96571296 #> Bgn           0.35033806 #> Col4a1        1.08994227 #> Plat          1.16879670 #> Nr3c2         1.81639594 #> Cbln1         0.64719536 #> Gab1          1.46719706 #> Pllp          2.83929320 #> Necab2        2.37856283 #> Dbndd1        1.20736269 #> Agt           2.30986060 #> Cryab         4.66577168 #> Tagln         0.42281179 #> Mcam          1.09629339 #> Olfm2         2.26084825 #> Icam5         3.07895079 #> Anxa2         0.38974761 #> Rora          2.58959747 #> Calml4        0.13459022 #> Htr3a         0.44621075 #> Paqr5         0.26346143 #> Rasgrf1       4.38499536 #> Zic1          1.45860493 #> Mobp          6.10458192 #> Hhatl         0.81980020 #> Trf           4.77173848 #> Cpne4         2.20413776 #> Cdhr4         0.06342928 #> Cd59a         1.43861027 #> Gng11         2.19151279 #> Chrm1         2.95772818 #> Prr5l         0.60336929 #> Ugt8a         2.00153051 #> Rims3         2.55188402 #> Sgpp2         0.57907461 #> Camkv         4.70088986 #> Sox10         1.65921654 #> Micall1       1.19040089 #> Tie1          0.30998037 #> Fa2h          2.11498241 #> Ucp2          0.83585966 #> Vav3          0.62844713 #> Ccp110        2.09204511 #> Gria2         4.68558326 #> Rasl10a       1.80985928 #> Foxj1         0.22307537 #> Trim59        0.99786278 #> Dynlrb2       0.07137860 #> Gjc1          0.34064045 #> Neurod1       0.84668834 #> Ttyh2         1.58859307 #> Cpne7         1.93052451 #> Nrip3         2.77075058 #> Tbr1          1.78988837 #> Lcat          1.41763369 #> Tmem98        0.56123415 #> Myo1d         0.66978023 #> Prdm8         1.25861063 #> Tgfbi         0.09177186 #> Kcnc2         2.67091282 #> Thrsp         2.06264951 #> Isg15         0.68267050 #> Acta2         0.53759005 #> H2-Q4         0.04403270 #> Dock4         2.45605205 #> Myrf          1.21563347 #> Lmo1          2.14353738 #> Igfbp7        2.07693868 #> P2ry12        1.54083467 #> Pcdh8         1.79334980 #> Lgi4          1.04604672 #> Fxyd1         3.12197726 #> Fxyd7         4.06784836 #> Mag           4.67393619 #> Zcchc12       1.52071335 #> Anln          0.68573737 #> Wnt4          0.90331411 #> C1ql2         1.16794137 #> Unc93b1       0.81959434 #> Tspan15       1.26549944 #> Ppp1r14a      2.58835889 #> Clic4         2.12422161 #> Galnt6        0.30211407 #> Ccn3          1.54742610 #> Rims2         2.28915772 #> Zmat4         1.49254831 #> Cldn11        4.78456149 #> Ccdc33        0.07363270 #> Slc32a1       1.83410423 #> Tgm2          0.40593632 #> Vstm2l        2.75978563 #> Neurod6       2.82060410 #> Crygn         0.09798658 #> Enpp6         0.58768814 #> Neurod2       2.71342401 #> Satb2         0.79402893 #> Pcp4l1        2.57535473 #> Txnip         0.68700917 #> Egr1          2.50492310 #> Otud7b        1.59728173 #> Car14         1.08944666 #> Rgs4          3.33547592 #> Dock10        1.73507733 #> Lpar1         1.60370465 #> Trps1         0.78861445 #> Ptpn3         2.00909251 #> Lefty1        0.81134858 #> Zfhx3         1.09077552 #> St6galnac5    2.56250778 #> Ak5           3.13566196 #> Hrh3          1.86482080 #> Nexn          0.48396001 #> Adgrl4        1.00117125 #> Rlbp1         0.99467230 #> Igfbp2        1.39985479 #> Wfs1          2.73229161 #> Cplx3         0.50906013 #> Orai2         2.26748066 #> Olig2         1.08102009 #> Gpr37         2.62296320 #> Plcb4         2.11957165 #> Nxph4         0.16686809 #> Ndufa4l2      0.68493998 #> Cacng5        0.73174308 #> Plekhg1       1.30868528 #> Cmtm5         3.15469470 #> Gpr161        0.70486753 #> Rfx3          1.26658762 #> Igsf21        1.76647020 #> Ramp3         1.81952795 #> Arhgap12      1.51450516 #> Nkx6-2        1.37399409 #> Ninj2         0.49197601 #> Cldn5         2.20681530 #> Htr2c         0.89371813 #> Hspb8         0.63868671 #> Fmod          0.04236641 #> Prelp         0.65903079 #> Mpped1        2.39482943 #> Rapgef5       2.40123292 #> Vwa1          1.17900956 #> Stab1         0.41544093 #> Arl15         1.13171031 #> Reln          0.89969889 #> Mustn1        0.05434083 #> Pbxip1        1.45561696 #> Dnali1        0.08601687 #> Id1           1.51472412 #> Lrrtm3        1.11618629 #> Tmem212       0.15113993 #> Epop          1.81153342 #> Gjc2          1.29166595 #> 1190005I06Rik 1.04935507 #> Ctla2a        1.32362644 #> Cnr1          2.12160609 #> Gpr4          0.48872287 #> Sowaha        2.97280378 #> Tent5c        0.25759204 #> Serpinb1a     0.95503066 #> S1pr5         0.68336274 #> Penk          1.45336436 #> Cdc42ep2      1.28679455 #> Slitrk6       0.18711931 #> Hpcal4        4.76118084 #> Olig1         4.10287912 #> Rprml         3.49550568 #> Stxbp6        1.80627634 #> Hs3st2        0.83422411 #> Rbp1          1.30611288 #> Ppm1e         3.21338301 #> Sox18         0.68029097 #> Kctd4         1.38510172 #> Nxph3         0.54103846 #> Vat1l         0.74698880 #> Cd24a         0.40742449 #> Odf3b         0.11363113 #> Gjb1          1.30976978 #> Selplg        1.18755362 #> Bcl11b        2.09150675 #> Lhfp          1.57670266 #> Ranbp3l       0.11161922 #> Msx1          0.15696548 #> Zdhhc22       1.49991394 #> Phldb1        2.21834915 #> Ctxn1         4.74797145 #> Tprn          0.99384427 #> Vstm2a        2.31470010 #> Ndnf          0.54665309 #> Pdp1          3.07130792 #> Scn3b         2.98404777 #> Cdc42ep1      0.92909667 #> Gal3st1       1.13100658 #> Rasd1         1.67572621 #> Spink8        1.68685087 #> Opalin        2.79718795 #> Gja4          0.18769692 #> Synpo2        1.01374359 #> Pcdh20        1.45659664 #> Adra1b        0.93910023 #> Fam131a       3.82104523 #> Tmem125       0.81514353 #> Mb21d2        1.76973253 #> Lingo3        0.92482011 #> Ncald         4.46018666 #> Siglech       0.87621547 #> Rgs14         1.48359693 #> Gm14964       0.23881197 #> Gpr17         0.73653293 #> Cx3cr1        0.95719342 #> Ezr           1.61193468 #> Adarb2        0.49534891 #> Cpne8         0.72932689 #> Plekhg3       0.58116792 #> Lamb2         0.91230505 #> Creb5         0.34033447 #> Cntn2         1.59843273 #> Aldh1a1       2.13762657 #> Phgdh         3.40225383 #> Tnfaip6       1.11901813 #> Camk2d        1.69034013 #> Shisa6        1.88370870 #> Cthrc1        0.86122853 #> Tmem119       0.96813052 #> Hmgb2         0.75379922 #> Tmem158       2.33485916 #> Dsp           0.56496508 #> Lrtm2         1.70069660 #> Gabra5        2.35473191 #> Tns1          0.68278002 #> Nell1         1.98912213 #> Slain1        2.70259995 #> Prr18         1.92474592 #> S100a8        0.35740871 #> S100a9        0.44543463 #> Col8a2        0.18741821 #> Synpr         2.65502986 #> Sertm1        1.18622154 #> Adgrf5        1.03373000 #> Capg          0.21266618 #> Gjc3          1.77287650 #> Fcer1g        1.07990094 #> Pde1a         2.36702109 #> Tafa1         1.26002983 #> Ddn           4.90921841 #> Hopx          2.98504911 #> Ptk2b         4.41025426 #> Rgs3          1.29883300 #> Kcng2         0.97869316 #> Ntng1         1.71046729 #> H2-Q7         0.09426609 #> Ifitm2        1.19277954 #> Plaat3        2.39613452 #> Plekhh1       1.42694370 #> Myl4          0.98021372 #> H2-K1         2.01438048 #> Dpp6          3.32538357 #> Tmem91        1.03303378 #> Cyp2d22       1.30268039 #> Ttr           6.25632335 #> Suclg2        0.47537351 #> Patj          0.59129471 #> Btbd3         3.54003655 #> Unc13c        0.76560805 #> Syt9          0.73367694 #> Shisal1       1.50139458 #> Grm4          0.67044200 #> Sox11         0.94133413 #> Slc22a8       0.74498851 #> Slc24a3       3.24439184 #> Klk8          1.46881306 #> Ipcef1        1.28184953 #> Tnnt1         1.17970564 #> Hhip          0.38943212 #> Spag8         0.05630185 #> Fxyd6         2.51761650 #> Ppp1r3c       1.32238705 #> Cbln4         0.72890041 #> Nnat          4.37366824 #> Myl9          1.25803289 #> Vxn           3.31594192 #> Lgals1        1.50991492 #> Gpr88         0.57929201 #> Ctxn3         0.39628055 #> Lyz2          0.46364032 #> Tmem100       0.65813793 #> Wfdc17        0.12579889 #> Ahnak         0.91869843 #> Hba-a2        5.95260496 #> Hba-a1        6.42665658 #> Ccdc153       0.15608004 #> Ccnd1         1.45258705 #> Serpinh1      0.88895100 #> Gad1          3.20243518 #> Arhgef10      1.14429536 #> 2410004P03Rik 0.17949586 #> Nt5dc2        1.11648381 #> Cebpd         1.09991152 #> Sod3          0.77167033 #> H2-D1         2.08413405 #> C4b           0.92330880 #> Tmem88b       2.17385844 #> Hbb-bt        5.36616636 #> Rhog          1.83048241 #> Rprm          1.73507034 #> Ly6a          2.50538847 #> Mog           3.46300407 #> Trbc2         1.23305101 #> Igkc          0.08856211 #> Smim1         1.01101079 #> Hs3st4        2.55684519 #> Evi2a         2.17418067 #> Prkcg         4.29179503 #> Ly6c1         2.71720127 #> Gbp4          0.11760288 #> Wipf3         3.44832475 #> BC039966      0.05227336 #> Gm13889       1.59952540 #> Plcxd2        1.35893527 #> Mia           0.17050296 #> Pou3f1        1.50999422 #> Lrrc10b       1.53819465 #> Apol11b       0.32937402 #> Gpr62         1.13247697 #> Shisa8        0.27554714 #> Gm2115        1.40123238 #> Kctd12        2.25485833 #> 1700047M11Rik 0.64729410 #> Lhfpl3        1.24297124 #> C030029H02Rik 0.34659023 #> Gm19935       0.24955801 #> 9630013A20Rik 0.33023852 #> 2900040C04Rik 0.32603957"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":null,"dir":"Reference","previous_headings":"","what":"create_average_detection_DT — create_average_detection_DT","title":"create_average_detection_DT — create_average_detection_DT","text":"calculates average gene detection cell metadata factor (e.g. cluster)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_average_detection_DT — create_average_detection_DT","text":"","code":"create_average_detection_DT(   gobject,   feat_type = NULL,   spat_unit = NULL,   meta_data_name,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   detection_threshold = 0 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"create_average_detection_DT — create_average_detection_DT","text":"gobject giotto object feat_type feature type spat_unit spatial unit meta_data_name name metadata column use expression_values expression values use detection_threshold detection threshold consider gene detected","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_average_detection_DT — create_average_detection_DT","text":"data.table average gene epression values factor","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_average_detection_DT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"create_average_detection_DT — create_average_detection_DT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  create_average_detection_DT(g, meta_data_name = \"leiden_clus\") #>                cluster_2  cluster_5  cluster_1   cluster_3  cluster_6 cluster_7 #> Gna12         0.83606557 0.83333333 0.82716049 0.787037037 0.80000000       0.8 #> Ccnd2         0.57377049 0.59523810 0.61728395 0.564814815 0.51111111       0.7 #> Btbd17        0.41803279 0.41666667 0.40123457 0.416666667 0.35555556       0.3 #> Sox9          0.47540984 0.52380952 0.52469136 0.388888889 0.57777778       0.3 #> Sez6          0.81147541 0.78571429 0.85802469 0.787037037 0.71111111       0.8 #> Serpinf1      0.16393443 0.21428571 0.13580247 0.166666667 0.08888889       0.1 #> S100a6        0.67213115 0.66666667 0.66666667 0.583333333 0.64444444       0.6 #> Col1a1        0.07377049 0.03571429 0.03703704 0.083333333 0.04444444       0.1 #> Vwf           0.23770492 0.33333333 0.27777778 0.268518519 0.31111111       0.2 #> Esam          0.28688525 0.26190476 0.34567901 0.361111111 0.35555556       0.3 #> Npas1         0.11475410 0.16666667 0.16049383 0.203703704 0.11111111       0.2 #> Tiam1         0.58196721 0.52380952 0.49382716 0.555555556 0.40000000       0.4 #> Bcam          0.19672131 0.16666667 0.14814815 0.305555556 0.28888889       0.1 #> Hmgn2         0.59016393 0.59523810 0.59259259 0.500000000 0.55555556       0.6 #> Rab3b         0.50819672 0.48809524 0.47530864 0.416666667 0.40000000       0.5 #> Inmt          0.04918033 0.01190476 0.03703704 0.018518519 0.00000000       0.0 #> Ddr1          0.63934426 0.60714286 0.62962963 0.592592593 0.60000000       0.3 #> Homer3        0.42622951 0.35714286 0.34567901 0.296296296 0.22222222       0.6 #> Cp            0.08196721 0.13095238 0.08024691 0.083333333 0.00000000       0.1 #> Calb2         0.40163934 0.39285714 0.31481481 0.379629630 0.24444444       0.5 #> Man1a         0.36885246 0.39285714 0.37654321 0.351851852 0.28888889       0.7 #> Efnb3         0.75409836 0.77380952 0.67901235 0.703703704 0.80000000       0.7 #> Hlf           0.82786885 0.78571429 0.81481481 0.750000000 0.77777778       0.8 #> Gstm7         0.48360656 0.41666667 0.38888889 0.388888889 0.40000000       0.5 #> Cavin1        0.25409836 0.25000000 0.26543210 0.231481481 0.17777778       0.2 #> Sst           0.79508197 0.79761905 0.87037037 0.814814815 0.86666667       0.8 #> Hapln2        0.31967213 0.21428571 0.24691358 0.250000000 0.28888889       0.3 #> Hspb1         0.16393443 0.21428571 0.20370370 0.157407407 0.20000000       0.0 #> Ndrg1         0.77049180 0.67857143 0.74691358 0.768518519 0.77777778       0.4 #> Nid1          0.07377049 0.05952381 0.06790123 0.064814815 0.17777778       0.0 #> Kit           0.17213115 0.16666667 0.27160494 0.259259259 0.24444444       0.2 #> Pvalb         0.77049180 0.77380952 0.77777778 0.731481481 0.77777778       0.7 #> Tmbim1        0.68852459 0.60714286 0.56790123 0.555555556 0.51111111       0.3 #> Crip1         0.43442623 0.36904762 0.43209877 0.333333333 0.37777778       0.4 #> Tek           0.21311475 0.10714286 0.17901235 0.101851852 0.17777778       0.2 #> Elovl1        0.56557377 0.52380952 0.44444444 0.398148148 0.44444444       0.4 #> Cyba          0.33606557 0.39285714 0.28395062 0.388888889 0.17777778       0.3 #> Itih3         0.38524590 0.41666667 0.38888889 0.453703704 0.31111111       0.3 #> Cnp           0.99180328 0.98809524 0.98148148 0.981481481 1.00000000       0.9 #> Hap1          0.50000000 0.48809524 0.38888889 0.398148148 0.26666667       0.6 #> Clic1         0.35245902 0.21428571 0.20987654 0.250000000 0.17777778       0.2 #> Stx1a         0.58196721 0.63095238 0.65432099 0.611111111 0.57777778       0.6 #> Arpp19        0.90983607 0.89285714 0.96913580 0.851851852 0.95555556       0.9 #> Dio2          0.31147541 0.32142857 0.32098765 0.240740741 0.31111111       0.1 #> Id3           0.77868852 0.79761905 0.72222222 0.731481481 0.75555556       0.7 #> Crlf1         0.19672131 0.26190476 0.20987654 0.203703704 0.17777778       0.3 #> Ttc9b         0.88524590 0.94047619 0.89506173 0.814814815 0.86666667       0.9 #> Carhsp1       0.74590164 0.63095238 0.59259259 0.638888889 0.60000000       0.5 #> Cabp7         0.53278689 0.59523810 0.57407407 0.601851852 0.73333333       0.5 #> Fam163b       0.61475410 0.65476190 0.62345679 0.518518519 0.53333333       0.5 #> Rarres2       0.37704918 0.25000000 0.24074074 0.296296296 0.35555556       0.3 #> Syn2          0.92622951 0.92857143 0.90740741 0.907407407 0.95555556       0.9 #> Ick           0.42622951 0.41666667 0.45061728 0.333333333 0.33333333       0.3 #> Prox1         0.34426230 0.41666667 0.27777778 0.398148148 0.31111111       0.3 #> Adssl1        0.40983607 0.42857143 0.37037037 0.351851852 0.42222222       0.3 #> Vipr2         0.12295082 0.11904762 0.11111111 0.138888889 0.06666667       0.2 #> Gltp          0.63934426 0.54761905 0.59259259 0.481481481 0.60000000       0.6 #> Amotl1        0.40983607 0.40476190 0.45679012 0.462962963 0.44444444       0.4 #> Bcas1         0.85245902 0.76190476 0.80246914 0.805555556 0.73333333       0.7 #> Aldh1a2       0.04918033 0.02380952 0.03703704 0.111111111 0.00000000       0.1 #> Tppp3         0.70491803 0.58333333 0.62345679 0.611111111 0.60000000       0.6 #> Sirt2         0.95081967 0.95238095 0.95061728 0.953703704 0.91111111       0.9 #> Lpl           0.25409836 0.20238095 0.25308642 0.212962963 0.31111111       0.2 #> Cers2         0.64754098 0.70238095 0.64814815 0.611111111 0.62222222       0.8 #> Qdpr          0.95901639 0.88095238 0.93209877 0.953703704 0.97777778       1.0 #> Stk32c        0.66393443 0.61904762 0.62962963 0.592592593 0.55555556       0.3 #> Lbp           0.07377049 0.08333333 0.07407407 0.120370370 0.08888889       0.0 #> Hsd11b1       0.40163934 0.46428571 0.42592593 0.481481481 0.42222222       0.5 #> Vtn           0.70491803 0.72619048 0.69135802 0.611111111 0.66666667       0.5 #> Stac2         0.41803279 0.45238095 0.50000000 0.314814815 0.46666667       0.3 #> Plxdc1        0.38524590 0.45238095 0.41975309 0.425925926 0.28888889       0.3 #> Igfbp4        0.63934426 0.55952381 0.64814815 0.592592593 0.64444444       0.7 #> Dbndd2        0.70491803 0.65476190 0.65432099 0.648148148 0.64444444       0.8 #> Pltp          0.65573770 0.58333333 0.59259259 0.564814815 0.62222222       0.4 #> Slc12a4       0.33606557 0.26190476 0.32098765 0.194444444 0.31111111       0.3 #> Cadps2        0.49180328 0.48809524 0.45679012 0.453703704 0.42222222       0.4 #> Erbb3         0.15573770 0.14285714 0.14197531 0.175925926 0.22222222       0.3 #> Pmp22         0.47540984 0.47619048 0.40740741 0.435185185 0.33333333       0.4 #> Kcnab3        0.40163934 0.35714286 0.45679012 0.324074074 0.22222222       0.2 #> Myh11         0.05737705 0.08333333 0.06172840 0.083333333 0.04444444       0.2 #> Plod1         0.40163934 0.42857143 0.36419753 0.398148148 0.33333333       0.4 #> Etnppl        0.27049180 0.23809524 0.35802469 0.333333333 0.24444444       0.3 #> Arhgef25      0.78688525 0.72619048 0.80246914 0.787037037 0.71111111       0.7 #> Rcn3          0.16393443 0.09523810 0.22222222 0.194444444 0.08888889       0.1 #> Vip           0.25409836 0.23809524 0.22222222 0.222222222 0.15555556       0.2 #> Utrn          0.40163934 0.39285714 0.39506173 0.388888889 0.42222222       0.3 #> Grm1          0.49180328 0.42857143 0.47530864 0.592592593 0.44444444       0.4 #> Reep3         0.45901639 0.44047619 0.51234568 0.277777778 0.44444444       0.7 #> Fabp7         0.54098361 0.51190476 0.50617284 0.509259259 0.44444444       0.4 #> Dcn           0.13934426 0.11904762 0.11728395 0.120370370 0.08888889       0.2 #> Slc17a8       0.04918033 0.03571429 0.08024691 0.018518519 0.04444444       0.0 #> Dusp6         0.39344262 0.34523810 0.37037037 0.361111111 0.37777778       0.3 #> Kitl          0.43442623 0.47619048 0.46296296 0.370370370 0.28888889       0.3 #> Ccn2          0.19672131 0.30952381 0.27777778 0.166666667 0.33333333       0.1 #> Timp3         0.67213115 0.58333333 0.61111111 0.574074074 0.64444444       0.7 #> Ascl1         0.17213115 0.15476190 0.16666667 0.083333333 0.15555556       0.0 #> Unc5b         0.36065574 0.32142857 0.24074074 0.370370370 0.28888889       0.2 #> Vsir          0.36065574 0.28571429 0.29012346 0.268518519 0.40000000       0.1 #> Gamt          0.68852459 0.58333333 0.62345679 0.601851852 0.64444444       0.6 #> Ptprb         0.27049180 0.15476190 0.27160494 0.194444444 0.28888889       0.4 #> Csrp2         0.21311475 0.20238095 0.16666667 0.129629630 0.20000000       0.3 #> Adarb1        0.86065574 0.78571429 0.79629630 0.768518519 0.62222222       0.7 #> Rnf130        0.60655738 0.60714286 0.61111111 0.555555556 0.55555556       0.6 #> Nefh          0.59016393 0.58333333 0.57407407 0.620370370 0.48888889       0.8 #> Aebp1         0.15573770 0.11904762 0.15432099 0.111111111 0.11111111       0.0 #> Sept4         0.94262295 0.90476190 0.89506173 0.907407407 0.95555556       0.8 #> Gria1         0.89344262 0.92857143 0.92592593 0.898148148 0.88888889       0.8 #> Sypl          0.63114754 0.53571429 0.61728395 0.592592593 0.64444444       0.9 #> Arsg          0.41803279 0.42857143 0.33950617 0.333333333 0.46666667       0.1 #> Cacng4        0.46721311 0.41666667 0.51234568 0.472222222 0.31111111       0.3 #> Rab37         0.28688525 0.14285714 0.17901235 0.138888889 0.13333333       0.1 #> Itgb4         0.22950820 0.30952381 0.21604938 0.250000000 0.26666667       0.2 #> Aspa          0.54918033 0.44047619 0.46296296 0.500000000 0.44444444       0.7 #> Cygb          0.47540984 0.47619048 0.48148148 0.500000000 0.35555556       0.3 #> Rflnb         0.26229508 0.20238095 0.32716049 0.324074074 0.17777778       0.3 #> Doc2b         0.27049180 0.23809524 0.19753086 0.212962963 0.26666667       0.2 #> Gfap          0.73770492 0.73809524 0.72839506 0.657407407 0.75555556       0.9 #> Npas3         0.23770492 0.21428571 0.25308642 0.212962963 0.35555556       0.0 #> Serpina3n     0.36885246 0.40476190 0.32716049 0.342592593 0.24444444       0.5 #> Clmn          0.64754098 0.54761905 0.59259259 0.648148148 0.55555556       0.5 #> Prkch         0.16393443 0.17857143 0.17901235 0.175925926 0.22222222       0.2 #> Fbln5         0.09836066 0.05952381 0.10493827 0.074074074 0.11111111       0.0 #> Akr1c18       0.08196721 0.03571429 0.06790123 0.083333333 0.00000000       0.1 #> Gng4          0.30327869 0.25000000 0.30246914 0.277777778 0.24444444       0.6 #> Sema4d        0.61475410 0.54761905 0.54938272 0.527777778 0.48888889       0.4 #> Cxcl14        0.72131148 0.79761905 0.70987654 0.759259259 0.75555556       0.9 #> Hexb          0.75409836 0.80952381 0.80864198 0.842592593 0.82222222       0.7 #> Iqgap2        0.27049180 0.26190476 0.29629630 0.250000000 0.28888889       0.3 #> Crhbp         0.16393443 0.19047619 0.22839506 0.166666667 0.28888889       0.1 #> Rab3c         0.80327869 0.75000000 0.83333333 0.768518519 0.80000000       0.8 #> Thbs4         0.17213115 0.19047619 0.15432099 0.120370370 0.28888889       0.0 #> Serinc5       0.58196721 0.54761905 0.55555556 0.601851852 0.44444444       0.5 #> Erbin         0.72950820 0.57142857 0.75308642 0.638888889 0.62222222       0.7 #> Prkcd         0.58196721 0.61904762 0.53086420 0.601851852 0.48888889       0.5 #> Pdlim2        0.69672131 0.55952381 0.59259259 0.555555556 0.66666667       0.3 #> Ednrb         0.55737705 0.61904762 0.58024691 0.564814815 0.51111111       0.6 #> Cpne6         0.73770492 0.75000000 0.72222222 0.759259259 0.64444444       0.7 #> Sema5a        0.53278689 0.50000000 0.43827160 0.481481481 0.31111111       0.7 #> Matn2         0.31967213 0.39285714 0.39506173 0.314814815 0.35555556       0.3 #> Nptxr         0.84426230 0.86904762 0.90740741 0.814814815 0.82222222       0.8 #> Enpp2         0.93442623 0.90476190 0.91975309 0.879629630 0.93333333       0.8 #> Efcab6        0.09836066 0.14285714 0.16666667 0.101851852 0.13333333       0.2 #> Ppp1r1a       0.86885246 0.96428571 0.90123457 0.916666667 0.93333333       0.9 #> Litaf         0.54098361 0.48809524 0.46296296 0.444444444 0.53333333       0.5 #> Il1rap        0.55737705 0.47619048 0.47530864 0.509259259 0.46666667       0.4 #> Apod          0.96721311 0.94047619 0.96913580 0.944444444 0.97777778       0.9 #> Cpox          0.60655738 0.52380952 0.52469136 0.490740741 0.48888889       0.4 #> Grik1         0.19672131 0.17857143 0.14197531 0.175925926 0.11111111       0.3 #> Clic6         0.09016393 0.07142857 0.11111111 0.175925926 0.08888889       0.1 #> Nr4a1         0.20491803 0.25000000 0.32098765 0.222222222 0.08888889       0.1 #> Igfbp6        0.44262295 0.42857143 0.49382716 0.472222222 0.33333333       0.3 #> Sncg          0.12295082 0.09523810 0.12962963 0.129629630 0.13333333       0.0 #> Gzma          0.02459016 0.03571429 0.03086420 0.046296296 0.04444444       0.1 #> Grm2          0.28688525 0.26190476 0.33333333 0.231481481 0.20000000       0.2 #> Prph          0.04918033 0.07142857 0.05555556 0.101851852 0.00000000       0.1 #> Rsph1         0.09836066 0.04761905 0.07407407 0.083333333 0.11111111       0.2 #> Sox8          0.36065574 0.41666667 0.32716049 0.277777778 0.35555556       0.3 #> Fam234a       0.32786885 0.35714286 0.33333333 0.287037037 0.28888889       0.4 #> Lims2         0.43442623 0.40476190 0.33950617 0.351851852 0.40000000       0.3 #> Aqp4          0.72131148 0.73809524 0.71604938 0.759259259 0.71111111       0.9 #> Slc12a2       0.72131148 0.70238095 0.69135802 0.703703704 0.60000000       0.8 #> Cd74          0.05737705 0.10714286 0.06172840 0.074074074 0.02222222       0.0 #> Pdgfrb        0.20491803 0.22619048 0.20370370 0.175925926 0.24444444       0.1 #> Csf1r         0.75409836 0.70238095 0.66666667 0.601851852 0.60000000       0.7 #> Cbln2         0.27868852 0.14285714 0.16049383 0.250000000 0.22222222       0.1 #> Frmd8         0.46721311 0.38095238 0.46296296 0.388888889 0.35555556       0.3 #> Gldc          0.27868852 0.32142857 0.30246914 0.305555556 0.24444444       0.2 #> Tcf7l2        0.45901639 0.46428571 0.41358025 0.453703704 0.42222222       0.3 #> Bhlhe22       0.38524590 0.41666667 0.46913580 0.351851852 0.28888889       0.4 #> Kcnip2        0.54098361 0.54761905 0.69135802 0.555555556 0.66666667       0.7 #> Alas2         0.37704918 0.32142857 0.34567901 0.259259259 0.24444444       0.4 #> Gdf11         0.30327869 0.27380952 0.27160494 0.240740741 0.28888889       0.2 #> Baiap2        0.74590164 0.75000000 0.73456790 0.666666667 0.60000000       0.7 #> Ifitm3        0.50819672 0.57142857 0.46913580 0.564814815 0.55555556       0.4 #> Phkg1         0.31147541 0.29761905 0.27777778 0.268518519 0.35555556       0.0 #> Nptx1         0.72950820 0.76190476 0.75308642 0.675925926 0.80000000       0.7 #> Pde8a         0.31967213 0.30952381 0.30864198 0.342592593 0.35555556       0.0 #> Itih5         0.22950820 0.19047619 0.21604938 0.277777778 0.20000000       0.1 #> Homer2        0.59836066 0.61904762 0.52469136 0.500000000 0.71111111       0.5 #> Fam20c        0.61475410 0.61904762 0.50000000 0.555555556 0.40000000       0.7 #> Cplx2         0.92622951 0.91666667 0.92592593 0.861111111 0.91111111       1.0 #> Myo5b         0.32786885 0.36904762 0.38271605 0.333333333 0.31111111       0.3 #> Snca          0.90163934 0.86904762 0.93209877 0.898148148 0.88888889       1.0 #> Col3a1        0.03278689 0.03571429 0.04320988 0.064814815 0.04444444       0.0 #> Ecrg4         0.16393443 0.10714286 0.19753086 0.157407407 0.26666667       0.2 #> Map4k4        0.68852459 0.63095238 0.67283951 0.629629630 0.60000000       0.7 #> 2010300C02Rik 0.71311475 0.78571429 0.77777778 0.666666667 0.73333333       0.7 #> Ogfrl1        0.87704918 0.86904762 0.93827160 0.879629630 0.91111111       0.8 #> Fn1           0.35245902 0.32142857 0.34567901 0.268518519 0.28888889       0.3 #> Efhd1         0.52459016 0.44047619 0.48148148 0.398148148 0.46666667       0.2 #> Ngef          0.69672131 0.65476190 0.77777778 0.648148148 0.64444444       0.6 #> Bok           0.72131148 0.65476190 0.70987654 0.648148148 0.60000000       0.8 #> Tmem163       0.40163934 0.36904762 0.37654321 0.425925926 0.37777778       0.6 #> Lct           0.17213115 0.23809524 0.15432099 0.111111111 0.17777778       0.4 #> Cfh           0.30327869 0.29761905 0.24691358 0.194444444 0.15555556       0.3 #> Ptpn4         0.76229508 0.71428571 0.73456790 0.703703704 0.68888889       0.8 #> Tnni1         0.29508197 0.21428571 0.20987654 0.194444444 0.31111111       0.1 #> Csrp1         0.98360656 0.92857143 0.96296296 0.944444444 0.95555556       1.0 #> Nfasc         0.84426230 0.78571429 0.84567901 0.777777778 0.75555556       0.9 #> Syt2          0.23770492 0.17857143 0.19135802 0.166666667 0.06666667       0.1 #> Atp2b4        0.53278689 0.36904762 0.51234568 0.416666667 0.33333333       0.3 #> Rgs16         0.30327869 0.25000000 0.21604938 0.277777778 0.13333333       0.2 #> Ncf2          0.07377049 0.09523810 0.09876543 0.009259259 0.06666667       0.0 #> Cnih3         0.43442623 0.55952381 0.54320988 0.435185185 0.33333333       0.7 #> Tmem63a       0.46721311 0.50000000 0.50000000 0.518518519 0.44444444       0.3 #> Cfap126       0.07377049 0.08333333 0.05555556 0.111111111 0.13333333       0.0 #> Meig1         0.10655738 0.09523810 0.10493827 0.101851852 0.11111111       0.2 #> Ccdc3         0.26229508 0.26190476 0.20370370 0.222222222 0.17777778       0.3 #> Rgs5          0.59016393 0.66666667 0.64197531 0.601851852 0.73333333       0.6 #> Enkur         0.06557377 0.04761905 0.06172840 0.064814815 0.11111111       0.0 #> Myoc          0.16393443 0.14285714 0.16666667 0.111111111 0.11111111       0.1 #> Vim           0.45901639 0.55952381 0.45679012 0.546296296 0.55555556       0.4 #> Prkcq         0.20491803 0.17857143 0.25308642 0.259259259 0.31111111       0.2 #> Gad2          0.70491803 0.73809524 0.61111111 0.620370370 0.64444444       0.5 #> Lcn2          0.04098361 0.08333333 0.03086420 0.027777778 0.06666667       0.0 #> Nr4a2         0.40163934 0.30952381 0.37037037 0.268518519 0.35555556       0.3 #> Ermn          0.65573770 0.60714286 0.66049383 0.583333333 0.57777778       0.5 #> Fibcd1        0.28688525 0.28571429 0.29629630 0.287037037 0.35555556       0.5 #> Gsn           0.83606557 0.73809524 0.78395062 0.759259259 0.75555556       0.6 #> Grb14         0.81147541 0.83333333 0.70370370 0.759259259 0.73333333       0.8 #> Notch1        0.27049180 0.22619048 0.25308642 0.268518519 0.24444444       0.1 #> Ube2l6        0.27868852 0.25000000 0.24691358 0.250000000 0.26666667       0.3 #> Gatm          0.84426230 0.72619048 0.79629630 0.759259259 0.82222222       0.9 #> Cd82          0.45901639 0.50000000 0.41975309 0.472222222 0.37777778       0.4 #> Mdk           0.50819672 0.47619048 0.51851852 0.509259259 0.42222222       0.4 #> Lamp5         0.47540984 0.48809524 0.54320988 0.379629630 0.35555556       0.7 #> Itpka         0.77049180 0.82142857 0.79012346 0.777777778 0.71111111       0.7 #> Chgb          0.96721311 0.91666667 0.93827160 0.935185185 0.97777778       1.0 #> Mal           0.95901639 0.95238095 0.95679012 0.972222222 0.95555556       1.0 #> Pdyn          0.25409836 0.17857143 0.19753086 0.157407407 0.08888889       0.2 #> Nkx2-2        0.18852459 0.20238095 0.17283951 0.148148148 0.15555556       0.0 #> Edn3          0.04918033 0.02380952 0.04320988 0.083333333 0.04444444       0.0 #> Car2          0.96721311 0.96428571 0.95061728 0.962962963 0.95555556       1.0 #> Col9a3        0.26229508 0.25000000 0.20370370 0.231481481 0.24444444       0.4 #> Chrna4        0.50000000 0.54761905 0.56172840 0.435185185 0.37777778       0.3 #> Gss           0.42622951 0.35714286 0.38271605 0.342592593 0.33333333       0.1 #> Slc7a11       0.21311475 0.23809524 0.22222222 0.277777778 0.20000000       0.4 #> Tm4sf1        0.28688525 0.22619048 0.27160494 0.259259259 0.28888889       0.1 #> Kcnab1        0.71311475 0.72619048 0.75308642 0.694444444 0.55555556       0.8 #> Shox2         0.22131148 0.17857143 0.21604938 0.203703704 0.20000000       0.1 #> Serpini1      0.77049180 0.77380952 0.80246914 0.712962963 0.75555556       0.8 #> Tspan2        0.90983607 0.82142857 0.85802469 0.879629630 0.82222222       0.9 #> S100a11       0.19672131 0.14285714 0.16666667 0.222222222 0.24444444       0.0 #> Vcam1         0.31147541 0.36904762 0.30864198 0.268518519 0.35555556       0.3 #> Lef1          0.23770492 0.23809524 0.22222222 0.203703704 0.13333333       0.1 #> Npy2r         0.20491803 0.25000000 0.25308642 0.185185185 0.22222222       0.2 #> F3            0.37704918 0.48809524 0.40123457 0.398148148 0.44444444       0.0 #> Calb1         0.73770492 0.67857143 0.70370370 0.611111111 0.60000000       0.6 #> Epha7         0.56557377 0.50000000 0.57407407 0.564814815 0.48888889       0.6 #> Slc44a1       0.78688525 0.70238095 0.74691358 0.685185185 0.71111111       0.6 #> 1110017D15Rik 0.16393443 0.15476190 0.12345679 0.064814815 0.11111111       0.1 #> Tpm2          0.16393443 0.09523810 0.13580247 0.212962963 0.17777778       0.1 #> Slc6a9        0.56557377 0.57142857 0.50000000 0.490740741 0.64444444       0.4 #> Laptm5        0.57377049 0.47619048 0.43209877 0.407407407 0.53333333       0.6 #> Sema3c        0.26229508 0.19047619 0.27160494 0.166666667 0.11111111       0.2 #> Hpca          0.95081967 0.96428571 0.97530864 0.898148148 0.97777778       1.0 #> Padi2         0.47540984 0.34523810 0.35802469 0.277777778 0.44444444       0.2 #> Slc4a2        0.46721311 0.51190476 0.43827160 0.435185185 0.42222222       0.2 #> Gabrd         0.65573770 0.65476190 0.64197531 0.564814815 0.57777778       0.7 #> Rgs12         0.41803279 0.39285714 0.34567901 0.361111111 0.33333333       0.4 #> Slc30a3       0.50819672 0.45238095 0.50617284 0.444444444 0.46666667       0.5 #> Emilin1       0.05737705 0.02380952 0.01234568 0.037037037 0.06666667       0.0 #> 1700001C02Rik 0.05737705 0.02380952 0.03086420 0.009259259 0.06666667       0.0 #> Gabra4        0.66393443 0.63095238 0.69135802 0.685185185 0.60000000       0.8 #> Pdgfra        0.27049180 0.28571429 0.30864198 0.342592593 0.28888889       0.2 #> Epha5         0.65573770 0.63095238 0.61111111 0.500000000 0.57777778       0.6 #> Tesc          0.58196721 0.52380952 0.64814815 0.527777778 0.60000000       0.6 #> Pitpnm2       0.61475410 0.70238095 0.63580247 0.555555556 0.66666667       0.6 #> Mmp17         0.59836066 0.59523810 0.67283951 0.611111111 0.60000000       0.4 #> Cit           0.69672131 0.59523810 0.68518519 0.666666667 0.60000000       0.7 #> Foxp2         0.30327869 0.30952381 0.32716049 0.333333333 0.22222222       0.1 #> Arpc1b        0.52459016 0.41666667 0.53086420 0.407407407 0.46666667       0.6 #> Col1a2        0.22131148 0.19047619 0.10493827 0.120370370 0.17777778       0.0 #> Eln           0.03278689 0.05952381 0.06172840 0.046296296 0.08888889       0.0 #> Pcolce        0.14754098 0.07142857 0.10493827 0.138888889 0.15555556       0.0 #> Tsc22d4       0.95901639 0.97619048 0.96296296 0.962962963 0.93333333       0.9 #> Cald1         0.35245902 0.32142857 0.31481481 0.240740741 0.28888889       0.3 #> Ccdc136       0.78688525 0.72619048 0.73456790 0.731481481 0.55555556       0.6 #> Npy           0.72131148 0.64285714 0.71604938 0.574074074 0.71111111       0.6 #> Slc13a4       0.11475410 0.03571429 0.04938272 0.064814815 0.04444444       0.0 #> Gkn3          0.18032787 0.10714286 0.14814815 0.203703704 0.06666667       0.0 #> Slc6a13       0.12295082 0.08333333 0.08024691 0.120370370 0.06666667       0.0 #> Mgp           0.49180328 0.23809524 0.42592593 0.388888889 0.31111111       0.1 #> Lmo3          0.62295082 0.63095238 0.64814815 0.611111111 0.62222222       0.6 #> Slco1c1       0.46721311 0.57142857 0.59876543 0.583333333 0.51111111       0.8 #> Cpne9         0.40983607 0.26190476 0.40740741 0.351851852 0.35555556       0.2 #> Itpr2         0.23770492 0.17857143 0.25308642 0.277777778 0.28888889       0.1 #> Slc6a11       0.72131148 0.71428571 0.68518519 0.666666667 0.57777778       0.7 #> Vamp1         0.63934426 0.63095238 0.65432099 0.685185185 0.60000000       0.7 #> Cd9           0.77868852 0.78571429 0.74691358 0.648148148 0.68888889       0.6 #> Pglyrp1       0.32786885 0.30952381 0.27160494 0.287037037 0.33333333       0.2 #> Slc17a6       0.41803279 0.44047619 0.46296296 0.407407407 0.31111111       0.3 #> Sipa1l3       0.43442623 0.47619048 0.43827160 0.444444444 0.46666667       0.5 #> Sh3gl3        0.71311475 0.63095238 0.56790123 0.592592593 0.62222222       0.7 #> Plekhb1       0.98360656 0.95238095 0.98148148 0.981481481 0.97777778       1.0 #> Nupr1         0.11475410 0.20238095 0.10493827 0.138888889 0.11111111       0.0 #> Dkk3          0.80327869 0.75000000 0.78395062 0.666666667 0.66666667       0.9 #> Cox6a2        0.47540984 0.34523810 0.38271605 0.435185185 0.31111111       0.3 #> Dkkl1         0.25409836 0.20238095 0.33333333 0.222222222 0.28888889       0.0 #> Fgfr2         0.54918033 0.44047619 0.47530864 0.500000000 0.46666667       0.4 #> Crym          0.63114754 0.64285714 0.70370370 0.574074074 0.55555556       0.7 #> Slc38a5       0.08196721 0.05952381 0.07407407 0.111111111 0.15555556       0.0 #> Flna          0.37704918 0.46428571 0.41358025 0.342592593 0.28888889       0.3 #> Bgn           0.18852459 0.20238095 0.17901235 0.185185185 0.20000000       0.1 #> Col4a1        0.36065574 0.32142857 0.37654321 0.324074074 0.35555556       0.6 #> Plat          0.37704918 0.42857143 0.41358025 0.324074074 0.35555556       0.3 #> Nr3c2         0.48360656 0.57142857 0.46296296 0.453703704 0.31111111       0.6 #> Cbln1         0.18032787 0.17857143 0.17283951 0.203703704 0.17777778       0.2 #> Gab1          0.46721311 0.46428571 0.51234568 0.453703704 0.48888889       0.4 #> Pllp          0.76229508 0.76190476 0.75308642 0.703703704 0.64444444       0.6 #> Necab2        0.61475410 0.51190476 0.60493827 0.583333333 0.62222222       0.4 #> Dbndd1        0.36065574 0.41666667 0.38271605 0.398148148 0.33333333       0.2 #> Agt           0.63934426 0.63095238 0.58024691 0.620370370 0.60000000       0.9 #> Cryab         0.98360656 0.95238095 0.94444444 0.944444444 0.88888889       0.9 #> Tagln         0.09836066 0.11904762 0.14197531 0.157407407 0.08888889       0.0 #> Mcam          0.40163934 0.29761905 0.31481481 0.277777778 0.28888889       0.3 #> Olfm2         0.60655738 0.55952381 0.62962963 0.518518519 0.55555556       0.7 #> Icam5         0.65573770 0.69047619 0.68518519 0.620370370 0.73333333       0.6 #> Anxa2         0.19672131 0.13095238 0.17283951 0.231481481 0.17777778       0.2 #> Rora          0.69672131 0.78571429 0.73456790 0.703703704 0.71111111       0.5 #> Calml4        0.04918033 0.09523810 0.06790123 0.083333333 0.04444444       0.1 #> Htr3a         0.08196721 0.10714286 0.06790123 0.083333333 0.13333333       0.0 #> Paqr5         0.09836066 0.10714286 0.09876543 0.111111111 0.13333333       0.1 #> Rasgrf1       0.87704918 0.92857143 0.88888889 0.898148148 0.88888889       0.9 #> Zic1          0.36885246 0.38095238 0.34567901 0.416666667 0.33333333       0.5 #> Mobp          1.00000000 0.98809524 0.99382716 1.000000000 1.00000000       1.0 #> Hhatl         0.32786885 0.34523810 0.30864198 0.333333333 0.37777778       0.4 #> Trf           0.98360656 0.95238095 0.96296296 0.907407407 0.95555556       1.0 #> Cpne4         0.54098361 0.45238095 0.54320988 0.509259259 0.44444444       0.3 #> Cdhr4         0.03278689 0.03571429 0.04320988 0.027777778 0.00000000       0.0 #> Cd59a         0.35245902 0.42857143 0.37654321 0.277777778 0.26666667       0.5 #> Gng11         0.68032787 0.77380952 0.67283951 0.703703704 0.64444444       0.8 #> Chrm1         0.64754098 0.64285714 0.69135802 0.546296296 0.64444444       0.5 #> Prr5l         0.28688525 0.26190476 0.20370370 0.222222222 0.20000000       0.3 #> Ugt8a         0.72131148 0.63095238 0.68518519 0.666666667 0.55555556       0.3 #> Rims3         0.72950820 0.53571429 0.66049383 0.675925926 0.64444444       0.5 #> Sgpp2         0.31967213 0.16666667 0.24691358 0.268518519 0.31111111       0.3 #> Camkv         0.90163934 0.90476190 0.95061728 0.916666667 0.91111111       1.0 #> Sox10         0.55737705 0.47619048 0.54320988 0.490740741 0.51111111       0.6 #> Micall1       0.37704918 0.35714286 0.41975309 0.342592593 0.40000000       0.5 #> Tie1          0.12295082 0.10714286 0.11111111 0.111111111 0.11111111       0.1 #> Fa2h          0.70491803 0.58333333 0.64814815 0.620370370 0.53333333       0.5 #> Ucp2          0.30327869 0.25000000 0.37037037 0.333333333 0.37777778       0.5 #> Vav3          0.30327869 0.22619048 0.20370370 0.231481481 0.08888889       0.2 #> Ccp110        0.67213115 0.63095238 0.70370370 0.537037037 0.51111111       0.8 #> Gria2         0.92622951 0.91666667 0.94444444 0.898148148 0.93333333       1.0 #> Rasl10a       0.45901639 0.48809524 0.47530864 0.388888889 0.40000000       0.4 #> Foxj1         0.21311475 0.22619048 0.12345679 0.166666667 0.17777778       0.0 #> Trim59        0.31147541 0.35714286 0.35185185 0.287037037 0.37777778       0.2 #> Dynlrb2       0.09016393 0.07142857 0.05555556 0.037037037 0.08888889       0.0 #> Gjc1          0.08196721 0.14285714 0.12962963 0.111111111 0.13333333       0.3 #> Neurod1       0.20491803 0.26190476 0.27777778 0.240740741 0.17777778       0.3 #> Ttyh2         0.58196721 0.48809524 0.44444444 0.462962963 0.53333333       0.5 #> Cpne7         0.50819672 0.46428571 0.51851852 0.490740741 0.55555556       0.4 #> Nrip3         0.73770492 0.67857143 0.72222222 0.638888889 0.62222222       0.7 #> Tbr1          0.51639344 0.51190476 0.58024691 0.481481481 0.44444444       0.5 #> Lcat          0.46721311 0.53571429 0.43827160 0.407407407 0.44444444       0.4 #> Tmem98        0.31147541 0.26190476 0.27160494 0.287037037 0.40000000       0.2 #> Myo1d         0.22131148 0.15476190 0.23456790 0.157407407 0.20000000       0.2 #> Prdm8         0.31967213 0.38095238 0.35185185 0.240740741 0.24444444       0.5 #> Tgfbi         0.05737705 0.04761905 0.03703704 0.120370370 0.11111111       0.0 #> Kcnc2         0.72131148 0.69047619 0.71604938 0.675925926 0.44444444       1.0 #> Thrsp         0.50819672 0.57142857 0.48765432 0.583333333 0.51111111       0.6 #> Isg15         0.24590164 0.27380952 0.20370370 0.212962963 0.22222222       0.2 #> Acta2         0.16393443 0.16666667 0.14197531 0.166666667 0.20000000       0.0 #> H2-Q4         0.04918033 0.04761905 0.04938272 0.037037037 0.11111111       0.0 #> Dock4         0.65573770 0.58333333 0.67901235 0.462962963 0.53333333       0.6 #> Myrf          0.51639344 0.46428571 0.45061728 0.500000000 0.46666667       0.7 #> Lmo1          0.48360656 0.60714286 0.56172840 0.527777778 0.46666667       0.7 #> Igfbp7        0.54918033 0.58333333 0.58641975 0.592592593 0.64444444       0.4 #> P2ry12        0.45081967 0.39285714 0.37037037 0.416666667 0.44444444       0.5 #> Pcdh8         0.34426230 0.39285714 0.31481481 0.370370370 0.28888889       0.5 #> Lgi4          0.44262295 0.33333333 0.37654321 0.361111111 0.53333333       0.2 #> Fxyd1         0.82786885 0.79761905 0.81481481 0.824074074 0.77777778       0.9 #> Fxyd7         0.89344262 0.91666667 0.92592593 0.861111111 0.73333333       0.9 #> Mag           0.96721311 0.90476190 0.93209877 0.953703704 0.88888889       1.0 #> Zcchc12       0.46721311 0.52380952 0.45061728 0.398148148 0.33333333       0.6 #> Anln          0.36065574 0.40476190 0.33950617 0.250000000 0.37777778       0.2 #> Wnt4          0.33606557 0.32142857 0.34567901 0.370370370 0.13333333       0.3 #> C1ql2         0.17213115 0.19047619 0.17283951 0.203703704 0.13333333       0.3 #> Unc93b1       0.23770492 0.25000000 0.21604938 0.185185185 0.33333333       0.3 #> Tspan15       0.50000000 0.41666667 0.48148148 0.351851852 0.37777778       0.5 #> Ppp1r14a      0.81147541 0.73809524 0.72839506 0.740740741 0.73333333       0.8 #> Clic4         0.71311475 0.66666667 0.61111111 0.666666667 0.71111111       0.6 #> Galnt6        0.27868852 0.29761905 0.20987654 0.222222222 0.28888889       0.1 #> Ccn3          0.47540984 0.48809524 0.53086420 0.416666667 0.55555556       0.6 #> Rims2         0.64754098 0.65476190 0.65432099 0.611111111 0.42222222       0.5 #> Zmat4         0.48360656 0.46428571 0.49382716 0.444444444 0.28888889       0.4 #> Cldn11        0.94262295 0.96428571 0.96913580 0.935185185 0.91111111       1.0 #> Ccdc33        0.04918033 0.03571429 0.02469136 0.018518519 0.04444444       0.0 #> Slc32a1       0.44262295 0.45238095 0.48765432 0.472222222 0.48888889       0.4 #> Tgm2          0.13934426 0.09523810 0.09259259 0.120370370 0.15555556       0.0 #> Vstm2l        0.61475410 0.63095238 0.64197531 0.527777778 0.53333333       0.6 #> Neurod6       0.66393443 0.61904762 0.66666667 0.629629630 0.60000000       0.5 #> Crygn         0.05737705 0.05952381 0.04320988 0.009259259 0.06666667       0.0 #> Enpp6         0.20491803 0.25000000 0.29012346 0.222222222 0.15555556       0.1 #> Neurod2       0.59836066 0.57142857 0.62962963 0.592592593 0.46666667       0.5 #> Satb2         0.31147541 0.28571429 0.33333333 0.157407407 0.35555556       0.2 #> Pcp4l1        0.73770492 0.77380952 0.72222222 0.740740741 0.60000000       0.6 #> Txnip         0.30327869 0.19047619 0.25308642 0.268518519 0.33333333       0.2 #> Egr1          0.57377049 0.54761905 0.64197531 0.564814815 0.55555556       0.8 #> Otud7b        0.50819672 0.47619048 0.54938272 0.425925926 0.46666667       0.3 #> Car14         0.39344262 0.38095238 0.34567901 0.370370370 0.35555556       0.2 #> Rgs4          0.79508197 0.83333333 0.79012346 0.833333333 0.75555556       0.6 #> Dock10        0.41803279 0.48809524 0.37037037 0.398148148 0.46666667       0.3 #> Lpar1         0.60655738 0.47619048 0.51851852 0.574074074 0.51111111       0.5 #> Trps1         0.31147541 0.35714286 0.32098765 0.212962963 0.26666667       0.3 #> Ptpn3         0.56557377 0.47619048 0.54938272 0.583333333 0.48888889       0.5 #> Lefty1        0.16393443 0.20238095 0.22839506 0.203703704 0.22222222       0.2 #> Zfhx3         0.28688525 0.28571429 0.29629630 0.296296296 0.28888889       0.3 #> St6galnac5    0.57377049 0.66666667 0.59876543 0.518518519 0.68888889       0.5 #> Ak5           0.73770492 0.76190476 0.67283951 0.685185185 0.66666667       0.5 #> Hrh3          0.64754098 0.48809524 0.56172840 0.537037037 0.40000000       0.4 #> Nexn          0.17213115 0.16666667 0.14197531 0.138888889 0.08888889       0.1 #> Adgrl4        0.31967213 0.29761905 0.30246914 0.287037037 0.33333333       0.2 #> Rlbp1         0.28688525 0.33333333 0.27777778 0.259259259 0.13333333       0.2 #> Igfbp2        0.46721311 0.42857143 0.42592593 0.425925926 0.44444444       0.3 #> Wfs1          0.59836066 0.61904762 0.61111111 0.629629630 0.75555556       0.4 #> Cplx3         0.25409836 0.28571429 0.28395062 0.157407407 0.31111111       0.3 #> Orai2         0.46721311 0.53571429 0.56790123 0.462962963 0.46666667       0.4 #> Olig2         0.50819672 0.44047619 0.39506173 0.342592593 0.42222222       0.7 #> Gpr37         0.77868852 0.64285714 0.70987654 0.703703704 0.68888889       0.8 #> Plcb4         0.59836066 0.60714286 0.59876543 0.629629630 0.40000000       0.5 #> Nxph4         0.07377049 0.07142857 0.07407407 0.064814815 0.06666667       0.1 #> Ndufa4l2      0.25409836 0.20238095 0.13580247 0.185185185 0.22222222       0.1 #> Cacng5        0.26229508 0.33333333 0.19753086 0.231481481 0.17777778       0.1 #> Plekhg1       0.46721311 0.39285714 0.43827160 0.453703704 0.28888889       0.3 #> Cmtm5         0.85245902 0.75000000 0.82098765 0.814814815 0.80000000       1.0 #> Gpr161        0.17213115 0.23809524 0.19135802 0.166666667 0.15555556       0.4 #> Rfx3          0.36885246 0.35714286 0.29012346 0.324074074 0.24444444       0.3 #> Igsf21        0.50000000 0.36904762 0.53086420 0.379629630 0.40000000       0.5 #> Ramp3         0.54918033 0.51190476 0.46913580 0.490740741 0.48888889       0.5 #> Arhgap12      0.39344262 0.35714286 0.43827160 0.453703704 0.35555556       0.5 #> Nkx6-2        0.55737705 0.44047619 0.44444444 0.444444444 0.48888889       0.5 #> Ninj2         0.16393443 0.13095238 0.20987654 0.129629630 0.11111111       0.2 #> Cldn5         0.60655738 0.59523810 0.57407407 0.620370370 0.75555556       0.6 #> Htr2c         0.21311475 0.23809524 0.30864198 0.268518519 0.20000000       0.4 #> Hspb8         0.24590164 0.19047619 0.15432099 0.175925926 0.28888889       0.1 #> Fmod          0.05737705 0.04761905 0.04320988 0.064814815 0.04444444       0.0 #> Prelp         0.30327869 0.20238095 0.23456790 0.259259259 0.20000000       0.3 #> Mpped1        0.66393443 0.61904762 0.66666667 0.481481481 0.55555556       0.6 #> Rapgef5       0.55737705 0.64285714 0.61111111 0.527777778 0.51111111       0.5 #> Vwa1          0.38524590 0.44047619 0.33950617 0.435185185 0.46666667       0.8 #> Stab1         0.15573770 0.14285714 0.14814815 0.129629630 0.13333333       0.1 #> Arl15         0.39344262 0.38095238 0.41358025 0.379629630 0.24444444       0.4 #> Reln          0.30327869 0.26190476 0.32716049 0.277777778 0.22222222       0.1 #> Mustn1        0.09836066 0.03571429 0.06172840 0.046296296 0.00000000       0.0 #> Pbxip1        0.44262295 0.44047619 0.48765432 0.342592593 0.37777778       0.7 #> Dnali1        0.04098361 0.02380952 0.03086420 0.037037037 0.08888889       0.0 #> Id1           0.53278689 0.40476190 0.42592593 0.435185185 0.53333333       0.3 #> Lrrtm3        0.42622951 0.38095238 0.43827160 0.324074074 0.22222222       0.3 #> Tmem212       0.08196721 0.03571429 0.05555556 0.055555556 0.04444444       0.1 #> Epop          0.50000000 0.59523810 0.58641975 0.453703704 0.42222222       0.5 #> Gjc2          0.45901639 0.45238095 0.39506173 0.370370370 0.40000000       0.6 #> 1190005I06Rik 0.45901639 0.41666667 0.37654321 0.324074074 0.33333333       0.6 #> Ctla2a        0.40983607 0.33333333 0.33950617 0.361111111 0.28888889       0.1 #> Cnr1          0.57377049 0.60714286 0.61728395 0.518518519 0.60000000       0.6 #> Gpr4          0.11475410 0.14285714 0.16666667 0.175925926 0.15555556       0.2 #> Sowaha        0.56557377 0.70238095 0.56790123 0.601851852 0.77777778       0.6 #> Tent5c        0.19672131 0.17857143 0.13580247 0.111111111 0.08888889       0.1 #> Serpinb1a     0.38524590 0.29761905 0.32098765 0.314814815 0.33333333       0.2 #> S1pr5         0.42622951 0.33333333 0.29629630 0.287037037 0.26666667       0.3 #> Penk          0.36885246 0.42857143 0.40740741 0.324074074 0.44444444       0.5 #> Cdc42ep2      0.43442623 0.36904762 0.43209877 0.407407407 0.35555556       0.2 #> Slitrk6       0.14754098 0.07142857 0.16049383 0.120370370 0.06666667       0.0 #> Hpcal4        0.92622951 0.89285714 0.93209877 0.805555556 0.91111111       1.0 #> Olig1         0.94262295 0.88095238 0.91358025 0.907407407 0.88888889       0.6 #> Rprml         0.72950820 0.64285714 0.74074074 0.685185185 0.71111111       0.7 #> Stxbp6        0.50000000 0.48809524 0.45679012 0.462962963 0.40000000       0.5 #> Hs3st2        0.31967213 0.28571429 0.35802469 0.277777778 0.24444444       0.2 #> Rbp1          0.43442623 0.42857143 0.40740741 0.425925926 0.33333333       0.2 #> Ppm1e         0.77049180 0.76190476 0.82098765 0.722222222 0.77777778       0.8 #> Sox18         0.18852459 0.23809524 0.14814815 0.212962963 0.11111111       0.2 #> Kctd4         0.36885246 0.39285714 0.26543210 0.324074074 0.22222222       0.3 #> Nxph3         0.29508197 0.21428571 0.32716049 0.203703704 0.20000000       0.1 #> Vat1l         0.31147541 0.30952381 0.23456790 0.203703704 0.31111111       0.1 #> Cd24a         0.29508197 0.21428571 0.21604938 0.129629630 0.24444444       0.2 #> Odf3b         0.07377049 0.03571429 0.04938272 0.018518519 0.04444444       0.1 #> Gjb1          0.52459016 0.38095238 0.37654321 0.361111111 0.40000000       0.4 #> Selplg        0.48360656 0.30952381 0.39506173 0.398148148 0.42222222       0.2 #> Bcl11b        0.56557377 0.66666667 0.62345679 0.518518519 0.51111111       0.6 #> Lhfp          0.42622951 0.51190476 0.47530864 0.370370370 0.35555556       0.6 #> Ranbp3l       0.01639344 0.08333333 0.01234568 0.046296296 0.00000000       0.1 #> Msx1          0.10655738 0.13095238 0.08024691 0.111111111 0.04444444       0.1 #> Zdhhc22       0.54098361 0.44047619 0.40123457 0.462962963 0.44444444       0.3 #> Phldb1        0.76229508 0.66666667 0.62962963 0.611111111 0.66666667       0.8 #> Ctxn1         0.88524590 0.90476190 0.88271605 0.898148148 0.86666667       0.8 #> Tprn          0.55737705 0.47619048 0.41975309 0.398148148 0.40000000       0.5 #> Vstm2a        0.61475410 0.59523810 0.59876543 0.601851852 0.60000000       0.6 #> Ndnf          0.16393443 0.16666667 0.11728395 0.148148148 0.13333333       0.2 #> Pdp1          0.73770492 0.72619048 0.72839506 0.685185185 0.68888889       0.7 #> Scn3b         0.60655738 0.70238095 0.71604938 0.685185185 0.68888889       0.8 #> Cdc42ep1      0.40163934 0.44047619 0.33950617 0.305555556 0.40000000       0.2 #> Gal3st1       0.50819672 0.47619048 0.41358025 0.407407407 0.37777778       0.5 #> Rasd1         0.37704918 0.39285714 0.37654321 0.361111111 0.37777778       0.4 #> Spink8        0.32786885 0.33333333 0.34567901 0.361111111 0.44444444       0.4 #> Opalin        0.77868852 0.78571429 0.72839506 0.712962963 0.75555556       0.7 #> Gja4          0.04918033 0.07142857 0.06790123 0.092592593 0.08888889       0.0 #> Synpo2        0.35245902 0.29761905 0.29012346 0.342592593 0.31111111       0.5 #> Pcdh20        0.29508197 0.35714286 0.38271605 0.351851852 0.24444444       0.4 #> Adra1b        0.37704918 0.34523810 0.38888889 0.305555556 0.31111111       0.3 #> Fam131a       0.79508197 0.83333333 0.78395062 0.694444444 0.66666667       0.7 #> Tmem125       0.34426230 0.25000000 0.30864198 0.370370370 0.28888889       0.4 #> Mb21d2        0.55737705 0.51190476 0.46296296 0.509259259 0.40000000       0.4 #> Lingo3        0.36065574 0.39285714 0.30864198 0.361111111 0.20000000       0.4 #> Ncald         0.92622951 0.95238095 0.93827160 0.888888889 0.88888889       1.0 #> Siglech       0.27868852 0.23809524 0.25925926 0.166666667 0.40000000       0.3 #> Rgs14         0.44262295 0.46428571 0.37037037 0.370370370 0.31111111       0.4 #> Gm14964       0.18852459 0.07142857 0.12962963 0.138888889 0.08888889       0.0 #> Gpr17         0.31147541 0.25000000 0.27777778 0.268518519 0.37777778       0.2 #> Cx3cr1        0.36885246 0.34523810 0.27160494 0.324074074 0.35555556       0.2 #> Ezr           0.54918033 0.53571429 0.45061728 0.425925926 0.51111111       0.4 #> Adarb2        0.24590164 0.23809524 0.27777778 0.287037037 0.22222222       0.1 #> Cpne8         0.27868852 0.22619048 0.24691358 0.231481481 0.20000000       0.2 #> Plekhg3       0.32786885 0.26190476 0.24074074 0.287037037 0.28888889       0.3 #> Lamb2         0.30327869 0.36904762 0.29012346 0.314814815 0.33333333       0.4 #> Creb5         0.20491803 0.14285714 0.14814815 0.166666667 0.15555556       0.2 #> Cntn2         0.64754098 0.55952381 0.66666667 0.555555556 0.62222222       0.4 #> Aldh1a1       0.65573770 0.67857143 0.67283951 0.712962963 0.64444444       0.4 #> Phgdh         0.81967213 0.84523810 0.82098765 0.814814815 0.84444444       0.8 #> Tnfaip6       0.42622951 0.41666667 0.35185185 0.342592593 0.17777778       0.1 #> Camk2d        0.58196721 0.52380952 0.62345679 0.481481481 0.46666667       0.4 #> Shisa6        0.40163934 0.44047619 0.46296296 0.444444444 0.33333333       0.6 #> Cthrc1        0.28688525 0.28571429 0.24074074 0.259259259 0.17777778       0.2 #> Tmem119       0.36065574 0.23809524 0.25308642 0.342592593 0.28888889       0.4 #> Hmgb2         0.33606557 0.20238095 0.24074074 0.185185185 0.13333333       0.3 #> Tmem158       0.63934426 0.59523810 0.62962963 0.555555556 0.46666667       0.7 #> Dsp           0.08196721 0.08333333 0.04938272 0.037037037 0.02222222       0.2 #> Lrtm2         0.51639344 0.47619048 0.54320988 0.537037037 0.35555556       0.4 #> Gabra5        0.54918033 0.57142857 0.61728395 0.537037037 0.48888889       0.6 #> Tns1          0.29508197 0.20238095 0.24691358 0.314814815 0.15555556       0.2 #> Nell1         0.53278689 0.52380952 0.47530864 0.500000000 0.44444444       0.2 #> Slain1        0.77868852 0.63095238 0.69753086 0.712962963 0.57777778       0.7 #> Prr18         0.72950820 0.63095238 0.57407407 0.537037037 0.71111111       0.6 #> S100a8        0.12295082 0.10714286 0.12345679 0.138888889 0.15555556       0.1 #> S100a9        0.15573770 0.07142857 0.14197531 0.148148148 0.11111111       0.1 #> Col8a2        0.02459016 0.02380952 0.03086420 0.046296296 0.13333333       0.0 #> Synpr         0.54918033 0.61904762 0.57407407 0.620370370 0.55555556       0.4 #> Sertm1        0.40163934 0.44047619 0.37037037 0.324074074 0.31111111       0.6 #> Adgrf5        0.31147541 0.23809524 0.36419753 0.379629630 0.33333333       0.3 #> Capg          0.13934426 0.11904762 0.07407407 0.092592593 0.08888889       0.0 #> Gjc3          0.58196721 0.61904762 0.54938272 0.527777778 0.57777778       0.3 #> Fcer1g        0.45081967 0.45238095 0.38888889 0.379629630 0.33333333       0.7 #> Pde1a         0.63114754 0.60714286 0.71604938 0.574074074 0.68888889       0.5 #> Tafa1         0.41803279 0.40476190 0.45679012 0.259259259 0.26666667       0.4 #> Ddn           0.90163934 0.90476190 0.92592593 0.888888889 0.91111111       1.0 #> Hopx          0.75409836 0.73809524 0.72839506 0.657407407 0.82222222       0.6 #> Ptk2b         0.90163934 0.92857143 0.91975309 0.935185185 0.88888889       0.6 #> Rgs3          0.47540984 0.50000000 0.47530864 0.500000000 0.44444444       0.3 #> Kcng2         0.25409836 0.28571429 0.24074074 0.277777778 0.13333333       0.3 #> Ntng1         0.45081967 0.39285714 0.41358025 0.425925926 0.35555556       0.4 #> H2-Q7         0.02459016 0.02380952 0.04320988 0.064814815 0.04444444       0.0 #> Ifitm2        0.31967213 0.36904762 0.31481481 0.296296296 0.35555556       0.5 #> Plaat3        0.66393443 0.69047619 0.72839506 0.629629630 0.77777778       0.8 #> Plekhh1       0.52459016 0.48809524 0.46296296 0.453703704 0.44444444       0.4 #> Myl4          0.32786885 0.34523810 0.40740741 0.277777778 0.40000000       0.4 #> H2-K1         0.41803279 0.47619048 0.53086420 0.537037037 0.60000000       0.5 #> Dpp6          0.77049180 0.73809524 0.77777778 0.740740741 0.66666667       0.7 #> Tmem91        0.28688525 0.32142857 0.31481481 0.222222222 0.28888889       0.2 #> Cyp2d22       0.40163934 0.34523810 0.39506173 0.388888889 0.51111111       0.2 #> Ttr           1.00000000 1.00000000 0.98765432 0.990740741 1.00000000       1.0 #> Suclg2        0.24590164 0.33333333 0.27777778 0.185185185 0.17777778       0.4 #> Patj          0.27049180 0.21428571 0.20987654 0.259259259 0.24444444       0.3 #> Btbd3         0.79508197 0.86904762 0.80864198 0.833333333 0.68888889       0.9 #> Unc13c        0.36065574 0.30952381 0.26543210 0.268518519 0.17777778       0.4 #> Syt9          0.23770492 0.21428571 0.25308642 0.203703704 0.08888889       0.3 #> Shisal1       0.50000000 0.44047619 0.49382716 0.462962963 0.37777778       0.6 #> Grm4          0.25409836 0.19047619 0.28395062 0.203703704 0.20000000       0.2 #> Sox11         0.27049180 0.32142857 0.30246914 0.287037037 0.26666667       0.4 #> Slc22a8       0.22131148 0.21428571 0.15432099 0.185185185 0.22222222       0.3 #> Slc24a3       0.81967213 0.77380952 0.80246914 0.787037037 0.73333333       0.6 #> Klk8          0.32786885 0.44047619 0.31481481 0.379629630 0.35555556       0.4 #> Ipcef1        0.42622951 0.35714286 0.51851852 0.324074074 0.44444444       0.6 #> Tnnt1         0.45901639 0.40476190 0.30864198 0.388888889 0.15555556       0.3 #> Hhip          0.11475410 0.17857143 0.12962963 0.194444444 0.17777778       0.1 #> Spag8         0.02459016 0.03571429 0.03086420 0.027777778 0.08888889       0.0 #> Fxyd6         0.69672131 0.70238095 0.74074074 0.648148148 0.71111111       0.5 #> Ppp1r3c       0.40163934 0.39285714 0.43209877 0.342592593 0.26666667       0.1 #> Cbln4         0.19672131 0.17857143 0.17901235 0.203703704 0.15555556       0.2 #> Nnat          0.96721311 0.86904762 0.90740741 0.888888889 0.88888889       0.9 #> Myl9          0.40163934 0.45238095 0.30864198 0.324074074 0.42222222       0.2 #> Vxn           0.77868852 0.75000000 0.72839506 0.703703704 0.73333333       0.8 #> Lgals1        0.45081967 0.51190476 0.53086420 0.472222222 0.48888889       0.1 #> Gpr88         0.29508197 0.19047619 0.21604938 0.203703704 0.24444444       0.0 #> Ctxn3         0.11475410 0.14285714 0.12345679 0.148148148 0.06666667       0.0 #> Lyz2          0.23770492 0.10714286 0.15432099 0.157407407 0.20000000       0.1 #> Tmem100       0.24590164 0.27380952 0.28395062 0.231481481 0.22222222       0.3 #> Wfdc17        0.01639344 0.01190476 0.02469136 0.037037037 0.08888889       0.0 #> Ahnak         0.29508197 0.26190476 0.26543210 0.314814815 0.42222222       0.2 #> Hba-a2        0.99180328 1.00000000 0.99382716 0.990740741 0.97777778       1.0 #> Hba-a1        1.00000000 0.97619048 1.00000000 0.990740741 1.00000000       1.0 #> Ccdc153       0.12295082 0.04761905 0.06790123 0.101851852 0.11111111       0.0 #> Ccnd1         0.46721311 0.45238095 0.56172840 0.490740741 0.51111111       0.5 #> Serpinh1      0.27868852 0.38095238 0.24691358 0.250000000 0.24444444       0.1 #> Gad1          0.73770492 0.66666667 0.74074074 0.777777778 0.71111111       0.6 #> Arhgef10      0.41803279 0.35714286 0.45061728 0.324074074 0.33333333       0.5 #> 2410004P03Rik 0.04098361 0.08333333 0.03703704 0.027777778 0.04444444       0.0 #> Nt5dc2        0.22950820 0.22619048 0.22222222 0.250000000 0.22222222       0.3 #> Cebpd         0.28688525 0.35714286 0.28395062 0.296296296 0.31111111       0.4 #> Sod3          0.24590164 0.20238095 0.12962963 0.231481481 0.22222222       0.2 #> H2-D1         0.67213115 0.76190476 0.66049383 0.611111111 0.64444444       0.8 #> C4b           0.40163934 0.33333333 0.36419753 0.296296296 0.37777778       0.2 #> Tmem88b       0.78688525 0.66666667 0.72222222 0.703703704 0.60000000       0.6 #> Hbb-bt        0.99180328 1.00000000 0.98148148 0.990740741 0.95555556       1.0 #> Rhog          0.58196721 0.54761905 0.59259259 0.583333333 0.48888889       0.4 #> Rprm          0.48360656 0.45238095 0.39506173 0.407407407 0.44444444       0.6 #> Ly6a          0.70491803 0.63095238 0.64814815 0.703703704 0.73333333       0.7 #> Mog           0.83606557 0.78571429 0.83333333 0.851851852 0.91111111       0.6 #> Trbc2         0.31967213 0.35714286 0.40740741 0.333333333 0.37777778       0.2 #> Igkc          0.04918033 0.07142857 0.04938272 0.037037037 0.02222222       0.1 #> Smim1         0.38524590 0.32142857 0.34567901 0.370370370 0.62222222       0.6 #> Hs3st4        0.63934426 0.55952381 0.62345679 0.657407407 0.66666667       0.7 #> Evi2a         0.60655738 0.55952381 0.57407407 0.574074074 0.71111111       0.6 #> Prkcg         0.86885246 0.86904762 0.90740741 0.833333333 0.80000000       0.8 #> Ly6c1         0.68032787 0.73809524 0.70370370 0.675925926 0.66666667       0.8 #> Gbp4          0.05737705 0.02380952 0.03086420 0.101851852 0.02222222       0.1 #> Wipf3         0.61475410 0.69047619 0.70987654 0.694444444 0.66666667       0.6 #> BC039966      0.03278689 0.03571429 0.04320988 0.027777778 0.08888889       0.0 #> Gm13889       0.46721311 0.47619048 0.48765432 0.444444444 0.33333333       0.2 #> Plcxd2        0.49180328 0.39285714 0.45679012 0.388888889 0.17777778       0.2 #> Mia           0.08196721 0.09523810 0.08641975 0.101851852 0.08888889       0.0 #> Pou3f1        0.53278689 0.57142857 0.50617284 0.481481481 0.42222222       0.7 #> Lrrc10b       0.33606557 0.42857143 0.35802469 0.379629630 0.37777778       0.5 #> Apol11b       0.13114754 0.08333333 0.06790123 0.092592593 0.06666667       0.1 #> Gpr62         0.40163934 0.36904762 0.40740741 0.379629630 0.35555556       0.2 #> Shisa8        0.14754098 0.10714286 0.11111111 0.111111111 0.15555556       0.3 #> Gm2115        0.24590164 0.34523810 0.28395062 0.351851852 0.31111111       0.3 #> Kctd12        0.66393443 0.55952381 0.63580247 0.601851852 0.60000000       0.6 #> 1700047M11Rik 0.32786885 0.29761905 0.25925926 0.277777778 0.22222222       0.2 #> Lhfpl3        0.40163934 0.44047619 0.37654321 0.342592593 0.20000000       0.5 #> C030029H02Rik 0.13114754 0.14285714 0.09876543 0.092592593 0.11111111       0.1 #> Gm19935       0.13114754 0.08333333 0.07407407 0.074074074 0.13333333       0.0 #> 9630013A20Rik 0.05737705 0.09523810 0.09259259 0.083333333 0.04444444       0.0 #> 2900040C04Rik 0.12295082 0.10714286 0.10493827 0.055555556 0.08888889       0.0 #>                cluster_4 #> Gna12         0.72043011 #> Ccnd2         0.49462366 #> Btbd17        0.39784946 #> Sox9          0.54838710 #> Sez6          0.80645161 #> Serpinf1      0.23655914 #> S100a6        0.55913978 #> Col1a1        0.05376344 #> Vwf           0.24731183 #> Esam          0.30107527 #> Npas1         0.19354839 #> Tiam1         0.52688172 #> Bcam          0.27956989 #> Hmgn2         0.55913978 #> Rab3b         0.41935484 #> Inmt          0.04301075 #> Ddr1          0.56989247 #> Homer3        0.48387097 #> Cp            0.08602151 #> Calb2         0.34408602 #> Man1a         0.39784946 #> Efnb3         0.67741935 #> Hlf           0.76344086 #> Gstm7         0.46236559 #> Cavin1        0.25806452 #> Sst           0.79569892 #> Hapln2        0.25806452 #> Hspb1         0.23655914 #> Ndrg1         0.72043011 #> Nid1          0.02150538 #> Kit           0.24731183 #> Pvalb         0.75268817 #> Tmbim1        0.52688172 #> Crip1         0.51612903 #> Tek           0.21505376 #> Elovl1        0.47311828 #> Cyba          0.35483871 #> Itih3         0.29032258 #> Cnp           0.96774194 #> Hap1          0.47311828 #> Clic1         0.20430108 #> Stx1a         0.62365591 #> Arpp19        0.94623656 #> Dio2          0.26881720 #> Id3           0.73118280 #> Crlf1         0.33333333 #> Ttc9b         0.91397849 #> Carhsp1       0.46236559 #> Cabp7         0.56989247 #> Fam163b       0.64516129 #> Rarres2       0.23655914 #> Syn2          0.87096774 #> Ick           0.34408602 #> Prox1         0.27956989 #> Adssl1        0.29032258 #> Vipr2         0.12903226 #> Gltp          0.54838710 #> Amotl1        0.38709677 #> Bcas1         0.70967742 #> Aldh1a2       0.03225806 #> Tppp3         0.62365591 #> Sirt2         0.92473118 #> Lpl           0.34408602 #> Cers2         0.66666667 #> Qdpr          0.94623656 #> Stk32c        0.60215054 #> Lbp           0.07526882 #> Hsd11b1       0.45161290 #> Vtn           0.72043011 #> Stac2         0.39784946 #> Plxdc1        0.31182796 #> Igfbp4        0.59139785 #> Dbndd2        0.59139785 #> Pltp          0.58064516 #> Slc12a4       0.31182796 #> Cadps2        0.50537634 #> Erbb3         0.18279570 #> Pmp22         0.39784946 #> Kcnab3        0.34408602 #> Myh11         0.03225806 #> Plod1         0.36559140 #> Etnppl        0.25806452 #> Arhgef25      0.77419355 #> Rcn3          0.25806452 #> Vip           0.18279570 #> Utrn          0.35483871 #> Grm1          0.54838710 #> Reep3         0.53763441 #> Fabp7         0.53763441 #> Dcn           0.15053763 #> Slc17a8       0.03225806 #> Dusp6         0.46236559 #> Kitl          0.46236559 #> Ccn2          0.17204301 #> Timp3         0.65591398 #> Ascl1         0.16129032 #> Unc5b         0.27956989 #> Vsir          0.22580645 #> Gamt          0.60215054 #> Ptprb         0.32258065 #> Csrp2         0.21505376 #> Adarb1        0.77419355 #> Rnf130        0.54838710 #> Nefh          0.56989247 #> Aebp1         0.11827957 #> Sept4         0.91397849 #> Gria1         0.88172043 #> Sypl          0.65591398 #> Arsg          0.31182796 #> Cacng4        0.43010753 #> Rab37         0.16129032 #> Itgb4         0.18279570 #> Aspa          0.41935484 #> Cygb          0.59139785 #> Rflnb         0.30107527 #> Doc2b         0.21505376 #> Gfap          0.70967742 #> Npas3         0.27956989 #> Serpina3n     0.39784946 #> Clmn          0.66666667 #> Prkch         0.16129032 #> Fbln5         0.15053763 #> Akr1c18       0.03225806 #> Gng4          0.35483871 #> Sema4d        0.52688172 #> Cxcl14        0.79569892 #> Hexb          0.81720430 #> Iqgap2        0.35483871 #> Crhbp         0.13978495 #> Rab3c         0.76344086 #> Thbs4         0.20430108 #> Serinc5       0.59139785 #> Erbin         0.58064516 #> Prkcd         0.46236559 #> Pdlim2        0.65591398 #> Ednrb         0.48387097 #> Cpne6         0.75268817 #> Sema5a        0.51612903 #> Matn2         0.39784946 #> Nptxr         0.91397849 #> Enpp2         0.95698925 #> Efcab6        0.13978495 #> Ppp1r1a       0.91397849 #> Litaf         0.51612903 #> Il1rap        0.40860215 #> Apod          0.92473118 #> Cpox          0.44086022 #> Grik1         0.18279570 #> Clic6         0.13978495 #> Nr4a1         0.29032258 #> Igfbp6        0.45161290 #> Sncg          0.13978495 #> Gzma          0.01075269 #> Grm2          0.34408602 #> Prph          0.08602151 #> Rsph1         0.11827957 #> Sox8          0.37634409 #> Fam234a       0.34408602 #> Lims2         0.35483871 #> Aqp4          0.69892473 #> Slc12a2       0.61290323 #> Cd74          0.05376344 #> Pdgfrb        0.19354839 #> Csf1r         0.68817204 #> Cbln2         0.19354839 #> Frmd8         0.49462366 #> Gldc          0.27956989 #> Tcf7l2        0.44086022 #> Bhlhe22       0.43010753 #> Kcnip2        0.65591398 #> Alas2         0.29032258 #> Gdf11         0.29032258 #> Baiap2        0.77419355 #> Ifitm3        0.50537634 #> Phkg1         0.31182796 #> Nptx1         0.77419355 #> Pde8a         0.19354839 #> Itih5         0.32258065 #> Homer2        0.64516129 #> Fam20c        0.51612903 #> Cplx2         0.96774194 #> Myo5b         0.38709677 #> Snca          0.89247312 #> Col3a1        0.04301075 #> Ecrg4         0.19354839 #> Map4k4        0.63440860 #> 2010300C02Rik 0.73118280 #> Ogfrl1        0.87096774 #> Fn1           0.33333333 #> Efhd1         0.36559140 #> Ngef          0.66666667 #> Bok           0.68817204 #> Tmem163       0.40860215 #> Lct           0.23655914 #> Cfh           0.26881720 #> Ptpn4         0.77419355 #> Tnni1         0.24731183 #> Csrp1         0.97849462 #> Nfasc         0.84946237 #> Syt2          0.13978495 #> Atp2b4        0.52688172 #> Rgs16         0.24731183 #> Ncf2          0.04301075 #> Cnih3         0.50537634 #> Tmem63a       0.50537634 #> Cfap126       0.07526882 #> Meig1         0.17204301 #> Ccdc3         0.19354839 #> Rgs5          0.65591398 #> Enkur         0.08602151 #> Myoc          0.12903226 #> Vim           0.43010753 #> Prkcq         0.20430108 #> Gad2          0.68817204 #> Lcn2          0.04301075 #> Nr4a2         0.30107527 #> Ermn          0.65591398 #> Fibcd1        0.37634409 #> Gsn           0.78494624 #> Grb14         0.68817204 #> Notch1        0.21505376 #> Ube2l6        0.25806452 #> Gatm          0.81720430 #> Cd82          0.45161290 #> Mdk           0.47311828 #> Lamp5         0.47311828 #> Itpka         0.76344086 #> Chgb          0.88172043 #> Mal           0.95698925 #> Pdyn          0.24731183 #> Nkx2-2        0.15053763 #> Edn3          0.04301075 #> Car2          0.97849462 #> Col9a3        0.31182796 #> Chrna4        0.48387097 #> Gss           0.52688172 #> Slc7a11       0.30107527 #> Tm4sf1        0.30107527 #> Kcnab1        0.75268817 #> Shox2         0.18279570 #> Serpini1      0.65591398 #> Tspan2        0.82795699 #> S100a11       0.21505376 #> Vcam1         0.33333333 #> Lef1          0.23655914 #> Npy2r         0.30107527 #> F3            0.43010753 #> Calb1         0.75268817 #> Epha7         0.63440860 #> Slc44a1       0.72043011 #> 1110017D15Rik 0.11827957 #> Tpm2          0.12903226 #> Slc6a9        0.55913978 #> Laptm5        0.45161290 #> Sema3c        0.21505376 #> Hpca          0.95698925 #> Padi2         0.26881720 #> Slc4a2        0.43010753 #> Gabrd         0.60215054 #> Rgs12         0.41935484 #> Slc30a3       0.49462366 #> Emilin1       0.07526882 #> 1700001C02Rik 0.03225806 #> Gabra4        0.69892473 #> Pdgfra        0.30107527 #> Epha5         0.63440860 #> Tesc          0.66666667 #> Pitpnm2       0.62365591 #> Mmp17         0.65591398 #> Cit           0.60215054 #> Foxp2         0.29032258 #> Arpc1b        0.48387097 #> Col1a2        0.09677419 #> Eln           0.09677419 #> Pcolce        0.10752688 #> Tsc22d4       0.93548387 #> Cald1         0.35483871 #> Ccdc136       0.78494624 #> Npy           0.64516129 #> Slc13a4       0.05376344 #> Gkn3          0.09677419 #> Slc6a13       0.09677419 #> Mgp           0.43010753 #> Lmo3          0.62365591 #> Slco1c1       0.52688172 #> Cpne9         0.34408602 #> Itpr2         0.25806452 #> Slc6a11       0.66666667 #> Vamp1         0.74193548 #> Cd9           0.70967742 #> Pglyrp1       0.27956989 #> Slc17a6       0.46236559 #> Sipa1l3       0.51612903 #> Sh3gl3        0.64516129 #> Plekhb1       0.97849462 #> Nupr1         0.12903226 #> Dkk3          0.74193548 #> Cox6a2        0.35483871 #> Dkkl1         0.17204301 #> Fgfr2         0.50537634 #> Crym          0.56989247 #> Slc38a5       0.18279570 #> Flna          0.32258065 #> Bgn           0.12903226 #> Col4a1        0.36559140 #> Plat          0.38709677 #> Nr3c2         0.48387097 #> Cbln1         0.22580645 #> Gab1          0.47311828 #> Pllp          0.73118280 #> Necab2        0.65591398 #> Dbndd1        0.39784946 #> Agt           0.58064516 #> Cryab         0.93548387 #> Tagln         0.11827957 #> Mcam          0.35483871 #> Olfm2         0.62365591 #> Icam5         0.68817204 #> Anxa2         0.15053763 #> Rora          0.66666667 #> Calml4        0.04301075 #> Htr3a         0.13978495 #> Paqr5         0.09677419 #> Rasgrf1       0.87096774 #> Zic1          0.37634409 #> Mobp          0.97849462 #> Hhatl         0.26881720 #> Trf           0.92473118 #> Cpne4         0.60215054 #> Cdhr4         0.03225806 #> Cd59a         0.47311828 #> Gng11         0.61290323 #> Chrm1         0.69892473 #> Prr5l         0.21505376 #> Ugt8a         0.56989247 #> Rims3         0.64516129 #> Sgpp2         0.18279570 #> Camkv         0.92473118 #> Sox10         0.47311828 #> Micall1       0.44086022 #> Tie1          0.11827957 #> Fa2h          0.55913978 #> Ucp2          0.30107527 #> Vav3          0.23655914 #> Ccp110        0.60215054 #> Gria2         0.89247312 #> Rasl10a       0.48387097 #> Foxj1         0.08602151 #> Trim59        0.34408602 #> Dynlrb2       0.03225806 #> Gjc1          0.10752688 #> Neurod1       0.25806452 #> Ttyh2         0.48387097 #> Cpne7         0.50537634 #> Nrip3         0.75268817 #> Tbr1          0.47311828 #> Lcat          0.45161290 #> Tmem98        0.19354839 #> Myo1d         0.23655914 #> Prdm8         0.32258065 #> Tgfbi         0.02150538 #> Kcnc2         0.68817204 #> Thrsp         0.58064516 #> Isg15         0.22580645 #> Acta2         0.17204301 #> H2-Q4         0.02150538 #> Dock4         0.62365591 #> Myrf          0.38709677 #> Lmo1          0.52688172 #> Igfbp7        0.61290323 #> P2ry12        0.49462366 #> Pcdh8         0.50537634 #> Lgi4          0.36559140 #> Fxyd1         0.80645161 #> Fxyd7         0.84946237 #> Mag           0.95698925 #> Zcchc12       0.47311828 #> Anln          0.22580645 #> Wnt4          0.31182796 #> C1ql2         0.25806452 #> Unc93b1       0.27956989 #> Tspan15       0.41935484 #> Ppp1r14a      0.65591398 #> Clic4         0.61290323 #> Galnt6        0.11827957 #> Ccn3          0.44086022 #> Rims2         0.65591398 #> Zmat4         0.49462366 #> Cldn11        0.95698925 #> Ccdc33        0.03225806 #> Slc32a1       0.51612903 #> Tgm2          0.13978495 #> Vstm2l        0.72043011 #> Neurod6       0.63440860 #> Crygn         0.04301075 #> Enpp6         0.18279570 #> Neurod2       0.62365591 #> Satb2         0.25806452 #> Pcp4l1        0.67741935 #> Txnip         0.25806452 #> Egr1          0.67741935 #> Otud7b        0.52688172 #> Car14         0.37634409 #> Rgs4          0.78494624 #> Dock10        0.53763441 #> Lpar1         0.45161290 #> Trps1         0.27956989 #> Ptpn3         0.55913978 #> Lefty1        0.24731183 #> Zfhx3         0.33333333 #> St6galnac5    0.64516129 #> Ak5           0.68817204 #> Hrh3          0.54838710 #> Nexn          0.17204301 #> Adgrl4        0.33333333 #> Rlbp1         0.33333333 #> Igfbp2        0.45161290 #> Wfs1          0.70967742 #> Cplx3         0.16129032 #> Orai2         0.61290323 #> Olig2         0.37634409 #> Gpr37         0.67741935 #> Plcb4         0.60215054 #> Nxph4         0.06451613 #> Ndufa4l2      0.21505376 #> Cacng5        0.25806452 #> Plekhg1       0.40860215 #> Cmtm5         0.80645161 #> Gpr161        0.22580645 #> Rfx3          0.40860215 #> Igsf21        0.52688172 #> Ramp3         0.47311828 #> Arhgap12      0.45161290 #> Nkx6-2        0.41935484 #> Ninj2         0.18279570 #> Cldn5         0.61290323 #> Htr2c         0.29032258 #> Hspb8         0.22580645 #> Fmod          0.02150538 #> Prelp         0.21505376 #> Mpped1        0.62365591 #> Rapgef5       0.64516129 #> Vwa1          0.38709677 #> Stab1         0.12903226 #> Arl15         0.34408602 #> Reln          0.31182796 #> Mustn1        0.02150538 #> Pbxip1        0.50537634 #> Dnali1        0.04301075 #> Id1           0.49462366 #> Lrrtm3        0.37634409 #> Tmem212       0.05376344 #> Epop          0.50537634 #> Gjc2          0.38709677 #> 1190005I06Rik 0.37634409 #> Ctla2a        0.40860215 #> Cnr1          0.58064516 #> Gpr4          0.15053763 #> Sowaha        0.74193548 #> Tent5c        0.10752688 #> Serpinb1a     0.33333333 #> S1pr5         0.23655914 #> Penk          0.38709677 #> Cdc42ep2      0.40860215 #> Slitrk6       0.06451613 #> Hpcal4        0.95698925 #> Olig1         0.91397849 #> Rprml         0.76344086 #> Stxbp6        0.50537634 #> Hs3st2        0.22580645 #> Rbp1          0.41935484 #> Ppm1e         0.76344086 #> Sox18         0.22580645 #> Kctd4         0.40860215 #> Nxph3         0.19354839 #> Vat1l         0.23655914 #> Cd24a         0.15053763 #> Odf3b         0.04301075 #> Gjb1          0.40860215 #> Selplg        0.38709677 #> Bcl11b        0.54838710 #> Lhfp          0.49462366 #> Ranbp3l       0.04301075 #> Msx1          0.05376344 #> Zdhhc22       0.40860215 #> Phldb1        0.61290323 #> Ctxn1         0.88172043 #> Tprn          0.34408602 #> Vstm2a        0.61290323 #> Ndnf          0.16129032 #> Pdp1          0.76344086 #> Scn3b         0.70967742 #> Cdc42ep1      0.31182796 #> Gal3st1       0.37634409 #> Rasd1         0.46236559 #> Spink8        0.43010753 #> Opalin        0.70967742 #> Gja4          0.06451613 #> Synpo2        0.29032258 #> Pcdh20        0.36559140 #> Adra1b        0.31182796 #> Fam131a       0.77419355 #> Tmem125       0.29032258 #> Mb21d2        0.54838710 #> Lingo3        0.31182796 #> Ncald         0.86021505 #> Siglech       0.29032258 #> Rgs14         0.43010753 #> Gm14964       0.08602151 #> Gpr17         0.22580645 #> Cx3cr1        0.33333333 #> Ezr           0.52688172 #> Adarb2        0.16129032 #> Cpne8         0.23655914 #> Plekhg3       0.24731183 #> Lamb2         0.33333333 #> Creb5         0.12903226 #> Cntn2         0.49462366 #> Aldh1a1       0.60215054 #> Phgdh         0.87096774 #> Tnfaip6       0.39784946 #> Camk2d        0.49462366 #> Shisa6        0.50537634 #> Cthrc1        0.27956989 #> Tmem119       0.35483871 #> Hmgb2         0.25806452 #> Tmem158       0.62365591 #> Dsp           0.13978495 #> Lrtm2         0.50537634 #> Gabra5        0.56989247 #> Tns1          0.25806452 #> Nell1         0.56989247 #> Slain1        0.74193548 #> Prr18         0.50537634 #> S100a8        0.10752688 #> S100a9        0.17204301 #> Col8a2        0.06451613 #> Synpr         0.62365591 #> Sertm1        0.35483871 #> Adgrf5        0.31182796 #> Capg          0.08602151 #> Gjc3          0.52688172 #> Fcer1g        0.36559140 #> Pde1a         0.59139785 #> Tafa1         0.34408602 #> Ddn           0.87096774 #> Hopx          0.76344086 #> Ptk2b         0.86021505 #> Rgs3          0.41935484 #> Kcng2         0.30107527 #> Ntng1         0.46236559 #> H2-Q7         0.04301075 #> Ifitm2        0.41935484 #> Plaat3        0.67741935 #> Plekhh1       0.44086022 #> Myl4          0.26881720 #> H2-K1         0.64516129 #> Dpp6          0.75268817 #> Tmem91        0.33333333 #> Cyp2d22       0.45161290 #> Ttr           1.00000000 #> Suclg2        0.15053763 #> Patj          0.18279570 #> Btbd3         0.82795699 #> Unc13c        0.22580645 #> Syt9          0.24731183 #> Shisal1       0.43010753 #> Grm4          0.21505376 #> Sox11         0.31182796 #> Slc22a8       0.23655914 #> Slc24a3       0.77419355 #> Klk8          0.40860215 #> Ipcef1        0.36559140 #> Tnnt1         0.27956989 #> Hhip          0.13978495 #> Spag8         0.02150538 #> Fxyd6         0.66666667 #> Ppp1r3c       0.45161290 #> Cbln4         0.22580645 #> Nnat          0.90322581 #> Myl9          0.40860215 #> Vxn           0.73118280 #> Lgals1        0.48387097 #> Gpr88         0.19354839 #> Ctxn3         0.13978495 #> Lyz2          0.16129032 #> Tmem100       0.21505376 #> Wfdc17        0.05376344 #> Ahnak         0.32258065 #> Hba-a2        1.00000000 #> Hba-a1        1.00000000 #> Ccdc153       0.05376344 #> Ccnd1         0.43010753 #> Serpinh1      0.31182796 #> Gad1          0.74193548 #> Arhgef10      0.37634409 #> 2410004P03Rik 0.06451613 #> Nt5dc2        0.35483871 #> Cebpd         0.31182796 #> Sod3          0.23655914 #> H2-D1         0.59139785 #> C4b           0.30107527 #> Tmem88b       0.56989247 #> Hbb-bt        0.96774194 #> Rhog          0.55913978 #> Rprm          0.45161290 #> Ly6a          0.68817204 #> Mog           0.81720430 #> Trbc2         0.30107527 #> Igkc          0.03225806 #> Smim1         0.33333333 #> Hs3st4        0.64516129 #> Evi2a         0.62365591 #> Prkcg         0.86021505 #> Ly6c1         0.72043011 #> Gbp4          0.04301075 #> Wipf3         0.78494624 #> BC039966      0.02150538 #> Gm13889       0.47311828 #> Plcxd2        0.40860215 #> Mia           0.07526882 #> Pou3f1        0.41935484 #> Lrrc10b       0.39784946 #> Apol11b       0.11827957 #> Gpr62         0.39784946 #> Shisa8        0.10752688 #> Gm2115        0.44086022 #> Kctd12        0.61290323 #> 1700047M11Rik 0.23655914 #> Lhfpl3        0.39784946 #> C030029H02Rik 0.12903226 #> Gm19935       0.08602151 #> 9630013A20Rik 0.11827957 #> 2900040C04Rik 0.10752688"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cell_meta_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_cell_meta_obj — create_cell_meta_obj","title":"create_cell_meta_obj — create_cell_meta_obj","text":"create_cell_meta_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cell_meta_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_cell_meta_obj — create_cell_meta_obj","text":"","code":"create_cell_meta_obj(   metaDT = NULL,   col_desc = NA_character_,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cell_meta_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_cell_meta_obj — create_cell_meta_obj","text":"cell_meta_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":null,"dir":"Reference","previous_headings":"","what":"create_cluster_matrix — create_cluster_matrix","title":"create_cluster_matrix — create_cluster_matrix","text":"creates aggregated matrix given clustering column","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_cluster_matrix — create_cluster_matrix","text":"","code":"create_cluster_matrix(   gobject,   spat_unit = NULL,   feat_type = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   cluster_column,   feat_subset = NULL,   gene_subset = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"create_cluster_matrix — create_cluster_matrix","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") expression_values name expression values use cluster_column name cluster column use, feat_subset subset features use gene_subset deprecated use.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_cluster_matrix — create_cluster_matrix","text":"matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_cluster_matrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"create_cluster_matrix — create_cluster_matrix","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  create_cluster_matrix(g, cluster_column = \"leiden_clus\") #> 634 x 7 Matrix of class \"dgeMatrix\" #>                cluster_2  cluster_5  cluster_1  cluster_3  cluster_6 cluster_7 #> 1110017D15Rik 0.44254321 0.42104894 0.38350624 0.19568207 0.28069313 0.3703106 #> 1190005I06Rik 1.35043254 1.35570109 1.12952302 1.02266077 1.17287740 1.8616339 #> 1700001C02Rik 0.18927101 0.05728738 0.07733503 0.01839425 0.15710555 0.0000000 #> 1700047M11Rik 0.95685380 0.88367167 0.76632284 0.86813679 0.55009271 0.8187913 #> 2010300C02Rik 2.95949381 3.37786454 3.14329561 2.84124569 3.02035452 3.4352495 #> 2410004P03Rik 0.14404681 0.17406545 0.08321509 0.08717661 0.17331548 0.0000000 #> 2900040C04Rik 0.32757163 0.28457067 0.32113707 0.17356740 0.32761432 0.0000000 #> 9630013A20Rik 0.17597264 0.29575033 0.28874834 0.26833691 0.09952757 0.0000000 #> Acta2         0.57752461 0.54501809 0.56501864 0.64096745 0.69354224 0.0000000 #> Adarb1        3.53550700 3.30058022 3.38098627 3.46216432 2.58062282 3.0655697 #> Adarb2        0.75636302 0.75530304 0.86623663 0.88371980 0.80480183 0.3976548 #> Adgrf5        0.89756501 0.66877532 1.13318007 1.20908964 0.95886855 1.1535245 #> Adgrl4        1.04985868 0.90483970 0.92898229 0.97800088 1.06809182 0.5068221 #> Adra1b        1.27403000 1.02719137 1.28061157 0.99103440 1.14741183 1.1441730 #> Adssl1        1.22683731 1.36701339 1.20495704 1.03050662 1.38292753 0.8528214 #> Aebp1         0.47659104 0.35614418 0.44012339 0.36315284 0.27892980 0.0000000 #> Agt           2.58344953 2.65131727 2.23244375 2.66909410 2.54067049 2.9915034 #> Ahnak         0.87442210 0.76469206 0.79734451 0.91531682 1.40794558 0.7167474 #> Ak5           2.81209723 2.96793488 2.67339895 2.68978028 2.65212379 2.2315317 #> Akr1c18       0.25486892 0.10717964 0.18107542 0.29201268 0.00000000 0.1371682 #> Alas2         1.24029336 1.11196961 1.15905023 0.92345850 0.83743496 1.5693706 #> Aldh1a1       2.29817855 2.52563080 2.35379228 2.65641791 2.47922311 1.5909304 #> Aldh1a2       0.12766617 0.06700689 0.09847394 0.30442144 0.00000000 0.3474831 #> Amotl1        1.59141088 1.52206874 1.67265575 1.88453192 1.80460555 1.5660657 #> Anln          1.06438290 1.22290140 1.02662252 0.75448601 1.21465958 0.6797875 #> Anxa2         0.57179514 0.34788829 0.50720952 0.70967632 0.45995659 0.6369316 #> Apod          5.11956478 5.00724135 4.93962837 4.96219926 5.42790752 3.9966022 #> Apol11b       0.35929836 0.24092320 0.20236074 0.27629799 0.17705447 0.2564135 #> Aqp4          2.67431922 2.75917648 2.54629507 2.82003279 2.84498269 2.9813845 #> Arhgap12      1.31951502 1.16740918 1.43679667 1.47682701 1.25994916 1.6957406 #> Arhgef10      1.30399703 1.11347707 1.43731120 1.03112802 0.99866752 1.5000659 #> Arhgef25      3.32395185 3.23853885 3.39800246 3.38567462 2.97064593 3.5291598 #> Arl15         1.26545235 1.28025241 1.37925059 1.28053546 0.71570803 1.4224155 #> Arpc1b        1.62470466 1.29123387 1.73839998 1.34042337 1.61413436 1.7838762 #> Arpp19        4.42595642 4.35163328 4.80397850 3.89752350 4.45562164 3.9427566 #> Arsg          1.27517546 1.23375248 0.99465993 1.03370270 1.58670989 0.2504086 #> Ascl1         0.42848925 0.46801984 0.49010822 0.23662938 0.52055771 0.0000000 #> Aspa          1.87909375 1.45680189 1.53833872 1.72369905 1.46958193 2.5777761 #> Atp2b4        1.84269558 1.15386024 1.80429076 1.41293692 1.27377631 1.2427699 #> BC039966      0.08464373 0.07695937 0.13722385 0.10447754 0.34869164 0.0000000 #> Baiap2        3.31778256 3.47637866 3.33135191 2.99228394 2.89563373 3.2529838 #> Bcam          0.55274955 0.46173183 0.45044757 0.95543213 0.93821439 0.2666210 #> Bcas1         3.64879117 3.22084650 3.42773536 3.41097031 3.13603555 2.8217151 #> Bcl11b        2.08720626 2.64724695 2.35003951 1.99581744 2.15090413 2.5578504 #> Bgn           0.55339634 0.55505453 0.52065451 0.54507218 0.63729383 0.2564135 #> Bhlhe22       1.26730535 1.57124430 1.63385086 1.27426865 1.07416336 1.8132305 #> Bok           2.71366296 2.47116725 2.82089779 2.77238677 2.50119762 2.6689739 #> Btbd17        1.18729607 1.29867174 1.21794661 1.43198694 1.25581641 0.7594994 #> Btbd3         3.23569186 3.66107529 3.30479961 3.62928422 2.70333505 4.1914698 #> C030029H02Rik 0.37708569 0.39173442 0.28273725 0.26811175 0.29861244 0.3741050 #> C1ql2         0.63756061 0.83656585 0.55546037 0.74039217 0.42425309 1.4792838 #> C4b           1.20912580 1.07666214 1.08784349 0.97983734 1.23896846 0.6141041 #> Cabp7         2.26141511 2.44514004 2.33171046 2.61207654 3.16472283 1.9179897 #> Cacng4        1.53992884 1.49452708 1.76753612 1.58747283 1.01433516 1.1549710 #> Cacng5        0.75850207 1.10563582 0.59535977 0.80880499 0.67086059 0.4663389 #> Cadps2        1.66298140 1.79355599 1.70677869 1.60769029 1.55996625 1.4189812 #> Calb1         2.75161481 2.64565739 2.66071371 2.35304449 2.24703356 2.8503507 #> Calb2         1.41862992 1.32679445 1.12525518 1.48135851 0.98242852 1.9040701 #> Cald1         1.00831433 1.09999147 0.96943989 0.73670233 0.93050467 0.8055152 #> Calml4        0.17812836 0.24026338 0.21439030 0.26489800 0.12279855 0.2564135 #> Camk2d        1.91013264 1.75440216 2.22769858 1.77491542 1.64604388 1.5496669 #> Camkv         4.44530499 4.39151834 4.74003800 4.44649869 4.41698046 5.4369734 #> Capg          0.38903655 0.35245856 0.21153810 0.28855782 0.27376925 0.0000000 #> Car14         1.24424269 1.11343694 1.07236797 1.21006471 1.11457941 0.5862004 #> Car2          4.79559426 4.66259955 4.63408113 4.92886903 4.97714175 5.0083894 #> Carhsp1       2.55785092 2.19549855 2.04605615 2.27045522 2.17840332 1.8752942 #> Cavin1        0.76178584 0.74779708 0.85791117 0.71491635 0.47148173 0.7352277 #> Cbln1         0.50677361 0.56843914 0.49778664 0.67986802 0.53191317 0.7215881 #> Cbln2         0.85233400 0.44056965 0.53927191 0.76469578 0.74219937 0.1371682 #> Cbln4         0.65457753 0.56382202 0.54803959 0.66918493 0.58515336 0.3758855 #> Ccdc136       3.19733978 2.90704090 2.90717882 3.07481517 2.32147603 2.3319452 #> Ccdc153       0.36423938 0.18890700 0.24146879 0.32301029 0.36814199 0.0000000 #> Ccdc3         0.78413847 0.73650858 0.63024330 0.68680921 0.59021747 1.1575822 #> Ccdc33        0.15646381 0.08911464 0.06165821 0.03512126 0.14687971 0.0000000 #> Ccn2          0.64678980 1.03034906 0.93286268 0.51762328 1.18479178 0.6489568 #> Ccn3          1.69445080 1.82519651 2.02261190 1.50804077 2.07883176 2.2958439 #> Ccnd1         1.49172433 1.43781973 1.87903187 1.67180559 1.71349654 1.6711655 #> Ccnd2         1.94201357 2.05141093 2.18616953 2.02323861 1.91616817 2.3163818 #> Ccp110        2.29732034 2.19807779 2.47177250 1.90358959 1.82606217 2.4110374 #> Cd24a         0.83585240 0.66717923 0.63308184 0.42952765 0.77319714 0.3935818 #> Cd59a         1.09204790 1.27182310 1.17265850 0.83537412 0.89930350 1.3773815 #> Cd74          0.16323129 0.28640037 0.16826600 0.26490651 0.08241013 0.0000000 #> Cd82          1.49922529 1.58499533 1.36301618 1.50503499 1.30925932 1.4534073 #> Cd9           3.11862023 3.00308144 2.84786535 2.72844377 2.86524077 2.3690098 #> Cdc42ep1      1.25933372 1.34260246 0.99908397 1.00464598 1.27408659 0.7373906 #> Cdc42ep2      1.31112799 1.03877484 1.33480677 1.30032413 1.17369038 0.6871979 #> Cdhr4         0.10169997 0.12003410 0.12457179 0.06082551 0.00000000 0.0000000 #> Cebpd         0.91772180 1.20032716 0.86517644 0.93989122 1.13127334 1.5196409 #> Cers2         2.35272710 2.57746727 2.31978260 2.28481964 2.52422789 3.1972147 #> Cfap126       0.22972328 0.20822942 0.17732501 0.33723331 0.34625506 0.0000000 #> Cfh           0.88970003 0.91487359 0.72403399 0.65726992 0.53960703 1.0474544 #> Chgb          4.88863946 4.69165476 5.02117029 4.85742016 4.98184272 5.0368354 #> Chrm1         2.58901145 2.56080761 2.84557636 2.32416159 2.60370776 2.0795552 #> Chrna4        1.65844964 1.85245203 1.94891048 1.54787324 1.42590930 1.1898229 #> Cit           2.54506390 2.26660798 2.68180498 2.55911909 2.31233140 2.5188545 #> Cldn11        5.12673269 4.91747338 4.91391632 4.85413605 4.93278681 5.2484757 #> Cldn5         2.05797803 2.16118255 2.01543084 2.15157241 2.88085137 1.9432223 #> Clic1         1.00898108 0.61047121 0.60289933 0.76176127 0.55957882 0.6369316 #> Clic4         2.58666667 2.36671046 2.12576758 2.38873272 2.69836201 2.0664659 #> Clic6         0.26628334 0.18558083 0.33574166 0.53274505 0.32058596 0.3474831 #> Clmn          2.16643116 1.82939053 2.08910818 2.32066560 2.04461206 1.5499308 #> Cmtm5         3.59912609 3.09342087 3.27582574 3.38148577 3.24189183 4.0948043 #> Cnih3         1.37787878 1.91073139 1.86309495 1.51923394 0.95664556 2.2298451 #> Cnp           6.03778097 5.82455446 5.72610313 5.77702510 6.08723395 5.0034797 #> Cnr1          1.99177163 2.19292993 2.33292360 2.01669127 2.45104316 2.1977566 #> Cntn2         2.19769046 1.98853482 2.31129249 1.83212021 2.27929936 1.2398097 #> Col1a1        0.22421466 0.10226721 0.10783051 0.29432743 0.15596186 0.3703106 #> Col1a2        0.68218467 0.49410901 0.33255629 0.40645615 0.51822386 0.0000000 #> Col3a1        0.10335846 0.09522224 0.14714881 0.21914560 0.13701240 0.0000000 #> Col4a1        1.02425466 0.93547399 1.18324437 1.02022529 1.15861721 1.8394679 #> Col8a2        0.06717989 0.05587790 0.09922726 0.10487230 0.42155426 0.0000000 #> Col9a3        0.73807814 0.71699776 0.55312249 0.70748193 0.83754395 1.2497755 #> Cox6a2        1.53223212 1.20097966 1.34653532 1.53161448 1.02634977 1.0002553 #> Cp            0.22881160 0.39256404 0.21860348 0.25071201 0.00000000 0.2504086 #> Cplx2         4.84253940 5.22427279 4.94190933 4.76831409 4.92894758 5.1011530 #> Cplx3         0.89687539 0.93155993 1.02811878 0.55739109 1.14881459 1.1910550 #> Cpne4         1.77621294 1.63315095 1.92080522 1.89454150 1.47925758 1.1136211 #> Cpne6         2.98364077 3.20817015 3.18107406 3.40839997 2.72992785 3.3275147 #> Cpne7         1.83558011 1.68264494 1.91383742 1.91205820 1.96437175 1.6219654 #> Cpne8         0.80722610 0.75749844 0.77400170 0.72723726 0.63598534 0.8251990 #> Cpne9         1.35270330 0.85277249 1.42153976 1.27506722 1.41430820 0.8109540 #> Cpox          1.88485507 1.55457452 1.67161441 1.48853842 1.68145051 1.2664507 #> Creb5         0.61650207 0.41841136 0.38959639 0.45888483 0.47775179 0.6407260 #> Crhbp         0.50371639 0.62988919 0.69393968 0.55015138 1.07634777 0.1371682 #> Crip1         1.41009971 1.25450326 1.39849965 1.15120273 1.20854459 1.0925703 #> Crlf1         0.68633559 0.92119629 0.62912246 0.71898084 0.58334100 1.0250248 #> Cryab         5.18551692 4.86790348 4.88570189 4.82335774 4.79686080 4.3052533 #> Crygn         0.16837963 0.15891147 0.11078299 0.02585192 0.25634860 0.0000000 #> Crym          2.59338157 2.77401687 2.90799042 2.55813201 2.23842391 2.8514304 #> Csf1r         2.66955319 2.53276487 2.42293815 2.23872947 2.61373883 2.8836846 #> Csrp1         5.01572073 4.68519528 4.78446126 4.80670914 5.05684827 5.1119679 #> Csrp2         0.59065362 0.63314040 0.47274840 0.39455994 0.51584406 0.8911345 #> Cthrc1        0.75791455 0.78019177 0.73432917 0.85975193 0.59578985 0.5068221 #> Ctla2a        1.24079344 0.98451329 1.06031270 1.13176646 0.99305478 0.3547843 #> Ctxn1         4.63620134 4.70894211 4.78510560 4.55425034 4.60291026 4.9102322 #> Ctxn3         0.36793834 0.44103903 0.31762107 0.54951397 0.33353101 0.0000000 #> Cx3cr1        1.02819592 1.13498291 0.84360013 1.02390163 1.29212364 0.7194057 #> Cxcl14        2.70461369 3.01340845 2.61703676 2.92785002 2.96684799 3.2410235 #> Cyba          1.03626710 1.15289251 0.86405628 1.23125127 0.63976179 1.2564585 #> Cygb          1.56224133 1.62942100 1.54136833 1.74061875 1.27509267 1.2047964 #> Cyp2d22       1.12801427 1.03854008 1.18972937 1.23368207 1.79398667 0.3935818 #> Dbndd1        1.15359092 1.34742373 1.27477861 1.35473435 1.17078218 0.7872716 #> Dbndd2        2.48931976 2.38269055 2.34673722 2.41390483 2.46122731 2.5249243 #> Dcn           0.47717856 0.33911219 0.31729641 0.46515059 0.30710267 0.6245136 #> Ddn           4.74116866 5.10769279 4.80497790 4.76725155 4.88958648 5.7241280 #> Ddr1          2.30055485 2.04984165 2.16648979 2.02195473 2.26367690 1.2358701 #> Dio2          0.96343624 1.01739656 0.91295021 0.76877531 0.96959609 0.3908687 #> Dkk3          3.43279965 3.25478191 3.65911228 3.12123621 3.00627044 3.6254150 #> Dkkl1         0.84140367 0.69790200 1.07608973 0.75568738 0.97585842 0.0000000 #> Dnali1        0.11444348 0.09526922 0.10768508 0.11466140 0.20920214 0.0000000 #> Doc2b         0.85036485 0.79605063 0.64340435 0.67876817 0.88942003 0.5897834 #> Dock10        1.28970847 1.57049487 1.14562505 1.29309427 1.52662939 1.1203111 #> Dock4         2.29163340 2.21266447 2.43823628 1.83282468 1.96590270 2.4823942 #> Dpp6          3.17192427 3.06393903 3.25492974 3.23346631 2.74675531 3.3143334 #> Dsp           0.32584473 0.34822123 0.15779537 0.13951865 0.04866590 0.8175892 #> Dusp6         1.25874421 1.07733803 1.23134055 1.17891621 1.18342817 1.2890468 #> Dynlrb2       0.26238060 0.21789545 0.17695090 0.13195426 0.24472416 0.0000000 #> Ecrg4         0.45018284 0.32103283 0.61516957 0.49927573 0.82417133 0.3875768 #> Edn3          0.13911894 0.05176152 0.10439934 0.24100412 0.17549881 0.0000000 #> Ednrb         1.74214831 2.06030247 1.98828402 1.88385559 1.81672934 1.8173021 #> Efcab6        0.31995630 0.44039143 0.53089320 0.32225920 0.43844731 0.8746874 #> Efhd1         1.68085370 1.43353602 1.55741521 1.35112243 1.69179593 0.8484207 #> Efnb3         3.00627172 3.13310020 2.69940050 2.74742453 3.06518311 3.0503625 #> Egr1          2.14886893 1.96359869 2.38581323 2.15333255 2.12058191 2.9450464 #> Eln           0.09061027 0.12437313 0.18921346 0.15069912 0.28733407 0.0000000 #> Elovl1        1.85542908 1.68257937 1.39440717 1.26707570 1.48335618 1.3114013 #> Emilin1       0.15988581 0.06982516 0.02383032 0.08950430 0.19240122 0.0000000 #> Enkur         0.19258484 0.16684621 0.19068893 0.19143594 0.27889672 0.0000000 #> Enpp2         4.43558458 4.31703048 4.29793558 4.11931597 4.59425832 3.7667837 #> Enpp6         0.61638331 0.76178677 0.88997335 0.67357231 0.41861134 0.2387173 #> Epha5         2.38930589 2.35544274 2.31345803 1.94187464 2.14475995 2.2749732 #> Epha7         2.07360225 1.93747690 2.12807952 2.16424935 1.78071038 2.7985356 #> Epop          1.70575981 2.20123934 2.11031292 1.70178432 1.65954865 2.0015656 #> Erbb3         0.41722543 0.37231331 0.41477667 0.49706419 0.60270594 0.9611556 #> Erbin         2.45095864 1.96542277 2.62172379 2.34742867 2.29976160 2.4205313 #> Ermn          2.49706251 2.35035913 2.53116196 2.23101740 2.34756426 1.6429710 #> Esam          0.81955988 0.70087106 1.01971007 1.15689072 1.34596491 0.7461961 #> Etnppl        0.79577091 0.73976180 1.07222053 1.11998472 0.75859382 0.7478169 #> Evi2a         2.06586106 2.00947394 1.94122254 1.99571269 2.67085999 1.9128370 #> Ezr           1.70220561 1.86477689 1.47255180 1.38241032 1.93366439 1.1799208 #> F3            1.17849759 1.49972532 1.29002259 1.29397785 1.59195340 0.0000000 #> Fa2h          2.70702598 2.15260925 2.41984825 2.42349903 2.22907359 1.7402922 #> Fabp7         1.70844146 1.67648177 1.53028626 1.74460669 1.56617051 1.2506639 #> Fam131a       3.58531575 3.79288244 3.59295331 3.26990512 2.77153982 3.6632339 #> Fam163b       2.33735544 2.69302626 2.28224543 1.98406086 2.14181837 2.2600349 #> Fam20c        2.02595270 2.06933668 1.66449848 1.96555317 1.41006144 2.5059174 #> Fam234a       0.87158086 1.01867176 1.00146330 0.90913099 0.92536879 1.2068740 #> Fbln5         0.27933271 0.16453232 0.30820530 0.23993262 0.27045984 0.0000000 #> Fcer1g        1.31521853 1.40151280 1.16901605 1.22187509 1.33067651 2.1634638 #> Fgfr2         1.78640295 1.47183801 1.58647443 1.62810292 1.71937644 1.4072603 #> Fibcd1        1.06700564 1.12347821 1.12803125 1.14066428 1.31491645 2.0072588 #> Flna          1.09557690 1.29788690 1.28178968 1.09731220 0.93128353 0.8206811 #> Fmod          0.16746162 0.12864624 0.12528572 0.18129535 0.13869958 0.0000000 #> Fn1           1.10491890 0.98838442 1.10338559 0.92355011 1.00517314 0.6760625 #> Foxj1         0.58587705 0.65336904 0.39514923 0.46595485 0.55686934 0.0000000 #> Foxp2         0.98678529 1.02917465 1.17179142 1.19784971 0.73538372 0.3436696 #> Frmd8         1.46489626 1.19688364 1.45831748 1.18313898 1.21407728 1.1267537 #> Fxyd1         3.14185573 3.03257244 3.09423916 3.31509575 3.39728196 3.1929004 #> Fxyd6         2.76320510 2.76118346 2.82867431 2.47509575 3.00110702 1.6754807 #> Fxyd7         4.24985766 4.36743132 4.51523820 4.11282865 3.66635135 3.9561871 #> Gab1          1.50292378 1.59756945 1.69453646 1.46556971 1.69383067 1.0986573 #> Gabra4        2.60497866 2.43929779 2.57947094 2.71908436 2.31227760 2.8052710 #> Gabra5        2.08271045 2.19042809 2.35036426 2.17363466 1.86402028 2.8035044 #> Gabrd         2.41994887 2.39963813 2.38924771 2.08800067 2.15819546 2.3539306 #> Gad1          3.11135615 2.86412058 3.21870359 3.36647334 2.93370810 2.2695200 #> Gad2          2.58905667 2.66586350 2.23435549 2.35198533 2.70805407 1.8277225 #> Gal3st1       1.58753819 1.44401350 1.29638097 1.31334863 1.32980736 1.8481187 #> Galnt6        0.79259003 0.86166055 0.59304957 0.62816013 0.94087487 0.3242240 #> Gamt          2.33360093 2.02585528 2.10745674 2.14681391 2.43994362 2.0382807 #> Gatm          3.55985522 2.98305682 3.24247224 3.01039727 3.50364606 3.8087241 #> Gbp4          0.14737745 0.05765225 0.07565243 0.32623728 0.05709014 0.2666210 #> Gdf11         0.89456013 0.78694878 0.85317097 0.80486474 1.06354474 0.5940782 #> Gfap          3.12155168 3.24198121 3.03211737 2.75172258 3.35167866 3.7201425 #> Gja4          0.12059199 0.22431300 0.18452209 0.26626134 0.32685198 0.0000000 #> Gjb1          1.63349091 1.24850559 1.23920304 1.25310596 1.40097070 1.0983238 #> Gjc1          0.25997653 0.40032750 0.38944777 0.32112771 0.39605926 0.9215004 #> Gjc2          1.50615090 1.47433026 1.34343557 1.24223850 1.31123383 2.0603772 #> Gjc3          2.05012612 2.15068339 1.93199599 1.85360953 2.02416301 0.9383281 #> Gkn3          0.61270038 0.38462317 0.52145131 0.66694451 0.19017267 0.0000000 #> Gldc          0.80769231 0.98218429 0.87414267 0.99385658 0.84366451 0.6635751 #> Gltp          2.15804351 1.84663313 2.04223111 1.76176658 2.14830600 1.9952998 #> Gm13889       1.46735997 1.54319311 1.51447377 1.42448664 1.08310793 0.7766758 #> Gm14964       0.50914628 0.24641944 0.35409220 0.44864513 0.24150887 0.0000000 #> Gm19935       0.35745016 0.29221866 0.23263621 0.21978974 0.42931808 0.0000000 #> Gm2115        0.82234763 1.22818773 1.03188783 1.23356153 1.12760221 1.2121439 #> Gna12         3.30737745 3.34082808 3.26309190 3.23263758 3.30171653 3.4313574 #> Gng11         2.51158658 2.82844009 2.39374372 2.58329008 2.65677985 2.6251262 #> Gng4          0.93611513 0.72142584 0.89823297 0.87199592 0.72353001 1.9499755 #> Gpr161        0.61508999 0.70157514 0.60472709 0.51476430 0.53725598 1.3769960 #> Gpr17         0.95594366 0.75231028 0.93072472 0.95879073 1.21728945 0.6845804 #> Gpr37         3.10942139 2.62248215 2.73938171 2.69477256 2.76208140 3.3843659 #> Gpr4          0.32994338 0.38349617 0.51193651 0.56655929 0.48262546 0.5230345 #> Gpr62         1.17578799 1.10082468 1.17761935 1.16650569 1.15881284 0.6983290 #> Gpr88         0.93007302 0.57660156 0.74518927 0.68161931 0.74959412 0.0000000 #> Grb14         3.42052836 3.36173213 2.77046062 3.08122822 3.00375570 2.9427657 #> Gria1         4.12795684 4.34492850 4.29095060 4.17984545 4.00398837 4.2329121 #> Gria2         4.59242525 4.64033571 4.81893386 4.40964277 4.66819325 5.2594264 #> Grik1         0.55123294 0.54706355 0.40812361 0.55433660 0.31160914 1.1483943 #> Grm1          1.67262407 1.55697786 1.67076335 2.15167949 1.61600199 1.3251047 #> Grm2          0.96663539 0.96544707 1.11083722 0.84242663 0.70178515 0.6245136 #> Grm4          0.82379382 0.55970502 0.91102293 0.77318015 0.76956595 0.9669871 #> Gsn           3.53057502 3.09333206 3.24377538 3.28817732 3.30329127 2.3946310 #> Gss           1.23676224 0.97623337 1.16285378 1.02848915 1.06035712 0.2504086 #> Gstm7         1.48500928 1.42703276 1.16225013 1.19766905 1.33959392 1.6747068 #> Gzma          0.07190143 0.11410847 0.08815679 0.16416438 0.15574311 0.2504086 #> H2-D1         2.26112351 2.59192070 2.24441472 2.23564957 2.31971537 2.4143860 #> H2-K1         1.33428078 1.59535735 1.74512473 1.78442778 2.14500032 1.5905231 #> H2-Q4         0.12644221 0.13312345 0.13251285 0.13326698 0.36279216 0.0000000 #> H2-Q7         0.07293258 0.07103938 0.11838827 0.19723209 0.14273118 0.0000000 #> Hap1          1.59121288 1.59382394 1.22734443 1.28449310 0.83700513 2.0214657 #> Hapln2        0.97869249 0.59951972 0.77294983 0.71085218 0.94971053 0.6425065 #> Hba-a1        6.77230847 6.68048781 6.62388866 6.48718732 6.78048518 6.7279361 #> Hba-a2        6.31671961 6.30178206 6.17605155 6.06596014 6.26167421 6.2308667 #> Hbb-bt        5.73427869 5.85482772 5.61558173 5.57224388 5.69711546 6.0253158 #> Hexb          3.00911612 3.37099821 3.18495493 3.30895148 3.64220022 2.5958016 #> Hhatl         0.93681733 1.06462245 0.98033459 1.11457753 1.24083725 1.0382275 #> Hhip          0.30280717 0.48120264 0.35418673 0.58559193 0.56028980 0.2666210 #> Hlf           3.24839637 3.18753475 3.31310560 3.16226642 3.13612021 3.0091062 #> Hmgb2         1.00275853 0.66241499 0.74258912 0.52707685 0.40160431 0.6541978 #> Hmgn2         2.06603581 2.04159933 1.99690865 1.76837367 1.84263924 2.1922319 #> Homer2        1.96389655 2.22129055 1.81406114 1.84286080 2.66051456 1.6458791 #> Homer3        1.26643552 1.15517582 1.11972968 1.01678407 0.71873936 1.6754294 #> Hopx          2.84716359 2.93676383 2.80524269 2.57688789 3.64036484 2.4846092 #> Hpca          5.42154696 5.77634500 5.65291624 5.30758332 5.48050058 6.0249872 #> Hpcal4        4.41959519 4.53852396 4.64722880 3.90770677 4.57671568 4.6085595 #> Hrh3          2.26063005 1.67483898 2.03100649 2.01218617 1.34537819 1.2703098 #> Hs3st2        1.12198006 1.02177563 1.24062153 0.97789314 0.88637304 0.5769102 #> Hs3st4        2.39012844 2.20126636 2.49203687 2.68146833 2.47900039 2.7906412 #> Hsd11b1       1.26986044 1.47931030 1.35631908 1.65409190 1.51951132 1.7326963 #> Hspb1         0.52971873 0.70520439 0.61274014 0.46869655 0.57186807 0.0000000 #> Hspb8         0.65264924 0.53639950 0.44501817 0.53386240 0.82568828 0.3703106 #> Htr2c         0.72402001 0.71674657 0.94921040 0.83540190 0.72370414 1.3014022 #> Htr3a         0.20623614 0.25779001 0.21562203 0.29249946 0.51795632 0.0000000 #> Icam5         2.81103374 2.98606878 2.87476056 2.66370075 3.01691101 3.2118431 #> Ick           1.33976866 1.21525841 1.35199145 0.94688793 0.97359053 0.6602028 #> Id1           1.62154126 1.37257775 1.28516523 1.47026285 1.89182064 1.2202405 #> Id3           2.94529544 3.10331664 2.78821879 2.78836190 3.03403342 2.3991619 #> Ifitm2        0.96906880 1.09064416 0.90269673 0.95391429 1.21353976 1.4021251 #> Ifitm3        1.66376351 1.90122708 1.56203622 1.98765479 2.12591695 1.2725191 #> Igfbp2        1.50043225 1.40823846 1.38463073 1.42376461 1.60911510 0.8100896 #> Igfbp4        2.56466752 2.20266690 2.60079633 2.39337399 2.70624219 3.0103030 #> Igfbp6        1.65030632 1.57194646 1.75294453 1.63411478 1.10892966 0.8347239 #> Igfbp7        1.77284339 1.99886593 1.93657362 2.05040476 2.33193718 1.0121604 #> Igkc          0.13555940 0.24448284 0.20547536 0.14835237 0.10338205 0.2504086 #> Igsf21        1.68603070 1.22147136 1.83816298 1.36185664 1.39103066 1.7312896 #> Il1rap        1.83932810 1.47409370 1.46592131 1.65888997 1.58001808 1.2359937 #> Inmt          0.13863241 0.05262011 0.10527864 0.03996412 0.00000000 0.0000000 #> Ipcef1        1.55486089 1.28809917 1.90560329 1.18308943 1.57157324 2.0242319 #> Iqgap2        0.90895923 0.78908630 0.98281143 0.83299641 0.98028629 1.0300316 #> Isg15         0.66931028 0.84537077 0.61051327 0.68058352 0.64991891 0.3935818 #> Itgb4         0.65964180 0.92831686 0.63561418 0.75968338 0.75914514 0.5053382 #> Itih3         1.13630590 1.27197529 1.23250522 1.54389062 0.89307587 0.7474588 #> Itih5         0.66908579 0.61358907 0.66298569 0.88788154 0.66934306 0.2564135 #> Itpka         3.38790169 3.77027935 3.64104099 3.56730816 3.20722970 3.6555564 #> Itpr2         0.68257703 0.50138653 0.75204281 0.89185105 0.91117434 0.3474831 #> Kcnab1        2.77547276 2.98507524 2.92440955 2.70075041 2.18772552 3.4374489 #> Kcnab3        1.30572178 1.20773147 1.52367819 1.07447598 0.74673275 0.4728139 #> Kcnc2         2.85238527 2.59184448 2.80120583 2.81393417 1.82541417 3.5675709 #> Kcng2         0.81096094 0.99894463 0.76329563 0.97884792 0.37033260 0.9943758 #> Kcnip2        2.25376431 2.23553466 2.76070190 2.34762087 2.53952800 3.1093760 #> Kctd12        2.20413606 2.03580757 2.30484518 2.27816759 2.13535177 2.3238084 #> Kctd4         1.22576360 1.28181598 0.87460770 1.13942354 0.62521228 1.2614962 #> Kit           0.56833963 0.53109779 0.81175354 0.88306169 0.87098881 0.6870762 #> Kitl          1.41888612 1.55266742 1.57897181 1.31670195 1.02985082 1.0221684 #> Klk8          1.14965101 1.48560121 1.13405184 1.37458564 1.32795052 1.4736128 #> Lamb2         0.89661890 1.11155264 0.88756112 1.02605030 1.13427781 1.4909428 #> Lamp5         1.72564609 1.84724258 2.09268336 1.37732734 1.24490303 2.3696344 #> Laptm5        1.75628277 1.68232228 1.38838393 1.44405341 1.98893577 2.1105590 #> Lbp           0.21986917 0.28440076 0.23720866 0.31418215 0.25051624 0.0000000 #> Lcat          1.48401002 1.79499129 1.41899153 1.42503144 1.49609368 1.4704056 #> Lcn2          0.11001342 0.23756140 0.08109622 0.07181696 0.23086015 0.0000000 #> Lct           0.55087056 0.90609934 0.47985112 0.37742620 0.63297348 1.2735187 #> Lef1          0.78796878 0.76062726 0.78915342 0.78366249 0.47511347 0.2564135 #> Lefty1        0.53841045 0.66308465 0.78954952 0.70686947 0.71217809 0.8436765 #> Lgals1        1.43037952 1.64432200 1.67221114 1.58771425 1.82899585 0.3436696 #> Lgi4          1.28584162 1.08700341 1.11107934 1.17937170 1.69896078 0.5068221 #> Lhfp          1.30109693 1.69313788 1.63660291 1.29043961 1.15576850 1.9859031 #> Lhfpl3        1.20532422 1.39255353 1.12989133 1.16122852 0.66136299 1.4522671 #> Lims2         1.27731649 1.25909487 1.00587185 1.06166966 1.35833723 1.0815706 #> Lingo3        1.08347499 1.27753513 1.01662036 1.12567323 0.70963331 1.2846233 #> Litaf         1.76599530 1.58304036 1.59402701 1.46871417 1.80087344 1.7484272 #> Lmo1          1.68561146 2.17490628 1.99279555 2.00818965 1.59998363 2.9855520 #> Lmo3          2.42932341 2.62194967 2.67226522 2.35574188 2.40708808 2.5245086 #> Lpar1         2.09900245 1.58915403 1.77779593 2.03084932 1.87624640 1.6533343 #> Lpl           0.74898467 0.73794230 0.84582531 0.73030980 0.96083767 0.6531023 #> Lrrc10b       1.20742881 1.61461967 1.26439875 1.45805132 1.47514670 1.9429702 #> Lrrtm3        1.33048713 1.24589537 1.37982293 1.11962727 0.75626311 1.0594517 #> Lrtm2         1.78561984 1.62725178 1.82437791 1.91200291 1.25072335 1.0239489 #> Ly6a          2.45182370 2.27519555 2.34222985 2.60751217 2.75894028 2.0413342 #> Ly6c1         2.47782910 2.71577070 2.59802701 2.53117760 2.70659596 2.7301925 #> Lyz2          0.64063495 0.29592774 0.40658358 0.50297824 0.68417195 0.3474831 #> Mag           5.12500474 4.67191908 4.65072225 4.92307953 4.78339942 5.0692949 #> Mal           5.52489949 5.32136589 5.25246346 5.50360680 5.67157535 5.4366287 #> Man1a         1.17187286 1.31869487 1.24676725 1.17223778 0.97405462 2.2950651 #> Map4k4        2.32223513 2.05759704 2.32236026 2.17313011 2.14955074 2.3387905 #> Matn2         1.02592291 1.31043133 1.24722461 1.06996228 1.28397813 1.0234107 #> Mb21d2        1.88319470 1.57101132 1.53801536 1.78219219 1.39135704 1.3609037 #> Mcam          1.17115913 0.82098156 0.95253117 0.80677507 0.93344433 0.9827394 #> Mdk           1.58694084 1.61605846 1.61063336 1.68377010 1.44990012 1.1585555 #> Meig1         0.29109497 0.27586998 0.35000531 0.26306041 0.28185530 0.5090908 #> Mgp           1.66148784 0.78793329 1.50269980 1.41650584 1.02778485 0.3436696 #> Mia           0.26367437 0.31952226 0.25723706 0.29690062 0.26626194 0.0000000 #> Micall1       1.05263096 1.00082961 1.24536063 1.03367055 1.12657206 1.6637881 #> Mmp17         2.44647351 2.48596867 2.83821830 2.60643100 2.31549141 1.9436145 #> Mobp          6.59632749 6.31520717 6.49676468 6.46728343 6.69364109 6.2946899 #> Mog           3.85434500 3.66219244 3.74512123 3.72785284 4.14058242 2.8615374 #> Mpped1        2.61638152 2.52593116 2.79221724 2.09534555 2.49422851 2.6844707 #> Msx1          0.27092155 0.36375093 0.21662745 0.36830708 0.12867615 0.2564135 #> Mustn1        0.26758770 0.09690683 0.16914040 0.12959606 0.00000000 0.0000000 #> Myh11         0.19846986 0.24588139 0.22678101 0.26793807 0.10543429 0.4196490 #> Myl4          1.18020420 1.28964125 1.57277445 0.96930487 1.49492177 0.9777995 #> Myl9          1.26493377 1.38354292 1.03635801 1.13510805 1.44268258 0.6635751 #> Myo1d         0.62446089 0.40878407 0.64095163 0.47877072 0.52474848 0.6478262 #> Myo5b         1.08991437 1.30942463 1.27752362 1.23667112 1.09982000 1.0071975 #> Myoc          0.58313508 0.62531156 0.54259460 0.46842173 0.37242729 0.2564135 #> Myrf          1.68052605 1.50964521 1.51786885 1.71116937 1.51161493 2.7020055 #> Ncald         4.47619030 4.63623903 4.66581202 4.35115584 4.38541089 4.7700048 #> Ncf2          0.19577536 0.30744226 0.28517955 0.04401388 0.22083523 0.0000000 #> Ndnf          0.51310409 0.58195774 0.38392762 0.50161323 0.43649448 0.3875768 #> Ndrg1         3.13863431 2.61730487 3.02006093 2.98727188 3.46588636 1.8026284 #> Ndufa4l2      0.76029564 0.59436411 0.42263532 0.59691739 0.75663938 0.2564135 #> Necab2        2.21168530 1.90715240 2.26504854 2.39376640 2.30668914 1.1476453 #> Nefh          2.05418571 2.14532273 2.08433434 2.32932866 1.89647811 2.7000541 #> Nell1         1.84269481 1.74220880 1.68494960 1.88827253 1.65591025 0.9011789 #> Neurod1       0.67678261 0.81565899 0.80869242 0.72888077 0.64958901 0.9152128 #> Neurod2       2.39954962 2.38922135 2.53563564 2.49431276 1.92186944 2.1457090 #> Neurod6       2.63428566 2.50013668 2.77025341 2.64586781 2.55916111 2.4965476 #> Nexn          0.56948760 0.48736435 0.47581899 0.49945862 0.27890296 0.2564135 #> Nfasc         3.34835525 3.13436419 3.45235108 3.13689334 2.88211743 3.9146409 #> Ngef          2.91242099 2.74592475 3.24004763 2.67797217 2.64117361 2.4591740 #> Nid1          0.21553865 0.17652907 0.19669062 0.21101093 0.57025089 0.0000000 #> Ninj2         0.44872324 0.37088683 0.60350690 0.38235840 0.30128077 0.3758855 #> Nkx2-2        0.56734724 0.56550690 0.48407154 0.49525147 0.43224503 0.0000000 #> Nkx6-2        1.90055006 1.39579282 1.44117547 1.54679054 1.80681039 1.7592271 #> Nnat          4.39845107 3.86182696 4.01859780 4.37346434 4.21748417 4.5339505 #> Notch1        0.73795047 0.57299505 0.76784734 0.79697664 0.79244038 0.3703106 #> Npas1         0.33784649 0.56748473 0.53158683 0.63813928 0.44098006 0.7215881 #> Npas3         0.72428750 0.61893080 0.75975639 0.67456185 1.19424107 0.0000000 #> Nptx1         3.44951987 3.60426494 3.51022093 3.32857508 3.53222106 3.4367115 #> Nptxr         3.98905107 4.10408925 4.54218333 4.02744883 3.77647703 4.0245328 #> Npy           2.70571597 2.42263758 2.73864823 2.31508768 2.82614785 1.9942862 #> Npy2r         0.57723444 0.84627539 0.80665137 0.67953308 0.73797688 0.4196490 #> Nr3c2         1.74298171 1.99898592 1.65044180 1.59818056 1.15467732 2.5707193 #> Nr4a1         0.64554738 0.73686764 0.99578525 0.71031972 0.25864240 0.2526861 #> Nr4a2         1.22250797 0.88546766 1.12822732 0.84090078 1.14285461 1.1404969 #> Nrip3         2.86404839 2.54543673 2.89416401 2.69424073 2.64936601 2.2236894 #> Nt5dc2        0.71051009 0.77568089 0.64458904 0.80447504 0.71280335 1.2502371 #> Ntng1         1.66959193 1.52111510 1.55641161 1.78292903 1.47126781 1.4775886 #> Nupr1         0.34593129 0.60897633 0.28826812 0.43127770 0.34710384 0.0000000 #> Nxph3         0.98709456 0.70831593 1.11105497 0.66187736 0.85333024 0.4936364 #> Nxph4         0.22263899 0.21444872 0.23321410 0.21511268 0.21381214 0.5123107 #> Odf3b         0.19472127 0.11610201 0.15056997 0.05604758 0.14914976 0.3703106 #> Ogfrl1        4.06706884 4.06803553 4.44373436 4.29416184 4.30641033 4.0158758 #> Olfm2         2.16938520 2.03888319 2.31740773 1.92146082 2.15946392 2.4801375 #> Olig1         4.59979138 4.17669248 4.25667919 4.33405253 4.42979786 2.9726222 #> Olig2         1.60203185 1.34909962 1.26060560 1.09819003 1.39070009 2.4657778 #> Opalin        3.34713558 3.25712117 2.96589080 2.98397388 3.26812150 3.1494090 #> Orai2         1.69283039 2.08994082 1.92667785 1.68048975 1.55877682 1.6261425 #> Otud7b        1.54728064 1.44846861 1.72710033 1.37022748 1.55159842 1.0621922 #> P2ry12        1.37878842 1.24887876 1.19884558 1.45998888 1.78452703 1.7301314 #> Padi2         1.47837486 1.10605178 1.07137082 0.92795207 1.38944203 0.4613923 #> Paqr5         0.28548196 0.34937823 0.26226962 0.31439479 0.41305397 0.1371682 #> Patj          0.94550036 0.73674309 0.75330778 0.87271454 0.90792393 1.0548719 #> Pbxip1        1.34938308 1.33038450 1.52504316 1.15143540 1.19436056 2.3029478 #> Pcdh20        1.02000367 1.35575835 1.33769133 1.26211034 0.83403675 1.7809842 #> Pcdh8         1.16073414 1.37681956 1.02213157 1.29615729 0.97496592 1.6198937 #> Pcolce        0.40835217 0.17567545 0.31943003 0.44060403 0.47988101 0.0000000 #> Pcp4l1        2.97992708 2.96077966 2.92023724 3.06136601 2.54141375 2.1498052 #> Pde1a         2.60443179 2.51600334 3.10065238 2.33133041 2.97094728 2.2677380 #> Pde8a         0.95549842 0.97877848 0.91299388 1.06086870 1.00052882 0.0000000 #> Pdgfra        0.78804945 0.93572625 1.03361028 1.15029471 0.90386397 0.7194057 #> Pdgfrb        0.53134815 0.69153085 0.59398354 0.55032243 0.82027150 0.2666210 #> Pdlim2        2.64100657 2.03304145 2.19677138 2.17522177 2.62607356 1.1154087 #> Pdp1          3.01037972 2.98742459 3.06598155 3.05666212 2.75897253 2.8148635 #> Pdyn          0.79158555 0.59079410 0.58304153 0.54279423 0.19734941 0.5758145 #> Penk          1.28150874 1.48804379 1.37118419 1.07752180 1.50500529 1.8658537 #> Pglyrp1       0.88571095 0.96683044 0.80009758 0.93906298 1.21806059 0.5068221 #> Phgdh         3.16186234 3.45444131 3.10165196 3.33673834 3.61300815 3.2276782 #> Phkg1         0.85701198 0.92818993 0.80632925 0.91264376 1.24705822 0.0000000 #> Phldb1        2.72674466 2.28226498 2.33404266 2.08710097 2.45410574 2.9918993 #> Pitpnm2       2.15711440 2.59388505 2.21222659 1.94021692 2.44767598 2.7039998 #> Plaat3        2.50487243 2.51184225 2.66509723 2.22563314 3.00090855 2.8468772 #> Plat          1.14540299 1.24250895 1.21317463 0.99302566 1.10865702 0.9816925 #> Plcb4         2.21541850 2.22112223 2.19114756 2.49093229 1.48135714 1.5824280 #> Plcxd2        1.64210575 1.30250470 1.60803209 1.32447479 0.56780985 0.4196490 #> Plekhb1       5.26989022 5.08766180 5.33292848 5.29172376 5.43168172 5.4000485 #> Plekhg1       1.63237476 1.45942596 1.58926683 1.67521499 1.07618807 0.9779528 #> Plekhg3       0.93540440 0.69588822 0.70566064 0.88679433 0.85559176 1.0493189 #> Plekhh1       1.74894875 1.68160253 1.50615974 1.50661273 1.58905469 1.2009855 #> Pllp          3.22415451 3.21743067 3.01274890 3.03544285 2.74681104 2.5136211 #> Plod1         1.12228671 1.27754944 1.09295150 1.23896140 1.13073327 1.2264941 #> Pltp          2.21518165 2.02049597 2.09493581 1.95665173 2.49435424 1.3305275 #> Plxdc1        1.22437375 1.44472440 1.42370524 1.50672610 1.12087763 0.8329171 #> Pmp22         1.47344250 1.44434883 1.32383976 1.40805034 1.14008930 1.1259126 #> Pou3f1        1.86305306 2.03310718 1.83260238 1.72681881 1.72651282 3.0430671 #> Ppm1e         3.14150738 3.06855235 3.37154134 3.05397217 3.21361904 3.4547617 #> Ppp1r14a      3.34120410 2.99944064 2.85879699 2.91610667 3.11068072 3.0766945 #> Ppp1r1a       4.01406097 4.69827590 4.31408620 4.26538646 4.36988396 4.3554185 #> Ppp1r3c       1.24356108 1.19575277 1.30680502 1.07985846 0.81875439 0.2666210 #> Prdm8         1.04292224 1.27702526 1.13657692 0.83121952 0.77800741 1.6912317 #> Prelp         0.89738015 0.60641398 0.70944223 0.79762136 0.64964328 0.9521178 #> Prkcd         2.57324385 2.61354668 2.38756697 2.87293417 2.13261309 2.2796092 #> Prkcg         4.14188600 4.17863055 4.46934041 4.14347947 3.94561260 4.3279904 #> Prkch         0.47655716 0.50607402 0.56185862 0.61083942 0.73205288 0.6261503 #> Prkcq         0.57988915 0.51531037 0.72080768 0.76230445 0.99688914 0.6372650 #> Prox1         1.12087834 1.34728136 0.86501440 1.33385558 0.96045485 1.0248782 #> Prph          0.17354909 0.25141501 0.14536617 0.34584096 0.00000000 0.3242240 #> Prr18         2.69529293 2.32592581 2.10526236 1.93626405 2.62882326 1.7417281 #> Prr5l         0.82610324 0.76269196 0.57957434 0.65938983 0.55913009 0.6862699 #> Ptk2b         4.25083755 4.58330163 4.44088016 4.56974541 4.09386716 3.4133443 #> Ptpn3         2.03505854 1.71841934 2.02237954 2.18976046 1.75715473 1.6801179 #> Ptpn4         2.95295578 2.77964915 2.93667271 2.84916240 2.78932644 3.1403560 #> Ptprb         0.78607075 0.42205639 0.82417310 0.58637400 0.96141466 1.2463021 #> Pvalb         3.28835059 3.07327787 3.23604114 3.04990097 3.21770290 2.9380384 #> Qdpr          5.23889427 4.77963136 4.90730301 4.97703997 5.36660249 4.9643569 #> Rab37         0.90145605 0.52665608 0.58522806 0.49870197 0.47213690 0.2564135 #> Rab3b         1.77459139 1.75638043 1.64899950 1.56796461 1.60138382 1.6748753 #> Rab3c         3.43988290 3.25891694 3.48259901 3.36089800 3.40901135 3.1297855 #> Ramp3         2.10765261 2.07922426 1.91348009 2.04867784 2.03535612 1.8926492 #> Ranbp3l       0.03242664 0.27743058 0.04010778 0.11302941 0.00000000 0.2824807 #> Rapgef5       1.96906516 2.42593863 2.26278751 1.91891904 1.81402583 1.9696632 #> Rarres2       1.15314942 0.79457001 0.76443331 0.97133349 1.13558301 0.7671321 #> Rasd1         1.29763417 1.41015801 1.31560461 1.43060189 1.44304974 1.1781116 #> Rasgrf1       4.15342599 4.27961595 4.33009229 4.13530341 4.16508849 4.5934711 #> Rasl10a       1.54192423 1.73460468 1.60630631 1.35696467 1.33128251 1.7335148 #> Rbp1          1.36164224 1.36587083 1.21432986 1.38511940 1.12779742 0.5328893 #> Rcn3          0.41078586 0.24734435 0.67825434 0.56174438 0.25650623 0.5212264 #> Reep3         1.45149503 1.30521540 1.63704715 0.88291932 1.55062552 2.0238562 #> Reln          0.86476575 0.83080429 1.00051023 0.96892689 0.77288492 0.1371682 #> Rflnb         0.73297921 0.58146422 1.01514315 1.03543508 0.54574352 0.9564919 #> Rfx3          1.19477919 1.18544260 0.89180005 1.05139857 0.66943743 0.8861989 #> Rgs12         1.22645589 1.21384074 1.12066235 1.14204164 1.11072187 1.1780739 #> Rgs14         1.49998504 1.67943201 1.31174597 1.36534501 1.12748511 1.3400020 #> Rgs16         0.95357582 0.77241859 0.79247107 1.00855874 0.53107269 0.4951308 #> Rgs3          1.48949093 1.63216949 1.50739170 1.75153065 1.47722520 1.1313837 #> Rgs4          3.46613950 3.57801726 3.66691030 3.69097731 3.26991343 2.2863177 #> Rgs5          2.02183992 2.33216198 2.25644205 2.17722922 2.79744251 2.4141827 #> Rhog          2.06081008 2.00638986 2.06360270 2.08136653 1.95855083 1.2839779 #> Rims2         2.29191029 2.32112167 2.29767291 2.16756388 1.45935355 1.7251028 #> Rims3         2.76819976 2.12361322 2.58159429 2.79867693 2.35592738 2.2271525 #> Rlbp1         0.77307162 1.09270069 0.79549368 0.85825563 0.41168285 0.7177937 #> Rnf130        1.98574201 2.22208533 2.13350127 1.94480595 2.01370330 2.0420282 #> Rora          2.72090769 3.14506075 2.91905783 2.85151295 2.69507749 1.8534747 #> Rprm          1.75743433 1.72853508 1.58142372 1.53667923 1.82211970 1.8632513 #> Rprml         3.07675148 2.89096108 3.24192141 3.01097068 3.15841849 3.0885792 #> Rsph1         0.27474608 0.16513017 0.23973773 0.20146095 0.31590239 0.6090279 #> S100a11       0.55821875 0.46909211 0.50687831 0.66359584 0.74313723 0.0000000 #> S100a6        2.42891377 2.33734168 2.42540182 2.09391026 2.41906585 1.8676702 #> S100a8        0.39841914 0.31742352 0.40403127 0.53159406 0.58116865 0.3474831 #> S100a9        0.45259758 0.22712797 0.47389134 0.48781378 0.40056456 0.1371682 #> S1pr5         1.28460786 0.98366694 0.86736555 0.86549324 0.81975136 0.7280132 #> Satb2         0.99178482 0.81658359 1.09482562 0.50963007 1.03455500 0.7250296 #> Scn3b         2.40820926 2.84722996 2.85438349 2.75251782 2.69454073 3.5098934 #> Selplg        1.46198870 0.95436411 1.26787210 1.27829013 1.58337965 0.8879271 #> Sema3c        0.79138634 0.46456785 0.85844214 0.52721566 0.30380740 0.6305185 #> Sema4d        2.03092581 1.86271608 1.89149412 1.77346033 1.74305382 1.3499372 #> Sema5a        1.74619383 1.75016526 1.40190974 1.65337013 1.00666994 2.4115971 #> Sept4         4.72125229 4.40519236 4.25235384 4.46364870 4.96708134 3.8270092 #> Serinc5       1.85389862 1.76190306 1.80870776 2.08593379 1.58414402 1.5293168 #> Serpina3n     1.23737941 1.38114731 1.07596381 1.15230991 0.81359560 1.8331696 #> Serpinb1a     1.16808584 0.95532207 0.97708237 1.03182567 1.20150453 0.5758145 #> Serpinf1      0.49689128 0.67245412 0.40614711 0.52461938 0.31016114 0.1371682 #> Serpinh1      0.77813139 1.16936908 0.77033088 0.75731999 0.68906297 0.2824807 #> Serpini1      3.30040994 3.29933835 3.60183670 3.19300777 3.26845870 3.4041277 #> Sertm1        1.35580865 1.46341900 1.25682736 1.08935281 1.13479998 2.0082069 #> Sez6          3.45947190 3.30180445 3.77961671 3.45034173 3.07211639 3.7882936 #> Sgpp2         0.93686313 0.51241116 0.76483544 0.87672988 1.07059811 0.9898886 #> Sh3gl3        2.42227350 2.18739040 1.96729858 2.11239853 2.11841189 2.1834760 #> Shisa6        1.40168284 1.60698652 1.61333210 1.72421787 1.27669855 2.1950510 #> Shisa8        0.41727316 0.26971254 0.31966186 0.31993890 0.47023109 0.8756489 #> Shisal1       1.63781235 1.58658496 1.63079867 1.72592166 1.27391482 1.8356435 #> Shox2         0.82458200 0.67605161 0.75661388 0.85502706 0.76525942 0.4929982 #> Siglech       0.82944635 0.65626474 0.78482842 0.55325551 1.51082291 1.0615638 #> Sipa1l3       1.46441270 1.87109964 1.53637225 1.57753377 1.71206764 1.7216736 #> Sirt2         4.50161397 4.42130053 4.35249062 4.42498751 4.26085093 4.2228421 #> Slain1        2.82831747 2.25443731 2.49507274 2.66298154 2.19900915 2.3975510 #> Slc12a2       2.61481381 2.48155481 2.45199470 2.58709031 2.28611363 2.7799110 #> Slc12a4       0.98062041 0.87515793 0.89853208 0.65237371 0.98230366 0.9809346 #> Slc13a4       0.32992903 0.09337211 0.14992969 0.18884589 0.12359795 0.0000000 #> Slc17a6       1.62291007 1.66658407 1.77797658 1.80386313 1.27191228 1.6023952 #> Slc17a8       0.17280684 0.10455841 0.28782050 0.04330752 0.17635608 0.0000000 #> Slc22a8       0.62010027 0.65232266 0.44280445 0.57180855 0.71534210 0.7740998 #> Slc24a3       3.34455169 3.06058189 3.38792495 3.35547202 2.89063604 2.6629890 #> Slc30a3       1.89363523 1.69620000 1.88026617 1.62812203 1.71538297 1.7453630 #> Slc32a1       1.59437851 1.52183497 1.70916749 1.78111100 1.95042305 1.1983679 #> Slc38a5       0.21605026 0.17444448 0.20752276 0.34937317 0.55424647 0.0000000 #> Slc44a1       3.03127766 2.73384982 2.76202669 2.62223174 2.91734606 2.2830737 #> Slc4a2        1.39994031 1.55371697 1.29468289 1.37431593 1.41444369 0.6038967 #> Slc6a11       2.61604162 2.62012288 2.50593623 2.66856608 2.30484151 2.5784086 #> Slc6a13       0.33661496 0.22670062 0.23966019 0.37448920 0.20501486 0.0000000 #> Slc6a9        1.76829554 1.79664252 1.68823316 1.74618441 2.14463735 1.3979006 #> Slc7a11       0.64926494 0.63902218 0.68024411 0.86961091 0.64560305 1.0871200 #> Slco1c1       1.54177117 2.06311666 2.01561258 1.99786085 1.87544335 2.5707408 #> Slitrk6       0.42813022 0.21470071 0.48738984 0.42940442 0.22577354 0.0000000 #> Smim1         1.09552768 0.96792008 1.05119351 1.16738202 1.91408576 1.7977655 #> Snca          4.62706705 4.73126980 4.85586143 4.61241596 4.60789463 5.0600640 #> Sncg          0.40304031 0.28474379 0.38255750 0.38044514 0.42697491 0.0000000 #> Sod3          0.71522440 0.61108203 0.37187077 0.72537202 0.70488595 0.7834772 #> Sowaha        2.11056381 2.81955510 2.20716759 2.34804256 2.87009279 2.6319992 #> Sox10         1.87523360 1.68483776 1.86954113 1.71488287 1.81402802 1.9575917 #> Sox11         0.72569496 0.98116963 0.90692982 0.91801201 0.78341938 1.3880737 #> Sox18         0.55977904 0.81528063 0.42582977 0.60139038 0.38481028 0.6037182 #> Sox8          1.05032952 1.22311243 1.03490994 0.88191218 1.22329141 1.1165167 #> Sox9          1.52919580 1.82629178 1.73707493 1.30671993 2.10794802 0.8765589 #> Spag8         0.07313899 0.11994541 0.07826858 0.07973453 0.24626610 0.0000000 #> Spink8        1.27139206 1.48848462 1.41945551 1.55335746 1.84664197 1.9907929 #> Sst           3.73684749 3.66376591 4.00841752 3.75201838 4.13871179 3.5194932 #> St6galnac5    2.16976535 2.53073593 2.28547222 2.07026295 2.41378148 2.3171005 #> Stab1         0.43845358 0.42299714 0.40552315 0.36719874 0.45872728 0.2504086 #> Stac2         1.37615453 1.44983037 1.68280224 1.10862295 1.67586917 0.9597937 #> Stk32c        2.43264753 2.31827006 2.27191999 2.16800239 2.11622851 1.1254119 #> Stx1a         2.43108017 2.42823381 2.88334873 2.45917900 2.37738140 2.2308187 #> Stxbp6        1.68982961 1.67759145 1.49422978 1.59922746 1.34631155 1.6554338 #> Suclg2        0.71876825 1.05265778 0.79135694 0.56916264 0.62196847 1.2940937 #> Syn2          4.48304876 4.69086545 4.68289652 4.49762071 4.61898034 4.2666136 #> Synpo2        1.30381698 1.05201536 1.04885488 1.25656357 1.22006726 1.5780861 #> Synpr         2.06776280 2.30042058 2.13497232 2.36693755 2.13873900 1.8655386 #> Sypl          2.06287982 1.84444490 2.16063146 2.07372883 2.56105551 3.2220890 #> Syt2          0.66474670 0.55319344 0.69937910 0.56156080 0.27321902 0.2666210 #> Syt9          0.73252808 0.66269409 0.74731851 0.70257922 0.30197116 0.9660008 #> Tafa1         1.43448588 1.38764327 1.53188164 0.93793749 0.83074187 1.2099745 #> Tagln         0.33838878 0.37546179 0.46356002 0.56298326 0.21107501 0.0000000 #> Tbr1          1.98502173 1.94914444 2.35409038 1.89777057 1.66296620 1.6540140 #> Tcf7l2        1.92964955 1.89001198 1.74476682 2.08429611 1.88492371 1.6457028 #> Tek           0.58846075 0.33380651 0.52905848 0.28965068 0.56496634 0.5935108 #> Tent5c        0.51357553 0.52555080 0.38222326 0.34015465 0.31439325 0.3976548 #> Tesc          2.30027805 1.98764453 2.43810163 2.14169984 2.12836973 2.4553152 #> Tgfbi         0.16242251 0.10086874 0.11706610 0.33153366 0.28952068 0.0000000 #> Tgm2          0.39655722 0.24013140 0.25795652 0.33902515 0.57609405 0.0000000 #> Thbs4         0.49765351 0.59669414 0.52533895 0.45375515 1.01070198 0.0000000 #> Thrsp         1.66670187 2.09722949 1.64618163 2.02629276 1.75051207 2.3582313 #> Tiam1         2.04082965 1.80812107 1.72900493 2.00111715 1.35007867 1.2827112 #> Tie1          0.34054619 0.32802029 0.30334945 0.33701117 0.32710426 0.2824807 #> Timp3         2.23409432 2.05459679 2.16335370 2.15665627 2.37840741 2.4935373 #> Tm4sf1        0.91410376 0.73984987 0.86342619 0.75260177 0.92873579 0.2666210 #> Tmbim1        2.37754522 2.08368796 1.92791556 1.88812870 1.74852239 1.1152814 #> Tmem100       0.72780347 0.76122785 0.83235817 0.73586833 0.72919557 0.8543052 #> Tmem119       1.01709217 0.81441820 0.77017322 1.08834503 1.01649421 1.1748484 #> Tmem125       1.06154618 0.77941710 0.91822041 1.19434335 0.92088619 1.2462929 #> Tmem158       2.27830361 2.23153622 2.33674527 2.00456458 1.79358921 2.6565355 #> Tmem163       1.33074915 1.18819754 1.27391290 1.38626655 1.19782563 2.0900730 #> Tmem212       0.26257481 0.14465794 0.17697560 0.18815656 0.16627582 0.3741050 #> Tmem63a       1.59770579 1.66244580 1.57718404 1.76645489 1.62173987 0.8654414 #> Tmem88b       3.07189636 2.53557020 2.75820730 2.74813759 2.36238987 1.9045927 #> Tmem91        0.91325311 1.01976509 0.90439258 0.71761435 0.98623491 0.6407260 #> Tmem98        0.84876609 0.78400162 0.76138953 0.85510839 1.28831323 0.6518838 #> Tnfaip6       1.30991237 1.27427386 0.99731184 1.03838146 0.58299791 0.3775465 #> Tnni1         0.78849723 0.56909482 0.59023884 0.60013499 0.99522997 0.2824807 #> Tnnt1         1.85088086 1.54993758 1.34763068 1.57888624 0.78988791 1.3366398 #> Tns1          0.86826741 0.57209402 0.76665670 0.99855609 0.51350110 0.6067047 #> Tpm2          0.47347063 0.28035363 0.43004655 0.65260676 0.53526026 0.2564135 #> Tppp3         2.60248409 2.12178859 2.28050208 2.27905129 2.24382333 2.2492398 #> Tprn          1.75470671 1.39721522 1.28822863 1.36993821 1.31152137 1.3917156 #> Trbc2         1.20583296 1.28703415 1.50146442 1.22354779 1.38336445 0.6090279 #> Trf           5.45009365 5.02241912 5.14522113 4.95783218 5.58619057 5.1389024 #> Trim59        0.87326383 1.06343482 1.05911906 0.80614020 1.19515684 0.7928307 #> Trps1         0.88635242 1.09999999 0.96537691 0.70914548 0.77885897 0.6262941 #> Tsc22d4       4.68481739 4.87820011 4.58044772 4.72661026 4.51677143 4.2072991 #> Tspan15       1.48416997 1.31211576 1.53793806 1.15584722 1.17124980 1.5972370 #> Tspan2        4.21697788 3.63807510 3.87527630 4.09312839 3.90853413 4.3763411 #> Ttc9b         4.29092470 4.57642934 4.57666226 4.01245305 4.26698811 4.2923582 #> Ttr           6.19462776 6.26366576 6.08356036 6.07872249 6.84390319 5.7097158 #> Ttyh2         2.00867858 1.61856659 1.52483405 1.73481250 1.94563902 1.9251238 #> Txnip         0.81687069 0.55199932 0.77762053 0.82753556 1.02713336 0.4566015 #> Ube2l6        0.79318618 0.71995881 0.73357527 0.72603253 0.68412857 0.7306790 #> Ucp2          0.79834906 0.75259766 1.12235205 1.13314304 1.32931986 1.5159634 #> Ugt8a         2.78339796 2.44413871 2.53914210 2.46467594 2.32760436 0.9639957 #> Unc13c        1.12647624 0.85563289 0.83457482 0.82026022 0.60663106 1.3103061 #> Unc5b         1.12443275 0.97559247 0.74116499 1.14892392 0.91670574 0.6871979 #> Unc93b1       0.65399313 0.72501458 0.64464940 0.57091079 1.05917378 1.2411060 #> Utrn          1.12996068 1.24445634 1.24669304 1.33442974 1.35301345 0.9244398 #> Vamp1         2.48963304 2.49782797 2.57893644 2.89025235 2.48330459 2.1890445 #> Vat1l         0.90595201 0.84805180 0.70829763 0.71705645 1.05167716 0.3474831 #> Vav3          0.98378113 0.76786652 0.63515849 0.75285785 0.26584800 0.5328893 #> Vcam1         0.90264419 1.11631737 0.91089476 0.85585352 1.14136059 1.0918987 #> Vim           1.63777758 1.87228319 1.50567183 1.96622246 1.92367017 1.2362695 #> Vip           0.83348717 0.73252192 0.69218987 0.83135659 0.52756790 0.5780129 #> Vipr2         0.41622431 0.36140341 0.35658828 0.46596769 0.22133447 0.6305185 #> Vsir          1.00682289 0.86527542 0.84954259 0.77101413 1.46413962 0.4970584 #> Vstm2a        2.28073151 2.26633071 2.15393733 2.28636983 2.22163146 2.1500628 #> Vstm2l        2.22098701 2.38136884 2.51948666 2.11308075 2.07506678 2.2089450 #> Vtn           2.72627600 2.74226687 2.48487479 2.41757776 2.62731419 1.6681123 #> Vwa1          1.13226660 1.31113787 1.04354593 1.31549050 1.40072163 2.2643882 #> Vwf           0.73980288 1.02125057 0.93244909 0.92739552 1.11699965 0.4919525 #> Vxn           3.53117569 3.31903989 3.47201305 3.21175235 3.32323417 3.4741524 #> Wfdc17        0.03592151 0.03125994 0.10073253 0.10269814 0.25262848 0.0000000 #> Wfs1          2.18927867 2.30295460 2.32184235 2.44810454 2.92937818 2.1068153 #> Wipf3         2.55544936 2.96123354 2.99511897 3.11271141 2.75874347 3.3429219 #> Wnt4          1.07266316 1.11076790 1.04697232 1.19598207 0.44986225 0.8317029 #> Zcchc12       1.52902191 1.75238761 1.50205089 1.30837531 1.18592398 2.1019134 #> Zdhhc22       1.89107607 1.70658932 1.55754351 1.79296320 1.68515227 1.1714144 #> Zfhx3         1.01463614 0.96580755 1.05374459 1.16390482 1.05445715 0.8927713 #> Zic1          1.47768397 1.44655695 1.39423152 1.80648344 1.34917327 2.0632232 #> Zmat4         1.55506361 1.57574686 1.53556433 1.42295301 1.05790010 1.4843569 #>                cluster_4 #> 1110017D15Rik 0.25822164 #> 1190005I06Rik 1.04935507 #> 1700001C02Rik 0.08247050 #> 1700047M11Rik 0.64729410 #> 2010300C02Rik 3.16523944 #> 2410004P03Rik 0.17949586 #> 2900040C04Rik 0.32603957 #> 9630013A20Rik 0.33023852 #> Acta2         0.53759005 #> Adarb1        3.34622701 #> Adarb2        0.49534891 #> Adgrf5        1.03373000 #> Adgrl4        1.00117125 #> Adra1b        0.93910023 #> Adssl1        0.83671153 #> Aebp1         0.30265744 #> Agt           2.30986060 #> Ahnak         0.91869843 #> Ak5           3.13566196 #> Akr1c18       0.10277605 #> Alas2         0.98245807 #> Aldh1a1       2.13762657 #> Aldh1a2       0.06307203 #> Amotl1        1.47332766 #> Anln          0.68573737 #> Anxa2         0.38974761 #> Apod          4.62594045 #> Apol11b       0.32937402 #> Aqp4          2.39931394 #> Arhgap12      1.51450516 #> Arhgef10      1.14429536 #> Arhgef25      3.50954343 #> Arl15         1.13171031 #> Arpc1b        1.56174316 #> Arpp19        4.54109612 #> Arsg          0.85763161 #> Ascl1         0.42467991 #> Aspa          1.43052716 #> Atp2b4        1.76384060 #> BC039966      0.05227336 #> Baiap2        3.57025234 #> Bcam          0.78622815 #> Bcas1         2.79866172 #> Bcl11b        2.09150675 #> Bgn           0.35033806 #> Bhlhe22       1.69768308 #> Bok           2.78164079 #> Btbd17        1.20395106 #> Btbd3         3.54003655 #> C030029H02Rik 0.34659023 #> C1ql2         1.16794137 #> C4b           0.92330880 #> Cabp7         2.48792771 #> Cacng4        1.43833695 #> Cacng5        0.73174308 #> Cadps2        1.81067037 #> Calb1         3.10570843 #> Calb2         1.44793211 #> Cald1         1.05283005 #> Calml4        0.13459022 #> Camk2d        1.69034013 #> Camkv         4.70088986 #> Capg          0.21266618 #> Car14         1.08944666 #> Car2          4.83859775 #> Carhsp1       1.57075592 #> Cavin1        0.70230817 #> Cbln1         0.64719536 #> Cbln2         0.53026081 #> Cbln4         0.72890041 #> Ccdc136       3.18618838 #> Ccdc153       0.15608004 #> Ccdc3         0.53051383 #> Ccdc33        0.07363270 #> Ccn2          0.56396116 #> Ccn3          1.54742610 #> Ccnd1         1.45258705 #> Ccnd2         1.75449691 #> Ccp110        2.09204511 #> Cd24a         0.40742449 #> Cd59a         1.43861027 #> Cd74          0.10955569 #> Cd82          1.39403665 #> Cd9           2.77532732 #> Cdc42ep1      0.92909667 #> Cdc42ep2      1.28679455 #> Cdhr4         0.06342928 #> Cebpd         1.09991152 #> Cers2         2.43882985 #> Cfap126       0.21236296 #> Cfh           0.71937055 #> Chgb          4.89580590 #> Chrm1         2.95772818 #> Chrna4        1.63380471 #> Cit           2.09743659 #> Cldn11        4.78456149 #> Cldn5         2.20681530 #> Clic1         0.51866093 #> Clic4         2.12422161 #> Clic6         0.42591897 #> Clmn          2.33553604 #> Cmtm5         3.15469470 #> Cnih3         1.78926516 #> Cnp           5.39410872 #> Cnr1          2.12160609 #> Cntn2         1.59843273 #> Col1a1        0.16085927 #> Col1a2        0.27025654 #> Col3a1        0.13151465 #> Col4a1        1.08994227 #> Col8a2        0.18741821 #> Col9a3        0.93330550 #> Cox6a2        1.13090877 #> Cp            0.28275109 #> Cplx2         5.27754568 #> Cplx3         0.50906013 #> Cpne4         2.20413776 #> Cpne6         3.56585260 #> Cpne7         1.93052451 #> Cpne8         0.72932689 #> Cpne9         1.15978487 #> Cpox          1.27439556 #> Creb5         0.34033447 #> Crhbp         0.49109958 #> Crip1         1.57047760 #> Crlf1         1.15496768 #> Cryab         4.66577168 #> Crygn         0.09798658 #> Crym          2.53876400 #> Csf1r         2.53418697 #> Csrp1         4.62308151 #> Csrp2         0.61034920 #> Cthrc1        0.86122853 #> Ctla2a        1.32362644 #> Ctxn1         4.74797145 #> Ctxn3         0.39628055 #> Cx3cr1        0.95719342 #> Cxcl14        3.03239260 #> Cyba          1.07571205 #> Cygb          2.20674896 #> Cyp2d22       1.30268039 #> Dbndd1        1.20736269 #> Dbndd2        2.03506595 #> Dcn           0.43218827 #> Ddn           4.90921841 #> Ddr1          1.94713727 #> Dio2          0.79573740 #> Dkk3          3.32926588 #> Dkkl1         0.54054309 #> Dnali1        0.08601687 #> Doc2b         0.59824740 #> Dock10        1.73507733 #> Dock4         2.45605205 #> Dpp6          3.32538357 #> Dsp           0.56496508 #> Dusp6         1.53022592 #> Dynlrb2       0.07137860 #> Ecrg4         0.59745978 #> Edn3          0.10673408 #> Ednrb         1.59033225 #> Efcab6        0.43987268 #> Efhd1         1.06229685 #> Efnb3         2.65042930 #> Egr1          2.50492310 #> Eln           0.23647582 #> Elovl1        1.46954470 #> Emilin1       0.27462874 #> Enkur         0.16460524 #> Enpp2         4.51135587 #> Enpp6         0.58768814 #> Epha5         2.46494758 #> Epha7         2.52694235 #> Epop          1.81153342 #> Erbb3         0.51423124 #> Erbin         1.98244265 #> Ermn          2.25647105 #> Esam          0.85819635 #> Etnppl        0.77888619 #> Evi2a         2.17418067 #> Ezr           1.61193468 #> F3            1.34499351 #> Fa2h          2.11498241 #> Fabp7         1.74874429 #> Fam131a       3.82104523 #> Fam163b       2.60011746 #> Fam20c        1.76695203 #> Fam234a       0.93518603 #> Fbln5         0.43630675 #> Fcer1g        1.07990094 #> Fgfr2         1.71329354 #> Fibcd1        1.39882457 #> Flna          0.96571296 #> Fmod          0.04236641 #> Fn1           1.07906684 #> Foxj1         0.22307537 #> Foxp2         1.05428719 #> Frmd8         1.45107637 #> Fxyd1         3.12197726 #> Fxyd6         2.51761650 #> Fxyd7         4.06784836 #> Gab1          1.46719706 #> Gabra4        2.73396239 #> Gabra5        2.35473191 #> Gabrd         2.14254530 #> Gad1          3.20243518 #> Gad2          2.50678278 #> Gal3st1       1.13100658 #> Galnt6        0.30211407 #> Gamt          1.93081585 #> Gatm          3.15793713 #> Gbp4          0.11760288 #> Gdf11         0.85765670 #> Gfap          2.78027907 #> Gja4          0.18769692 #> Gjb1          1.30976978 #> Gjc1          0.34064045 #> Gjc2          1.29166595 #> Gjc3          1.77287650 #> Gkn3          0.32377812 #> Gldc          0.81997077 #> Gltp          1.76140268 #> Gm13889       1.59952540 #> Gm14964       0.23881197 #> Gm19935       0.24955801 #> Gm2115        1.40123238 #> Gna12         2.60609824 #> Gng11         2.19151279 #> Gng4          1.09385812 #> Gpr161        0.70486753 #> Gpr17         0.73653293 #> Gpr37         2.62296320 #> Gpr4          0.48872287 #> Gpr62         1.13247697 #> Gpr88         0.57929201 #> Grb14         2.61113828 #> Gria1         4.44084827 #> Gria2         4.68558326 #> Grik1         0.52200308 #> Grm1          1.93235928 #> Grm2          1.19803763 #> Grm4          0.67044200 #> Gsn           3.05493280 #> Gss           1.63093165 #> Gstm7         1.46685037 #> Gzma          0.01537066 #> H2-D1         2.08413405 #> H2-K1         2.01438048 #> H2-Q4         0.04403270 #> H2-Q7         0.09426609 #> Hap1          1.61910843 #> Hapln2        0.76712800 #> Hba-a1        6.42665658 #> Hba-a2        5.95260496 #> Hbb-bt        5.36616636 #> Hexb          3.27353577 #> Hhatl         0.81980020 #> Hhip          0.38943212 #> Hlf           3.09046018 #> Hmgb2         0.75379922 #> Hmgn2         1.82635952 #> Homer2        2.19581914 #> Homer3        1.57341038 #> Hopx          2.98504911 #> Hpca          5.92641822 #> Hpcal4        4.76118084 #> Hrh3          1.86482080 #> Hs3st2        0.83422411 #> Hs3st4        2.55684519 #> Hsd11b1       1.52920468 #> Hspb1         0.66489715 #> Hspb8         0.63868671 #> Htr2c         0.89371813 #> Htr3a         0.44621075 #> Icam5         3.07895079 #> Ick           0.92748210 #> Id1           1.51472412 #> Id3           2.79703382 #> Ifitm2        1.19277954 #> Ifitm3        1.65475491 #> Igfbp2        1.39985479 #> Igfbp4        2.18737537 #> Igfbp6        1.55487402 #> Igfbp7        2.07693868 #> Igkc          0.08856211 #> Igsf21        1.76647020 #> Il1rap        1.40773267 #> Inmt          0.12421173 #> Ipcef1        1.28184953 #> Iqgap2        1.20430675 #> Isg15         0.68267050 #> Itgb4         0.52681245 #> Itih3         0.95701386 #> Itih5         1.08149119 #> Itpka         3.73740983 #> Itpr2         0.70815555 #> Kcnab1        3.04226008 #> Kcnab3        1.11418182 #> Kcnc2         2.67091282 #> Kcng2         0.97869316 #> Kcnip2        2.85003650 #> Kctd12        2.25485833 #> Kctd4         1.38510172 #> Kit           0.77771411 #> Kitl          1.58339868 #> Klk8          1.46881306 #> Lamb2         0.91230505 #> Lamp5         1.81610150 #> Laptm5        1.38439411 #> Lbp           0.19627608 #> Lcat          1.41763369 #> Lcn2          0.12253289 #> Lct           0.85846186 #> Lef1          0.82801917 #> Lefty1        0.81134858 #> Lgals1        1.50991492 #> Lgi4          1.04604672 #> Lhfp          1.57670266 #> Lhfpl3        1.24297124 #> Lims2         0.98938857 #> Lingo3        0.92482011 #> Litaf         1.79792102 #> Lmo1          2.14353738 #> Lmo3          2.63058172 #> Lpar1         1.60370465 #> Lpl           1.07121408 #> Lrrc10b       1.53819465 #> Lrrtm3        1.11618629 #> Lrtm2         1.70069660 #> Ly6a          2.50538847 #> Ly6c1         2.71720127 #> Lyz2          0.46364032 #> Mag           4.67393619 #> Mal           5.04683942 #> Man1a         1.23827535 #> Map4k4        2.08664581 #> Matn2         1.35789783 #> Mb21d2        1.76973253 #> Mcam          1.09629339 #> Mdk           1.53376080 #> Meig1         0.43572822 #> Mgp           1.36713519 #> Mia           0.17050296 #> Micall1       1.19040089 #> Mmp17         2.76300035 #> Mobp          6.10458192 #> Mog           3.46300407 #> Mpped1        2.39482943 #> Msx1          0.15696548 #> Mustn1        0.05434083 #> Myh11         0.14259988 #> Myl4          0.98021372 #> Myl9          1.25803289 #> Myo1d         0.66978023 #> Myo5b         1.38504287 #> Myoc          0.35233935 #> Myrf          1.21563347 #> Ncald         4.46018666 #> Ncf2          0.09961637 #> Ndnf          0.54665309 #> Ndrg1         2.73408497 #> Ndufa4l2      0.68493998 #> Necab2        2.37856283 #> Nefh          1.89682064 #> Nell1         1.98912213 #> Neurod1       0.84668834 #> Neurod2       2.71342401 #> Neurod6       2.82060410 #> Nexn          0.48396001 #> Nfasc         3.34781941 #> Ngef          2.75647904 #> Nid1          0.04243022 #> Ninj2         0.49197601 #> Nkx2-2        0.38872638 #> Nkx6-2        1.37399409 #> Nnat          4.37366824 #> Notch1        0.58981274 #> Npas1         0.61792941 #> Npas3         0.82203709 #> Nptx1         3.83192513 #> Nptxr         4.61099196 #> Npy           2.51459626 #> Npy2r         1.04472256 #> Nr3c2         1.81639594 #> Nr4a1         0.85403244 #> Nr4a2         0.95915164 #> Nrip3         2.77075058 #> Nt5dc2        1.11648381 #> Ntng1         1.71046729 #> Nupr1         0.35617664 #> Nxph3         0.54103846 #> Nxph4         0.16686809 #> Odf3b         0.11363113 #> Ogfrl1        4.14079304 #> Olfm2         2.26084825 #> Olig1         4.10287912 #> Olig2         1.08102009 #> Opalin        2.79718795 #> Orai2         2.26748066 #> Otud7b        1.59728173 #> P2ry12        1.54083467 #> Padi2         0.79418108 #> Paqr5         0.26346143 #> Patj          0.59129471 #> Pbxip1        1.45561696 #> Pcdh20        1.45659664 #> Pcdh8         1.79334980 #> Pcolce        0.29688338 #> Pcp4l1        2.57535473 #> Pde1a         2.36702109 #> Pde8a         0.48703240 #> Pdgfra        0.91472515 #> Pdgfrb        0.56980162 #> Pdlim2        2.33042211 #> Pdp1          3.07130792 #> Pdyn          0.83021815 #> Penk          1.45336436 #> Pglyrp1       0.83805061 #> Phgdh         3.40225383 #> Phkg1         0.95307076 #> Phldb1        2.21834915 #> Pitpnm2       2.26748973 #> Plaat3        2.39613452 #> Plat          1.16879670 #> Plcb4         2.11957165 #> Plcxd2        1.35893527 #> Plekhb1       5.03052367 #> Plekhg1       1.30868528 #> Plekhg3       0.58116792 #> Plekhh1       1.42694370 #> Pllp          2.83929320 #> Plod1         1.01513955 #> Pltp          2.01247707 #> Plxdc1        1.00394069 #> Pmp22         1.22235809 #> Pou3f1        1.50999422 #> Ppm1e         3.21338301 #> Ppp1r14a      2.58835889 #> Ppp1r1a       4.59851094 #> Ppp1r3c       1.32238705 #> Prdm8         1.25861063 #> Prelp         0.65903079 #> Prkcd         2.14637020 #> Prkcg         4.29179503 #> Prkch         0.49976063 #> Prkcq         0.53553084 #> Prox1         1.02388754 #> Prph          0.26203379 #> Prr18         1.92474592 #> Prr5l         0.60336929 #> Ptk2b         4.41025426 #> Ptpn3         2.00909251 #> Ptpn4         3.05481348 #> Ptprb         0.95638887 #> Pvalb         3.09893154 #> Qdpr          4.73326809 #> Rab37         0.52556290 #> Rab3b         1.46259667 #> Rab3c         3.27239312 #> Ramp3         1.81952795 #> Ranbp3l       0.11161922 #> Rapgef5       2.40123292 #> Rarres2       0.60835906 #> Rasd1         1.67572621 #> Rasgrf1       4.38499536 #> Rasl10a       1.80985928 #> Rbp1          1.30611288 #> Rcn3          0.75698657 #> Reep3         1.57246606 #> Reln          0.89969889 #> Rflnb         0.86553427 #> Rfx3          1.26658762 #> Rgs12         1.37988885 #> Rgs14         1.48359693 #> Rgs16         0.82849384 #> Rgs3          1.29883300 #> Rgs4          3.33547592 #> Rgs5          2.22307367 #> Rhog          1.83048241 #> Rims2         2.28915772 #> Rims3         2.55188402 #> Rlbp1         0.99467230 #> Rnf130        1.79891419 #> Rora          2.58959747 #> Rprm          1.73507034 #> Rprml         3.49550568 #> Rsph1         0.26057185 #> S100a11       0.55417837 #> S100a6        1.92737468 #> S100a8        0.35740871 #> S100a9        0.44543463 #> S1pr5         0.68336274 #> Satb2         0.79402893 #> Scn3b         2.98404777 #> Selplg        1.18755362 #> Sema3c        0.66432371 #> Sema4d        1.68305206 #> Sema5a        1.87068636 #> Sept4         4.18425152 #> Serinc5       1.99901133 #> Serpina3n     1.34144027 #> Serpinb1a     0.95503066 #> Serpinf1      0.61207785 #> Serpinh1      0.88895100 #> Serpini1      2.94974436 #> Sertm1        1.18622154 #> Sez6          3.40864347 #> Sgpp2         0.57907461 #> Sh3gl3        2.10938506 #> Shisa6        1.88370870 #> Shisa8        0.27554714 #> Shisal1       1.50139458 #> Shox2         0.74921670 #> Siglech       0.87621547 #> Sipa1l3       1.97744447 #> Sirt2         4.27459459 #> Slain1        2.70259995 #> Slc12a2       2.10404227 #> Slc12a4       0.85628245 #> Slc13a4       0.11711368 #> Slc17a6       1.74404575 #> Slc17a8       0.11292223 #> Slc22a8       0.74498851 #> Slc24a3       3.24439184 #> Slc30a3       1.95904506 #> Slc32a1       1.83410423 #> Slc38a5       0.52886519 #> Slc44a1       2.59962787 #> Slc4a2        1.22137346 #> Slc6a11       2.31871251 #> Slc6a13       0.34682235 #> Slc6a9        1.73057613 #> Slc7a11       0.85798499 #> Slco1c1       1.79393540 #> Slitrk6       0.18711931 #> Smim1         1.01101079 #> Snca          4.82591434 #> Sncg          0.39717035 #> Sod3          0.77167033 #> Sowaha        2.97280378 #> Sox10         1.65921654 #> Sox11         0.94133413 #> Sox18         0.68029097 #> Sox8          1.07632871 #> Sox9          1.65161246 #> Spag8         0.05630185 #> Spink8        1.68685087 #> Sst           3.66156380 #> St6galnac5    2.56250778 #> Stab1         0.41544093 #> Stac2         1.29603399 #> Stk32c        2.22177632 #> Stx1a         2.57695025 #> Stxbp6        1.80627634 #> Suclg2        0.47537351 #> Syn2          4.69831340 #> Synpo2        1.01374359 #> Synpr         2.65502986 #> Sypl          2.28179773 #> Syt2          0.45448942 #> Syt9          0.73367694 #> Tafa1         1.26002983 #> Tagln         0.42281179 #> Tbr1          1.78988837 #> Tcf7l2        1.78881915 #> Tek           0.62410035 #> Tent5c        0.25759204 #> Tesc          2.63279774 #> Tgfbi         0.09177186 #> Tgm2          0.40593632 #> Thbs4         0.61252956 #> Thrsp         2.06264951 #> Tiam1         2.08517521 #> Tie1          0.30998037 #> Timp3         2.12169068 #> Tm4sf1        0.89917395 #> Tmbim1        1.79891682 #> Tmem100       0.65813793 #> Tmem119       0.96813052 #> Tmem125       0.81514353 #> Tmem158       2.33485916 #> Tmem163       1.34780537 #> Tmem212       0.15113993 #> Tmem63a       1.60914217 #> Tmem88b       2.17385844 #> Tmem91        1.03303378 #> Tmem98        0.56123415 #> Tnfaip6       1.11901813 #> Tnni1         0.63957991 #> Tnnt1         1.17970564 #> Tns1          0.68278002 #> Tpm2          0.37449563 #> Tppp3         2.18130652 #> Tprn          0.99384427 #> Trbc2         1.23305101 #> Trf           4.77173848 #> Trim59        0.99786278 #> Trps1         0.78861445 #> Tsc22d4       4.38214380 #> Tspan15       1.26549944 #> Tspan2        3.66338603 #> Ttc9b         4.45687988 #> Ttr           6.25632335 #> Ttyh2         1.58859307 #> Txnip         0.68700917 #> Ube2l6        0.73267755 #> Ucp2          0.83585966 #> Ugt8a         2.00153051 #> Unc13c        0.76560805 #> Unc5b         0.88591120 #> Unc93b1       0.81959434 #> Utrn          1.01510328 #> Vamp1         2.87882461 #> Vat1l         0.74698880 #> Vav3          0.62844713 #> Vcam1         0.90587290 #> Vim           1.55448093 #> Vip           0.61427950 #> Vipr2         0.32945893 #> Vsir          0.62922846 #> Vstm2a        2.31470010 #> Vstm2l        2.75978563 #> Vtn           2.53775487 #> Vwa1          1.17900956 #> Vwf           0.77167716 #> Vxn           3.31594192 #> Wfdc17        0.12579889 #> Wfs1          2.73229161 #> Wipf3         3.44832475 #> Wnt4          0.90331411 #> Zcchc12       1.52071335 #> Zdhhc22       1.49991394 #> Zfhx3         1.09077552 #> Zic1          1.45860493 #> Zmat4         1.49254831"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_dim_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_dim_obj — create_dim_obj","title":"create_dim_obj — create_dim_obj","text":"create_dim_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_dim_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_dim_obj — create_dim_obj","text":"","code":"create_dim_obj(   name = \"test\",   reduction = \"cells\",   reduction_method = NA_character_,   coordinates = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL,   my_rownames = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_dim_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_dim_obj — create_dim_obj","text":"dim_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_expr_obj — create_expr_obj","title":"create_expr_obj — create_expr_obj","text":"create_expr_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_expr_obj — create_expr_obj","text":"","code":"create_expr_obj(   name = \"test\",   exprMat = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"create_expr_obj — create_expr_obj","text":"exprMat matrix expression information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_expr_obj — create_expr_obj","text":"expr_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_expr_obj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"create_expr_obj — create_expr_obj","text":"","code":"x_expr <- readRDS(system.file(\"extdata/toy_matrix.RDS\",     package = \"GiottoClass\" ))  create_expr_obj(exprMat = x_expr) #> Warning: `create_expr_obj()` was deprecated in GiottoClass 3.3.0. #> ℹ Please use `createExprObj()` instead. #> An object of class exprObj : \"test\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #>  #> contains: #>   A B C D E F G H I J #> a 0 0 0 0 0 0 0 0 0 0 #> b 0 0 0 0 1 0 0 0 0 0 #> c 0 0 0 0 0 0 1 0 0 0 #> d 0 0 0 0 0 0 0 0 0 1 #> e 0 0 1 0 0 0 0 0 0 0 #> f 0 0 0 0 0 0 0 0 1 0 #> g 1 0 0 0 0 0 0 0 0 0 #> h 1 0 0 0 0 0 0 0 0 1 #> i 0 0 0 0 0 0 0 0 0 0 #> j 0 0 0 1 0 1 0 0 0 0 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_feat_meta_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_feat_meta_obj — create_feat_meta_obj","title":"create_feat_meta_obj — create_feat_meta_obj","text":"create_feat_meta_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_feat_meta_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_feat_meta_obj — create_feat_meta_obj","text":"","code":"create_feat_meta_obj(   metaDT = NULL,   col_desc = NA_character_,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_feat_meta_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_feat_meta_obj — create_feat_meta_obj","text":"feat_meta_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_featureNetwork_object.html","id":null,"dir":"Reference","previous_headings":"","what":"Create feature network object — create_featureNetwork_object","title":"Create feature network object — create_featureNetwork_object","text":"Create feature network object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_featureNetwork_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create feature network object — create_featureNetwork_object","text":"","code":"create_featureNetwork_object(   name = \"feat_network\",   network_datatable = NULL,   network_lookup_id = NULL,   full = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_featureNetwork_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create feature network object — create_featureNetwork_object","text":"name name assign created feature network object network_datatable network data.table object network_lookup_id network lookup id full fully connected status","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_featureNetwork_object.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create feature network object — create_featureNetwork_object","text":"featureNetwork_object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_points_object.html","id":null,"dir":"Reference","previous_headings":"","what":"Create giotto points object — create_giotto_points_object","title":"Create giotto points object — create_giotto_points_object","text":"Create giotto points object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_points_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create giotto points object — create_giotto_points_object","text":"","code":"create_giotto_points_object(   feat_type = \"rna\",   spatVector = NULL,   networks = NULL,   unique_IDs = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_points_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create giotto points object — create_giotto_points_object","text":"feat_type feature type spatVector terra spatVector object containing point data networks (optional) feature network object unique_IDs (optional) unique IDs spatVector cacheing","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_points_object.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create giotto points object — create_giotto_points_object","text":"giotto_points_object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_polygon_object.html","id":null,"dir":"Reference","previous_headings":"","what":"Create a giotto polygon object — create_giotto_polygon_object","title":"Create a giotto polygon object — create_giotto_polygon_object","text":"Create giotto polygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_polygon_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create a giotto polygon object — create_giotto_polygon_object","text":"","code":"create_giotto_polygon_object(   name = \"cell\",   spatVector = NULL,   spatVectorCentroids = NULL,   overlaps = NULL,   unique_IDs = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_polygon_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create a giotto polygon object — create_giotto_polygon_object","text":"name name polygon object spatVector SpatVector polygons spatVectorCentroids (optional) SpatVector polygon centroids overlaps (optional) feature overlaps polygons unique_IDs unique polygon IDs cacheing","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_giotto_polygon_object.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create a giotto polygon object — create_giotto_polygon_object","text":"giotto_polygon_object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_nn_net_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_nn_net_obj — create_nn_net_obj","title":"create_nn_net_obj — create_nn_net_obj","text":"create_nn_net_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_nn_net_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_nn_net_obj — create_nn_net_obj","text":"","code":"create_nn_net_obj(   name = \"test\",   nn_type = NA_character_,   igraph = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_nn_net_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_nn_net_obj — create_nn_net_obj","text":"nn_net_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_enr_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_spat_enr_obj — create_spat_enr_obj","title":"create_spat_enr_obj — create_spat_enr_obj","text":"create_spat_enr_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_enr_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_spat_enr_obj — create_spat_enr_obj","text":"","code":"create_spat_enr_obj(   name = \"test\",   method = NA_character_,   enrichDT = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_enr_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_spat_enr_obj — create_spat_enr_obj","text":"spat_enr_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Create S4 spatialGridObj — create_spat_grid_obj","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"Create S4 spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"","code":"create_spat_grid_obj(   name = \"test\",   method = NA_character_,   parameters = NULL,   gridDT = NULL,   spat_unit = \"cell\",   feat_type = \"rna\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"name name spatialGridObj method method used generate spatial grid parameters additional method-specific parameters used spatial grid generation gridDT data.table holding spatial grid information spat_unit spatial unit feat_type feature type provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_grid_obj.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create S4 spatialGridObj — create_spat_grid_obj","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatialGridObj\")  create_spat_grid_obj(name = \"test\", gridDT = x) #> An object of class spatialGridObj : \"test\" #> Contains annotations for spatial unit: \"cell\" and feature type: \"rna\" #> Contains spatial grid defined for: #>    5 intervals from x range: 6400.82 to 6900.82  #>    5 intervals from y range: -5173.441 to -4673.441 #>  #> Contains spatial grid generated with: NA  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_locs_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_spat_locs_obj — create_spat_locs_obj","title":"create_spat_locs_obj — create_spat_locs_obj","text":"create_spat_locs_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_locs_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_spat_locs_obj — create_spat_locs_obj","text":"","code":"create_spat_locs_obj(   name = \"test\",   coordinates = NULL,   spat_unit = \"cell\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_locs_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_spat_locs_obj — create_spat_locs_obj","text":"spat_locs_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_net_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"create_spat_net_obj — create_spat_net_obj","title":"create_spat_net_obj — create_spat_net_obj","text":"create_spat_net_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_net_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_spat_net_obj — create_spat_net_obj","text":"","code":"create_spat_net_obj(   name = \"test\",   method = NA_character_,   parameters = NULL,   outputObj = NULL,   networkDT = NULL,   networkDT_before_filter = NULL,   cellShapeObj = NULL,   crossSectionObjects = NULL,   spat_unit = \"cell\",   provenance = NULL,   misc = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_spat_net_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"create_spat_net_obj — create_spat_net_obj","text":"spat_net_obj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":null,"dir":"Reference","previous_headings":"","what":"Crop to a spatial subset — crop","title":"Crop to a spatial subset — crop","text":"Spatially subset object x using object y. Giotto spatial subobjects respond terra::crop. giottoPoints giottoPolygon, alternative faster crop operation implemented data.table manipulation geometry information used default. mode also allows rectangular subsetting. Additionally, giottoPolygons cropped using centroids entire polygon either present instead default crop behavior keep portion polygon fall within selected crop region. Set DT = FALSE order use default style terra::crop behavior also allows usage additional params ...","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Crop to a spatial subset — crop","text":"","code":"# S4 method for class 'giottoLargeImage' crop(x, y, ...)  # S4 method for class 'giottoAffineImage' crop(x, y, ...)  # S4 method for class 'spatLocsObj' crop(x, y, ...)  # S4 method for class 'spatialNetworkObj' crop(x, y, ...)  # S4 method for class 'giottoPoints' crop(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)  # S4 method for class 'giottoPolygon' crop(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Crop to a spatial subset — crop","text":"x object y object SpatExtent returns SpatExtent ... additional params pass terra::crop DT logical. Use alternative DT subsetting crop operation xmin, xmax, ymin, ymax used DT = TRUE. Set extent bounds independently","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Crop to a spatial subset — crop","text":"SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/crop.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Crop to a spatial subset — crop","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\") crop(g_image, g_image) #> An object of class giottoLargeImage : \"alignment\" #> Image extent            : 2364.5, 6522.5, -5425.25, -2620.75 (xmin, xmax, ymin, ymax) #> Original image extent   : 2364.5, 6522.5, -5425.25, -2620.75 (xmin, xmax, ymin, ymax) #> Scale factor            : 13.2420382165605, 13.2287735849057 (x, y) #> Resolution              : 0.0755170755170755, 0.0755927972900695 (x, y) #> Layers                  : 4  #> Estimated max intensity : 174  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoData/Mini_datasets/Visium/VisiumObject/Images/alignment_spatRaster'"},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Crop a giotto largeImage object — cropGiottoLargeImage","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"Crop giottoLargeImage based crop_extent argument given values","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"","code":"cropGiottoLargeImage(   gobject = NULL,   largeImage_name = NULL,   giottoLargeImage = NULL,   crop_name = \"image\",   crop_extent = NULL,   xmax_crop = NULL,   xmin_crop = NULL,   ymax_crop = NULL,   ymin_crop = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"gobject gobject holding giottoLargeImage largeImage_name name giottoLargeImage within gobject giottoLargeImage alternative input param using giottoLargeImage object instead gobject largeImage_name params crop_name arbitrary name cropped giottoLargeImage crop_extent terra extent object used crop giottoLargeImage xmax_crop, xmin_crop, ymax_crop, ymin_crop crop min/max x y bounds","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"giottoLargeImage object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/cropGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Crop a giotto largeImage object — cropGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  cropGiottoLargeImage(g, largeImage_name = \"image\") #> An object of class giottoLargeImage : \"image\" #> Image extent            : 2000.5, 6790.5, -5730.25, -2380.75 (xmin, xmax, ymin, ymax) #> Original image extent   : 2000.5, 6790.5, -5730.25, -2380.75 (xmin, xmax, ymin, ymax) #> Scale factor            : 19.7119341563786, 19.4738372093023 (x, y) #> Resolution              : 0.0507306889352818, 0.051350947902672 (x, y) #> Layers                  : 4  #> Estimated max intensity : 133  #> Estimated min intensity : 36  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoData/Mini_datasets/Visium/VisiumObject/Images/image_spatRaster'"},{"path":"https://drieslab.github.io/GiottoClass/reference/data_access_params.html","id":null,"dir":"Reference","previous_headings":"","what":"data_access_params — data_access_params","title":"data_access_params — data_access_params","text":"data_access_params","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/data_access_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"data_access_params — data_access_params","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class) output format get information (e.g. \"data.table\") set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. copy_obj whether deep copy/duplicate getting object (default = TRUE) initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/data_access_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"data_access_params — data_access_params","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":null,"dir":"Reference","previous_headings":"","what":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"Affine transforms linear transformations cover scaling, rotation, shearing, translations. can represented matrices 2x3 3x3 values. function reads matrix extracts values needed perform list class affine. Works 2D transforms. Logic https://math.stackexchange.com//3521141","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"","code":".decomp_affine(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"x object coercible matrix 2x3 3x3 affine matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"list transforms information.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/decomp_affine.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Decompose affine matrix into scale, rotation, and shear operations — decomp_affine","text":"","code":"# load example data sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  # affine transform matrices m <- diag(rep(1, 3)) shear_m <- trans_m <- m trans_m[seq(2), 3] <- c(200, 300) scale_m <- diag(c(2, 3, 1)) shear_m[2, 1] <- 2 aff_m <- matrix(c(     2, 0.5, 1000,     -0.3, 3, 20,     100, 29, 1 ), nrow = 3, byrow = TRUE)  # create affine objects # values are shown in order of operations affine(m) #> <affine2d> #> anchor    : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> rotate    : 0  (rad) #> shear     : 0, 0  (x, y) #> scale     : 1, 1  (x, y) #> translate : 0, 0  (x, y) affine(trans_m) #> <affine2d> #> anchor    : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> rotate    : 0  (rad) #> shear     : 0, 0  (x, y) #> scale     : 1, 1  (x, y) #> translate : 200, 300  (x, y) affine(scale_m) #> <affine2d> #> anchor    : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> rotate    : 0  (rad) #> shear     : 0, 0  (x, y) #> scale     : 2, 3  (x, y) #> translate : 0, 0  (x, y) s <- affine(shear_m) a <- affine(aff_m) force(a) #> <affine2d> #> anchor    : -180, 180, -90, 90  (xmin, xmax, ymin, ymax) #> rotate    : -0.165148677414627  (rad) #> shear     : 0.016260162601626, 0  (x, y) #> scale     : 2.02210754385589, 3.04138126514911  (x, y) #> translate : 1000, 20  (x, y)  # perform piecewise transforms with decomp  sl_shear_piecewise <- sl |>     spin(GiottoUtils::degrees(s$rotate), x0 = 0, y0 = 0) |>     shear(fx = s$shear[[\"x\"]], fy = s$shear[[\"y\"]], x0 = 0, y0 = 0) |>     rescale(fx = s$scale[[\"x\"]], fy = s$scale[[\"y\"]], x0 = 0, y0 = 0) |>     spatShift(dx = s$translate[[\"x\"]], dy = s$translate[[\"y\"]])  sl_aff_piecewise <- sl |>     spin(GiottoUtils::degrees(a$rotate), x0 = 0, y0 = 0) |>     shear(fx = a$shear[[\"x\"]], fy = a$shear[[\"y\"]], x0 = 0, y0 = 0) |>     rescale(fx = a$scale[[\"x\"]], fy = a$scale[[\"y\"]], x0 = 0, y0 = 0) |>     spatShift(dx = a$translate[[\"x\"]], dy = a$translate[[\"y\"]])  plot(affine(sl, shear_m))  plot(sl_shear_piecewise) plot(affine(sl, aff_m))  plot(sl_aff_piecewise)"},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":null,"dir":"Reference","previous_headings":"","what":"Density plot — density","title":"Density plot — density","text":"Create density plots pixel values giottoLargeImage. Wrapper around terra::density().","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Density plot — density","text":"","code":"# S4 method for class 'giottoLargeImage' density(x, show_max = TRUE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Density plot — density","text":"x giottoLargeImage show_max logical. Plot set max intensity vertical red line ... Arguments passed terra::density","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Density plot — density","text":"density plot","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/density.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Density plot — density","text":"","code":"f <- system.file(package = \"GiottoClass\", \"extdata/toy_intensity.tif\") gimg <- createGiottoLargeImage(f, use_rast_ext = TRUE) #> use_rast_ext == TRUE #>  extent from input raster_object will be used.  density(gimg)"},{"path":"https://drieslab.github.io/GiottoClass/reference/density_giottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","title":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","text":"Plot smoothed curve giotto largeImage intensity values","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/density_giottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","text":"","code":".dist_giottolargeimage(   gobject = NULL,   image_name = NULL,   giottoLargeImage = NULL,   method = \"dens\",   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/density_giottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","text":"gobject giotto object giottoLargeImage giotto large image object method method plotting image distribution ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/density_giottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot smoothed curve of giotto largeImage intensity values — density_giottoLargeImage","text":"density histogram plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 dimObj Class — dimObj-class","title":"S4 dimObj Class — dimObj-class","text":"Framework store dimension reduction information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 dimObj Class — dimObj-class","text":"dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 dimObj Class — dimObj-class","text":"name name dimObject feat_type feature type data spat_unit spatial unit data provenance origin aggregated information (applicable) reduction whether reduction performed 'feats' 'cells' reduction_method method used generate dimension reduction coordinates embedding coordinates misc method-specific additional outputs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 dimObj Class — dimObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"dimObj\") #> An object of class dimObj : \"pca\" #> --| Contains dimension reduction generated with: pca  #> ----| for feat_type: rna  #> ----|     spat_unit: aggregate  #>  #>    100 dimensions for 462 data points #>  #> Additional included info: #> [1] \"eigenvalues\" \"loadings\"    #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":null,"dir":"Reference","previous_headings":"","what":"Dimnames of an object — dimnames","title":"Dimnames of an object — dimnames","text":"Retrieve set dimnames object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dimnames of an object — dimnames","text":"","code":"# S4 method for class 'giotto' dimnames(x)  # S4 method for class 'exprObj' dimnames(x)  # S4 method for class 'dimObj' dimnames(x)  # S4 method for class 'spatLocsObj' dimnames(x)  # S4 method for class 'metaData' dimnames(x)  # S4 method for class 'enrData' dimnames(x)  # S4 method for class 'dimObj' dimnames(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dimnames of an object — dimnames","text":"x object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dimnames of an object — dimnames","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dimnames.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dimnames of an object — dimnames","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  dimnames(g) #> [[1]] #>           1           2           3           4           5           6  #>      \"Mlc1\"    \"Gprc5b\"      \"Gfap\"     \"Ednrb\"      \"Sox9\"      \"Aqp4\"  #>           7           8           9          10          11          12  #>      \"Gjc3\"      \"Sox8\"     \"Ntsr2\" \"Adcyap1r1\"       \"Smo\"    \"Gpr161\"  #>          13          14          15          16          17          18  #>      \"C1qb\"     \"Olig1\"      \"C1qa\"     \"Lmtk2\"     \"Pth1r\"     \"Ephb6\"  #>          19          20          21          22          23          24  #>     \"Gpr26\"    \"Gabbr1\"    \"Adra2a\"    \"Gabbr2\"     \"Timp4\"     \"Abcc9\"  #>          25          26          27          28          29          30  #>     \"Csf1r\"     \"Ntrk2\"    \"Adgrg1\"     \"Ntrk3\"      \"Ddr1\"     \"Erbb4\"  #>          31          32          33          34          35          36  #>    \"Selplg\"     \"Cspg5\"      \"Dlk1\"   \"Gpr37l1\"      \"Fzd1\"     \"Fgfr3\"  #>          37          38          39          40          41          42  #>  \"Slc25a18\"     \"Igf1r\"    \"Adgrl1\"     \"S1pr1\"       \"Ryk\"      \"Grm5\"  #>          43          44          45          46          47          48  #>     \"Eomes\"       \"Axl\"    \"Efemp1\"    \"Adgrb3\"     \"Sstr4\"       \"Fn1\"  #>          49          50          51          52          53          54  #>    \"Adora1\"     \"Erbb2\"     \"Gper1\"    \"Gramd3\"     \"Mertk\"   \"Slc32a1\"  #>          55          56          57          58          59          60  #>    \"Adgra1\"    \"Adgrl2\"     \"Ptgfr\"      \"Fzd2\"   \"Aldh1l1\"    \"Adgrg6\"  #>          61          62          63          64          65          66  #>      \"Egfr\"    \"Gpr162\"     \"Lpar4\"       \"Kit\"     \"Ptgdr\"      \"Gad1\"  #>          68          69          71          72          73          74  #>      \"Lgr4\"     \"Tyro3\"   \"Atp13a5\"      \"Ddr2\"     \"Rspo3\"  \"Arhgap29\"  #>          75          76          77          78          80          82  #>     \"Ackr3\"    \"Gpr146\"      \"Fzd7\"   \"Slc47a1\"      \"Insr\"    \"Ptger3\"  #>          83          84          85          86          87          88  #>    \"Bdkrb1\"     \"Traf4\"    \"Celsr2\"      \"Fzd4\"     \"Fgfr2\"    \"Cx3cr1\"  #>          89          90          91          92          93          94  #>    \"Anxa11\"    \"Adgrb1\"     \"Lpar1\"     \"Gpr17\"    \"Gpr173\"      \"Ror1\"  #>          95          96          97          99         100         101  #>    \"Cxcl12\"    \"Kiss1r\"     \"Epha4\"    \"Gpr182\"     \"Man1a\"      \"Gpr4\"  #>         102         103         104         105         106         107  #>    \"P2ry14\"     \"Hcar1\"     \"Ephb1\"     \"Adrb1\"      \"Grm3\"     \"P2ry1\"  #>         109         110         111         112         113         114  #>      \"Nrp2\"      \"Ptk7\"   \"Slco1a4\"   \"Tmem108\"      \"Hrh3\"     \"Insrr\"  #>         115         116         117         118         119         120  #>    \"Cmklr1\"      \"Opn3\"    \"Adra1b\"     \"Gpr62\"     \"Npy1r\"      \"Nrp1\"  #>         121         122         123         125         126         127  #>      \"Fzd6\"     \"S1pr5\"    \"Pdgfrb\"      \"Flt1\"     \"Chrm3\"    \"Agtr1a\"  #>         128         129         130         132         133         134  #>    \"Adgrl4\"     \"Ephb3\"     \"Lpar6\"     \"Epha6\"      \"Fzd5\"      \"Emcn\"  #>         135         136         137         138         139         140  #>     \"Cldn5\"     \"Sstr1\"      \"Fzd3\"    \"P2ry12\"    \"Adgrl3\"    \"Sema4d\"  #>         141         142         143         144         145         146  #>    \"Adgrf5\"    \"Gpr160\"    \"Mrgpre\"    \"Amigo2\"    \"Adgra3\"    \"P2yr13\"  #>         147         148         149         150         151         152  #>     \"Epha3\"    \"Adgre1\"     \"P2ry6\"    \"Cx3cl1\"    \"Epha10\"     \"Tacr1\"  #>         153         154         155         156         157         158  #>     \"Peg10\"     \"Ednra\"    \"Plxnb3\"      \"Flt4\"   \"Slc17a7\"      \"Drd2\"  #>         159         160         161         162         163         164  #>     \"Tjap1\"      \"Fzd8\"   \"Cd300c2\"      \"Htr4\"     \"Gpr52\"       \"Tek\"  #>         165         166         167         168         170         171  #>     \"S1pr2\"       \"Kdr\"      \"Ror2\"     \"Kcnj8\"      \"Hrh1\"    \"Celsr1\"  #>         172         173         176         177         178         180  #>    \"Gpr153\"     \"S1pr3\"    \"Adgra2\"    \"Fgfrl1\"      \"Tie1\"   \"Slc15a3\"  #>         181         182         183         184         185         186  #>     \"Ccr10\"    \"Pdgfra\"     \"Lhcgr\"    \"Mrgprf\"     \"Ascl1\"    \"Baiap2\"  #>         187         188         189         190         191         193  #>     \"Gpr85\"     \"Gpr22\"      \"Gcgr\"      \"Grm1\"     \"Ptafr\"    \"Calcrl\"  #>         194         195         197         198         199         200  #>     \"Gpr34\"     \"Cenpe\"   \"Adora2b\"     \"Adrb2\"      \"Ccr2\"       \"Alk\"  #>         201         203         204         205         207         208  #>     \"Tacr3\"     \"Chrm5\"     \"Erbb3\"      \"Ccr9\"     \"Gpr21\"     \"Epha7\"  #>         209         210         211         212         214         216  #>    \"Adra2b\"    \"Pcdh15\" \"Blank-104\"   \"Adora2a\"      \"Drd1\"  \"Blank-57\"  #>         218         219         220         221         223         225  #>      \"Grm7\"     \"Htr1b\"      \"Fzd9\"      \"Grm4\" \"Blank-152\"     \"Aplnr\"  #>         226         227         228         229         230         231  #>    \"Gpr176\"       \"F2r\"   \"Vmn1r43\"    \"Gpr156\"     \"Gpr55\" \"Blank-155\"  #>         232         233         234         235         236         237  #>    \"Bdkrb2\"     \"C5ar2\"    \"Gpbar1\"    \"Adgrv1\"    \"Gprc5c\"     \"Lmod1\"  #>         238         240         241         242         243         244  #>    \"Gpr135\"     \"Rxfp3\"    \"Tbxa2r\"     \"Fzd10\"       \"Ret\"  \"Blank-80\"  #>         246         247         248         250         251         253  #>     \"Epha8\"     \"Gpr75\"     \"Ackr1\"    \"Adgrg4\"     \"Chrm1\"     \"Epha1\"  #>         254         255         256         257         259         261  #>    \"Vmn2r1\"      \"Syt4\"  \"Tas2r135\"      \"Ccr1\"     \"Lpar2\"     \"Myh11\"  #>         262         263         267         271         272         274  #>      \"Gipr\"      \"Musk\"    \"Gpr183\"      \"Cnr1\"     \"C3ar1\"     \"S1pr4\"  #>         278         280         281         283         284         285  #>      \"Grm2\"     \"C5ar1\"     \"Ephb2\"      \"Fpr1\"       \"Rho\"     \"Gpr27\"  #>         288         289         290         291         294         296  #>    \"Adra1d\"    \"Gpr157\"    \"Adgrg2\"  \"Blank-45\"     \"Gpr20\"      \"Casr\"  #>         297         298         299         302         305         306  #>     \"Avpr2\"      \"Mc5r\"      \"Sctr\"     \"Epha5\"    \"Gpr158\"     \"Cxcr4\"  #>         313         315         316         321         322         323  #>     \"Vipr1\"      \"Gpr6\" \"Blank-148\"    \"Celsr3\"     \"Uts2r\"      \"Hrh2\"  #>         324         325         328         329         330         331  #>      \"Htr6\"   \"Slc17a6\"      \"Gpr1\"     \"Glp2r\"   \"Ppp1r3g\"     \"V1ra8\"  #>         332         333         334         335         337         339  #>      \"Trhr\"     \"Sstr3\"     \"Gpr63\"     \"Htr1a\"     \"F2rl3\"       \"Pln\"  #>         340         341         347         348         350         351  #>    \"Grin2b\"     \"Gpr37\"     \"Chrm4\"      \"Lgr6\"     \"Gpr61\"    \"Taar7e\"  #>         352         353         354         356         358         360  #>      \"Mas1\"     \"Npy2r\"    \"Ptger2\"     \"P2ry2\"     \"Oprm1\"    \"Prokr2\"  #>         362         364         365         366         369         372  #>    \"Adra1a\"     \"Gpr45\"      \"Mc4r\" \"Blank-128\"     \"Sstr2\"      \"Flt3\"  #>         375         376         381         382         383         387  #>     \"Htr5a\"      \"Ghsr\"     \"Galr1\"  \"Blank-95\"     \"Gpr83\"     \"Crhr1\"  #>         388         389         390         393         396         399  #>      \"Brs3\"      \"Drd5\"    \"Gpr139\"     \"Taar6\"     \"Htr5b\"   \"Vmn1r40\"  #>         401         402         407         410         411         412  #>       \"Rrh\"  \"Blank-83\"     \"Crhr2\" \"Blank-161\"   \"Vmn1r50\"    \"Tas1r3\"  #>         414         417         418         420         428         434  #>     \"Taar2\"     \"P2ry4\"     \"Mchr1\"    \"Tas1r1\"  \"Blank-69\"      \"Htr7\"  #>         436         441         446         448         452         458  #>    \"Hcrtr2\"     \"Htr2a\"   \"Cysltr2\"   \"Vmn1r46\"      \"Grpr\"    \"Adgrf2\"  #>         461         463         464         468         474         475  #> \"Blank-127\"      \"Opn5\"     \"Taar3\"      \"Oxtr\"     \"Cckbr\"      \"Nmbr\"  #>         476         477         481         482         487         492  #>    \"Ptger4\" \"Blank-145\"    \"Gpr101\"   \"Slc17a8\"    \"Adgrf4\"     \"Epha2\"  #>         528  #> \"Blank-139\"  #>  #> [[2]] #>                                         2  #> \"240649020551054330404932383065726870513\"  #>                                         3  #> \"274176126496863898679934791272921588227\"  #>                                         4  #> \"323754550002953984063006506310071917306\"  #>                                         5  #>  \"87260224659312905497866017323180367450\"  #>                                         6  #>  \"17817477728742691260808256980746537959\"  #>                                         7  #> \"182132384503107798660396708280285136358\"  #>                                         9  #> \"316289522368890354495930310222776908199\"  #>                                        10  #> \"318995879282318989627235045690211636294\"  #>                                        11  #> \"104570855383158731814075192607294301741\"  #>                                        12  #> \"115370283894795045523368609208878185314\"  #>                                        13  #> \"123860671559578247432410194986927758864\"  #>                                        14  #> \"126981423897188762239468136959275655616\"  #>                                        15  #> \"134398773695365619188678200952912609063\"  #>                                        16  #>  \"15242486364109501724975900940581726845\"  #>                                        17  #> \"152684748256642370929802439227360458069\"  #>                                        18  #> \"153751792203577791006158581642177087065\"  #>                                        19  #>  \"16326589507615554063401897357427439030\"  #>                                        20  #> \"165786478473465185470745991122188406667\"  #>                                        21  #> \"167710327060928309829388429279250508392\"  #>                                        22  #> \"172181421897607556322673704318102678295\"  #>                                        23  #> \"176844289786228093052039491926955764947\"  #>                                        24  #> \"182235958169292445695483205478317795477\"  #>                                        25  #> \"183227745956657225549068107012033843521\"  #>                                        26  #> \"186988931894710833920932112634285943415\"  #>                                        27  #> \"190687643154627893064711601675234362640\"  #>                                        28  #>  \"20548793658722995878220914240286086757\"  #>                                        29  #> \"206702762285684421190019779213421380201\"  #>                                        30  #> \"216701996099683814512199402223708471323\"  #>                                        31  #>  \"21934936165997373583174173761929761438\"  #>                                        32  #> \"230344318208995342827768566280706457626\"  #>                                        33  #> \"251905496166492083168644493421091558216\"  #>                                        34  #> \"262996653580953175020435707363716649390\"  #>                                        35  #>  \"27666206735695437393204421885258583706\"  #>                                        37  #> \"286906689872367261752702769926754066848\"  #>                                        38  #> \"288822108801800165318171357739905375883\"  #>                                        39  #> \"301054712356664458042996323827909441002\"  #>                                        40  #> \"304842190541754537761816256358565562302\"  #>                                        41  #> \"318439340668767417720582355350205310941\"  #>                                        42  #> \"335295524680090725199231409883288198017\"  #>                                        43  #>  \"35118346554513854436644695033199584696\"  #>                                        44  #>  \"41054036480225512911591384807281320971\"  #>                                        45  #>  \"43731708947199618294982749003938483862\"  #>                                        46  #>  \"48024672048124996997588408479044670509\"  #>                                        47  #>  \"51348907619842676963078202479438175138\"  #>                                        49  #>  \"67532821514617092397935003422482443295\"  #>                                        50  #>  \"77151711298730578178892667721058396928\"  #>                                        51  #>  \"77782228870577724567477221255169934206\"  #>                                        52  #>   \"8777587181320516093160667806451882030\"  #>                                        53  #>  \"95838678880751873613229512065975406368\"  #>                                        54  #>  \"95947958963963707263153541936375959179\"  #>                                        55  #>   \"9668748337336721830701975018211142813\"  #>                                        56  #>  \"97411078642927912684859796714759494710\"  #>                                        57  #> \"101161259912191124732236989250178928032\"  #>                                        58  #> \"110615983935499449765434338770904504245\"  #>                                        59  #> \"110858042010405247711695373195937122852\"  #>                                        60  #> \"110900719814678261966908552089216814729\"  #>                                        61  #>  \"12925323527075390484710711277617599454\"  #>                                        63  #> \"137348923180371322628727011975895485209\"  #>                                        64  #> \"138859376429590720661963324654447571708\"  #>                                        65  #> \"140543565961583233746802451796981444137\"  #>                                        66  #> \"143386081176260440019925196855300710659\"  #>                                        67  #> \"143408196806895889016075556052288734233\"  #>                                        68  #> \"145421744145915784890159499930205641713\"  #>                                        69  #> \"148336156782096202859532636956126767457\"  #>                                        70  #> \"150082699777048696177232440639953146354\"  #>                                        71  #>  \"15247055772869406897093633424720409278\"  #>                                        72  #>  \"15834776842182822801451197571763335013\"  #>                                        73  #> \"170833460535439412738579124041592991444\"  #>                                        74  #> \"173780780834031059819946658163431921979\"  #>                                        75  #> \"174306823762889142173283452439684229948\"  #>                                        76  #> \"175540604452034099044348476236813150837\"  #>                                        77  #> \"177757177666889772027017950398587309639\"  #>                                        78  #>  \"17868848607867654301368031294266874310\"  #>                                        79  #> \"180947508370750255585892730777436680945\"  #>                                        80  #> \"187952627468949069447188707715308813657\"  #>                                        81  #>   \"1900302715660571356090444774019116326\"  #>                                        82  #> \"203192161403397797138670022274582721699\"  #>                                        83  #> \"206016050634629330546630679047044021073\"  #>                                        85  #> \"214394514156259228118188949454902817376\"  #>                                        86  #> \"221669638772738575000116137509912039310\"  #>                                        87  #> \"224458376429228506642398057779371677646\"  #>                                        88  #> \"226912346807310637711937183879196326571\"  #>                                        89  #> \"227232155811404089141823608874580791245\"  #>                                        91  #> \"236677629222667262221261861475728542818\"  #>                                        93  #> \"244015124549889909957742476033146111487\"  #>                                        94  #> \"244247765904337326625465691380839405459\"  #>                                        95  #> \"244448312826260498647079278647004353269\"  #>                                        96  #> \"244840145612854293464477850603474951260\"  #>                                        97  #> \"262797098003740683881650619022037793005\"  #>                                        98  #> \"265185306239991354232232246957204545228\"  #>                                        99  #> \"266413162898429280572455841453688616870\"  #>                                       101  #> \"275784684664527332374777211328350223506\"  #>                                       102  #> \"277057315125198906319398446608128392905\"  #>                                       104  #> \"291975341311453330406711526698967834209\"  #>                                       105  #> \"295193149306421749943849825086053455411\"  #>                                       106  #>  \"30222355550742125173065032035537805062\"  #>                                       107  #> \"304560432600831995659079356647103974886\"  #>                                       108  #>  \"30571638947438619177947320407779261750\"  #>                                       109  #> \"306415949245581212081161219410047325001\"  #>                                       110  #> \"311565496674213535805029947713320284697\"  #>                                       111  #> \"314397389362641167108869069386457433770\"  #>                                       112  #>   \"3188909098022617910378369321966273882\"  #>                                       113  #> \"322879686187630160969459793861944841206\"  #>                                       114  #> \"330850389163886577071114668277958486114\"  #>                                       115  #> \"334199301045926627171760429217123408914\"  #>                                       116  #> \"339814056401091912617621500767389941735\"  #>                                       117  #>  \"36648998424868029072860674954666559763\"  #>                                       118  #>  \"39033692777509843205319060807429911979\"  #>                                       119  #>   \"3942785923272820952395109293003259310\"  #>                                       120  #>  \"47275912178029130797780898068213599096\"  #>                                       121  #>  \"56815638009315000170441964570512336625\"  #>                                       122  #>  \"57203625626451579261315887898923502046\"  #>                                       123  #>  \"62669443199671326763841071380380779477\"  #>                                       124  #>  \"64228015236811922665804882776457047292\"  #>                                       126  #>  \"68418314542386876178693610244900595267\"  #>                                       127  #>  \"70219882915166469874938407731799217344\"  #>                                       128  #>  \"75660428514717127988983246148828583482\"  #>                                       129  #>  \"75682347267697870039469591993208007445\"  #>                                       130  #>  \"87903363874776475366779322866396664731\"  #>                                       131  #>  \"88743795534206169429467675642537392511\"  #>                                       133  #>   \"9538866320245722231901445225545432644\"  #>                                       134  #>  \"96091484747656303270745913028146994621\"  #>                                       135  #> \"116860147088450350976374609398998546737\"  #>                                       136  #> \"133061403473432310288273623600023558748\"  #>                                       137  #> \"137154375879163008723188861204335796821\"  #>                                       138  #> \"185903314401459366597627436588666236388\"  #>                                       139  #> \"217996462208701069168232210617040322639\"  #>                                       140  #> \"226667648171626631993624597360362535576\"  #>                                       141  #> \"254829253202043893331055483138743800247\"  #>                                       142  #> \"271967915636064836314881508293335292245\"  #>                                       143  #> \"273673567134859598195435250950149370161\"  #>                                       144  #> \"305306955532868686456926844192964831687\"  #>                                       145  #> \"307030440204593378842812081935039092344\"  #>                                       146  #> \"311587331826654155209560142756469108973\"  #>                                       147  #>  \"44197902970141946871502798467323259089\"  #>                                       148  #>  \"44721220002773982161418195292536576043\"  #>                                       150  #>  \"65855854848879329159292019718060662708\"  #>                                       151  #>  \"76322781861215450124167009829890606622\"  #>                                       152  #>  \"11065258297873257226330942251431244138\"  #>                                       153  #> \"118071411587380747913796380721014165557\"  #>                                       154  #> \"123540785709544435621019288242840920053\"  #>                                       156  #> \"130428604684362047522418850101908720496\"  #>                                       157  #> \"134509424346276649608483685115101376571\"  #>                                       158  #> \"136341171141277731884608634279863298546\"  #>                                       160  #> \"137356600627014280700323828086313714576\"  #>                                       161  #> \"151798130004305208790801168757831384604\"  #>                                       162  #> \"162684318525520950869468479178769741207\"  #>                                       163  #> \"164424478098970510930576318421517316799\"  #>                                       164  #> \"166456955228473064319115194076209471689\"  #>                                       165  #> 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                         178  #> \"254538897036257180617662178141894962698\"  #>                                       179  #> \"257184545464839903394564555141875300987\"  #>                                       180  #> \"266246243070401825856501948379131507953\"  #>                                       181  #> \"280661554698226730422771895627995747059\"  #>                                       182  #> \"283821893476134729825893155000887153128\"  #>                                       183  #> \"286146294981380023269011675378975275188\"  #>                                       184  #> \"292254379263157279159966458654907155929\"  #>                                       185  #> \"293900582929631255788566880963197704396\"  #>                                       186  #> \"296019945099320175547230863498668480924\"  #>                                       187  #> \"307915098305811968258082436904262060268\"  #>                                       188  #>  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                        493  #> \"262323915115773877344473192484876459225\"  #>                                       494  #> \"264234489423886906860498828392801290668\"  #>                                       495  #> \"328891726607418454659643302361160567789\"  #>                                       496  #>   \"6380671372744430258754116433861320161\"  #>                                       497  #>  \"75286702783716447443887872812098770697\"  #>                                       498  #>   \"9677424102111816817518421117250891895\"  #>                                       499  #>  \"17685062374745280598492217386845129350\"  #>                                       501  #>  \"32422253415776258079819139802733069941\"  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Dimensions of giotto objects — dims-generic","title":"Dimensions of giotto objects — dims-generic","text":"Find dimensions object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dimensions of giotto objects — dims-generic","text":"","code":"# S4 method for class 'giotto' nrow(x)  # S4 method for class 'giottoPoints' nrow(x)  # S4 method for class 'giottoPolygon' nrow(x)  # S4 method for class 'spatLocsObj' nrow(x)  # S4 method for class 'exprData' nrow(x)  # S4 method for class 'metaData' nrow(x)  # S4 method for class 'spatialNetworkObj' nrow(x)  # S4 method for class 'enrData' nrow(x)  # S4 method for class 'dimObj' nrow(x)  # S4 method for class 'giotto' ncol(x)  # S4 method for class 'exprData' ncol(x)  # S4 method for class 'metaData' ncol(x)  # S4 method for class 'enrData' ncol(x)  # S4 method for class 'dimObj' ncol(x)  # S4 method for class 'giotto' dim(x)  # S4 method for class 'spatLocsObj' dim(x)  # S4 method for class 'exprData' dim(x)  # S4 method for class 'metaData' dim(x)  # S4 method for class 'enrData' dim(x)  # S4 method for class 'giottoLargeImage' dim(x)  # S4 method for class 'giottoPolygon' dim(x)  # S4 method for class 'giottoPoints' dim(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dimensions of giotto objects — dims-generic","text":"x object check dimensions ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dimensions of giotto objects — dims-generic","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dims-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dimensions of giotto objects — dims-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  nrow(g) #> [1] 79761"},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot distribution of image intensity values — distGiottoImage","title":"Plot distribution of image intensity values — distGiottoImage","text":"Plot distribution intensity values using either density plot histogram. Useful finding image artefact outliers determining reasonable scaling cutoffs.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot distribution of image intensity values — distGiottoImage","text":"","code":"distGiottoImage(   gobject = NULL,   image_type = \"largeImage\",   image_name = NULL,   giottoLargeImage = NULL,   method = c(\"dens\", \"hist\"),   show_max = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot distribution of image intensity values — distGiottoImage","text":"gobject giotto object image_type image object type (supports largeImage set default) image_name name image object use giottoLargeImage giotto large image object method plot type show image intensity distribution show_max logical. Plot set max intensity vertical red line ... additional params pass terra::hist() terra::density()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot distribution of image intensity values — distGiottoImage","text":"density histogram plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Plot distribution of image intensity values — distGiottoImage","text":"Plot generated downsampling original image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"plotting-method-dens-","dir":"Reference","previous_headings":"","what":"Plotting method 'dens'","title":"Plot distribution of image intensity values — distGiottoImage","text":"Density plot intensity values image objects. N total values examined. Bandwidth refers curve smoothing value applied.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"plotting-method-hist-","dir":"Reference","previous_headings":"","what":"Plotting method 'hist'","title":"Plot distribution of image intensity values — distGiottoImage","text":"Histogram intensity values image objects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/distGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot distribution of image intensity values — distGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  distGiottoImage(g, image_name = \"image\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/doDeferred.html","id":null,"dir":"Reference","previous_headings":"","what":"Perform deferred/lazy operations — doDeferred","title":"Perform deferred/lazy operations — doDeferred","text":"Force deferred/lazy operations.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/doDeferred.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Perform deferred/lazy operations — doDeferred","text":"","code":"# S4 method for class 'giottoAffineImage' doDeferred(x, size = 5e+05, filename = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/doDeferred.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Perform deferred/lazy operations — doDeferred","text":"x object force deferred operations size numeric. Minimum number image pixels render evaluating filename character. Full filepath write rendered image . NULL, file tempdir() generated. ... additional args pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/doDeferred.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Perform deferred/lazy operations — doDeferred","text":"","code":"gimg <- GiottoData::loadSubObjectMini(\"giottoLargeImage\") affimg <- spin(gimg, 45) # lazily performs affine  # force the affine operation and render the output with at least 5e5 px gimg2 <- doDeferred(affimg, size = 5e5) # **This is mainly intended for visualization.** # This process saves with image depth of 8. # Spatially transformed raster values are not preferred for analysis"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_mat.html","id":null,"dir":"Reference","previous_headings":"","what":"Print abbreviated matrix — .abbrev_mat","title":"Print abbreviated matrix — .abbrev_mat","text":"print abbreviated matrix exprObj. Works Matrix pkg denseMatrix, matrix, data.frame classes inherit .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_mat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print abbreviated matrix — .abbrev_mat","text":"","code":".abbrev_mat(exprObj, nrows, ncols, header = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_mat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print abbreviated matrix — .abbrev_mat","text":"abbreviated matrix exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_spatlocs.html","id":null,"dir":"Reference","previous_headings":"","what":"Print abbreviated spatlocs — .abbrev_spatlocs","title":"Print abbreviated spatlocs — .abbrev_spatlocs","text":"print abbreviated spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_spatlocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print abbreviated spatlocs — .abbrev_spatlocs","text":"","code":".abbrev_spatlocs(spatLocsObj, nrows)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-abbrev_spatlocs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Print abbreviated spatlocs — .abbrev_spatlocs","text":"abbreviated spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-bitdepth.html","id":null,"dir":"Reference","previous_headings":"","what":"Guess likely bitdepth from value(s) — .bitdepth","title":"Guess likely bitdepth from value(s) — .bitdepth","text":"Guess likely bitdepth value(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-bitdepth.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Guess likely bitdepth from value(s) — .bitdepth","text":"","code":".bitdepth(x, return_max = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-bitdepth.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Guess likely bitdepth from value(s) — .bitdepth","text":"x numeric vector. Values representative data assessed bitdepth. usually sampled subset values raster. return_max logical. default FALSE. Whether return maximum possible value detected bitdepth instead bitdepth ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-bitdepth.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Guess likely bitdepth from value(s) — .bitdepth","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_centroids_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate polygon centroids — .calculate_centroids_polygons","title":"Calculate polygon centroids — .calculate_centroids_polygons","text":"calculates centroids selected polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_centroids_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate polygon centroids — .calculate_centroids_polygons","text":"","code":".calculate_centroids_polygons(   gpolygon,   name = \"centroids\",   append_gpolygon = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_centroids_polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate polygon centroids — .calculate_centroids_polygons","text":"SpatVector giotto polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_distance_and_weight.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate spatial network distance and weight — .calculate_distance_and_weight","title":"Calculate spatial network distance and weight — .calculate_distance_and_weight","text":"Calculate distance weight metrics data.table spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_distance_and_weight.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate spatial network distance and weight — .calculate_distance_and_weight","text":"","code":".calculate_distance_and_weight(   networkDT = NULL,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   sdimz = \"sdimz\",   d2_or_d3 = c(2, 3) )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_distance_and_weight.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate spatial network distance and weight — .calculate_distance_and_weight","text":"networkDT spatial network data.table sdimx spatial dimension x sdimy spatial dimension y sdimz spatial dimension z d2_or_d3 number dimensions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_distance_and_weight.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate spatial network distance and weight — .calculate_distance_and_weight","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_overlap_raster.html","id":null,"dir":"Reference","previous_headings":"","what":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","title":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","text":"Core workflow function accepts simple SpatVector inputs, performs rasterization polys checks overlaps.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_overlap_raster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","text":"","code":".calculate_overlap_raster(   spatvec,   pointvec,   count_info_column = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_overlap_raster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","text":"spatvec SpatVector polygon giottoPolygon object pointvec SpatVector points giottoPoints object count_info_column column count information (optional) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-calculate_overlap_raster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Find feature points overlapped by rasterized polygon. — .calculate_overlap_raster","text":"SpatVector overlapped points info","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_cell_meta_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check cell metadata object — .check_cell_meta_obj","title":"Check cell metadata object — .check_cell_meta_obj","text":"Function check S4 cellMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_cell_meta_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check cell metadata object — .check_cell_meta_obj","text":"","code":".check_cell_meta_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_cell_meta_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check cell metadata object — .check_cell_meta_obj","text":"object S4 cellMetaObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_cell_meta_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check cell metadata object — .check_cell_meta_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_dim_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check dimObj — .check_dim_obj","title":"Check dimObj — .check_dim_obj","text":"check function S4 dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_dim_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check dimObj — .check_dim_obj","text":"","code":".check_dim_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_dim_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check dimObj — .check_dim_obj","text":"object S4 dimObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_dim_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check dimObj — .check_dim_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_expr_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check exprObj — .check_expr_obj","title":"Check exprObj — .check_expr_obj","text":"Check function S4 exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_expr_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check exprObj — .check_expr_obj","text":"","code":".check_expr_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_expr_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check exprObj — .check_expr_obj","text":"object S4 exprObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_expr_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check exprObj — .check_expr_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_feat_meta_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check feature metadata object — .check_feat_meta_obj","title":"Check feature metadata object — .check_feat_meta_obj","text":"Function check S4 featMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_feat_meta_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check feature metadata object — .check_feat_meta_obj","text":"","code":".check_feat_meta_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_feat_meta_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check feature metadata object — .check_feat_meta_obj","text":"object S4 featMetaObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_feat_meta_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check feature metadata object — .check_feat_meta_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_giotto_python_modules.html","id":null,"dir":"Reference","previous_headings":"","what":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","title":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","text":"Check core python packages Giotto uses. internal currently called giotto initialize() method","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_giotto_python_modules.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","text":"","code":".check_giotto_python_modules(my_python_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_giotto_python_modules.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","text":"my_python_path path python environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_giotto_python_modules.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check if Giotto python modules are in python environment — .check_giotto_python_modules","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_grid_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check spatialGridObj — .check_spat_grid_obj","title":"Check spatialGridObj — .check_spat_grid_obj","text":"Check function S4 spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_grid_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check spatialGridObj — .check_spat_grid_obj","text":"","code":".check_spat_grid_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_grid_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check spatialGridObj — .check_spat_grid_obj","text":"object S4 spatialGridObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_grid_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check spatialGridObj — .check_spat_grid_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_locs_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check spatLocsObj — .check_spat_locs_obj","title":"Check spatLocsObj — .check_spat_locs_obj","text":"Check function S4 spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_locs_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check spatLocsObj — .check_spat_locs_obj","text":"","code":".check_spat_locs_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_locs_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check spatLocsObj — .check_spat_locs_obj","text":"object S4 spatLocsObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_locs_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check spatLocsObj — .check_spat_locs_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_net_obj.html","id":null,"dir":"Reference","previous_headings":"","what":"Check spatialNetworkObj — .check_spat_net_obj","title":"Check spatialNetworkObj — .check_spat_net_obj","text":"Check function S4 spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_net_obj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check spatialNetworkObj — .check_spat_net_obj","text":"","code":".check_spat_net_obj(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_net_obj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check spatialNetworkObj — .check_spat_net_obj","text":"object S4 spatialNetworkObj check","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spat_net_obj.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check spatialNetworkObj — .check_spat_net_obj","text":"character TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spatial_location_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Check spatial location data — .check_spatial_location_data","title":"Check spatial location data — .check_spatial_location_data","text":"check cell ID (spatial unit) names spatial location expression data. look identical IDs sorting.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spatial_location_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check spatial location data — .check_spatial_location_data","text":"","code":".check_spatial_location_data(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-check_spatial_location_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check spatial location data — .check_spatial_location_data","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-combine_stack_spatvectors.html","id":null,"dir":"Reference","previous_headings":"","what":".combine_stack_spatvectors — .combine_stack_spatvectors","title":".combine_stack_spatvectors — .combine_stack_spatvectors","text":"combines/aggregates polygons cell ID different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-combine_stack_spatvectors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".combine_stack_spatvectors — .combine_stack_spatvectors","text":"","code":".combine_stack_spatvectors(   gobject,   spat_units,   for_loop = FALSE,   for_loop_group_size = 100 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-combine_stack_spatvectors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".combine_stack_spatvectors — .combine_stack_spatvectors","text":"SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_2d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_2d — .create_delaunaynetwork_2d","title":".create_delaunaynetwork_2d — .create_delaunaynetwork_2d","text":"Create spatial 2D Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_2d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_2d — .create_delaunaynetwork_2d","text":"","code":".create_delaunaynetwork_2d(   gobject,   method = c(\"delaunayn_geometry\", \"RTriangle\", \"deldir\"),   spat_unit = NULL,   spat_loc_name = \"raw\",   sdimx = \"sdimx\",   sdimy = \"sdimy\",   name = \"delaunay_network\",   maximum_distance = \"auto\",   minimum_k = 0,   options = \"Pp\",   Y = TRUE,   j = TRUE,   S = 0,   verbose = TRUE,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_2d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_2d — .create_delaunaynetwork_2d","text":"spatial 2D Delaunay network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_3d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_3d — .create_delaunaynetwork_3d","title":".create_delaunaynetwork_3d — .create_delaunaynetwork_3d","text":"Create spatial 3D Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_3d — .create_delaunaynetwork_3d","text":"","code":".create_delaunaynetwork_3d(   gobject,   method = \"delaunayn_geometry\",   spat_unit = NULL,   spat_loc_name = \"raw\",   sdimx = \"sdimx\",   sdimy = \"sdimy\",   sdimz = \"sdimz\",   name = \"delaunay_network_3D\",   maximum_distance = \"auto\",   minimum_k = 0,   options = \"Pp\",   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_3d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_3d — .create_delaunaynetwork_3d","text":"spatial 3D Delaunay network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_RTriangle.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_RTriangle — .create_delaunaynetwork_RTriangle","title":".create_delaunaynetwork_RTriangle — .create_delaunaynetwork_RTriangle","text":"Create spatial Delaunay network RTriangle","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_RTriangle.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_RTriangle — .create_delaunaynetwork_RTriangle","text":"","code":".create_delaunaynetwork_RTriangle(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   Y = TRUE,   j = TRUE,   S = 0,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_RTriangle.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_RTriangle — .create_delaunaynetwork_RTriangle","text":"spatial Delaunay network RTriangle","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_deldir.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_deldir — .create_delaunaynetwork_deldir","title":".create_delaunaynetwork_deldir — .create_delaunaynetwork_deldir","text":"Create spatial Delaunay network deldir","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_deldir.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_deldir — .create_delaunaynetwork_deldir","text":"","code":".create_delaunaynetwork_deldir(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_deldir.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_deldir — .create_delaunaynetwork_deldir","text":"spatial Delaunay network deldir","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_geometry — .create_delaunaynetwork_geometry","title":".create_delaunaynetwork_geometry — .create_delaunaynetwork_geometry","text":"Create spatial Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_geometry — .create_delaunaynetwork_geometry","text":"","code":".create_delaunaynetwork_geometry(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   options = \"Pp\",   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_geometry — .create_delaunaynetwork_geometry","text":"spatial Delaunay network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry_3d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_delaunaynetwork_geometry_3d — .create_delaunaynetwork_geometry_3d","title":".create_delaunaynetwork_geometry_3d — .create_delaunaynetwork_geometry_3d","text":"Create spatial 3D Delaunay network geometry","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry_3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_delaunaynetwork_geometry_3d — .create_delaunaynetwork_geometry_3d","text":"","code":".create_delaunaynetwork_geometry_3d(   spatial_locations,   sdimx = \"sdimx\",   sdimy = \"sdimy\",   sdimz = \"sdimz\",   options = options,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_delaunaynetwork_geometry_3d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_delaunaynetwork_geometry_3d — .create_delaunaynetwork_geometry_3d","text":"spatial 3D Delaunay network geometry","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_2d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_spatialgrid_default_2d — .create_spatialgrid_default_2d","title":".create_spatialgrid_default_2d — .create_spatialgrid_default_2d","text":"create 2D spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_2d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_spatialgrid_default_2d — .create_spatialgrid_default_2d","text":"","code":".create_spatialgrid_default_2d(   gobject,   spat_unit = NULL,   spat_loc_name = \"raw\",   sdimx_stepsize = NULL,   sdimy_stepsize = NULL,   minimum_padding = 1 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_2d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_spatialgrid_default_2d — .create_spatialgrid_default_2d","text":"2D spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_3d.html","id":null,"dir":"Reference","previous_headings":"","what":".create_spatialgrid_default_3d — .create_spatialgrid_default_3d","title":".create_spatialgrid_default_3d — .create_spatialgrid_default_3d","text":"create 3D spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".create_spatialgrid_default_3d — .create_spatialgrid_default_3d","text":"","code":".create_spatialgrid_default_3d(   gobject,   spat_unit = NULL,   spat_loc_name = \"raw\",   sdimx_stepsize = NULL,   sdimy_stepsize = NULL,   sdimz_stepsize = NULL,   minimum_padding = 1 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatialgrid_default_3d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".create_spatialgrid_default_3d — .create_spatialgrid_default_3d","text":"3D spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatvector_object_from_dfr.html","id":null,"dir":"Reference","previous_headings":"","what":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","title":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","text":"create terra spatvector data.frame cols 1 2 must x y coordinates respectively. Additional columns set attributes points first additional (col 3) feat_ID.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatvector_object_from_dfr.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","text":"","code":".create_spatvector_object_from_dfr(   x,   x_colname = NULL,   y_colname = NULL,   feat_ID_colname = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatvector_object_from_dfr.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","text":"x data.frame object x_colname column name x-coordinates y_colname column name y-coordinates feat_ID_colname column name feature ids verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_spatvector_object_from_dfr.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create terra spatvector object from a data.frame — .create_spatvector_object_from_dfr","text":"SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_terra_spatraster.html","id":null,"dir":"Reference","previous_headings":"","what":"Load image as a terra spatRaster object — .create_terra_spatraster","title":"Load image as a terra spatRaster object — .create_terra_spatraster","text":"Load image terra spatRaster object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_terra_spatraster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Load image as a terra spatRaster object — .create_terra_spatraster","text":"","code":".create_terra_spatraster(image_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_terra_spatraster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Load image as a terra spatRaster object — .create_terra_spatraster","text":"image_path existing full filepath image loaded terra spatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-create_terra_spatraster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Load image as a terra spatRaster object — .create_terra_spatraster","text":"spatRaster object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-do_gpoly.html","id":null,"dir":"Reference","previous_headings":"","what":"Do giottoPolygon — .do_gpoly","title":"Do giottoPolygon — .do_gpoly","text":"giottoPolygon objects carry 3 pieces spatial information. polygons, centroids, polygon overlapped features. need updated spatial manipulations applied. function simplifies performing functions SpatVector-based slots.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-do_gpoly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Do giottoPolygon — .do_gpoly","text":"","code":".do_gpoly(x, what, args = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-do_gpoly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Do giottoPolygon — .do_gpoly","text":"x giottoPolygon call args list additional args","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-do_gpoly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Do giottoPolygon — .do_gpoly","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_points.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert point data data.table to spatVector — .dt_to_spatvector_points","title":"Convert point data data.table to spatVector — .dt_to_spatvector_points","text":"data.table spatVector points","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_points.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert point data data.table to spatVector — .dt_to_spatvector_points","text":"","code":".dt_to_spatvector_points(dt, include_values = TRUE, specific_values = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_points.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert point data data.table to spatVector — .dt_to_spatvector_points","text":"dt data.table include_values boolean. Include additional values data.table attributes paired created terra spatVector specific_values specific values include attributes include_values == TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_points.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert point data data.table to spatVector — .dt_to_spatvector_points","text":"spatVector points","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","title":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","text":"convert data.table spatVector polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","text":"","code":".dt_to_spatvector_polygon(   dt,   include_values = TRUE,   specific_values = NULL,   sort_geom = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_polygon.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","text":"dt data.table. terra geometry information include_values logical. Whether include additional columns geometry information SpatVector attributes. Default TRUE. specific_values character. Specific subset columns include attributes include_values = TRUE. sort_geom logical. Whether sort key data.table input 'geom', 'part', 'hole' columns.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-dt_to_spatvector_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert data.table to polygon spatVector — .dt_to_spatvector_polygon","text":"polygon spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-edge_coords_array.html","id":null,"dir":"Reference","previous_headings":"","what":"Numerical array of edge start and end — .edge_coords_array","title":"Numerical array of edge start and end — .edge_coords_array","text":"Generate \\(2\\) x \\(j\\) x \\(k\\) numerical array edge start end coordinates. Rows correspond  start end. Cols variable ie x, y, (z) whatever variable used measure sample location graph space. third dim sample. layout makes easy iterate across matrix slices array [stats::dist()].","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-edge_coords_array.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Numerical array of edge start and end — .edge_coords_array","text":"","code":".edge_coords_array(x, y, x_node_ids = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-edge_coords_array.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Numerical array of edge start and end — .edge_coords_array","text":"x matrix nodes info coords y network data.table cols x_node_ids y indexed character cols, node IDs apply coords x must supplied character vector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-edge_coords_array.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Numerical array of edge start and end — .edge_coords_array","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-filter_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Filter spatial network — .filter_network","title":"Filter spatial network — .filter_network","text":"Filter spatial network spatial characteristics","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-filter_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Filter spatial network — .filter_network","text":"","code":".filter_network(networkDT = NULL, maximum_distance = NULL, minimum_k = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-filter_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Filter spatial network — .filter_network","text":"networkDT spatial network data.table format maximum_distance maximum distance cell centroids minimum_k minimum number neighbors","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-filter_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Filter spatial network — .filter_network","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_2d.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_2d — .find_grid_2d","title":".find_grid_2d — .find_grid_2d","text":"find grid location 2D","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_2d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_2d — .find_grid_2d","text":"","code":".find_grid_2d(grid_DT, x_loc, y_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_2d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_2d — .find_grid_2d","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_3d.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_3d — .find_grid_3d","title":".find_grid_3d — .find_grid_3d","text":"find grid location 3D","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_3d.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_3d — .find_grid_3d","text":"","code":".find_grid_3d(grid_DT, x_loc, y_loc, z_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_3d.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_3d — .find_grid_3d","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_x.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_x — .find_grid_x","title":".find_grid_x — .find_grid_x","text":"find grid location x-axis","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_x.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_x — .find_grid_x","text":"","code":".find_grid_x(grid_DT, x_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_x.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_x — .find_grid_x","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_y.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_y — .find_grid_y","title":".find_grid_y — .find_grid_y","text":"find grid location y-axis","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_y.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_y — .find_grid_y","text":"","code":".find_grid_y(grid_DT, y_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_y.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_y — .find_grid_y","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_z.html","id":null,"dir":"Reference","previous_headings":"","what":".find_grid_z — .find_grid_z","title":".find_grid_z — .find_grid_z","text":"find grid location z-axis","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_z.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".find_grid_z — .find_grid_z","text":"","code":".find_grid_z(grid_DT, z_loc)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-find_grid_z.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".find_grid_z — .find_grid_z","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-fix_multipart_geoms.html","id":null,"dir":"Reference","previous_headings":"","what":"Split multi-part polygons — .fix_multipart_geoms","title":"Split multi-part polygons — .fix_multipart_geoms","text":"function split geoms (polygons) multiple parts","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-fix_multipart_geoms.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split multi-part polygons — .fix_multipart_geoms","text":"","code":".fix_multipart_geoms(spatVector)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-fix_multipart_geoms.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split multi-part polygons — .fix_multipart_geoms","text":"SpatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-giotto_alloc_dt.html","id":null,"dir":"Reference","previous_headings":"","what":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","title":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","text":"Finds DT based objects, overallocates data.tables, sets objects back giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-giotto_alloc_dt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","text":"","code":".giotto_alloc_dt(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-giotto_alloc_dt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-giotto_alloc_dt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Over-allocation for giotto DT-based info — .giotto_alloc_dt","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-identify_background_range_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Identify background range polygons — .identify_background_range_polygons","title":"Identify background range polygons — .identify_background_range_polygons","text":"function remove background polygon comparing individual polygon vertex xy ranges overall SpatVector extent. SpatVector function run MUST contain polygons generated part FOV. individual polygons compared overall extent assumed roughly original mask image.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-identify_background_range_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Identify background range polygons — .identify_background_range_polygons","text":"","code":".identify_background_range_polygons(spatVector, threshold = 0.9)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-identify_background_range_polygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Identify background range polygons — .identify_background_range_polygons","text":"spatVector terra polygon spatvector threshold polygon's x y range exceeds fraction overall SpatVector extent, flagged removal.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-identify_background_range_polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Identify background range polygons — .identify_background_range_polygons","text":"character vector polygon IDs variable length (usually either length 0 .e. background poly remove, 1, background poly remove) used correct threshold.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_giotto_environment.html","id":null,"dir":"Reference","previous_headings":"","what":".install_giotto_environment — .install_giotto_environment","title":".install_giotto_environment — .install_giotto_environment","text":"installation options giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_giotto_environment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".install_giotto_environment — .install_giotto_environment","text":"","code":".install_giotto_environment(   force_environment = FALSE,   packages_to_install = c(\"pandas\", \"networkx\", \"python-igraph\", \"leidenalg\",     \"python-louvain\", \"python.app\", \"scikit-learn\", \"smfishhmrf\", \"session-info\"),   pip_packages = c(\"python-louvain\", \"smfishhmrf\", \"session-info\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   confirm = TRUE,   envname = \"giotto_env\",   conda = \"auto\",   verbose = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_giotto_environment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".install_giotto_environment — .install_giotto_environment","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_github_link_pip.html","id":null,"dir":"Reference","previous_headings":"","what":"Install Package from GitHub Link — .install_github_link_pip","title":"Install Package from GitHub Link — .install_github_link_pip","text":"Installs link python env","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_github_link_pip.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install Package from GitHub Link — .install_github_link_pip","text":"","code":".install_github_link_pip(link = NULL, env = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_github_link_pip.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install Package from GitHub Link — .install_github_link_pip","text":"link link github repository containing python package, e.g. git+https://github.com/TencentAILabHealthcare/pysodb.git env conda environment link installed via pip","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_github_link_pip.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install Package from GitHub Link — .install_github_link_pip","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":null,"dir":"Reference","previous_headings":"","what":"Install Python Package with Reticulate — .install_py_pkg_reticulate","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"Install Python Package Reticulate","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"","code":".install_py_pkg_reticulate(package = NULL, env = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"package name python package env name environment python package installed.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"character NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-install_py_pkg_reticulate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Install Python Package with Reticulate — .install_py_pkg_reticulate","text":"Installs package python env prompting user. Installation done via py_install reticulate package.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-merge_spatial_enrich_info.html","id":null,"dir":"Reference","previous_headings":"","what":".merge_spatial_enrich_info — .merge_spatial_enrich_info","title":".merge_spatial_enrich_info — .merge_spatial_enrich_info","text":"take combine data.table result append spatial enrichment results.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-merge_spatial_enrich_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".merge_spatial_enrich_info — .merge_spatial_enrich_info","text":"","code":".merge_spatial_enrich_info(   gobject,   comb_dt,   spat_unit,   feat_type,   spat_enr_names = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-merge_spatial_enrich_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".merge_spatial_enrich_info — .merge_spatial_enrich_info","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Overlap points per polgyon — .overlap_points_per_polygon","title":"Overlap points per polgyon — .overlap_points_per_polygon","text":"Loop overlap single polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overlap points per polgyon — .overlap_points_per_polygon","text":"","code":".overlap_points_per_polygon(spatvec, pointvec, poly_ID_names, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overlap points per polgyon — .overlap_points_per_polygon","text":"spatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon_wrapped.html","id":null,"dir":"Reference","previous_headings":"","what":"Overlap points per polygon – wrapped — .overlap_points_per_polygon_wrapped","title":"Overlap points per polygon – wrapped — .overlap_points_per_polygon_wrapped","text":"overlap wrapped polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon_wrapped.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overlap points per polygon – wrapped — .overlap_points_per_polygon_wrapped","text":"","code":".overlap_points_per_polygon_wrapped(   spatvec_wrapped,   pointvec_wrapped,   poly_ID_names )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_per_polygon_wrapped.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overlap points per polygon – wrapped — .overlap_points_per_polygon_wrapped","text":"Packed object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_single_polygon.html","id":null,"dir":"Reference","previous_headings":"","what":"Overlap points – single polygon — .overlap_points_single_polygon","title":"Overlap points – single polygon — .overlap_points_single_polygon","text":"overlap single polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_single_polygon.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Overlap points – single polygon — .overlap_points_single_polygon","text":"","code":".overlap_points_single_polygon(spatvec, poly_ID_name, pointvec_dt)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-overlap_points_single_polygon.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Overlap points – single polygon — .overlap_points_single_polygon","text":"terra::intersect","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottoimage_mg.html","id":null,"dir":"Reference","previous_headings":"","what":".plot_giottoimage_mg — .plot_giottoimage_mg","title":".plot_giottoimage_mg — .plot_giottoimage_mg","text":"get plot giottoImage either directly giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottoimage_mg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".plot_giottoimage_mg — .plot_giottoimage_mg","text":"","code":".plot_giottoimage_mg(gobject = NULL, image_name = NULL, giottoImage = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottoimage_mg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":".plot_giottoimage_mg — .plot_giottoimage_mg","text":"gobject giotto object image_name name giotto image showGiottoImageNames giottoImage giottoImage object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottoimage_mg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".plot_giottoimage_mg — .plot_giottoimage_mg","text":"plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottolargeimage.html","id":null,"dir":"Reference","previous_headings":"","what":".plot_giottolargeimage — .plot_giottolargeimage","title":".plot_giottolargeimage — .plot_giottolargeimage","text":"Plot downsampled version giottoLargeImage. Cropping can increase plot resolution region interest.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottolargeimage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".plot_giottolargeimage — .plot_giottolargeimage","text":"","code":".plot_giottolargeimage(   gobject = NULL,   largeImage_name = NULL,   giottoLargeImage = NULL,   crop_extent = NULL,   xmax_crop = NULL,   xmin_crop = NULL,   ymax_crop = NULL,   ymin_crop = NULL,   max_intensity = NULL,   asRGB = FALSE,   stretch = NULL,   axes = TRUE,   smooth = TRUE,   mar = c(3, 5, 1.5, 1),   legend = FALSE,   maxcell = 5e+05,   col = grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1),   asp = 1,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottolargeimage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":".plot_giottolargeimage — .plot_giottolargeimage","text":"gobject giotto object largeImage_name name giottoLargeImage giottoLargeImage giottoLargeImage object crop_extent (optional) extent object focus specific region image xmax_crop, xmin_crop, ymax_crop, ymin_crop (optional) crop min/max x y bounds max_intensity (optional) value treat maximum intensity color scale asRGB (optional) logical. Force RGB plotting automatically detected stretch character. Option stretch values increase contrast: \"lin\" linear \"hist\" (histogram) axes boolean. Default = TRUE. Whether draw axes smooth boolean. default = TRUE. whether apply smoothing image mar plot margins default = c(3,5,1.5,1) legend whether plot legend color scale (grayscale ). default = FALSE maxcell positive integer. Maximum number image cells use plot col character. Colors single channel images. default grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1). can also data.frame two columns (value, color) get \"classes\" type legend three columns (, , color) get \"interval\" type legend asp numeric. (default = 1) specific aspect ratio use ... additional params pass terra::plot terra::plotRGB depending depending image type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-plot_giottolargeimage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".plot_giottolargeimage — .plot_giottolargeimage","text":"plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":null,"dir":"Reference","previous_headings":"","what":"Hierarchical tree printing — .print_leaf","title":"Hierarchical tree printing — .print_leaf","text":"Hierarchical tree printing","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hierarchical tree printing — .print_leaf","text":"","code":".print_leaf(level_index, availableDT, inherit_last = TRUE, indent)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hierarchical tree printing — .print_leaf","text":"level_index col availability matrix start print availableDT availability matrix given data.table inherit_last (boolean) determine behavior previous level last level (intended values print) TRUE behavior defined. #TODO indent indent characters print level (top level ”)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Hierarchical tree printing — .print_leaf","text":"Hierarchical tree","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-print_leaf.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Hierarchical tree printing — .print_leaf","text":"Much inspiration taken https://rdrr.io/cran/fs/src/R/tree.R","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-prov_match.html","id":null,"dir":"Reference","previous_headings":"","what":"Check provenance info matches across list of S4 subobjects — .prov_match","title":"Check provenance info matches across list of S4 subobjects — .prov_match","text":"Check provenance info matches across list S4 subobjects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-prov_match.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check provenance info matches across list of S4 subobjects — .prov_match","text":"","code":".prov_match(..., verbose = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-prov_match.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check provenance info matches across list of S4 subobjects — .prov_match","text":"... list s4 subobjects match provenance verbose print discovered provenance info","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-prov_match.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check provenance info matches across list of S4 subobjects — .prov_match","text":"logical NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-py_install_prompt.html","id":null,"dir":"Reference","previous_headings":"","what":"Prompt User for Python Install — .py_install_prompt","title":"Prompt User for Python Install — .py_install_prompt","text":"prompts user install package","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-py_install_prompt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prompt User for Python Install — .py_install_prompt","text":"","code":".py_install_prompt(package = NULL, env = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-py_install_prompt.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prompt User for Python Install — .py_install_prompt","text":"package python package/github url env environment package installed","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-py_install_prompt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prompt User for Python Install — .py_install_prompt","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-read_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read cell metadata — .read_cell_metadata","title":"Read cell metadata — .read_cell_metadata","text":"read cell metadata list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-read_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read cell metadata — .read_cell_metadata","text":"","code":".read_cell_metadata(   metadata,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-read_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read cell metadata — .read_cell_metadata","text":"metadata nested list cell metadata information provenance provenance information (optional) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-read_cell_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read cell metadata — .read_cell_metadata","text":"cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rescale_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Rescale polygons — .rescale_polygons","title":"Rescale polygons — .rescale_polygons","text":"rescale individual polygons factor x y","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rescale_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rescale polygons — .rescale_polygons","text":"","code":".rescale_polygons(spatVector, spatVectorCentroids, fx = 0.5, fy = 0.5)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rescale_polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rescale polygons — .rescale_polygons","text":"polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Rotate spatial locations — .rotate_spatial_locations","title":"Rotate spatial locations — .rotate_spatial_locations","text":"Rotate given spatlocs given radians","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rotate spatial locations — .rotate_spatial_locations","text":"","code":".rotate_spatial_locations(   spatlocs,   rotateradians = c(xy = 0, zy = 0, xz = 0),   rcenter = c(0, 0, 0),   geom = c(\"sdimx\", \"sdimy\", \"sdimz\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rotate spatial locations — .rotate_spatial_locations","text":"spatlocs spatial locations use rotateradians Named vector radians rotation along 3 coordinate axes. single value provided, treated xy rotation. rcenter center rotation given vector xy(z) coordinates (defaults coordinate center) geom character. Named vector colames x, y, z coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rotate spatial locations — .rotate_spatial_locations","text":"spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-rotate_spatial_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Rotate spatial locations — .rotate_spatial_locations","text":"Radians provided rotateradians param named vector values xy (yaw), zy (pitch), xz (roll)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Scale spatial locations — .scale_spatial_locations","title":"Scale spatial locations — .scale_spatial_locations","text":"Simple scaling spatial locations given scale_factor. Values scaled coordinate origin coordinates provided scenter param. Default values supply values z axis, values applied input data.table z information detected third item geom param.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Scale spatial locations — .scale_spatial_locations","text":"","code":".scale_spatial_locations(   spatlocs,   scale_factor = c(1, 1, 1),   scenter = c(0, 0, 0),   geom = c(\"sdimx\", \"sdimy\", \"sdimz\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scale spatial locations — .scale_spatial_locations","text":"spatlocs data.table. spatial locations information scale scale_factor scaling factor apply coordinates. Default c(1, 1, 1) scenter center scale spatial coordinates. Given vector xy(z) coordinates. Default c(0, 0, 0) geom character. Named vector colnames x, y, (z) coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Scale spatial locations — .scale_spatial_locations","text":"spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-scale_spatial_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Scale spatial locations — .scale_spatial_locations","text":"scale_factor either given single value applied x, y, z (available) dimensions vector named values 'x', y', ('z').","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Shift spatial locations — .shift_spatial_locations","title":"Shift spatial locations — .shift_spatial_locations","text":"Shift given coordinates given translation values","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shift spatial locations — .shift_spatial_locations","text":"","code":".shift_spatial_locations(   spatlocs,   dx = 0,   dy = 0,   dz = 0,   geom = c(\"sdimx\", \"sdimy\", \"sdimz\"),   copy_obj = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shift spatial locations — .shift_spatial_locations","text":"spatlocs spatial locations use dx value shift coordinates positive x direction dy value shift coordinates positive y direction dz value shift coordinates positive z direction geom character vector. Expected colnames x, y, z coords copy_obj logical. copy/duplicate object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shift spatial locations — .shift_spatial_locations","text":"spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_network.html","id":null,"dir":"Reference","previous_headings":"","what":"Shift spatial network — .shift_spatial_network","title":"Shift spatial network — .shift_spatial_network","text":"Shift spatial network coordinates","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Shift spatial network — .shift_spatial_network","text":"","code":".shift_spatial_network(spatnet, dx = 0, dy = 0, dz = 0, copy_obj = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Shift spatial network — .shift_spatial_network","text":"spatnet spatial network data.table dx distance shift x axis dy distance shift y axis dz distance shift z axis copy_obj copy/duplicate object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-shift_spatial_network.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Shift spatial network — .shift_spatial_network","text":"spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatraster_sample_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Sample values from SpatRaster — .spatraster_sample_values","title":"Sample values from SpatRaster — .spatraster_sample_values","text":"Sample numerical values SpatRaster. output format depends value output param.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatraster_sample_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sample values from SpatRaster — .spatraster_sample_values","text":"","code":".spatraster_sample_values(   raster_object,   size = 5000,   output = c(\"data.frame\", \"array\", \"magick\", \"EBImage\"),   verbose = NULL,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatraster_sample_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sample values from SpatRaster — .spatraster_sample_values","text":"raster_object terra SpatRaster sample size rough maximum pixels allowed resampling output output return . Defaults \"data.frame\" verbose verbose ... additional params pass terra::spatSample","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatraster_sample_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sample values from SpatRaster — .spatraster_sample_values","text":"magick EBImage image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatvector_to_dt.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert spatVector to data.table — .spatvector_to_dt","title":"Convert spatVector to data.table — .spatvector_to_dt","text":"convert spatVector data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatvector_to_dt.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert spatVector to data.table — .spatvector_to_dt","text":"","code":".spatvector_to_dt(spatvector, include_values = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spatvector_to_dt.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert spatVector to data.table — .spatvector_to_dt","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spline_poly.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert spline to polygon — .spline_poly","title":"Convert spline to polygon — .spline_poly","text":"spline polynomial smooth polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spline_poly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert spline to polygon — .spline_poly","text":"","code":".spline_poly(xy, vertices = 20, k = 3, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spline_poly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert spline to polygon — .spline_poly","text":"xy xy vertices vertices k k ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-spline_poly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert spline to polygon — .spline_poly","text":"polygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-subset_giotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset Giotto — .subset_giotto","title":"Subset Giotto — .subset_giotto","text":"Internal subset Giotto object including previous analyses specific spatial unit feature type. master workflow aggregate data subsetting. subsetGiotto, subsetGiottoLocs, subsetGiottoLocsMulti provide params pass function. function also hides confusing needed internal params exported functions. x_max, x_min, y_max, y_min params provided subsetting feature info downstream subsetGiottoLocs. polygon subsetting: Polygons subset subset using poly_ID values MUST match cell_ids, otherwise incorrect empty polygons can returned. subsetting subcellular information without editing aggregate information, use subsetGiottoLocsSubcellular","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-subset_giotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset Giotto — .subset_giotto","text":"","code":".subset_giotto(   gobject,   spat_unit = \":all:\",   feat_type = \"rna\",   spat_unit_fsub = \":all:\",   feat_type_ssub = \":all:\",   cell_ids = NULL,   feat_ids = NULL,   poly_info = spat_unit,   x_max = NULL,   x_min = NULL,   y_max = NULL,   y_min = NULL,   verbose = FALSE,   toplevel_params = 2 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-subset_giotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset Giotto — .subset_giotto","text":"gobject giotto object spat_unit, feat_type character vector. (default = '::') One spatial units feature types subset. Accepts '::' token subset across available. spat_unit_fsub character vector. (default = '::') limit feat_id subsets spat_units feat_type_ssub character vector. (default = '::') limit cell_id subsets feat_types cell_ids character. cell IDs keep feat_ids character. feature IDs keep poly_info character. polygon info(s) subset present. (defaults spat_unit) x_max, x_min, y_max, y_min feature info . minimum maximum x y coordinates keep verbose verbose toplevel_params expected stackframe parameters extracted","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-subset_giotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset Giotto — .subset_giotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-terra_writeraster_datatype.html","id":null,"dir":"Reference","previous_headings":"","what":".terra_writeraster_datatype — .terra_writeraster_datatype","title":".terra_writeraster_datatype — .terra_writeraster_datatype","text":"find likely compatible datatype given image characteristics. Values given arguments take priority found giottoLargeImage metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-terra_writeraster_datatype.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":".terra_writeraster_datatype — .terra_writeraster_datatype","text":"","code":".terra_writeraster_datatype(   giottoLargeImage = NULL,   quick_INTS_maxval = NULL,   max_intensity = NULL,   min_intensity = NULL,   is_int = NULL,   signed = NULL,   bitDepth = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-terra_writeraster_datatype.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":".terra_writeraster_datatype — .terra_writeraster_datatype","text":"giottoLargeImage giottoLargeImage object determine max_intensity, min_intensity, is_int settings quick_INTS_maxval Treat maximum intensity find compatible unsigned integer settings max_intensity, min_intensity value given image maximum/minimum intensity is_int image integer (TRUE) floating point (FALSE) signed image signed (TRUE) unsigned (TRUE) bitDepth image bitDepth verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/dot-terra_writeraster_datatype.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":".terra_writeraster_datatype — .terra_writeraster_datatype","text":"datatype terra writeRaster function","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate network edge euclidean distances — edge_distances","title":"Calculate network edge euclidean distances — edge_distances","text":"Calculate network edge euclidean distances","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Calculate network edge euclidean distances — edge_distances","text":"","code":"edge_distances(x, y, x_node_ids = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Calculate network edge euclidean distances — edge_distances","text":"x matrix nodes info coords. Rows samples, Cols variables y network data.table cols. Usually integer indices matching rows x. x_node_ids y indexed character cols, node IDs apply coords x must supplied character vector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Calculate network edge euclidean distances — edge_distances","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/edge_distances.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate network edge euclidean distances — edge_distances","text":"","code":"m <- matrix(c(0, 0, 0, 1, 1, 1, 3, 2, 4), byrow = TRUE, nrow = 3) edges <- data.table::data.table(     from = c(1, 1),     to = c(2, 3) )  edge_distances(m, edges) #> [1] 1.732051 5.385165"},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":null,"dir":"Reference","previous_headings":"","what":"estimateImageBg — estimateImageBg","title":"estimateImageBg — estimateImageBg","text":"helps estimate color background color plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"estimateImageBg — estimateImageBg","text":"","code":"estimateImageBg(mg_object, top_color_range = seq_len(50))"},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"estimateImageBg — estimateImageBg","text":"mg_object magick image Giotto image object top_color_range top possible background colors return","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"estimateImageBg — estimateImageBg","text":"vector pixel color frequencies associated barplot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/estimateImageBg.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"estimateImageBg — estimateImageBg","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, name = \"image\") mgimg <- as(g_image, \"giottoImage\")  estimateImageBg(mgimg)  #> Most abundant pixel colors: #> 276 261 159 155 132 103 100 79 73 69 67 66 64 55 48 43 43 43 43 39 39 39 36 36 #>  36 35 35 34 34 33 33 33 33 32 32 31 31 31 31 31 31 30 30 30 30 30 30 30 30 30"},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":null,"dir":"Reference","previous_headings":"","what":"Evaluate raw inputs to Giotto formatting — evaluate_input","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"Experimental. Evaluate raw inputs formats directly compatible Giotto's functionality. Note function formats data. output function still needs put Giotto subobject. wrapper function individual GiottoClass evaluation functions.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"","code":"evaluate_input(type, x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"type character. Type giotto data evaluate . x data evaluate ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"character class x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/evaluate_input.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Evaluate raw inputs to Giotto formatting — evaluate_input","text":"","code":"x <- GiottoData::loadSubObjectMini(\"exprObj\", 1)  evaluate_input(type = \"expression\", x) #> An object of class exprObj : \"normalized\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                                                                           #> Mlc1    .       .        .        .        . .  5.291601 . .        5.821597 . .        . #> Gprc5b  .       6.398031 .        7.454658 . .  6.273066 . 7.680054 6.808785 . 5.082989 . #> Gfap   10.48137 .        7.901442 5.886051 . . 10.746982 . 5.701006 5.821597 . .        . #>               #> Mlc1   ...... #> Gprc5b ...... #> Gfap   ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/exprObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 exprObj — exprObj-class","title":"S4 exprObj — exprObj-class","text":"Framework store aggregated expression information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/exprObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 exprObj — exprObj-class","text":"exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/exprObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 exprObj — exprObj-class","text":"name name exprObj exprMat matrix expression information spat_unit spatial unit expression (e.g. 'cell') feat_type feature type expression (e.g. 'rna', 'protein') provenance origin data expression information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/exprObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 exprObj — exprObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"exprObj\") #> An object of class exprObj : \"normalized\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                                                                           #> Mlc1    .       .        .        .        . .  5.291601 . .        5.821597 . .        . #> Gprc5b  .       6.398031 .        7.454658 . .  6.273066 . 7.680054 6.808785 . 5.082989 . #> Gfap   10.48137 .        7.901442 5.886051 . . 10.746982 . 5.701006 5.821597 . .        . #>               #> Mlc1   ...... #> Gprc5b ...... #> Gfap   ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a SpatExtent — ext","title":"Get a SpatExtent — ext","text":"Get SpatExtent object. spatial minmax x y object mapped .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a SpatExtent — ext","text":"","code":"# S4 method for class 'spatLocsObj' ext(x, ...)  # S4 method for class 'giottoPolygon' ext(x, ...)  # S4 method for class 'giottoPoints' ext(x, ...)  # S4 method for class 'spatialNetworkObj' ext(x, ...)  # S4 method for class 'giottoLargeImage' ext(x, ...)  # S4 method for class 'giottoImage' ext(x, ...)  # S4 method for class 'giotto' ext(   x,   spat_unit = \":all:\",   feat_type = \":all:\",   all_data = TRUE,   prefer = c(\"polygon\", \"spatlocs\", \"points\", \"images\"),   name = list(spatlocs = \":all:\"),   verbose = NULL,   ... )  # S4 method for class 'giottoAffineImage' ext(x, ...)  # S4 method for class 'affine2d' ext(x, ...)  # S4 method for class 'giottoPoints,SpatExtent' ext(x) <- value  # S4 method for class 'giottoPolygon,SpatExtent' ext(x) <- value  # S4 method for class 'giottoLargeImage,SpatExtent' ext(x) <- value  # S4 method for class 'ANY,ANY' ext(x) <- value  # S4 method for class 'giottoImage,SpatExtent' ext(x) <- value  # S4 method for class 'affine2d,ANY' ext(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a SpatExtent — ext","text":"x spatial object ... additional params pass spat_unit character. Spatial unit limit search . provided, default set. feat_type character. Feature type limit search \"points\" information. provided, default set. all_data logical. TRUE (default), spatial information designated prefer searched combined SpatExtent returned. FALSE, SpatExtent first existing data ordered prefer returned. prefer character vector. Order preferred data get extent . allowed terms \"polygon\", \"spatlocs\", \"points\", \"images\". also default ordering. Omitting terms removes search. name named list. Specific object names check. List names correspond allowed terms prefer. one name allowed \"images\" moment, produces combined SpatExtent verbose verbose value value set. Accepts object ext() work ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get a SpatExtent — ext","text":"SpatExtent","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get a SpatExtent — ext","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" # giotto %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% ext(g) # defaults to checking first giottoPolygon extent #> SpatExtent : 6391.46568586489, 6903.57332779812, -5153.89721175534, -4694.86823300896 (xmin, xmax, ymin, ymax) ext(g, prefer = \"spatlocs\") # check first spatLocsObj extent #> SpatExtent : 6401.14818002375, 6899.3228463116, -5147.19306531348, -4700.15708342436 (xmin, xmax, ymin, ymax) # first spatLocsObj from a different spat_unit ext(g, spat_unit = \"aggregate\", prefer = \"spatlocs\") #> SpatExtent : 6401.41164725267, 6899.10802819571, -5146.74746408943, -4700.32590047134 (xmin, xmax, ymin, ymax)  # from first image object ext(g, prefer = \"image\") #> SpatExtent : 6400.029, 6900.037, -5150.007, -4699.967 (xmin, xmax, ymin, ymax)  # add a dummy image with different spatial extent r <- terra::rast(array(seq(25), dim = c(5, 5))) test <- createGiottoLargeImage(r) ext(test) <- c(1e5, 1.1e5, 0, 10) g <- setGiotto(g, test) # add image  # combined from all image objects ext(g, prefer = \"image\", name = list(images = list_images_names(g))) #> SpatExtent : 6400.029, 110000, -5150.007, 10 (xmin, xmax, ymin, ymax)  # combined from all spatial data types in giotto object ext(g, all_data = TRUE, name = list(images = list_images_names(g))) #> SpatExtent : 6391.46568586489, 110000, -5153.89721175534, 10 (xmin, xmax, ymin, ymax)  # spatLocsObj %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% sl <- getSpatialLocations(g) ext(sl) #> SpatExtent : 6402.43781589887, 6899.20308651186, -5146.72565198022, -4700.15708342436 (xmin, xmax, ymin, ymax)  # giottoPolygon %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # get extent gpoly <- getPolygonInfo(g, return_giottoPolygon = TRUE) ext(gpoly) #> SpatExtent : 6399.24384990901, 6903.24298517207, -5152.38959073896, -4694.86823300896 (xmin, xmax, ymin, ymax)  # set extent plot(gpoly) # before  ext(gpoly) <- ext(0, 20, 30, 60) plot(gpoly) # after   # giottoPoints %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% # get extent gpoints <- getFeatureInfo(g, return_giottoPoints = TRUE) ext(gpoints) #> SpatExtent : 6400.037, 6900.0317, -5149.9834, -4699.9785 (xmin, xmax, ymin, ymax)  # set extent plot(gpoints) # before  ext(gpoints) <- ext(0, 2000, 3000, 6000) plot(gpoints) # after"},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":null,"dir":"Reference","previous_headings":"","what":"fDataDT — fDataDT","title":"fDataDT — fDataDT","text":"show feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"fDataDT — fDataDT","text":"","code":"fDataDT(gobject, spat_unit = NULL, feat_type = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"fDataDT — fDataDT","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"fDataDT — fDataDT","text":"data.table feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/fDataDT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"fDataDT — fDataDT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  fDataDT(g) #>            feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det #>             <char>    <int>      <num>      <num>     <num>         <num> #>   1:         Gna12      502  80.448718  1987.1333 3.1845085      3.958433 #>   2:         Ccnd2      357  57.211538  1254.4730 2.0103734      3.513930 #>   3:        Btbd17      252  40.384615   781.9747 1.2531645      3.103074 #>   4:          Sox9      309  49.519231  1019.7255 1.6341755      3.300083 #>   5:          Sez6      504  80.769231  2177.4740 3.4895416      4.320385 #>  ---                                                                      #> 630:        Lhfpl3      235  37.660256   732.3595 1.1736530      3.116423 #> 631: C030029H02Rik       72  11.538462   203.0811 0.3254506      2.820572 #> 632:       Gm19935       57   9.134615   172.1079 0.2758139      3.019436 #> 633: 9630013A20Rik       52   8.333333   157.2602 0.2520196      3.024235 #> 634: 2900040C04Rik       61   9.775641   179.7015 0.2879831      2.945926 #>         hvf #>      <char> #>   1:     no #>   2:     no #>   3:     no #>   4:     no #>   5:     no #>  ---        #> 630:     no #> 631:     no #> 632:     no #> 633:     no #> 634:     no"},{"path":"https://drieslab.github.io/GiottoClass/reference/featMetaObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 featMetaObj — featMetaObj-class","title":"S4 featMetaObj — featMetaObj-class","text":"Framework store feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featMetaObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 featMetaObj — featMetaObj-class","text":"featMetaObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featMetaObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 featMetaObj — featMetaObj-class","text":"metaDT metadata info col_desc (optional) character vector describing columns metadata spat_unit spatial unit aggregated expression (e.g. 'cell') feat_type feature type aggregated expression (e.g. 'rna', 'protein') provenance origin data aggregated expression information (applicable)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featMetaObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 featMetaObj — featMetaObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"featMetaObj\") #> An object of class featMetaObj  #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #>    feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det hvg_orig #>     <char>    <int>      <num>      <num>     <num>         <num>   <char> #> 1:    Mlc1       80   17.31602   526.5915  1.139808      6.582394       no #> 2:  Gprc5b      138   29.87013   944.0153  2.043323      6.840690       no #> 3:    Gfap      151   32.68398  1229.1943  2.660594      8.140359      yes #>          var    hvf #>        <num> <char> #> 1:  1.815718    yes #> 2:  2.388911    yes #> 3: 12.899599    yes"},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Feature type information — featType-generic","title":"Feature type information — featType-generic","text":"access set feat_type slot S4 subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Feature type information — featType-generic","text":"","code":"# S4 method for class 'ANY' featType(x)  # S4 method for class 'list' featType(x)  # S4 method for class 'featData' featType(x)  # S4 method for class 'featData' featType(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Feature type information — featType-generic","text":"x Giotto S4 class subobject feature type value value set feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Feature type information — featType-generic","text":"feat_type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Feature type information — featType-generic","text":"featType(): Get feature type information featType(featData): Get feature type information featType(featData) <- value: Set feature type information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featType-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Feature type information — featType-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"featMetaObj\")  featType(g) #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giotto feature network Class — featureNetwork-class","title":"S4 giotto feature network Class — featureNetwork-class","text":"Giotto class store operate feature network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giotto feature network Class — featureNetwork-class","text":"featureNetwork","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giotto feature network Class — featureNetwork-class","text":"contains feature network information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giotto feature network Class — featureNetwork-class","text":"name name feature network network_datatable feature network data.table format network_lookup_id table mapping numeric network ID unique feature numerical IDs full fully connected network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/featureNetwork-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giotto feature network Class — featureNetwork-class","text":"","code":"featureNetwork() #> An object of class \"featureNetwork\" #> Slot \"network_datatable\": #> NULL #>  #> Slot \"network_lookup_id\": #> NULL #>  #> Slot \"full\": #> NULL #>  #> Slot \"name\": #> [1] NA #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":null,"dir":"Reference","previous_headings":"","what":"Flip an object — flip","title":"Flip an object — flip","text":"Flip object designated x y value depending direction param input. Note behavior may different terra's","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flip an object — flip","text":"","code":"# S4 method for class 'giotto' flip(   x,   direction = \"vertical\",   x0 = 0,   y0 = 0,   spat_unit = \":all:\",   feat_type = \":all:\",   ... )  # S4 method for class 'giottoPolygon' flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for class 'giottoPoints' flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for class 'spatLocsObj' flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for class 'spatialNetworkObj' flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for class 'giottoLargeImage' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)  # S4 method for class 'SpatExtent' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)  # S4 method for class 'giottoLargeImage' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)  # S4 method for class 'giottoAffineImage' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)  # S4 method for class 'affine2d' flip(x, direction = \"vertical\", x0 = 0, y0 = 0)"},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flip an object — flip","text":"x object direction character. Direction flip. either partial match 'vertical' 'horizontal' x0 x value flip horizontally (ignored vertical). Pass NULL flip extent y0 y value flip vertically (ignored horizontal). Pass NULL flip extent spat_unit character vector. spatial units affect feat_type character vector. feature types affect ... additional args pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Flip an object — flip","text":"flipped object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/flip.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Flip an object — flip","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  flip(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx    sdimy                                 cell_ID #>       <num>    <num>                                  <char> #> 1: 6637.881 5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx    sdimy #> [1,] 6401.412 4700.326 #> [2,] 6899.108 5146.747 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert gef to Giotto — gefToGiotto","title":"Convert gef to Giotto — gefToGiotto","text":"Converts .gef file (output stereo-seq pipeline) giotto subcellular object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert gef to Giotto — gefToGiotto","text":"","code":"gefToGiotto(gef_file, bin_size = \"bin100\", verbose = FALSE, h5_file = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert gef to Giotto — gefToGiotto","text":"gef_file path .gef file bin_size bin size select .gef file verbose verbose h5_file name create -disk HDF5 file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert gef to Giotto — gefToGiotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/gefToGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert gef to Giotto — gefToGiotto","text":"Function beta. Converts .gef object Giotto object. six possible choices bin_size: bin1, bin10, bin20, bin50, bin100, bin200. See SAW pipeline additional information gef file.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial grids — generate_grid","title":"Spatial grids — generate_grid","text":"Generate spatial grid spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial grids — generate_grid","text":"","code":"triGrid(extent, ccd, id_prefix = \"ID_\")  orthoGrid(extent, ccd, id_prefix = \"ID_\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial grids — generate_grid","text":"extent SpatExtent anything else SpatExtent can extracted created ccd center center distance id_prefix character. prefix add ID names generated","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial grids — generate_grid","text":"spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/generate_grid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial grids — generate_grid","text":"","code":"e <- ext(0, 100, 0, 100) x <- triGrid(extent = e, ccd = 10) plot(x$sdimx, x$sdimy, asp = 1L)   x <- orthoGrid(extent = e, ccd = 10) plot(x$sdimx, x$sdimy, asp = 1L)"},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"getCellMetadata — getCellMetadata","title":"getCellMetadata — getCellMetadata","text":"Get cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getCellMetadata — getCellMetadata","text":"","code":"getCellMetadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   output = c(\"cellMetaObj\", \"data.table\"),   copy_obj = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getCellMetadata — getCellMetadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") output return either 'data.table' 'cellMetaObj' copy_obj whether deep copy/duplicate getting object (default = TRUE) set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getCellMetadata — getCellMetadata","text":"data.table cellMetaObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getCellMetadata — getCellMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getCellMetadata(g) #> An object of class cellMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #> dimensions: 624 7  #>  #>               cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                <char>     <int>    <int>      <num>      <num>       <num> #> 1: AACTCGATGGCGCAGT-1         1      265   41.79811  1057.9308           2 #> 2: GGCTGGCTAGCTTAAA-1         1      279   44.00631  1064.7493           5 #> 3: GACGCCTGTTGCAGGG-1         1      219   34.54259   964.9294           2 #>    custom_leiden #>            <num> #> 1:             4 #> 2:             3 #> 3:             3"},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dimension reduction — getDimReduction","title":"Get dimension reduction — getDimReduction","text":"Function get dimension reduction object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dimension reduction — getDimReduction","text":"","code":"getDimReduction(   gobject,   spat_unit = NULL,   feat_type = NULL,   reduction = c(\"cells\", \"feats\"),   reduction_method = NULL,   name = NULL,   output = c(\"dimObj\", \"matrix\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dimension reduction — getDimReduction","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") reduction reduction cells features (e.g. \"cells\", \"feats\") reduction_method reduction method (e.g. \"pca\", \"umap\", \"tsne\") name name reduction results output object type return . Either 'dimObj' (default) 'matrix' embedding coordinates. set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dimension reduction — getDimReduction","text":"dim reduction object (default) dim reduction coordinates","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getDimReduction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get dimension reduction — getDimReduction","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getDimReduction(g) #> An object of class dimObj : \"pca\" #> --| Contains dimension reduction generated with: pca  #> ----| for feat_type: rna  #> ----|     spat_unit: cell  #>  #>    100 dimensions for 624 data points #>  #> Additional included info: #> [1] \"eigenvalues\" \"loadings\"    #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":null,"dir":"Reference","previous_headings":"","what":"Get expression values — getExpression","title":"Get expression values — getExpression","text":"Function get expression values giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get expression values — getExpression","text":"","code":"getExpression(   gobject,   values = NULL,   spat_unit = NULL,   feat_type = NULL,   output = c(\"exprObj\", \"matrix\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get expression values — getExpression","text":"gobject giotto object values expression values extract (e.g. \"raw\", \"normalized\", \"scaled\") spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") output object type retrieve expression . Currently either matrix' matrix object contained exprObj 'exprObj' (default) exprObj allowed. set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get expression values — getExpression","text":"exprObj matrix depending output param","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getExpression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get expression values — getExpression","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getExpression(g) #> An object of class exprObj : \"raw\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #>  #> contains: #> 634 x 624 sparse Matrix of class \"dgCMatrix\" #>                                          #> Gna12  1 2 1 1 9 1 3 5 3 . . 10 7 ...... #> Ccnd2  . 1 1 . . 1 . 1 1 . .  . 3 ...... #> Btbd17 . 1 1 1 . . 2 . . . .  . . ...... #>  #>  ........suppressing 611 columns and 628 rows in show(); maybe adjust options(max.print=, width=) #>                                                #> Gm19935       . 1 . . . . . . . . 1 . . ...... #> 9630013A20Rik . . . . . . . . . . 1 . . ...... #> 2900040C04Rik 1 . . . . . . . . 1 . . . ...... #>  #>  First four colnames: #>  AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 #>  AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1"},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"Get feature info — getFeatureInfo","title":"Get feature info — getFeatureInfo","text":"Get giotto points spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get feature info — getFeatureInfo","text":"","code":"getFeatureInfo(   gobject = gobject,   feat_type = NULL,   return_giottoPoints = FALSE,   set_defaults = TRUE,   simplify = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get feature info — getFeatureInfo","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_giottoPoints return giottoPoints object set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. simplify logical. Whether take object list length 1.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get feature info — getFeatureInfo","text":"giotto points spatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get feature info — getFeatureInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getFeatureInfo(g) #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  source      : rna_feature_spatVector.shp #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3"},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"getFeatureMetadata — getFeatureMetadata","title":"getFeatureMetadata — getFeatureMetadata","text":"Get feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getFeatureMetadata — getFeatureMetadata","text":"","code":"getFeatureMetadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   output = c(\"featMetaObj\", \"data.table\"),   copy_obj = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getFeatureMetadata — getFeatureMetadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") output return either 'data.table' 'featMetaObj' copy_obj whether perform deepcopy data.table information set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getFeatureMetadata — getFeatureMetadata","text":"data.table featMetaObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getFeatureMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"getFeatureMetadata — getFeatureMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getFeatureMetadata(g) #> An object of class featMetaObj  #> spat_unit : \"z0\" #> feat_type : \"rna\" #> provenance: z0  #>  #>    feat_ID #>     <char> #> 1:    Mlc1 #> 2:  Gprc5b #> 3:    Gfap"},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get giotto image object — getGiottoImage","title":"Get giotto image object — getGiottoImage","text":"Get giotto one image objects gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get giotto image object — getGiottoImage","text":"","code":"getGiottoImage(gobject, image_type = NULL, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get giotto image object — getGiottoImage","text":"gobject giotto object image_type deprecated name character vector. Names giotto image object(s) showGiottoImageNames get","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get giotto image object — getGiottoImage","text":"giotto image object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get giotto image object — getGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getGiottoImage(gobject = g) #> An object of class giottoLargeImage : \"dapi_z0\" #> Image extent            : 6400.029, 6900.037, -5150.007, -4699.967 (xmin, xmax, ymin, ymax) #> Original image extent   : 6400.029, 6900.037, -5150.007, -4699.967 (xmin, xmax, ymin, ymax) #> Scale factor            : 0.108626547903541, 0.10862659908279 (x, y) #> Resolution              : 9.2058527063567, 9.20584836903386 (x, y) #> Layers                  : 1  #> Estimated max intensity : 255  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoData/Mini_datasets/Vizgen/VizgenObject/Images/dapi_z0_spatRaster'"},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Get multiomics integration results — getMultiomics","title":"Get multiomics integration results — getMultiomics","text":"Get multiomics integration result Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get multiomics integration results — getMultiomics","text":"","code":"getMultiomics(   gobject = NULL,   spat_unit = NULL,   feat_type = NULL,   integration_method = \"WNN\",   result_name = \"theta_weighted_matrix\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get multiomics integration results — getMultiomics","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') feat_type integrated feature type (e.g. 'rna_protein') integration_method multiomics integration method used. Default = 'WNN' result_name Default = 'theta_weighted_matrix'","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get multiomics integration results — getMultiomics","text":"multiomics integration result (e.g. theta_weighted_matrix WNN)","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getMultiomics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get multiomics integration results — getMultiomics","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- setMultiomics(     gobject = g, result = matrix(rnorm(100), nrow = 10),     spat_unit = \"cell\", feat_type = \"rna_protein\" )  getMultiomics(gobject = g, spat_unit = \"cell\", feat_type = \"rna_protein\") #>               [,1]        [,2]       [,3]        [,4]        [,5]       [,6] #>  [1,]  0.573351259 -0.77007572  1.0805134 -0.27499746  0.81051411 -1.7947501 #>  [2,]  0.653506513 -0.10392922  1.0956876  1.18512009  0.16798153 -1.5936760 #>  [3,]  1.102562583 -0.59883015 -0.8235445  0.03108054 -0.82634150 -0.5880921 #>  [4,] -0.331979510  0.86307592 -0.7896969 -0.20427061  0.48015487 -2.4436502 #>  [5,] -0.006015914  1.53498056 -2.2300375 -1.34758305 -0.22734637  0.8733072 #>  [6,]  0.542548136 -0.07677495  1.2682960  0.32840023 -0.38144334 -1.5700947 #>  [7,]  1.073179083  0.36398407  0.7477098  1.50785612 -0.51130892  1.2064433 #>  [8,]  0.431113801  0.80003990  0.2902944  0.51282324  1.61615062 -0.6020315 #>  [9,]  0.899647924 -1.51114608 -0.2336790  0.27261523  0.05862038  0.6160790 #> [10,]  0.906390447  1.66677279 -1.2574555  0.37969672 -0.20135846 -0.2994089 #>              [,7]        [,8]        [,9]       [,10] #>  [1,] -0.54314989  0.86164700 -0.36930863 -0.23013339 #>  [2,] -0.11165896  0.88285986 -0.10648446  1.82750672 #>  [3,] -0.59879136  0.25782948 -0.52105633  1.63416402 #>  [4,] -0.64283303 -2.41919619 -0.31239384 -0.30347819 #>  [5,] -2.18494492  0.98255604 -1.73132386  0.05761964 #>  [6,]  0.11409361  0.73347719  1.46947149 -0.50750744 #>  [7,]  0.01148282  0.76860157  0.01044213 -1.61633811 #>  [8,]  0.35329552 -0.01777067  0.40827683  0.89181656 #>  [9,]  2.29670311 -1.10088452  1.70418504 -0.03268551 #> [10,]  0.61040765  0.21277709 -0.43014614 -0.16986547"},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Get nearest neighbor network — getNearestNetwork","title":"Get nearest neighbor network — getNearestNetwork","text":"Get NN-network Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get nearest neighbor network — getNearestNetwork","text":"","code":"getNearestNetwork(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_type = NULL,   name = NULL,   output = c(\"nnNetObj\", \"igraph\", \"data.table\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get nearest neighbor network — getNearestNetwork","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_type \"kNN\" \"sNN\" name name NN network used output return giotto nnNetObj, igraph, data.table object. Default 'nnNetObj' set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get nearest neighbor network — getNearestNetwork","text":"Giotto nnNetObj, igraph data.table object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getNearestNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get nearest neighbor network — getNearestNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getNearestNetwork(gobject = g) #> The NN network type was not specified, default to the #>  first: \"sNN\" #> The NN network name was not specified, default to the #>  first: \"sNN.pca\" #> An object of class nnNetObj : \"sNN.pca\" #> --| Contains nearest neighbor network generated with: sNN  #> ----| for feat_type: rna  #> ----|     spat_unit: cell  #> ----|     provenance: cell  #>  #> IGRAPH 999a381 DNW- 624 3748 --  #> + attr: name (v/c), weight (e/n), distance (e/n), shared (e/n), rank #> | (e/n) #> + edges from 999a381 (vertex names): #>  [1] AAAGGGATGTAGCAAG-1->CAGTGTCCGCAGAATG-1 #>  [2] AAAGGGATGTAGCAAG-1->ACGTAGATTGCTGATG-1 #>  [3] AAAGGGATGTAGCAAG-1->CGTACCTGATAGGCCT-1 #>  [4] AAAGGGATGTAGCAAG-1->GATAAATCGGTGGATG-1 #>  [5] AAAGGGATGTAGCAAG-1->AACCCAGAGACGGAGA-1 #>  [6] AAAGGGATGTAGCAAG-1->GCCTTCAGCCCTACCG-1 #>  [7] AAATGGCATGTCTTGT-1->ACCCTTCATCTGCGAA-1 #> + ... omitted several edges #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"Get polygon info — getPolygonInfo","title":"Get polygon info — getPolygonInfo","text":"Get giotto polygon spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get polygon info — getPolygonInfo","text":"","code":"getPolygonInfo(   gobject = NULL,   polygon_name = NULL,   polygon_overlap = NULL,   return_giottoPolygon = FALSE,   verbose = TRUE,   simplify = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get polygon info — getPolygonInfo","text":"gobject giotto object polygon_name name polygons. Default \"cell\" polygon_overlap include polygon overlap information return_giottoPolygon (Defaults FALSE) Return giottoPolygon S4 object verbose verbose simplify logical. Whether take object list length 1.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get polygon info — getPolygonInfo","text":"spatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getPolygonInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get polygon info — getPolygonInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getPolygonInfo(g) #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 498, 1  (geometries, attributes) #>  extent      : 6399.244, 6903.243, -5152.39, -4694.868  (xmin, xmax, ymin, ymax) #>  source      : z0_spatInfo_spatVector.shp #>  coord. ref. :   #>  names       :                                 poly_ID #>  type        :                                   <chr> #>  values      :  40951783403982682273285375368232495429 #>                240649020551054330404932383065726870513 #>                274176126496863898679934791272921588227"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial enrichment — getSpatialEnrichment","title":"Get spatial enrichment — getSpatialEnrichment","text":"Function get spatial enrichment data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial enrichment — getSpatialEnrichment","text":"","code":"getSpatialEnrichment(   gobject,   spat_unit = NULL,   feat_type = NULL,   name = \"DWLS\",   output = c(\"spatEnrObj\", \"data.table\"),   copy_obj = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial enrichment — getSpatialEnrichment","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name spatial enrichment results. Default \"DWLS\" output format get information (e.g. \"data.table\") copy_obj whether deep copy/duplicate getting object (default = TRUE) set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial enrichment — getSpatialEnrichment","text":"spatEnrObj data.table fractions","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialEnrichment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get spatial enrichment — getSpatialEnrichment","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getSpatialEnrichment(g, spat_unit = \"aggregate\", name = \"cluster_metagene\") #> An object of class spatEnrObj : \"cluster_metagene\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>    ------------------------ #>  #> preview: #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #>  #> ...first 20 remaining colnames: #>  #>    #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial grid — getSpatialGrid","title":"Get spatial grid — getSpatialGrid","text":"Function get spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial grid — getSpatialGrid","text":"","code":"getSpatialGrid(   gobject,   spat_unit = NULL,   feat_type = NULL,   name = NULL,   return_grid_Obj = FALSE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial grid — getSpatialGrid","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name spatial grid return_grid_Obj return grid object (default = FALSE) set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial grid — getSpatialGrid","text":"spatialGridObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get spatial grid — getSpatialGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  getSpatialGrid(g) #> The grid name was not specified, default to the first: \"spatial_grid\" #>         x_start y_start  x_end y_end   gr_name gr_x_name gr_y_name #>           <num>   <num>  <num> <num>    <char>    <char>    <char> #>      1:  3067.5   -5445 3072.5 -5440      gr_1    gr_x_1    gr_y_1 #>      2:  3072.5   -5445 3077.5 -5440      gr_2    gr_x_2    gr_y_1 #>      3:  3077.5   -5445 3082.5 -5440      gr_3    gr_x_3    gr_y_1 #>      4:  3082.5   -5445 3087.5 -5440      gr_4    gr_x_4    gr_y_1 #>      5:  3087.5   -5445 3092.5 -5440      gr_5    gr_x_5    gr_y_1 #>     ---                                                            #> 388796:  6417.5   -2570 6422.5 -2565 gr_388796  gr_x_671  gr_y_576 #> 388797:  6422.5   -2570 6427.5 -2565 gr_388797  gr_x_672  gr_y_576 #> 388798:  6427.5   -2570 6432.5 -2565 gr_388798  gr_x_673  gr_y_576 #> 388799:  6432.5   -2570 6437.5 -2565 gr_388799  gr_x_674  gr_y_576 #> 388800:  6437.5   -2570 6442.5 -2565 gr_388800  gr_x_675  gr_y_576"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial locations — getSpatialLocations","title":"Get spatial locations — getSpatialLocations","text":"Function get spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial locations — getSpatialLocations","text":"","code":"getSpatialLocations(   gobject,   spat_unit = NULL,   name = NULL,   output = c(\"spatLocsObj\", \"data.table\"),   copy_obj = TRUE,   verbose = TRUE,   set_defaults = TRUE,   simplify = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial locations — getSpatialLocations","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") name name spatial locations (defaults first name spatial_locs slot, e.g. \"raw\") output object type get spatial locations . Default 'spatLocsObj'. Returning 'data.table' also possible. copy_obj whether copy/duplicate getting object (default = TRUE) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. simplify logical. Whether take object list length 1.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial locations — getSpatialLocations","text":"data.table coordinates spatLocsObj depending output","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialLocations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get spatial locations — getSpatialLocations","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getSpatialLocations(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"z0\" #> provenance: z0  #> dimensions: 498 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6405.067 -4780.499  40951783403982682273285375368232495429 #> 2: 6426.020 -4972.519 240649020551054330404932383065726870513 #> 3: 6428.456 -4799.158 274176126496863898679934791272921588227 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6402.438 -5146.726 #> [2,] 6899.203 -4700.157 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial network — getSpatialNetwork","title":"Get spatial network — getSpatialNetwork","text":"Function get spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial network — getSpatialNetwork","text":"","code":"getSpatialNetwork(   gobject,   spat_unit = NULL,   name = NULL,   output = c(\"spatialNetworkObj\", \"networkDT\", \"networkDT_before_filter\", \"outputObj\"),   set_defaults = TRUE,   copy_obj = TRUE,   verbose = TRUE,   simplify = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial network — getSpatialNetwork","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") name name spatial network output object type return . Options: 'spatialNetworkObj' (default), 'networkDT' 'networkDT_before_filter' data.table outputs. set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. copy_obj whether copy/duplicate getting object (default = TRUE) verbose verbose simplify logical. Whether take object list length 1.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial network — getSpatialNetwork","text":"spatialNetworkObj data.table","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getSpatialNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get spatial network — getSpatialNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  getSpatialNetwork(g) #> An object of class spatialNetworkObj : \"Delaunay_network\" #> Contains spatial network generated with: deldir  #> spat_unit : \"cell\" #> provenance: cell  #>    1770 connections (filtered) #>    1814 connections (before filter) #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_adj_rescale_img.html","id":null,"dir":"Reference","previous_headings":"","what":"get_adj_rescale_img — get_adj_rescale_img","title":"get_adj_rescale_img — get_adj_rescale_img","text":"get_adj_rescale_img","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_adj_rescale_img.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_adj_rescale_img — get_adj_rescale_img","text":"","code":"get_adj_rescale_img(img_minmax, spatial_locs, scale_factor = 1)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_adj_rescale_img.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_adj_rescale_img — get_adj_rescale_img","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_adj_rescale_img.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get_adj_rescale_img — get_adj_rescale_img","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_spatlocs <- getSpatialLocations(g) g_image <- getGiottoImage(g, name = \"image\") mgimg <- as(g_image, \"giottoImage\") minmax <- get_img_minmax(slot(mgimg, \"mg_object\")) #> Warning: `get_img_minmax()` was deprecated in GiottoClass 0.3.1. #> ℹ Please use `ext()` instead.  get_adj_rescale_img(img_minmax = minmax, spatial_locs = g_spatlocs) #> Warning: `get_adj_rescale_img()` was deprecated in GiottoClass 0.3.1. #> ℹ this is too specific to the inner workings of `giottoImage` #> ℹ We can simply use `ext<-` to set a new extent instead of this. #> xmin_adj_orig xmax_adj_orig ymin_adj_orig ymax_adj_orig  #>          3069         -6198         -5270          2568"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":null,"dir":"Reference","previous_headings":"","what":"get_distance — get_distance","title":"get_distance — get_distance","text":"estimate average distance neighboring cells network table input","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_distance — get_distance","text":"","code":"get_distance(networkDT, method = c(\"mean\", \"median\"))"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_distance — get_distance","text":"networkDT networkDT method method","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_distance — get_distance","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_distance.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get_distance — get_distance","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spat_net <- getSpatialNetwork(g, output = \"networkDT\")  get_distance(spat_net, method = \"mean\") #> [1] 137.93"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":null,"dir":"Reference","previous_headings":"","what":"get_img_minmax — get_img_minmax","title":"get_img_minmax — get_img_minmax","text":"get_img_minmax","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_img_minmax — get_img_minmax","text":"","code":"get_img_minmax(mg_img, negative_y = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_img_minmax — get_img_minmax","text":"mg_img magick object negative_y Map image negative y spatial values TRUE automatic alignment. Meaning origin upper left instead lower left.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"get_img_minmax — get_img_minmax","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_img_minmax.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"get_img_minmax — get_img_minmax","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, name = \"image\") mgimg <- as(g_image, \"giottoImage\")  get_img_minmax(slot(mgimg, \"mg_object\")) #> $img_xmax #> [1] 243 #>  #> $img_xmin #> [1] 0 #>  #> $img_ymax #> [1] 0 #>  #> $img_ymin #> [1] -172 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Get multiomics integration results — get_multiomics","title":"Get multiomics integration results — get_multiomics","text":"Get multiomics integration result Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get multiomics integration results — get_multiomics","text":"","code":"get_multiomics(   gobject,   spat_unit = NULL,   feat_type = NULL,   integration_method = \"WNN\",   result_name = \"theta_weighted_matrix\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get multiomics integration results — get_multiomics","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') feat_type integrated feature type (e.g. 'rna_protein') integration_method multiomics integration method used. Default = 'WNN' result_name Default = 'theta_weighted_matrix'","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get multiomics integration results — get_multiomics","text":"multiomics integration result (e.g. theta_weighted_matrix WNN)","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_multiomics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get multiomics integration results — get_multiomics","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- setMultiomics(     gobject = g, result = matrix(rnorm(100), nrow = 10),     spat_unit = \"cell\", feat_type = \"rna_protein\" )  get_multiomics(gobject = g, spat_unit = \"cell\", feat_type = \"rna_protein\") #>             [,1]        [,2]       [,3]       [,4]       [,5]        [,6] #>  [1,]  1.1884979  1.47605219 -1.9719497  1.7008620 -1.1675388 -0.05642605 #>  [2,] -0.6211862 -0.07589098 -0.4848200 -0.4662269 -0.7923482  1.19142146 #>  [3,] -0.4248148  0.62842700 -1.3848879 -0.3168777 -0.3003550 -0.02745457 #>  [4,] -1.2693983  0.19674511 -0.1762610 -1.2131392  0.1794639  0.88144485 #>  [5,] -0.2533625  0.08158049  0.2596137  0.2466786 -0.9374372 -3.09168198 #>  [6,] -0.1116180 -0.89830298 -0.2510197  0.1118254  1.4479660  1.12917805 #>  [7,] -0.1315426 -0.61990929 -1.0445444 -1.0078516  1.3361280  1.96047642 #>  [8,]  0.8725992 -1.06214909 -2.0920704  1.2416995  0.4995538  0.24592419 #>  [9,] -0.1657629  0.78311754 -0.5391583  1.3815616 -2.7557557 -0.43052706 #> [10,] -1.2409544 -2.78007372 -1.5206390 -2.5197112  0.4713136 -0.28259708 #>              [,7]       [,8]        [,9]       [,10] #>  [1,] -0.37221254 -0.4087357 -0.87151065  1.04067074 #>  [2,]  0.18263134 -2.2371918 -0.50174591  0.48370651 #>  [3,]  0.06055847  1.6845247  0.61345388 -1.38514216 #>  [4,] -0.28844587  0.8478142 -2.27293071 -0.98822934 #>  [5,]  1.40416927 -1.4393261 -0.02903636 -0.81254630 #>  [6,]  1.96437541  0.7074581 -1.31878087 -0.03695966 #>  [7,] -1.76916228  2.4144420 -1.59245568  0.12226510 #>  [8,]  0.11502054 -0.9043406 -0.15879473 -0.74855108 #>  [9,] -0.47298787  0.4745312  0.39397965  0.09353390 #> [10,] -0.95256772 -0.6146149  0.01302273  1.73000527"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giotto Class — giotto-class","title":"S4 giotto Class — giotto-class","text":"Giotto's core object encapsulates components spatial-omic project facilitates analyses.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giotto Class — giotto-class","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giotto Class — giotto-class","text":"[initialize] giotto class robust initialize() method automatically called upon setting data object, updates giottoInstructions, loading saved objects. performs following steps: Update object subobjects class definition changes needed Ensure set giottoInstructions available, otherwise generate defaults Ensure giotto python environment accessible options giotto.has_conda giotto.use_conda TRUE Check active spat_unit feat_type Ensure spatial/cell ID consistency initialize cell_ID feat_ID slots active spat_unit feat_type, well cell feature metadata exist. Values IDs metadata pulled existing data spatial_info/feat_info expression slots, preference latter. Perform slot-specific hierarchical checks ensure dependent pieces information added data depend existing information consistent across slots. Object validity checking","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giotto Class — giotto-class","text":"expression expression information expression_feat different features modalities rna, protein, metabolites, ... provided expression slot. spatial_locs spatial location coordinates cells/spots/grids spatial_info information spatial units (Giotto spatVector) cell_metadata metadata cells feat_metadata metadata available features feat_info information features (Giotto spatVector) cell_ID unique cell IDs feat_ID unique feature IDs features modalities spatial_network spatial network data.table/data.frame format spatial_grid spatial grid data.table/data.frame format spatial_enrichment slot save spatial enrichment-like results dimension_reduction slot save dimension reduction coordinates nn_network nearest neighbor network igraph format images slot store giotto image objects parameters slot save parameters used instructions slot global function instructions offset_file offset file used stitch together image fields versions giotto object metadata versioning info join_info information joined Giotto objects multiomics multiomics integration results h5_file path h5 file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giotto Class — giotto-class","text":"","code":"giotto() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> An object of class giotto  #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoAffineImage-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giottoAffineImage Class — giottoAffineImage-class","title":"S4 giottoAffineImage Class — giottoAffineImage-class","text":"Class extending giottoLargeImage. shear() spin() operations performed giottoLargeImage, class instantiated. provides way storing affine transformation also lazily performing required plotting preview. possible force deferred affine transform using doDeferred() return processed giottoLargeImage.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoAffineImage-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giottoAffineImage Class — giottoAffineImage-class","text":"giottoAffineImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoAffineImage-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giottoAffineImage Class — giottoAffineImage-class","text":"affine contains affine2d object allowing lazily performed spatial transforms funs list functions associated object. Primarily perform delayed/lazy operation","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giottoImage Class — giottoImage-class","title":"S4 giottoImage Class — giottoImage-class","text":"Framework giotto object store work spatial expression data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giottoImage Class — giottoImage-class","text":"giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giottoImage Class — giottoImage-class","text":"[mg_object] Core object image can read magick package [boundaries] Boundary adjustments can used manually automatically script adjust image spatial data.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giottoImage Class — giottoImage-class","text":"name name Giotto image mg_object magick image object minmax minimum maximum associated spatial location coordinates boundaries x y coordinate adjustments (default 0) scale_factor image scaling relative spatial locations resolution spatial location units covered per pixel file_path file path image given OS_platform Operating System run Giotto analysis ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoImage-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giottoImage Class — giottoImage-class","text":"","code":"giottoImage() #> An object of class ' giottoImage ' with name  test  #>   #> Min and max values are:  #>  Max on x-axis:   #>  Min on x-axis:   #>  Max on y-axis:   #>  Min on y-axis:   #>   #> Boundary adjustment are:  #>  Max adjustment on x-axis:   #>  Min adjustment on x-axis:   #>  Max adjustment on y-axis:   #>  Min adjustment on y-axis:   #>   #> Boundaries are:  #>  Image x-axis max boundary:    #>  Image x-axis min boundary:    #>  Image y-axis max boundary:    #>  Image y-axis min boundary:    #>   #> Scale factor:  #> NULL #>  #>  Resolution:  #> NULL #>  #>  File Path:  #> NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoLargeImage-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giottoLargeImage Class — giottoLargeImage-class","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"Image class Giotto uses terra SpatRaster backend. images loaded file disk worked lazily, values needed moment loaded/sampled memory. Since SpatRaster objects C pointers, giottoLargeImage inheriting classes need run reconnect() loading saved object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoLargeImage-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"giottoLargeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoLargeImage-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"name name large Giotto image raster_object terra SpatRaster object extent tracks extent raster object. Note processes rely extent raster object instead . overall_extent terra extent object covering original extent image scale_factor image scaling relative spatial locations resolution spatial location units covered per pixel max_intensity approximate maximum value min_intensity approximate minimum value max_window value set maximum intensity color scaling colors color mappings hex codes is_int values integers file_path file path image given OS_platform Operating System run Giotto analysis ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoLargeImage-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"","code":"giottoLargeImage() #> NULL giottoLargeImage"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoMasterToSuite.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a master Giotto object to suite — giottoMasterToSuite","title":"Convert a master Giotto object to suite — giottoMasterToSuite","text":"Convert master Giotto object suite","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoMasterToSuite.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a master Giotto object to suite — giottoMasterToSuite","text":"","code":"giottoMasterToSuite(gobject, expression_feat = \"rna\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoMasterToSuite.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a master Giotto object to suite — giottoMasterToSuite","text":"gobject Giotto object created master version expression_feat available features (e.g. rna, protein, ...)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoMasterToSuite.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a master Giotto object to suite — giottoMasterToSuite","text":"Giotto object compatible suite version","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giotto points Class — giottoPoints-class","title":"S4 giotto points Class — giottoPoints-class","text":"Giotto class store operate points data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giotto points Class — giottoPoints-class","text":"giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giotto points Class — giottoPoints-class","text":"Contains vector-type feature data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giotto points Class — giottoPoints-class","text":"feat_type name feature type spatVector terra spatVector store point shapes networks feature networks unique_ID_cache cached unique feature IDs match spatVector slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPoints-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giotto points Class — giottoPoints-class","text":"","code":"giottoPoints() #> An object of class giottoPoints #> feat_type : \"NA\" #> Feature Information: #> NULL #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giotto polygon Class — giottoPolygon-class","title":"S4 giotto polygon Class — giottoPolygon-class","text":"Giotto class store operate polygon-like data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 giotto polygon Class — giottoPolygon-class","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 giotto polygon Class — giottoPolygon-class","text":"holds polygon data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 giotto polygon Class — giottoPolygon-class","text":"name name polygon shapes spatVector terra spatVector store polygon shapes spatVectorCentroids centroids polygon shapes overlaps information overlapping points polygons unique_ID_cache cached unique spatial IDs match spatVector slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoPolygon-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 giotto polygon Class — giottoPolygon-class","text":"","code":"giottoPolygon() #> An object of class giottoPolygon #> spat_unit : \"NA\" #> Spatial Information: #> NULL #>  centroids   : NULL #>  overlaps    : NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Giotto to anndata — giottoToAnnData","title":"Convert Giotto to anndata — giottoToAnnData","text":"Converts Giotto object spatial anndata (e.g. scanpy) .h5ad file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Giotto to anndata — giottoToAnnData","text":"","code":"giottoToAnnData(   gobject = NULL,   spat_unit = NULL,   feat_type = NULL,   python_path = NULL,   env_name = \"giotto_env\",   save_directory = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Giotto to anndata — giottoToAnnData","text":"gobject giotto object converted spat_unit spatial unit used conversion. feat_type feature type used conversion. python_path path python executable within conda/miniconda environment env_name name environment containing python_path executable save_directory directory file saved.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Giotto to anndata — giottoToAnnData","text":"vector containing .h5ad file path(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToAnnData.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert Giotto to anndata — giottoToAnnData","text":"Function beta. Converts Giotto object .h5ad file(s). multiple spatial units /feature types, one spatial unit /feature type specified, specified spatial unit /feature type used. NULL, default, spatial units used conversion. multiple spatial units feature types specified, multiple AnnData object created returned. function create .txt files record key_added parameters networks. named corresponding spatial unit feature type pair. save_directory created already exist. default save_directory working directory.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeurat.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated — giottoToSeurat","title":"Deprecated — giottoToSeurat","text":"Deprecated. Please use either giottoToSeuratV4 giottoToSeuratV5","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeurat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated — giottoToSeurat","text":"","code":"giottoToSeurat(gobject, spat_unit = NULL, obj_use = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeurat.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deprecated — giottoToSeurat","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') obj_use Giotto object (deprecated, use gobject) ... additional params pass get_spatial_locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeurat.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deprecated — giottoToSeurat","text":"Seurat object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV4.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Giotto to Seurat V4 — giottoToSeuratV4","title":"Convert Giotto to Seurat V4 — giottoToSeuratV4","text":"Converts Giotto object Seurat object. functions extracts specific sets data belonging specified spatial unit. default values 'cell' 'rna' respectively.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV4.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Giotto to Seurat V4 — giottoToSeuratV4","text":"","code":"giottoToSeuratV4(gobject, spat_unit = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV4.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Giotto to Seurat V4 — giottoToSeuratV4","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') ... additional params pass get_spatial_locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV4.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Giotto to Seurat V4 — giottoToSeuratV4","text":"Seurat object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV5.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Giotto to Seurat V5 — giottoToSeuratV5","title":"Convert Giotto to Seurat V5 — giottoToSeuratV5","text":"Converts Giotto object Seurat object. functions extracts specific sets data belonging specified spatial unit. default values 'cell' 'rna' respectively.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV5.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Giotto to Seurat V5 — giottoToSeuratV5","text":"","code":"giottoToSeuratV5(   gobject,   spat_unit = NULL,   res_type = c(\"hires\", \"lowres\", \"fullres\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV5.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Giotto to Seurat V5 — giottoToSeuratV5","text":"gobject Giotto object spat_unit spatial unit (e.g. 'cell') res_type type 10x image output resolution ... additional params pass get_spatial_locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSeuratV5.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Giotto to Seurat V5 — giottoToSeuratV5","text":"Seurat object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Giotto to SpatialData — giottoToSpatialData","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"Converts Giotto object SpatialData object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"","code":"giottoToSpatialData(   gobject = NULL,   spat_unit = NULL,   feat_type = NULL,   spot_radius = NULL,   python_path = NULL,   env_name = NULL,   save_directory = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"gobject giotto object converted spat_unit spatial unit used conversion feat_type feature type used conversion spot_radius radius spots python_path path python executable within conda/miniconda environment env_name name environment containing python_path executable save_directory directory SpatialData object saved","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"SpatialData object saved disk.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialData.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert Giotto to SpatialData — giottoToSpatialData","text":"Function beta. Converts saves Giotto object SpatialData format disk.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"Utility function convert Giotto object SpatialExperiment object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"","code":"giottoToSpatialExperiment(giottoObj, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"giottoObj Input Giotto object convert SpatialExperiment object verbose boolean value specifying progress messages displayed . Default TRUE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"SpatialExperiment object contains data input Giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giottoToSpatialExperiment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Utility function to convert a Giotto object to a SpatialExperiment object. — giottoToSpatialExperiment","text":"","code":"if (FALSE) { # \\dontrun{ mini_gobject <- GiottoData::loadGiottoMini(\"vizgen\") giottoToSpatialExperiment(mini_gobject) } # }"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto instructions — createGiottoInstructions","title":"Giotto instructions — createGiottoInstructions","text":"Giotto instructions default settings applied giotto object level. added object, affect way object behaves. can create giottoInstructions object using createGiottoInstructions() add giotto object creation using instructions() generic. Specific settings can replaced retrieved using param argument. Additionally, using instructions<-() replacement function, initialize() called giotto object initialize = TRUE. giottoInstructions object provided giotto object creation, default one created giotto object initialization.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto instructions — createGiottoInstructions","text":"","code":"createGiottoInstructions(   python_path = getOption(\"giotto.py_path\"),   show_plot = NULL,   return_plot = NULL,   save_plot = NULL,   save_dir = NULL,   plot_format = NULL,   dpi = NULL,   units = NULL,   height = NULL,   width = NULL,   is_docker = FALSE,   plot_count = 0,   fiji_path = NULL,   no_python_warn = FALSE )  # S4 method for class 'missing,missing' instructions(gobject, param, ...)  # S4 method for class 'giotto,missing' instructions(gobject)  # S4 method for class 'giotto,character' instructions(gobject, param)  # S4 method for class 'giottoInstructions,character' instructions(gobject, param)  # S4 method for class 'giotto,missing,missing' instructions(gobject, initialize) <- value  # S4 method for class 'giotto,missing,logical' instructions(gobject, initialize) <- value  # S4 method for class 'giotto,character,missing' instructions(gobject, param, initialize) <- value  # S4 method for class 'giotto,character,logical' instructions(gobject, param, initialize) <- value  # S4 method for class 'giottoInstructions,character,ANY' instructions(gobject, param) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto instructions — createGiottoInstructions","text":"python_path path python binary use directory one level env directory (similar output reticulate::miniconda_path()) show_plot print plot console, default = TRUE return_plot return plot object, default = TRUE save_plot automatically save plot, dafault = FALSE save_dir path directory save plots plot_format format plots (defaults png) dpi resolution raster images units units format (defaults ) height height plots width width  plots is_docker using docker implementation Giotto (defaults FALSE) plot_count (global option) start count creating automatic unique plots fiji_path path fiji executable no_python_warn turn warning compatible python env detected gobject giotto object param Specific param instructions access modify ... params pass createGiottoInstructions() initialize (boolean, default = TRUE) whether initialize giotto object value value set","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto instructions — createGiottoInstructions","text":"giottoInstructions, instructions settings, giotto objects modified instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_instructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto instructions — createGiottoInstructions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  # create instructions ins <- instructions() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  # get instructions instrs <- instructions(g) force(instrs) #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : TRUE #> return_plot      : FALSE #> save_plot        : FALSE #> save_dir         : NA #> plot_format      : png #> dpi              : 300 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna  # get single instructions param instructions(g, \"show_plot\") #> [1] TRUE  # replace an instruction param instructions(g, \"show_plot\") <- FALSE instructions(g, \"show_plot\") #> [1] FALSE  # replace multiple instruction params instructions(g) #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : FALSE #> return_plot      : FALSE #> save_plot        : FALSE #> save_dir         : NA #> plot_format      : png #> dpi              : 300 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna instructions(g, c(\"show_plot\", \"dpi\")) <- list(TRUE, 600) instructions(g) #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : TRUE #> return_plot      : FALSE #> save_plot        : FALSE #> save_dir         : NA #> plot_format      : png #> dpi              : 600 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna  # replace instructions i <- createGiottoInstructions() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" instructions(g) <- i instructions(g) #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : TRUE #> return_plot      : TRUE #> save_plot        : FALSE #> save_dir         : /home/runner/work/GiottoClass/GiottoClass/docs/reference #> plot_format      : png #> dpi              : 300 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto python environment — giotto_python","title":"Giotto python environment — giotto_python","text":"Giotto several functions utilize python packages. facilitate , utilities provided creating, removing, attaching python environments. Python environments currently handled entirely reticulate. Creating environment installGiottoEnvironment() can used create default miniconda environment called giotto_env includes commonly used python packages. See python versions section specific packages version numbers. Custom environments manageable reticulate also compatible can hooked Giotto creation. checkGiottoEnvironment() can used order test envname full python path accessible Giotto. also check \"giotto.py_path\" option. Choosing environments one python environment may initialized used reticulate single R session. order switch another environment, R session must restarted. Whenever following happens first time session: giotto object creation (due creation default giottoInstructions) giottoInstructions creation (createGiottoInstructions()) GiottoClass::set_giotto_python_path() called (direct) , Giotto automatically detects activates python environment based following defaults decreasing priority: User provided (python_path param NULL) provided path envname option \"giotto.py_path\" Default expected giotto environment location based reticulate::miniconda_path() Envname \"giotto_env\" System default python environment behavior mediated set_giotto_python_path() utility function, find environment initialize .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto python environment — giotto_python","text":"","code":"checkGiottoEnvironment(   envname = NULL,   mini_install_path = deprecated(),   verbose = NULL )  installGiottoEnvironment(   packages_to_install = c(\"pandas==1.5.1\", \"networkx==2.8.8\", \"python-igraph==0.10.2\",     \"leidenalg==0.9.0\", \"python-louvain==0.16\", \"python.app==1.4\", \"scikit-learn==1.1.3\",     \"smfishhmrf\", \"session-info\"),   pip_packages = c(\"python-louvain\", \"smfishhmrf\", \"session-info\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   confirm = TRUE,   envname = \"giotto_env\",   conda = \"auto\",   force_miniconda = FALSE,   force_environment = FALSE,   verbose = NULL )  removeGiottoEnvironment(   envname = \"giotto_env\",   mini_path = deprecated(),   conda = \"auto\",   verbose = TRUE )  set_giotto_python_path(python_path = NULL, verbose = NULL, initialize = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto python environment — giotto_python","text":"envname character. (optional) name miniconda conda environment path python executable. using installGiottoEnvironment(), default \"giotto_env\" mini_install_path (optional) desired miniconda installation location. Default chosen reticulate::install_miniconda() verbose verbose packages_to_install python modules (packages) install Giotto. pip_packages python packages mush installed pip, names needed python_version python version use within giotto conda environment. Default v3.10.2 confirm whether pause confirmation conda environment install location (default = TRUE) conda either \"auto\" (default) allow reticulate handle , full filepath conda executable. can also set option \"reticulate.conda_binary\" Sys.setenv() \"RETICULATE_CONDA\" tell reticulate look. force_miniconda force reinstallation miniconda force_environment force reinstallation giotto environment mini_path deprecated python_path character. Name environment full path python executable. initialize force initialization set python path. Default = TRUE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto python environment — giotto_python","text":"installed Giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Giotto python environment — giotto_python","text":"checkGiottoEnvironment(): Based envname, detect conda miniconda environment accessible Giotto. default, envname \"giotto_env\", option \"giotto.py_path\" checked, alternative can provided. Setting envname \":auto:\" let  Giotto autodetect python env use. See section set_giotto_python_path() details autodetection. Returns TRUE env detected accessible Giotto. FALSE . initialize python environment detection. installGiottoEnvironment(): Install giotto python environment using miniconda reticulate. default, envname used \"giotto_env\". another name used, provide envname start session (see Choosing environment ).  includes miniconda installation also set python packages Giotto may often use. See details information setting environment .yml Returns NULL removeGiottoEnvironment(): Remove python environment Returns NULL set_giotto_python_path(): Detect activate python path. python_path param accepts full filepaths python executable envnames. final path use determined follows decreasing priority: User provided (python_path NULL) provided path envname option \"giotto.py_path\" Default expected giotto environment location based reticulate::miniconda_path() Envname \"giotto_env\" System default python environment function exits without anything option \"giotto.use_conda\" FALSE. default function force initialization python environment set, locking session environment. can skipped initialize = FALSE, however case, actual python path set downstream may differ expected reported function. Returns detected path python binary NULL none found.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"python-versions","dir":"Reference","previous_headings":"","what":"python versions","title":"Giotto python environment — giotto_python","text":"default, Python v3.10.2 used following python modules giotto environment installation: giotto environment can custom installed changing python_version parameter module versions packages_to_install parameter. example, giotto environment works well, default environment status past releases Giotto. Python  v3.6","code":"- pandas==1.5.1    - networkx==2.8.8    - python-igraph==0.10.2    - leidenalg==0.9.0    - python-louvain==0.16    - python.app==1.4    - scikit-learn==1.1.3 - pandas==1.1.5   - networkx==2.6.3   - python-igraph==0.9.6   - leidenalg==0.8.7   - python-louvain==0.15   - python.app==2 # macOS only   - scikit-learn==0.24.2"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"-yml-installs","dir":"Reference","previous_headings":"","what":".yml installs","title":"Giotto python environment — giotto_python","text":"Please note multiple .yml files provided repository advanced installation convenience. install --date Giotto environment using .yml file, open shell compatible conda/miniconda navigate directory specified system.file(package = \"Giotto\", \"python/configuration\"). directory, run following create environment one step:","code":"conda env create -n giotto_env -f ./genv.yml"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_python.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto python environment — giotto_python","text":"","code":"# detect without initialization # check default env location checkGiottoEnvironment() #> Giotto can access environment found at: #>  '/usr/share/miniconda/envs/giotto_env/bin/python' #>  If this is the wrong environment, try specifying `envname` param #>  or set option \"giotto.py_path\" with the desired envname or path #> [1] TRUE  # use environment name checkGiottoEnvironment(\"giotto_env\") #> Giotto can access environment found at: #>  '/usr/share/miniconda/envs/giotto_env/bin/python' #>  If this is the wrong environment, try specifying `envname` param #>  or set option \"giotto.py_path\" with the desired envname or path #> [1] TRUE  # full path # (use this if a different install location specified with .condarc) if (FALSE) {     checkGiottoEnvironment(         \"/Users/example/Library/r-miniconda-arm64/envs/giotto_env/bin/pythonw\"     ) } if (FALSE) {     # default environment installation     installGiottoEnvironment()      # install to alternate location     temp_env <- tempdir()     installGiottoEnvironment(mini_install_path = temp_env) } # detect AND initialize a python environment if (FALSE) {     set_giotto_python_path() }"},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate regular hexagon vertices — hexVertices","title":"Generate regular hexagon vertices — hexVertices","text":"Generates vertex coordinates regular hexagon.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate regular hexagon vertices — hexVertices","text":"","code":"hexVertices(radius, major_axis = c(\"v\", \"h\"))"},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate regular hexagon vertices — hexVertices","text":"radius radius hexagon major_axis orientation major axis 'v' vertical (default) 'h' horizontal","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate regular hexagon vertices — hexVertices","text":"data.table regular hexagon vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/hexVertices.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate regular hexagon vertices — hexVertices","text":"","code":"hexVertices(radius = 10) #>            x     y #>        <num> <num> #> 1:  0.000000    10 #> 2:  8.660254     5 #> 3:  8.660254    -5 #> 4:  0.000000   -10 #> 5: -8.660254    -5 #> 6: -8.660254     5"},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":null,"dir":"Reference","previous_headings":"","what":"Histogram — hist","title":"Histogram — hist","text":"Create histogram pixel values giottoLargeImage. Wrapper around terra::hist()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Histogram — hist","text":"","code":"# S4 method for class 'giottoLargeImage' hist(x, show_max = TRUE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Histogram — hist","text":"x giottoLargeImage show_max logical. Plot set max intensity vertical red line ... Arguments passed terra::hist","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Histogram — hist","text":"histogram","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/hist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Histogram — hist","text":"","code":"f <- system.file(package = \"GiottoClass\", \"extdata/toy_intensity.tif\") gimg <- createGiottoLargeImage(f, use_rast_ext = TRUE, verbose = FALSE)  hist(gimg) #> Warning: [hist] a sample of 83% of the cells was used"},{"path":"https://drieslab.github.io/GiottoClass/reference/init_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize cell metadata slot — init_cell_metadata","title":"Initialize cell metadata slot — init_cell_metadata","text":"Generate cellMetaObjs hold cell metadata spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize cell metadata slot — init_cell_metadata","text":"","code":"init_cell_metadata(gobject, provenance = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/init_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize cell metadata slot — init_cell_metadata","text":"gobject giotto object provenance provenance information (optional) feature type giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_cell_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize cell metadata slot — init_cell_metadata","text":"cellMetaObjs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_feat_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Initialize feature metadata slot — init_feat_metadata","title":"Initialize feature metadata slot — init_feat_metadata","text":"Generate featMetaObjs hold feature metadata spatial unit feature type giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_feat_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Initialize feature metadata slot — init_feat_metadata","text":"","code":"init_feat_metadata(gobject, provenance = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/init_feat_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Initialize feature metadata slot — init_feat_metadata","text":"gobject giotto object provenance provenance information (optional)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/init_feat_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Initialize feature metadata slot — init_feat_metadata","text":"featMetaObjs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":null,"dir":"Reference","previous_headings":"","what":"Join giotto objects — joinGiottoObjects","title":"Join giotto objects — joinGiottoObjects","text":"Function join multiple giotto objects together","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Join giotto objects — joinGiottoObjects","text":"","code":"joinGiottoObjects(   gobject_list,   gobject_names = NULL,   join_method = c(\"shift\", \"z_stack\", \"no_change\"),   z_vals = 1000,   x_shift = NULL,   y_shift = NULL,   x_padding = NULL,   y_padding = NULL,   dry_run = FALSE,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Join giotto objects — joinGiottoObjects","text":"gobject_list list giotto objects gobject_names unique giotto names giotto object join_method method join giotto objects, see details z_vals distance(s) along z-axis method z-stack (default step 1000) x_shift numeric vector values shift along x-axis method \"shift\" y_shift numeric vector values shift along y-axis method \"shift\" x_padding x padding datasets method shift y_padding y padding datasets method shift. applied y shifts given. dry_run logical. Plot expected object locations join, actually perform . verbose verbose Preview gobject space bounding polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Join giotto objects — joinGiottoObjects","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Join giotto objects — joinGiottoObjects","text":"function joins expression spatial information multiple giotto objects single one. Giotto supports multiple ways joining spatial information selected param join_method: \"shift\" (default) Spatial locations different datasets shifted numeric vectors values supplied x_shift, y_shift, x_padding, y_padding. particularly useful data provided tiles ROIs analyzing multiple spatial datasets together keeping spatial data separate. shift values given value needed giotto object joined gobject_list. Order matters. regular step value desired instead specific list values, use x_padding y_padding. shift padding values can used time. x_shift NULL, defaults x range gobjects list datasets xshifted exactly next overlaps. additional default x_padding = 1000 applied x_shift, x_padding, y_shift, y_padding NULL. \"z_stack\" Datasets spatially combined change x y spatial locations, z value incorporated dataset based input supplied param z_vals. specify z value dataset join, numeric vector must given value element gobject_list. Order matters. Alternatively, single numeric value can supplied z_vals case input treated z step value. \"no_change\" changes applied spatial locations datasets joining.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/joinGiottoObjects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Join giotto objects — joinGiottoObjects","text":"","code":"# joining objects with no spatial information m1 <- matrix(rnorm(100), nrow = 10) m2 <- matrix(rnorm(100), nrow = 10) colnames(m1) <- paste0(\"cell_\", seq_len(10)) colnames(m2) <- paste0(\"cell_\", seq_len(10)) rownames(m1) <- rownames(m2) <- paste0(\"feat_\", seq_len(10))  g1 <- createGiottoObject(expression = m1) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed g2 <- createGiottoObject(expression = m2) #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed  joinGiottoObjects(     gobject_list = list(g1, g2),     gobject_names = c(\"g1\", \"g2\") ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 10, 20 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw #> spatial locations ---------------- #>   [cell] raw #>  #>  #> Use objHistory() to see steps and params used  # dry run joining objects with spatial information # a default x_padding of 1000 is applied viz <- GiottoData::loadGiottoMini(\"viz\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" joinGiottoObjects(     list(viz, viz),     gobject_names = c(\"v1\", \"v2\"),     dry_run = TRUE )   # place them right next to each other # note that this means generated spatial networks will be more likely to # link across the datasets joinGiottoObjects(     list(viz, viz),     gobject_names = c(\"v1\", \"v2\"),     dry_run = TRUE,     x_padding = 0 )   # join the spatial objects joined_viz <- joinGiottoObjects(     list(viz, viz),     gobject_names = c(\"v1\", \"v2\") ) #> Warning: spatial locations have been modified. #>  Relevant spatial networks may need to be #>  regenerated #> Warning: spatial locations have been modified. #>  Relevant spatial networks may need to be #>  regenerated #> Warning: spat_unit: z1 spatloc name: raw #>  cell IDs in spatial locations are missing from spatial #>  polygon info #> Warning: spat_unit: aggregate spatloc name: raw #>  cell IDs in spatial locations are missing from spatial #>  polygon info"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":null,"dir":"Reference","previous_headings":"","what":"List cell ID names — list_cell_id_names","title":"List cell ID names — list_cell_id_names","text":"lists available cell id names. effect, names spat_units poly info gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List cell ID names — list_cell_id_names","text":"","code":"list_cell_id_names(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List cell ID names — list_cell_id_names","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List cell ID names — list_cell_id_names","text":"vector names available sets cell_IDs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_id_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List cell ID names — list_cell_id_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_cell_id_names(g) #> [1] \"cell\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"list_cell_metadata — list_cell_metadata","title":"list_cell_metadata — list_cell_metadata","text":"lists available cell metadata.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_cell_metadata — list_cell_metadata","text":"","code":"list_cell_metadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_cell_metadata — list_cell_metadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_cell_metadata — list_cell_metadata","text":"names locations available cell metadata data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_cell_metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_cell_metadata — list_cell_metadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_cell_metadata(g) #>    spat_unit feat_type #>       <char>    <char> #> 1:      cell       rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":null,"dir":"Reference","previous_headings":"","what":"list_dim_reductions — list_dim_reductions","title":"list_dim_reductions — list_dim_reductions","text":"return available dimension reductions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_dim_reductions — list_dim_reductions","text":"","code":"list_dim_reductions(   gobject,   data_type = NULL,   spat_unit = NULL,   feat_type = NULL,   dim_type = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_dim_reductions — list_dim_reductions","text":"gobject giotto object data_type \"cells\" \"feats\" data used dim reduction spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") dim_type dimensional reduction method (e.g. \"pca\", \"umap\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_dim_reductions — list_dim_reductions","text":"names locations dimension reduction data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_dim_reductions — list_dim_reductions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_dim_reductions(g) #>    data_type spat_unit feat_type dim_type        name #>       <char>    <char>    <char>   <char>      <char> #> 1:     cells      cell       rna      pca         pca #> 2:     cells      cell       rna      pca  custom_pca #> 3:     cells      cell       rna     umap        umap #> 4:     cells      cell       rna     umap custom_umap #> 5:     cells      cell       rna     tsne        tsne"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_dim_reductions_names — list_dim_reductions_names","title":"list_dim_reductions_names — list_dim_reductions_names","text":"return available dimension reductions object names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_dim_reductions_names — list_dim_reductions_names","text":"","code":"list_dim_reductions_names(   gobject,   data_type = \"cells\",   spat_unit = NULL,   feat_type = NULL,   dim_type = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_dim_reductions_names — list_dim_reductions_names","text":"gobject giotto object data_type cells feats dim reduction spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") dim_type dimensional reduction type (method)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_dim_reductions_names — list_dim_reductions_names","text":"names dimension reduction object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"list_dim_reductions_names — list_dim_reductions_names","text":"function can used find names used","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_dim_reductions_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_dim_reductions_names — list_dim_reductions_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_dim_reductions_names(g,     spat_unit = \"cell\", feat_type = \"rna\",     dim_type = \"pca\" ) #> [1] \"pca\"        \"custom_pca\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":null,"dir":"Reference","previous_headings":"","what":"list_expression — list_expression","title":"list_expression — list_expression","text":"lists available matrices","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_expression — list_expression","text":"","code":"list_expression(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_expression — list_expression","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_expression — list_expression","text":"names locations available matrices data.table. col order matters.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_expression — list_expression","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_expression(g) #>    spat_unit feat_type       name #>       <char>    <char>     <char> #> 1:      cell       rna        raw #> 2:      cell       rna normalized #> 3:      cell       rna     scaled"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_expression_names — list_expression_names","title":"list_expression_names — list_expression_names","text":"lists available matrices names given spatial unit feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_expression_names — list_expression_names","text":"","code":"list_expression_names(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_expression_names — list_expression_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_expression_names — list_expression_names","text":"vector names available matrices","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_expression_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_expression_names — list_expression_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_expression_names(g, spat_unit = \"cell\", feat_type = \"rna\") #> [1] \"raw\"        \"normalized\" \"scaled\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":null,"dir":"Reference","previous_headings":"","what":"List feat ID names — list_feat_id_names","title":"List feat ID names — list_feat_id_names","text":"lists available feat id names effect, names feat_types feature info gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"List feat ID names — list_feat_id_names","text":"","code":"list_feat_id_names(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"List feat ID names — list_feat_id_names","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"List feat ID names — list_feat_id_names","text":"vector names available sets feat_IDs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_id_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"List feat ID names — list_feat_id_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_feat_id_names(g) #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"list_feat_metadata — list_feat_metadata","title":"list_feat_metadata — list_feat_metadata","text":"lists available feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_feat_metadata — list_feat_metadata","text":"","code":"list_feat_metadata(   gobject,   spat_unit = NULL,   feat_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_feat_metadata — list_feat_metadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_feat_metadata — list_feat_metadata","text":"names locations available feature metadata data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feat_metadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_feat_metadata — list_feat_metadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_feat_metadata(g) #>    spat_unit feat_type #>       <char>    <char> #> 1:      cell       rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":null,"dir":"Reference","previous_headings":"","what":"list_feature_info — list_feature_info","title":"list_feature_info — list_feature_info","text":"return available giotto spatial feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_feature_info — list_feature_info","text":"","code":"list_feature_info(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_feature_info — list_feature_info","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_feature_info — list_feature_info","text":"names available feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_feature_info — list_feature_info","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_feature_info(g) #>    feat_info #>       <char> #> 1:       rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_feature_info_names — list_feature_info_names","title":"list_feature_info_names — list_feature_info_names","text":"return available names giotto feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_feature_info_names — list_feature_info_names","text":"","code":"list_feature_info_names(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_feature_info_names — list_feature_info_names","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_feature_info_names — list_feature_info_names","text":"vector names available feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_feature_info_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_feature_info_names — list_feature_info_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_feature_info_names(g) #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":null,"dir":"Reference","previous_headings":"","what":"list_giotto_data — list_giotto_data","title":"list_giotto_data — list_giotto_data","text":"list available data within specified giotto object slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_giotto_data — list_giotto_data","text":"","code":"list_giotto_data(gobject = NULL, slot = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_giotto_data — list_giotto_data","text":"gobject giotto object slot giotto object slot interest (e.g. \"expression\", \"spatial_locs\", etc.) ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_giotto_data — list_giotto_data","text":"names locations data within giotto object slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_giotto_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_giotto_data — list_giotto_data","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_giotto_data(gobject = g, slot = \"expression\") #>    spat_unit feat_type       name #>       <char>    <char>     <char> #> 1:      cell       rna        raw #> 2:      cell       rna normalized #> 3:      cell       rna     scaled"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":null,"dir":"Reference","previous_headings":"","what":"list_images — list_images","title":"list_images — list_images","text":"Prints available giotto images attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_images — list_images","text":"","code":"list_images(gobject, img_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_images — list_images","text":"gobject giotto object img_type \"image\" \"largeImage\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_images — list_images","text":"data.table giotto image names attached giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_images — list_images","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" list_images(g) #> Index: <img_type> #>        name   img_type #>      <char>     <char> #> 1:  dapi_z0 largeImage #> 2:  dapi_z1 largeImage #> 3: polyT_z0 largeImage #> 4: polyT_z1 largeImage list_images(g, img_type = \"largeImage\") #>        name   img_type #>      <char>     <char> #> 1:  dapi_z0 largeImage #> 2:  dapi_z1 largeImage #> 3: polyT_z0 largeImage #> 4: polyT_z1 largeImage"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_images_names — list_images_names","title":"list_images_names — list_images_names","text":"return available image names given image type attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_images_names — list_images_names","text":"","code":"list_images_names(gobject, img_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_images_names — list_images_names","text":"gobject giotto object img_type passing NULL (default) gets image names. Can specify \"image\" \"largeImage\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_images_names — list_images_names","text":"vector names available image names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_images_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_images_names — list_images_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" list_images_names(g) #> [1] \"dapi_z0\"  \"dapi_z1\"  \"polyT_z0\" \"polyT_z1\" list_images_names(g, img_type = \"largeImage\") #> [1] \"dapi_z0\"  \"dapi_z1\"  \"polyT_z0\" \"polyT_z1\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":null,"dir":"Reference","previous_headings":"","what":"list_nearest_networks — list_nearest_networks","title":"list_nearest_networks — list_nearest_networks","text":"return available nearest neighbor network information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_nearest_networks — list_nearest_networks","text":"","code":"list_nearest_networks(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_nearest_networks — list_nearest_networks","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_type nearest neighbor method (e.g. \"sNN\", \"kNN\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_nearest_networks — list_nearest_networks","text":"names locations nearest neighbor networks data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_nearest_networks — list_nearest_networks","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_nearest_networks(g) #>    spat_unit feat_type nn_type      name #>       <char>    <char>  <char>    <char> #> 1:      cell       rna     sNN   sNN.pca #> 2:      cell       rna     sNN custom_NN"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_nearest_networks_names — list_nearest_networks_names","title":"list_nearest_networks_names — list_nearest_networks_names","text":"return available nearest neighbor network object names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_nearest_networks_names — list_nearest_networks_names","text":"","code":"list_nearest_networks_names(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_type = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_nearest_networks_names — list_nearest_networks_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_type nearest neighbor method (e.g. \"sNN\", \"kNN\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_nearest_networks_names — list_nearest_networks_names","text":"names nearest neighbor network object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"list_nearest_networks_names — list_nearest_networks_names","text":"function can used find names used","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_nearest_networks_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_nearest_networks_names — list_nearest_networks_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_nearest_networks_names(g,     spat_unit = \"cell\", feat_type = \"rna\",     nn_type = \"sNN\" ) #> [1] \"sNN.pca\"   \"custom_NN\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_enrichments — list_spatial_enrichments","title":"list_spatial_enrichments — list_spatial_enrichments","text":"return available spatial enrichment results","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_enrichments — list_spatial_enrichments","text":"","code":"list_spatial_enrichments(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_enrichments — list_spatial_enrichments","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_enrichments — list_spatial_enrichments","text":"names locations available data data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_enrichments — list_spatial_enrichments","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_enrichments(g) #>    spat_unit feat_type             name #>       <char>    <char>           <char> #> 1: aggregate       rna cluster_metagene"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_enrichments_names — list_spatial_enrichments_names","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"returns available spatial enrichment names given spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"","code":"list_spatial_enrichments_names(gobject, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"vector names available spatial enrichments","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_enrichments_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_enrichments_names — list_spatial_enrichments_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_enrichments_names(g, spat_unit = \"aggregate\", feat_type = \"rna\") #> [1] \"cluster_metagene\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_grids — list_spatial_grids","title":"list_spatial_grids — list_spatial_grids","text":"return available spatial grids attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_grids — list_spatial_grids","text":"","code":"list_spatial_grids(   gobject,   spat_unit = NULL,   feat_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_grids — list_spatial_grids","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_grids — list_spatial_grids","text":"data.table names locations available spatial grids. col order matters","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_grids — list_spatial_grids","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  list_spatial_grids(g) #>    spat_unit feat_type         name #>       <char>    <char>       <char> #> 1:      cell       rna spatial_grid"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_grids_names — list_spatial_grids_names","title":"list_spatial_grids_names — list_spatial_grids_names","text":"return available spatial grids name given spatial unit attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_grids_names — list_spatial_grids_names","text":"","code":"list_spatial_grids_names(   gobject,   spat_unit = NULL,   feat_type = NULL,   return_uniques = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_grids_names — list_spatial_grids_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_grids_names — list_spatial_grids_names","text":"vector names available spatial grids names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_grids_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_grids_names — list_spatial_grids_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  list_spatial_grids_names(g, spat_unit = \"cell\", feat_type = \"rna\") #> [1] \"spatial_grid\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_info — list_spatial_info","title":"list_spatial_info — list_spatial_info","text":"return available giotto spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_info — list_spatial_info","text":"","code":"list_spatial_info(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_info — list_spatial_info","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_info — list_spatial_info","text":"names available spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_info — list_spatial_info","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_info(g) #>    spat_info #>       <char> #> 1:        z0 #> 2:        z1 #> 3: aggregate"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_info_names — list_spatial_info_names","title":"list_spatial_info_names — list_spatial_info_names","text":"return available names giotto spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_info_names — list_spatial_info_names","text":"","code":"list_spatial_info_names(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_info_names — list_spatial_info_names","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_info_names — list_spatial_info_names","text":"vector names available spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_info_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_info_names — list_spatial_info_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_info_names(g) #> [1] \"z0\"        \"z1\"        \"aggregate\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_locations — list_spatial_locations","title":"list_spatial_locations — list_spatial_locations","text":"shows available spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_locations — list_spatial_locations","text":"","code":"list_spatial_locations(gobject, spat_unit = NULL, return_uniques = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_locations — list_spatial_locations","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_locations — list_spatial_locations","text":"names locations available data.table data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_locations — list_spatial_locations","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_locations(g) #>    spat_unit   name #>       <char> <char> #> 1:      cell    raw"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_locations_names — list_spatial_locations_names","title":"list_spatial_locations_names — list_spatial_locations_names","text":"lists available spatial location names given spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_locations_names — list_spatial_locations_names","text":"","code":"list_spatial_locations_names(gobject, spat_unit = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_locations_names — list_spatial_locations_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_locations_names — list_spatial_locations_names","text":"vector names available spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_locations_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_locations_names — list_spatial_locations_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_locations_names(g, spat_unit = \"cell\") #> [1] \"raw\""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_networks — list_spatial_networks","title":"list_spatial_networks — list_spatial_networks","text":"return available spatial networks attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_networks — list_spatial_networks","text":"","code":"list_spatial_networks(gobject, spat_unit = NULL, return_uniques = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_networks — list_spatial_networks","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") return_uniques return unique nesting names (ignores final object exists/correct class)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_networks — list_spatial_networks","text":"data.table names locations available spatial networks, col order matters list unique nestings","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_networks — list_spatial_networks","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_networks(g) #>    spat_unit             name #>       <char>           <char> #> 1: aggregate Delaunay_network #> 2: aggregate      kNN_network"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":null,"dir":"Reference","previous_headings":"","what":"list_spatial_networks_names — list_spatial_networks_names","title":"list_spatial_networks_names — list_spatial_networks_names","text":"return available names giotto feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"list_spatial_networks_names — list_spatial_networks_names","text":"","code":"list_spatial_networks_names(gobject, spat_unit = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"list_spatial_networks_names — list_spatial_networks_names","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"list_spatial_networks_names — list_spatial_networks_names","text":"vector names available feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/list_spatial_networks_names.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"list_spatial_networks_names — list_spatial_networks_names","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  list_spatial_networks_names(g, spat_unit = \"cell\") #> [1] \"Delaunay_network\" \"spatial_network\""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"loadGiotto — loadGiotto","title":"loadGiotto — loadGiotto","text":"Saves Giotto object specific folder structure","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"loadGiotto — loadGiotto","text":"","code":"loadGiotto(   path_to_folder,   load_params = list(),   reconnect_giottoImage = TRUE,   python_path = NULL,   init_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"loadGiotto — loadGiotto","text":"path_to_folder path folder Giotto object stored saveGiotto load_params additional parameters loading reading giotto object reconnect_giottoImage (default = TRUE) whether attempt reconnection magick based image objects python_path (optional) manually set python path init_gobject logical. Whether initialize giotto object loading. (default = TRUE) verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"loadGiotto — loadGiotto","text":"Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"loadGiotto — loadGiotto","text":"Works together saveGiotto save re-load Giotto objects. Additional load_params need provided list go readRDS qread can set python path, alternatively look existing Giotto python environment.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/loadGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"loadGiotto — loadGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" td <- tempdir() saveGiotto(gobject = g, dir = td) #> 1. Start writing feature information #> 2. Start writing spatial information #> For spatial information: cell #> 3. Start writing image information #> For image information: alignment #> For image information: image  loadGiotto(path_to_folder = paste0(td, \"/saveGiottoDir\")) #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":null,"dir":"Reference","previous_headings":"","what":"makePseudoVisium — makePseudoVisium","title":"makePseudoVisium — makePseudoVisium","text":"Generates pseudo-visium grid spots across provided spatial extent","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"makePseudoVisium — makePseudoVisium","text":"","code":"makePseudoVisium(extent = NULL, micron_size = 1, name = \"pseudo_visium\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"makePseudoVisium — makePseudoVisium","text":"extent SpatExtent anything else SpatExtent can extracted created micron_size size micrometer relative spatial coordinates name character. (default 'pseudo_visium') Name giottoPolygon object create","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"makePseudoVisium — makePseudoVisium","text":"giottoPolygon pseudo-visium spots.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"makePseudoVisium — makePseudoVisium","text":"function generates pseudo-Visium grid spots based input spatial locations. micron_size param used determine size spots","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/makePseudoVisium.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"makePseudoVisium — makePseudoVisium","text":"","code":"e <- ext(0, 2000, 0, 2000) x <- makePseudoVisium(extent = e, micron_size = 1) #> 390 polygons generated plot(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"mean_flex — mean_flex","title":"mean_flex — mean_flex","text":"mean_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"mean_flex — mean_flex","text":"","code":"mean_flex(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"mean_flex — mean_flex","text":"x data use ... arguments pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"mean_flex — mean_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/mean_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"mean_flex — mean_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  mean_flex(m) #> [1] 0.05046857"},{"path":"https://drieslab.github.io/GiottoClass/reference/miscData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic class for additional miscellaneous information — miscData-class","title":"Basic class for additional miscellaneous information — miscData-class","text":"Classes (dimObj) can hold information multiple types methods use misc slot hold additional information specific method. Information may stored within S3 structures.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/miscData-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basic class for additional miscellaneous information — miscData-class","text":"slot miscellaneous information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/miscData-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Basic class for additional miscellaneous information — miscData-class","text":"","code":"g <- GiottoData::loadSubObjectMini(\"dimObj\")  slot(g, \"misc\") #> $eigenvalues #>   [1] 33.2534135 32.0046063 30.0502213 23.4352729 14.9873873 14.4036736 #>   [7] 11.8499793 10.6893086  9.3040152  6.9800585  6.8538084  6.0485295 #>  [13]  5.7915560  5.1138968  4.9417237  4.7024725  4.3698509  4.1615473 #>  [19]  3.9581798  3.5429980  3.4268141  3.3099700  3.2350908  3.1648805 #>  [25]  3.0439582  2.9064535  2.8524063  2.7202686  2.6799304  2.5689859 #>  [31]  2.5279120  2.4568203  2.4413820  2.4043215  2.2542061  2.2058793 #>  [37]  2.1896105  2.1608223  2.1332721  2.0909430  2.0288850  1.9923129 #>  [43]  1.9176801  1.8699125  1.8353129  1.7768831  1.7700422  1.7509328 #>  [49]  1.7226019  1.6894990  1.6530223  1.6411241  1.5851496  1.5687056 #>  [55]  1.5454645  1.5241935  1.4727217  1.4685526  1.4528981  1.4055974 #>  [61]  1.3715253  1.3659691  1.3286971  1.2883263  1.2804195  1.2507976 #>  [67]  1.2475448  1.2363812  1.1837924  1.1801315  1.1659735  1.1448418 #>  [73]  1.1201655  1.0999292  1.0838246  1.0546067  1.0483329  1.0319266 #>  [79]  0.9870703  0.9835202  0.9510675  0.9296043  0.9225639  0.9045214 #>  [85]  0.8797710  0.8550994  0.8356013  0.8292998  0.8066431  0.8016031 #>  [91]  0.7671520  0.7594730  0.7402408  0.7279798  0.7131876  0.6834403 #>  [97]  0.6823937  0.6489129  0.6446519  0.6206416 #>  #> $loadings #>                  Dim.1         Dim.2         Dim.3         Dim.4         Dim.5 #> Mlc1      0.0497209920  0.0516028482 -0.0788876048  0.0032493081  6.602336e-02 #> Gprc5b    0.0776530195  0.0767287111 -0.1003795798 -0.0429921843 -6.838634e-02 #> Gfap      0.2737382490  0.2308157480 -0.2703730778 -0.1253583035 -3.101030e-01 #> Ednrb     0.0840708314  0.0699607215 -0.0933344159 -0.0320003544  3.835691e-02 #> Sox9      0.0701589058  0.0648677354 -0.0882498978 -0.0089310657  8.022850e-02 #> Aqp4      0.1648074467  0.1639844662 -0.2047222491 -0.0886550945  3.217967e-02 #> Gjc3      0.0787488199  0.0902074332 -0.0900546455 -0.0683712434 -3.690813e-01 #> Sox8      0.0239282810  0.0501925669 -0.0283113185 -0.0160920618 -1.362323e-01 #> Ntsr2     0.1704425415  0.1601869753 -0.2146941517 -0.0504471528  2.278867e-01 #> Smo       0.0101445414 -0.0602267061 -0.0080775417 -0.0514860143 -8.651041e-05 #> C1qb      0.3469055234 -0.0556488977  0.2697640508  0.0633723690 -4.540910e-03 #> Olig1     0.0649931574  0.0709296076 -0.0604750868 -0.0437817503 -3.264669e-01 #> C1qa      0.3435753209 -0.0679235461  0.2732874719  0.0596583452 -1.168577e-02 #> Pth1r     0.0269966628 -0.0234988709 -0.0578083113  0.0128749364 -5.972937e-02 #> Gabbr2   -0.0968959099  0.0393425389  0.0697732292  0.0299199523 -9.626442e-04 #> Timp4     0.0536090931  0.0280895417 -0.0753163592  0.0158564413  4.382947e-02 #> Abcc9     0.0165480319 -0.0466802006 -0.0509001991  0.0153604110 -1.197030e-01 #> Csf1r     0.2636662717 -0.0386831102  0.2243084956  0.0669753056  9.956118e-03 #> Ntrk2     0.0881426645  0.1012229752 -0.1330898636 -0.0116179071  1.422470e-01 #> Adgrg1    0.0956322507  0.0336898984 -0.0983375842  0.0360269420  8.868170e-02 #> Ntrk3    -0.1084430931  0.0220051827  0.0772323289  0.0089486275 -1.086369e-02 #> Erbb4    -0.0061492024  0.0287309846 -0.0052711701 -0.0106869915 -2.363755e-02 #> Selplg    0.2163849803 -0.0146272024  0.1797440166  0.0711729672 -3.951132e-05 #> Cspg5     0.0508038447  0.1051590276 -0.1171638694 -0.0073861327  1.627924e-01 #> Dlk1      0.0319763185  0.0403762064 -0.0285589767 -0.0211066951 -7.607112e-02 #> Gpr37l1   0.1435865057  0.1348871702 -0.1928914087 -0.0302268679  2.051102e-01 #> Fgfr3     0.0996140210  0.0850286103 -0.1355375615 -0.0118240087  1.574511e-01 #> Slc25a18  0.0698809750  0.0686974956 -0.0947152143 -0.0096511715  1.026733e-01 #> Igf1r    -0.0014116337 -0.0596930778 -0.0528646487  0.0773945525  1.281184e-02 #> S1pr1     0.0822799744  0.0362846623 -0.1354970039  0.0181807874  1.784681e-01 #> Grm5     -0.1118001691  0.0475255721  0.0861476556  0.0347360399 -1.072351e-02 #> Axl       0.0858668222 -0.0487149935 -0.0215858560 -0.0347855205  5.258418e-03 #> Efemp1    0.0261969437 -0.1986612549 -0.0252210424 -0.2406020556  5.172519e-02 #> Adgrb3   -0.0544048314  0.0550664169  0.0217421136  0.0173602267  4.369901e-02 #> Fn1       0.0197391341 -0.3432218159 -0.0678838022 -0.2440058578  5.826913e-02 #> Mertk     0.1227479861  0.0330014625 -0.0359677503  0.0058191331  1.050344e-01 #> Adgrl2    0.0181563638 -0.0994313729 -0.0215071929 -0.0455756732  1.688788e-02 #> Fzd2      0.0166298244 -0.1219469652 -0.0205442251 -0.1621939124  3.165561e-02 #> Aldh1l1   0.0621044803  0.0450324509 -0.0755769710 -0.0463455168  4.455743e-02 #> Adgrg6    0.0049233608 -0.0962329171 -0.0395936687  0.0275253785  1.009561e-02 #> Egfr      0.0095100368 -0.0457057148 -0.0148372962 -0.1032193882  7.474851e-02 #> Kit      -0.0111042732 -0.0886068185  0.0082155796 -0.1106598956 -7.255914e-02 #> Ptgdr     0.0045409154 -0.0885371528  0.0038310671 -0.1341326756  7.176816e-02 #> Gad1     -0.0860206201  0.0439393653  0.0519458282  0.0080321157 -8.142480e-03 #> Tyro3     0.0171943705  0.0416572563 -0.0222654682 -0.0109172887 -1.119973e-01 #> Atp13a5   0.0206112315 -0.1426519762 -0.0496623163 -0.1027289390 -2.015837e-01 #> Ddr2      0.0197099222 -0.1317915730 -0.0023189303 -0.1419593244 -9.013596e-03 #> Rspo3    -0.0315132700 -0.0820764063  0.0224241276 -0.0986280620  4.999107e-02 #> Arhgap29  0.0170582653 -0.1760750472 -0.0446192339 -0.0791462003 -8.717547e-02 #> Fzd7      0.0013466497 -0.0541730858  0.0065291313 -0.0491961687 -3.135484e-02 #> Slc47a1   0.0070042606 -0.2605398556  0.0078046531 -0.4140449341  2.305858e-01 #> Ptger3    0.0028027777 -0.0436933914  0.0017106060 -0.0496212778 -4.140198e-02 #> Bdkrb1    0.0071407966 -0.0148844898 -0.0111734972 -0.0343489894  1.922939e-02 #> Traf4     0.0127022727 -0.0131715780 -0.0050164887 -0.0471016364 -8.346302e-02 #> Cx3cr1    0.2910208672 -0.0295179146  0.2327469236  0.0753681382  2.887251e-02 #> Anxa11   -0.0350383434 -0.0444961512  0.0227879282 -0.0003838839 -8.668919e-03 #> Adgrb1   -0.0912517077  0.0522565195  0.0642316823  0.0288516773 -2.134981e-02 #> Lpar1     0.0309961553 -0.0892477881 -0.0138536553 -0.1042763602 -9.845681e-02 #> Gpr17     0.0210630145  0.0267569595 -0.0347693627 -0.0180771947 -2.030246e-01 #> Cxcl12   -0.0205191339 -0.1197577846 -0.0109975056 -0.0464815062 -3.201204e-02 #> Epha4    -0.0933744058  0.0227970528  0.0629049097  0.0199398111  1.216961e-02 #> Gpr182    0.0217907242 -0.1307174869 -0.0290431428 -0.0359762880 -7.534909e-02 #> P2ry14    0.0061803999 -0.0464150639 -0.0177050305 -0.0297627807 -5.987862e-02 #> Hcar1     0.0112922586 -0.1115686468 -0.0095453473 -0.1018621177 -2.872211e-02 #> Ephb1     0.0142380691  0.0436005945 -0.0301308696 -0.0124731567 -3.450293e-02 #> Grm3      0.0503104535  0.0462853583 -0.0795484416 -0.0249577215 -5.127534e-02 #> P2ry1     0.0082016818 -0.0596404982 -0.0106745751 -0.0548097432 -1.740224e-02 #> Ptk7     -0.0066957877 -0.0125314706  0.0086372160 -0.0162025281 -1.046542e-02 #> Slco1a4   0.0223657930 -0.1657536092 -0.1369393395  0.2191105340 -5.040751e-03 #> Insrr     0.0104466450 -0.0690139103  0.0026752471 -0.0726142014 -8.709213e-02 #> Cmklr1    0.0763628647 -0.0475073233  0.0501998735  0.0350138248 -4.970904e-03 #> Fzd6      0.0192202128 -0.0748877500 -0.0529204409  0.0429010577  7.222569e-03 #> S1pr5     0.0284583918  0.0327079131 -0.0317267539 -0.0271689854 -1.673905e-01 #> Pdgfrb    0.0231063599 -0.0968995924 -0.0605968579 -0.0255074465 -1.062949e-01 #> Flt1      0.0246441573 -0.2259779787 -0.1861946652  0.2724661325 -1.032480e-02 #> Adgrl4    0.0280961325 -0.1382446041 -0.1168323871  0.1888979843  1.109663e-02 #> Lpar6     0.0625796806 -0.0137831249  0.0367979155  0.0174625835  7.205206e-03 #> Epha6    -0.0883902219  0.0310861900  0.0643222427  0.0286811098 -9.171165e-03 #> Emcn      0.0083437378 -0.0598648781 -0.0522568392  0.0706115352 -2.681291e-02 #> Cldn5     0.0311045271 -0.2946074660 -0.2310564448  0.3717678593  1.299561e-02 #> P2ry12    0.2344889997 -0.0116937160  0.1840545925  0.0754388728  2.322359e-02 #> Adgrf5    0.0266564647 -0.1775220011 -0.1348469482  0.2125852103 -9.071991e-03 #> P2yr13    0.1070261760 -0.0040461073  0.0854383239  0.0344185804  7.275986e-03 #> Adgre1    0.1063901755 -0.0230391639  0.0925878260  0.0249118824 -1.363161e-03 #> Cx3cl1   -0.1207742925  0.0391257213  0.0897826344  0.0332051052 -7.772283e-03 #> Plxnb3    0.0465977442  0.0271233361 -0.0068886248 -0.0066219585 -3.097681e-02 #> Flt4      0.0062416946 -0.0660399618 -0.0507326584  0.0868945900  8.260962e-03 #> Slc17a7  -0.1921862304  0.0788625906  0.1402943023  0.0679087015  9.239846e-03 #> Cd300c2   0.1054073418 -0.0143207295  0.0880892016  0.0232454239 -1.552302e-03 #> Tek       0.0133424704 -0.1214264457 -0.0950472703  0.1538389566 -5.129120e-03 #> Kdr       0.0022649406 -0.1017476134 -0.0655678924  0.0854487303 -8.440583e-03 #> Kcnj8     0.0057131652 -0.0600056637 -0.0504989633  0.0313678625 -1.127657e-01 #> S1pr3     0.0090193031 -0.0304064386 -0.0348778543  0.0102899655 -7.646302e-02 #> Tie1      0.0121630145 -0.0911768640 -0.0585413651  0.1039348344 -6.046745e-04 #> Pdgfra    0.0232382302 -0.0434901119 -0.0259810889 -0.0291148512 -1.264767e-01 #> Baiap2   -0.1134937277  0.0312269711  0.0847938141  0.0446083687 -2.995924e-04 #> Calcrl    0.0172670916 -0.0648868288 -0.0450806533  0.0565117118  2.899586e-03 #> Adrb2     0.0565699931 -0.0791478593  0.0446794048 -0.0935164553  3.025000e-02 #> Ccr2      0.0799214988 -0.0207712131  0.0667926120  0.0112386552 -1.135570e-02 #> Alk      -0.0010488678 -0.0386206408 -0.0004323964 -0.0506666242 -7.061478e-02 #> Tacr3    -0.0106678914  0.0043610542  0.0246442035  0.0067405818  9.965484e-04 #> Erbb3     0.0362406240  0.0303559518 -0.0228320219 -0.0204566277 -1.253986e-01 #> Pcdh15    0.0080932950  0.0218323904 -0.0177765291 -0.0113617353 -1.402757e-01 #> Grm7     -0.0892227313  0.0383326484  0.0626967229  0.0281851690 -2.794878e-02 #> F2r       0.0085739763 -0.0195181421 -0.0178674193  0.0234289168 -2.745732e-02 #> Bdkrb2    0.0084295968 -0.0521024891  0.0011408388 -0.0498454028 -5.117463e-02 #> Adgrv1    0.0052015216 -0.0634093489 -0.0061167662 -0.1132172762  7.952108e-02 #> Gprc5c    0.0218727090 -0.0799980468 -0.0023058938 -0.0650826276 -7.341098e-02 #> Tbxa2r    0.0115847334 -0.0363309895 -0.0153433217 -0.0168574532 -7.206869e-02 #> Ackr1    -0.0370746086 -0.0755354129 -0.0157640192  0.1054937156 -6.277259e-03 #> Lpar2     0.0096101481 -0.0183460648  0.0146876147 -0.0096323289 -1.428391e-02 #> Myh11     0.0002481764 -0.0253004153 -0.0093169064  0.0047274734 -1.017785e-02 #> Musk     -0.0062468259 -0.0002631417  0.0015877339 -0.0097866189 -3.799166e-04 #> Cnr1     -0.0381544081  0.0136333966  0.0235657726  0.0089730684  8.090727e-03 #> C3ar1     0.0938388877 -0.0167860039  0.0829960890  0.0252519568 -9.482789e-04 #> S1pr4     0.0084920039 -0.0293263522 -0.0121548940  0.0406779781 -5.382158e-04 #> C5ar1     0.0407262608 -0.0242408168  0.0197387038  0.0060726039  2.093155e-04 #> Fpr1      0.0102649869 -0.0089007948  0.0016960977 -0.0065596254 -6.134903e-03 #> Sctr      0.0120875632  0.0147438127 -0.0194051222 -0.0085722504  2.082209e-02 #> Gpr158   -0.0719496806  0.0266717042  0.0513712092  0.0216498668  2.935536e-03 #> Cxcr4     0.0211939611  0.0230622688 -0.0245363058 -0.0109080198  9.472430e-03 #> Hrh2     -0.0157438030  0.0061802567  0.0113053430  0.0029460645 -1.708804e-03 #> Slc17a6   0.0075493320  0.0126347130 -0.0160556510 -0.0084332711  1.170607e-02 #> Ppp1r3g   0.0149426987  0.0057072636 -0.0289783198  0.0056083236  2.498537e-02 #> Pln       0.0014566290 -0.0267677730 -0.0169765597  0.0225011657  1.028331e-03 #> Grin2b   -0.1116344588  0.0446090148  0.0803789620  0.0382154030  3.556127e-03 #> Taar7e   -0.0084726099  0.0011463210  0.0061755177 -0.0003439554 -1.293362e-03 #> Ptger2   -0.0141897939  0.0058535637  0.0102115853  0.0044346091  2.976632e-03 #> Mc4r     -0.0127097543  0.0043602053  0.0225416940  0.0110976884  3.705846e-03 #> Ghsr     -0.0154668954  0.0060562428  0.0124322219  0.0057590823  3.963661e-03 #> Nmbr     -0.0074165903  0.0065195240  0.0020395102 -0.0012619081  2.023811e-03 #>                  Dim.6         Dim.7         Dim.8         Dim.9        Dim.10 #> Mlc1      0.0182761915  0.0523347399 -0.0032111655  0.0230235230 -0.0565248194 #> Gprc5b   -0.0262843505 -0.0142032221 -0.0142765047 -0.0192770183 -0.1838368268 #> Gfap     -0.1432109312 -0.4711696419  0.1988483486 -0.0869773334  0.2599315051 #> Ednrb     0.0253695787  0.0240351780 -0.0244233651 -0.0168323839  0.0570961610 #> Sox9      0.0194617958  0.0161285816  0.0068747388  0.0009833111 -0.0370000232 #> Aqp4      0.0168151610 -0.2000194904  0.0644950601 -0.1064427544  0.1678385426 #> Gjc3     -0.2249668222  0.0187125465  0.0092513338  0.0300164662 -0.3656457906 #> Sox8     -0.1029165155  0.1565858604 -0.0842068247  0.0378807824  0.0503488863 #> Ntsr2     0.0884161928  0.0601591399 -0.0371910160 -0.0121313690 -0.0967083510 #> Smo       0.0204032629 -0.0058044858 -0.0164654277 -0.0517538708 -0.0178307007 #> C1qb     -0.0045146343  0.0134397160 -0.0040260989 -0.0055953051  0.0022908235 #> Olig1    -0.2183227094  0.2992207978 -0.1164606632  0.0861061922 -0.0153730282 #> C1qa      0.0265435115  0.0352839876 -0.0058782320 -0.0609901020  0.0776634792 #> Pth1r     0.1192601525 -0.0822562649 -0.0551762874  0.1662151256  0.0796146349 #> Gabbr2   -0.0060420466 -0.0368598736  0.0037237541 -0.0011252517  0.0028840412 #> Timp4     0.0221961075  0.0189454104 -0.0167912932  0.0384199346 -0.0328686964 #> Abcc9     0.2182095325 -0.1094258097 -0.1166292107  0.3197324458  0.1021869060 #> Csf1r    -0.0039872866  0.0069499252 -0.0041173345  0.0380562065 -0.0336859045 #> Ntrk2     0.0511733493  0.0717327091 -0.0538904965 -0.0099616986  0.0022584798 #> Adgrg1    0.0025298039  0.0678773694 -0.0206161289  0.0118832364 -0.0138546410 #> Ntrk3    -0.0182734701 -0.0303329643 -0.0569219300 -0.0239051225  0.0257590069 #> Erbb4     0.0337810072  0.1114888125  0.3676286293  0.1321977194  0.0391943206 #> Selplg   -0.0166492391 -0.0325701147  0.0124583651  0.0443160605 -0.0694815595 #> Cspg5     0.0588053237  0.2497969941 -0.0838835292  0.0292717363 -0.0184636223 #> Dlk1     -0.0370457788 -0.1189503512  0.0509739104 -0.0419006607  0.0493256471 #> Gpr37l1   0.0734524486  0.1365465240 -0.0665429465  0.0053271636 -0.0120350632 #> Fgfr3     0.0614918237  0.0683553459 -0.0434531749  0.0043267879 -0.0333005827 #> Slc25a18  0.0460450575  0.0471420472 -0.0256322576  0.0074784083 -0.0294715381 #> Igf1r    -0.0263860700 -0.0048914895  0.0237747562  0.0040855296 -0.0238764256 #> S1pr1     0.0426441384  0.0926183601 -0.0370001534  0.0361212152 -0.0885373515 #> Grm5     -0.0136265137 -0.0253368634 -0.0126006461  0.0083492739  0.0137399997 #> Axl       0.0615630618  0.0589631247 -0.0269283237 -0.1510596057  0.0873346031 #> Efemp1   -0.0977795336 -0.0093346860 -0.0148519474 -0.0732247206  0.0319738411 #> Adgrb3    0.0145943190  0.0249535626 -0.0514289160  0.0065675597 -0.0325743291 #> Fn1      -0.1096320687 -0.0409607248  0.0152232255  0.0225005722 -0.1048090707 #> Mertk     0.0538613613  0.0560714056 -0.0498987058  0.0259874221 -0.0544846829 #> Adgrl2   -0.0366391336  0.0140412802  0.0017077132  0.0088470687  0.0197063658 #> Fzd2      0.0216025019  0.0307080767  0.0038099869 -0.0627489303 -0.0376647634 #> Aldh1l1   0.0394606780 -0.0008650916 -0.0000883376 -0.0235530985 -0.0243189179 #> Adgrg6   -0.0455938014 -0.0190336401  0.0132880950 -0.0100387100  0.0025972170 #> Egfr     -0.0401506692  0.0092118002  0.0368625802  0.0997577331 -0.0045246001 #> Kit       0.1643328179  0.1499310890  0.3135276581 -0.1312016816 -0.0493314123 #> Ptgdr    -0.1020698484 -0.0355963141 -0.0090650888  0.0866547249  0.0186403635 #> Gad1      0.0848189702  0.1838049694  0.6135398399  0.2338461742  0.0557006851 #> Tyro3    -0.0738582593  0.0109487326 -0.0099308167  0.0201310895 -0.1868869758 #> Atp13a5   0.4156398041 -0.0355734050 -0.1188530829  0.1366726192 -0.0923436606 #> Ddr2      0.0040989042  0.0267001405  0.0209132411 -0.0491070756 -0.0262668026 #> Rspo3    -0.0756654554 -0.0391532961 -0.0063675757  0.0419050952 -0.0126148277 #> Arhgap29  0.1372343146  0.0027473224  0.0019229703 -0.0976372311 -0.0599879224 #> Fzd7      0.0661308956  0.0011388257  0.0005691529 -0.0592336654 -0.0302951848 #> Slc47a1  -0.3312521538 -0.0982370651 -0.0191476757  0.3045847111  0.0636210042 #> Ptger3    0.0823116370  0.0008631737 -0.0126837316 -0.0556000006 -0.0561456432 #> Bdkrb1   -0.0110628329  0.0038829796 -0.0126303100 -0.0015596184  0.0385526580 #> Traf4    -0.0808205267  0.2112513817 -0.0882192494  0.0448418656  0.1575704037 #> Cx3cr1   -0.0129814026 -0.0068088011  0.0008859339  0.0592343574 -0.0152954051 #> Anxa11    0.0021707801 -0.0237110949 -0.0335613289 -0.0294535031  0.0110179284 #> Adgrb1   -0.0219547105 -0.0172104134 -0.0214982229 -0.0009003600  0.0378630598 #> Lpar1     0.0783012522  0.0226794982  0.0067210488 -0.1607157529 -0.1337221635 #> Gpr17    -0.1526390784  0.3688384783 -0.1294798463  0.0839906271  0.3339011675 #> Cxcl12    0.0526751453  0.0134351442 -0.0094111965 -0.2086585188  0.0699296202 #> Epha4    -0.0200133275 -0.0480430223 -0.0678625229 -0.0189400851 -0.0229643168 #> Gpr182    0.1079706752  0.0638529181 -0.0076090173 -0.2943283561  0.0600448604 #> P2ry14    0.1220119244 -0.0366363062 -0.0565692745  0.0900498243 -0.0062950824 #> Hcar1     0.0576000275  0.0198625904  0.0091702233 -0.1221614800 -0.0310066152 #> Ephb1    -0.0292070142  0.0004742995 -0.0236911493  0.0113924043 -0.1542648150 #> Grm3      0.0351743531  0.0571313420 -0.0725842424  0.1151556875 -0.1887728158 #> P2ry1     0.0358421937  0.0111424937  0.0177445814 -0.1054133335  0.0425056551 #> Ptk7      0.0260353345 -0.0136236204 -0.0294950704 -0.0679230151  0.0395012941 #> Slco1a4  -0.0961948275  0.0102387245  0.0287978466  0.0077820664  0.0249941964 #> Insrr     0.1781679883  0.0548541029  0.0222958755 -0.1361325513 -0.1062319262 #> Cmklr1    0.0099328492  0.0193009821 -0.0099965038 -0.0915459348  0.0360559183 #> Fzd6      0.0049384870  0.0037551518  0.0119213403 -0.0466852506 -0.0302180426 #> S1pr5    -0.0963220515 -0.0200308654  0.0157231644  0.0152259591 -0.2850641058 #> Pdgfrb    0.2444966016 -0.0199654261 -0.1009689639  0.1049792714  0.0321909308 #> Flt1     -0.0480002049 -0.0339990747  0.0201293447  0.0775369960 -0.0335155759 #> Adgrl4   -0.0540856447 -0.0192198062  0.0214288318  0.0394870638 -0.0123241612 #> Lpar6     0.0152195164 -0.0119031659 -0.0097962263 -0.0018392043 -0.0208473398 #> Epha6     0.0008702446 -0.0431423394 -0.0342848963  0.0084888638 -0.0062207879 #> Emcn      0.0362734114 -0.0132948332 -0.0258691475  0.0708762937  0.0047825581 #> Cldn5    -0.1392357468 -0.0097382495  0.0652331858 -0.0444962737 -0.0120198376 #> P2ry12   -0.0177365118 -0.0370678484  0.0276946109  0.0997067491 -0.0721659528 #> Adgrf5   -0.0413667325 -0.0329967612  0.0198819317  0.0161114927  0.0033448417 #> P2yr13   -0.0082818847 -0.0144377919  0.0084739744  0.0408468585 -0.0348846960 #> Adgre1   -0.0011878222 -0.0045784911  0.0032807719  0.0095419015  0.0322537272 #> Cx3cl1   -0.0107519255 -0.0421281655 -0.0584679024 -0.0313878944  0.0043828950 #> Plxnb3   -0.0229208157 -0.0145414992  0.0206280347  0.0098718099 -0.0151000542 #> Flt4     -0.0407707809 -0.0005811435  0.0145972334 -0.0212555132 -0.0004953907 #> Slc17a7  -0.0242712193 -0.0979783263 -0.1285110480 -0.0386990784 -0.0099813102 #> Cd300c2  -0.0073314833 -0.0059082275 -0.0032696116 -0.0103259388 -0.0118695369 #> Tek      -0.0573345418 -0.0022282707  0.0165178813  0.0087699128  0.0262024416 #> Kdr      -0.0107854074 -0.0025793169  0.0115552863 -0.0180621328 -0.0250915484 #> Kcnj8     0.2045155436 -0.0946506905 -0.1068115750  0.3042285899  0.0935257937 #> S1pr3     0.1386004900 -0.0674970925 -0.0666056885  0.2159729786  0.0750633031 #> Tie1     -0.0548695049 -0.0166445194  0.0189586577  0.0192321890  0.0162260876 #> Pdgfra   -0.0297257338  0.2386784657 -0.0848398924 -0.0967451134  0.2110233808 #> Baiap2   -0.0115012871 -0.0583945948 -0.0714922429 -0.0309682971 -0.0044146994 #> Calcrl   -0.0071179870  0.0524515412 -0.0178244031 -0.0861124287  0.0411015504 #> Adrb2    -0.0332014648 -0.0070854688 -0.0264526840  0.0668783186  0.0975938139 #> Ccr2     -0.0132483753 -0.0013696773 -0.0088841233 -0.0388934439  0.0405884747 #> Alk       0.1114862567  0.1088347245  0.1240958399 -0.0336476065 -0.0480216416 #> Tacr3    -0.0032662136 -0.0164904025 -0.0212280263 -0.0152076821  0.0093712519 #> Erbb3    -0.0755090443 -0.0476671923  0.0253089240  0.0038305963 -0.1736720944 #> Pcdh15   -0.0986505507  0.2108748802 -0.0616036616  0.0582094530  0.0995608816 #> Grm7     -0.0117355616 -0.0472979114 -0.0517445020  0.0052776521 -0.0303220363 #> F2r       0.0025829869  0.0448033026 -0.0441688051  0.0343268188  0.0459188791 #> Bdkrb2    0.0965724175  0.0225397516 -0.0149999178 -0.0513786240  0.0381847660 #> Adgrv1   -0.0956791788 -0.0140641034 -0.0192251505  0.0832828316  0.0196034708 #> Gprc5c    0.1159648986  0.0361277804 -0.0085545908 -0.0805841731  0.0241521925 #> Tbxa2r    0.1332069647 -0.0487187735 -0.0578621117  0.1351736582  0.0983806334 #> Ackr1    -0.0402437814 -0.0218632455 -0.0083402505 -0.0896553691  0.0483979616 #> Lpar2     0.0287285454  0.0132225173  0.0077164653 -0.0818933444 -0.0038463804 #> Myh11    -0.0036734615 -0.0055023409  0.0014547530 -0.0327252066  0.0157818985 #> Musk      0.0231233802  0.0116212710 -0.0012895142 -0.0483731970  0.0115294539 #> Cnr1      0.0505729503  0.0964790514  0.3168813572  0.1196215675  0.0073378777 #> C3ar1     0.0007318926  0.0010301581 -0.0061584228 -0.0135860793  0.0483668571 #> S1pr4    -0.0180446600 -0.0102688902  0.0149532714 -0.0170945729 -0.0196138485 #> C5ar1     0.0186444390  0.0018633778 -0.0030160165 -0.0258686179 -0.0023665300 #> Fpr1      0.0157190855 -0.0105032449  0.0088762163 -0.0436370035  0.0104033105 #> Sctr      0.0105464895 -0.0154293556  0.0079620554 -0.0492531151  0.1157915984 #> Gpr158   -0.0013906665 -0.0285510908  0.0066147622 -0.0063789614  0.0156349912 #> Cxcr4     0.0079715926 -0.0270573006  0.0392406051 -0.0736354782  0.2009611041 #> Hrh2      0.0037567682  0.0042090412  0.0363706629  0.0104729169 -0.0027312019 #> Slc17a6   0.0094554493 -0.0371135225  0.0294658628 -0.0940261543  0.2309738144 #> Ppp1r3g   0.0064060794 -0.0023706537 -0.0041348103 -0.0038533715 -0.0182513720 #> Pln      -0.0079839216  0.0027920698 -0.0001577965 -0.0259833660 -0.0028082592 #> Grin2b   -0.0098278028 -0.0376438960 -0.0441121734  0.0020787405 -0.0057836993 #> Taar7e    0.0018212011 -0.0050037885 -0.0027950221 -0.0293574790  0.0418934633 #> Ptger2   -0.0004158681 -0.0088473544 -0.0103205013 -0.0023845578 -0.0041437677 #> Mc4r     -0.0049557329 -0.0168116324 -0.0257267649 -0.0072906204  0.0015155054 #> Ghsr     -0.0014022151 -0.0115142582 -0.0161237546 -0.0047397372 -0.0017167726 #> Nmbr      0.0155946934  0.0311940862  0.0926225820  0.0275221170  0.0021430226 #>                Dim.11        Dim.12       Dim.13        Dim.14        Dim.15 #> Mlc1     -0.020038499  4.368805e-02  0.017658374  0.0237889875 -0.0014887323 #> Gprc5b   -0.068977469  4.674161e-02 -0.002836844  0.0284616446  0.0248883319 #> Gfap      0.048051535 -2.123727e-01 -0.044360958  0.0176188656 -0.0349386185 #> Ednrb    -0.015601154 -1.024983e-01 -0.015521455 -0.0016168062 -0.0242628718 #> Sox9     -0.022351154 -1.628976e-02  0.022344373  0.0160212396 -0.0068392065 #> Aqp4      0.059265354 -8.562509e-02  0.009188955  0.0018077803 -0.0133083070 #> Gjc3     -0.114414832  1.943950e-01  0.014800378  0.0434896008  0.0195239198 #> Sox8      0.053299106 -4.882687e-02  0.011487680 -0.0189883241 -0.0213036740 #> Ntsr2    -0.001226814 -7.304461e-02 -0.046950518  0.0078976770  0.0190433563 #> Smo       0.054121946 -3.341464e-02 -0.007959094  0.0061000344  0.0509233702 #> C1qb     -0.101234587 -2.376866e-02  0.037292350 -0.0698355400  0.0100176748 #> Olig1     0.019274275  2.066780e-02  0.046628180 -0.0067943529 -0.0130086862 #> C1qa     -0.327690347 -8.079755e-02  0.187035639 -0.0143639919 -0.0764908759 #> Pth1r    -0.033888270  2.302678e-02 -0.067313192  0.0058266081 -0.0035007286 #> Gabbr2    0.002082942 -1.281311e-02  0.004470428  0.0213185548 -0.0088500700 #> Timp4    -0.011867477  3.201045e-02  0.013056866 -0.0017636056  0.0318700042 #> Abcc9    -0.055676500  7.322120e-02 -0.048006826 -0.0971730542 -0.0148455220 #> Csf1r     0.090485252  1.870855e-02 -0.039799256  0.1299624621  0.1228744218 #> Ntrk2    -0.002305177  8.433210e-02  0.077825345 -0.0130551067 -0.0231232906 #> Adgrg1    0.037618933 -8.115803e-03 -0.004499510  0.0239912380 -0.0160994961 #> Ntrk3     0.001613438 -5.524433e-02 -0.026061707  0.0141709575  0.0365869334 #> Erbb4    -0.031161339  3.359559e-03 -0.041391658 -0.0245055347  0.0150867771 #> Selplg    0.360991432  1.350267e-01 -0.225287845 -0.1795895858 -0.2757356520 #> Cspg5     0.008299183  3.079263e-02  0.011680749 -0.0200124690 -0.0131399212 #> Dlk1      0.059565965  6.223031e-03  0.001409311  0.0231149143  0.0268276298 #> Gpr37l1   0.024192425  9.223149e-03  0.015303567 -0.0185641211 -0.0086416711 #> Fgfr3    -0.003980442 -5.142991e-03 -0.021400008  0.0046432699  0.0009511007 #> Slc25a18 -0.035707907  1.989756e-02  0.010314425 -0.0021704947 -0.0054221087 #> Igf1r     0.032290062  6.592975e-02  0.030046617  0.0029889587  0.0690760677 #> S1pr1    -0.025646773  8.776936e-03 -0.016551446 -0.0107987934 -0.0082841000 #> Grm5      0.001272481 -2.842221e-02 -0.019232234  0.0199228111 -0.0132919475 #> Axl      -0.224627641  4.057458e-02 -0.140459983 -0.0431340380 -0.0972244586 #> Efemp1   -0.063983319  1.050285e-01 -0.214728944 -0.0561439709  0.0317470021 #> Adgrb3   -0.007785840 -1.453906e-02 -0.015905161  0.0054159650 -0.0058714403 #> Fn1       0.138224315 -1.450282e-01  0.131583990 -0.3005558461  0.1004061129 #> Mertk     0.057607747  1.264080e-02 -0.011221515  0.0791285694  0.0045157935 #> Adgrl2    0.005448365 -4.522455e-02  0.016707469  0.1167408842  0.0349196891 #> Fzd2      0.021456793 -4.520484e-03 -0.031130641  0.0229075191  0.0411838705 #> Aldh1l1  -0.023774029 -3.310673e-02 -0.008989503 -0.0305344894  0.0121229100 #> Adgrg6   -0.002028408  1.417053e-02 -0.068536134 -0.0802461509 -0.0976092037 #> Egfr     -0.032643563  4.620965e-03  0.012019488  0.0680026874 -0.0385026926 #> Kit       0.062544512 -2.977408e-05  0.041694999  0.1179445218 -0.0477153865 #> Ptgdr    -0.018796432  3.768817e-02 -0.028867877 -0.0162704191 -0.0358041253 #> Gad1     -0.081662277  2.961620e-02 -0.074720040 -0.0425537856  0.0122241666 #> Tyro3    -0.060221733  9.530014e-02  0.017485340  0.0082586590  0.0116224161 #> Atp13a5   0.112565194 -7.938054e-02  0.189537016 -0.0156263922 -0.0443578053 #> Ddr2      0.030475355 -8.566765e-02  0.064196123 -0.0702987777  0.0288278930 #> Rspo3     0.013146570 -2.064306e-02  0.020612609 -0.0389510848 -0.0097748976 #> Arhgap29  0.086391089 -8.757781e-02  0.054522767  0.0140487132 -0.0008055760 #> Fzd7      0.067595298 -1.422837e-02 -0.013572216 -0.0669776365 -0.0656715065 #> Slc47a1  -0.050996249  5.620700e-02  0.012737699  0.1145287300 -0.0825635458 #> Ptger3    0.060555965 -6.480637e-02  0.091237575  0.0322293786 -0.0394575438 #> Bdkrb1   -0.023814487  9.738136e-03 -0.063245451  0.0795604817 -0.0031514369 #> Traf4     0.083523840 -6.639744e-02  0.003518718  0.0001757780 -0.0212051429 #> Cx3cr1    0.053597388 -2.543381e-02  0.040688981  0.0683239127  0.0999276030 #> Anxa11   -0.003010427  2.152018e-02 -0.071228730  0.0077393588 -0.0219749559 #> Adgrb1    0.015425028 -4.084913e-02 -0.003809899  0.0194410205 -0.0032592180 #> Lpar1     0.014754245 -2.576004e-02  0.061073459 -0.0013049857  0.0621189330 #> Gpr17     0.138087162 -1.506092e-01  0.033908953 -0.0329730922 -0.0349453212 #> Cxcl12    0.010472411  1.618876e-01 -0.039533546  0.0813602459  0.0562750941 #> Epha4     0.010078760 -3.572675e-02  0.006354623  0.0003399448  0.0215361453 #> Gpr182   -0.109821109  9.717282e-02 -0.342385852  0.0263718387  0.0780167142 #> P2ry14    0.025744756 -3.130308e-02  0.064018359 -0.0698339489  0.0004043104 #> Hcar1     0.023663773 -1.996512e-02 -0.020023651  0.0115497981 -0.0252107528 #> Ephb1    -0.041200461  8.964523e-02  0.006980214  0.0055263742  0.0093595685 #> Grm3     -0.081837046  1.407191e-01 -0.039754260 -0.0130252228  0.0270471365 #> P2ry1     0.019465520  1.159565e-01 -0.035449554  0.0327524591  0.0232735723 #> Ptk7     -0.054204872  4.565399e-02 -0.093852867  0.0296128220  0.0292700301 #> Slco1a4   0.026249502 -3.491470e-02  0.042919890  0.0730236054 -0.1022275730 #> Insrr     0.095621861 -1.533824e-01  0.204867785  0.1376381615 -0.0902709094 #> Cmklr1   -0.139354247  2.837330e-02 -0.097973780 -0.1828790083  0.1532248356 #> Fzd6      0.019700882 -3.153353e-02  0.060359651  0.0336855298 -0.0473389691 #> S1pr5    -0.099641429  1.650677e-01  0.012417042  0.0160684983  0.0138651449 #> Pdgfrb   -0.038634441  4.812030e-02 -0.085069028  0.0498834091  0.0042292514 #> Flt1      0.032912792 -2.501097e-02  0.104390299  0.0463256622 -0.0241453908 #> Adgrl4    0.006514742 -1.111846e-02  0.037774748  0.1104409943 -0.0438263950 #> Lpar6     0.027827744 -2.145519e-02  0.035808458 -0.0112963829  0.0082153393 #> Epha6    -0.003052361 -3.446541e-02  0.010886529  0.0035294614 -0.0218302935 #> Emcn     -0.016019154  1.716235e-02  0.012921194  0.0353054068  0.0213335308 #> Cldn5    -0.021538240 -2.382138e-02 -0.013384328  0.0471020173  0.0442081829 #> P2ry12    0.386611849  3.758621e-02 -0.150877086  0.1362033992  0.2274988614 #> Adgrf5   -0.028749322 -1.470955e-04  0.021316722  0.0678092908 -0.0358465017 #> P2yr13    0.207066615  2.565520e-02 -0.089833735  0.0422417903  0.0750839493 #> Adgre1   -0.095656927 -1.756532e-02  0.107954947 -0.0227176085 -0.0383590848 #> Cx3cl1    0.021479037 -4.089392e-02  0.013394243  0.0319552624 -0.0267426785 #> Plxnb3    0.065918965 -9.441912e-03 -0.048090419  0.0222511744  0.0355124826 #> Flt4      0.001237470 -2.865386e-03 -0.026920011  0.0194351234 -0.0670762547 #> Slc17a7   0.009820295 -5.657356e-02  0.022882705  0.0289331122 -0.0288857867 #> Cd300c2  -0.124936281  9.072016e-03  0.043270492 -0.1179520783 -0.1136348081 #> Tek      -0.026549529 -6.871399e-03 -0.033318674 -0.0250430705  0.0945011680 #> Kdr       0.052464221 -1.417103e-02  0.073185734 -0.0580878424 -0.0499141067 #> Kcnj8    -0.065786997  9.127713e-02 -0.084275580 -0.0697282946 -0.0022770086 #> S1pr3    -0.051759416  5.563742e-02 -0.059414484 -0.0998813301  0.1009654089 #> Tie1     -0.002356740 -3.315768e-02  0.038728151 -0.0028230776  0.0074174825 #> Pdgfra    0.010513231 -5.051568e-03 -0.138495694  0.0242937847  0.0676010310 #> Baiap2    0.007200391 -2.414732e-02  0.034097473  0.0250554738 -0.0192283730 #> Calcrl   -0.060814149  5.472863e-02 -0.132005341 -0.0018959508 -0.0293391108 #> Adrb2    -0.123244758  2.106492e-02  0.020081861  0.4879664947 -0.0445119354 #> Ccr2     -0.283568784 -1.601459e-02  0.085028130 -0.1841681385 -0.1812689180 #> Alk       0.076684898 -1.207731e-01  0.148315607  0.0466881448 -0.0547710748 #> Tacr3     0.049412737  4.400015e-02  0.009896008  0.0921289200  0.0396572347 #> Erbb3    -0.044241686  9.601851e-02 -0.002442638  0.0032250763 -0.0051474845 #> Pcdh15    0.053854483 -3.008760e-02  0.023461279 -0.0073391578 -0.0196114268 #> Grm7     -0.007287395 -1.344405e-02  0.005035987  0.0023805202 -0.0154317516 #> F2r       0.001451940 -2.096208e-02 -0.010549611 -0.0738825588  0.0958259817 #> Bdkrb2   -0.029166120  9.077230e-02 -0.120356979  0.2531860520 -0.0304536349 #> Adgrv1   -0.009712447  5.085587e-02  0.023711517 -0.0108005355 -0.0247119858 #> Gprc5c   -0.035661611 -3.970576e-03 -0.039994591 -0.0012071195  0.0548320266 #> Tbxa2r   -0.097691236  1.003580e-01 -0.139867799  0.1638783163 -0.0169647743 #> Ackr1    -0.046878595  7.685558e-02 -0.109219154 -0.0541586716 -0.0375944823 #> Lpar2     0.099609394  1.351002e-01 -0.157220735 -0.0437225369 -0.2436105833 #> Myh11    -0.009800230 -2.402366e-02 -0.046643726 -0.2708892012  0.3534617551 #> Musk      0.023765552  6.188543e-02 -0.020671571  0.0881352148  0.0108528417 #> Cnr1     -0.044705047  2.661707e-02 -0.032900404 -0.0432178116  0.0170531212 #> C3ar1    -0.217256238 -6.165339e-02  0.148903746  0.0115011540 -0.0015004071 #> S1pr4     0.122986307  8.022143e-02 -0.082475141 -0.1293823329 -0.3283005053 #> C5ar1    -0.023902383  1.758769e-02  0.043925717 -0.1656464882 -0.3114631520 #> Fpr1      0.124247047  1.377279e-01 -0.062998951 -0.1326442696 -0.2698508684 #> Sctr      0.058895464  2.507629e-01  0.187262382 -0.0276457442  0.0464031290 #> Gpr158    0.010388267  2.916726e-02  0.027324178  0.0135457379 -0.0009297620 #> Cxcr4     0.078613675  3.731709e-01  0.294305974 -0.0264462299  0.0683632093 #> Hrh2     -0.007431172 -2.976020e-03 -0.003014343  0.0056026710  0.0005081364 #> Slc17a6   0.108970045  4.884665e-01  0.363774343 -0.0446393170  0.0800956523 #> Ppp1r3g  -0.009724545 -1.351029e-02 -0.004009719  0.0350344285  0.0006084764 #> Pln      -0.018882124 -2.320328e-02 -0.027951321 -0.2258460285  0.3369657983 #> Grin2b    0.002923810 -2.836359e-02  0.008477210  0.0141848516 -0.0053046041 #> Taar7e    0.032187101  1.041645e-01  0.051049250  0.0559371230  0.0346327649 #> Ptger2   -0.002746009 -7.342839e-03  0.003745769  0.0042079710  0.0007848482 #> Mc4r     -0.012113758 -1.633702e-02  0.029642096  0.0401400378  0.0136978701 #> Ghsr      0.005407458 -1.780903e-02 -0.003365696  0.0051626510 -0.0045798759 #> Nmbr     -0.006712408 -4.749770e-03 -0.006284959  0.0077549790 -0.0082885593 #>                 Dim.16        Dim.17        Dim.18        Dim.19        Dim.20 #> Mlc1     -0.0085195737  0.0454076670  0.1141469728  0.1513094573 -0.0766586895 #> Gprc5b   -0.0500574777 -0.0298408946 -0.0207443142 -0.0103294732  0.0051805356 #> Gfap      0.0216685881 -0.0083902605  0.1127647026  0.0847494263 -0.1004269992 #> Ednrb    -0.0104222666 -0.0317058324 -0.0683060104 -0.0132046955 -0.0030006882 #> Sox9      0.0210271532 -0.0028138266  0.1016544006  0.1087184388 -0.0800062370 #> Aqp4     -0.0170123248  0.0008515506 -0.0907580762 -0.1102144520  0.0660046002 #> Gjc3     -0.0122032831  0.0037671917 -0.0596671988 -0.0384069600  0.0132272069 #> Sox8     -0.0066824876  0.0004354844 -0.0098163567 -0.0109910258  0.0209243325 #> Ntsr2    -0.0112551622 -0.0153751094 -0.1713090778 -0.1075917045  0.1482549542 #> Smo       0.0306897168  0.0219460791  0.0233310357 -0.0136375939  0.0884135721 #> C1qb     -0.0409410741 -0.0511507092  0.0487433495 -0.0211217942  0.0098252555 #> Olig1    -0.0119025347 -0.0019798549 -0.0099140478  0.0033068686  0.0017079799 #> C1qa     -0.0209453769 -0.0218387278 -0.0107061349  0.0245603448 -0.0424701592 #> Pth1r    -0.0347251586 -0.0085555092 -0.0610277157  0.0208458915 -0.0262114002 #> Gabbr2   -0.0154657559  0.0071990985  0.0104283824 -0.0101539791 -0.0209078076 #> Timp4     0.0324223011 -0.0283840251  0.0942773611  0.0487786526 -0.0750493254 #> Abcc9    -0.0389316092 -0.0625035564  0.0385656652  0.0335835478 -0.0523465666 #> Csf1r    -0.0248393156  0.0476564696 -0.0203139565  0.0009389249 -0.0019761272 #> Ntrk2    -0.0159508375  0.0113695354  0.0865325152  0.0968588564 -0.0755840856 #> Adgrg1   -0.0307271364 -0.0147501566 -0.0001438173  0.0147913832 -0.0750199213 #> Ntrk3     0.0384152848  0.0360930244 -0.0191884919 -0.0445150077 -0.0183318294 #> Erbb4    -0.0333265208 -0.0106397540 -0.0338524500 -0.0190270225  0.1184402252 #> Selplg    0.1489658753  0.0036772270  0.0463846756 -0.0732508326  0.0116206437 #> Cspg5    -0.0071345916  0.0596091816  0.1057696857  0.0874017671 -0.0322829174 #> Dlk1     -0.0064684238  0.0330054653 -0.0452406001 -0.0958555918  0.1600062159 #> Gpr37l1  -0.0048062606 -0.0242112009  0.0231265309 -0.0142099244 -0.0106654361 #> Fgfr3    -0.0315245960 -0.0002881528 -0.1252693313 -0.0772715734  0.0847207016 #> Slc25a18 -0.0087766563 -0.0122841616  0.0686878388  0.1072909913 -0.0958635702 #> Igf1r     0.0670524753  0.0349615396  0.1066345624  0.0793229270 -0.0239854144 #> S1pr1     0.0087940692 -0.0021814639 -0.0241949414  0.0217024555 -0.0867462026 #> Grm5      0.0058530966 -0.0588878975 -0.0260135281  0.0112729399  0.0045433718 #> Axl       0.0144491795 -0.0533305361  0.1180891246 -0.0866044244  0.0060023412 #> Efemp1   -0.1698305577 -0.0640437451  0.1243797084  0.0533954899  0.0463348934 #> Adgrb3   -0.0006359178  0.0336053743  0.0031116729 -0.0125861508  0.0634926068 #> Fn1      -0.0765182478  0.0321032722 -0.1279909228  0.2748594327  0.1051273413 #> Mertk     0.0612397009  0.0869306803 -0.0775929957 -0.0607464315  0.1358840897 #> Adgrl2    0.0648811954  0.0754398659 -0.1147039779  0.0723471751 -0.1100928177 #> Fzd2      0.0535511337 -0.0646638993 -0.0060897911  0.0581720171 -0.0296291388 #> Aldh1l1  -0.0103812490 -0.0096530135  0.0042989221 -0.0053076862  0.0380473153 #> Adgrg6   -0.1681465359  0.0804366158 -0.3559356963  0.1330779361 -0.1290750023 #> Egfr      0.0464905737 -0.0305696569 -0.0154221700 -0.1066828423 -0.0808547713 #> Kit       0.0624612115 -0.0486648677  0.0096271870  0.0102961991 -0.3893420909 #> Ptgdr    -0.0369411258 -0.0209260964  0.0177430452 -0.0347500635 -0.0504868547 #> Gad1     -0.0413188454  0.0368202075  0.0369085803  0.0404838547  0.1797804460 #> Tyro3    -0.0128712224  0.0178923762 -0.0158121756 -0.0089876886 -0.0381978325 #> Atp13a5  -0.0794982137 -0.0900595277  0.0579663552 -0.3027185909  0.0691629020 #> Ddr2     -0.0192656947  0.0322949084 -0.0301332691  0.1766780402  0.0829158321 #> Rspo3    -0.0646678479 -0.0416882439 -0.0073931027  0.0109789258  0.0182446502 #> Arhgap29 -0.0217738556  0.0966237051 -0.0282157908  0.1917526928  0.0515756960 #> Fzd7     -0.0060437078  0.0428452705  0.0023495968  0.0354589147  0.0796198080 #> Slc47a1   0.0390428076 -0.0591409839  0.0819137807 -0.2825177989 -0.1198303360 #> Ptger3    0.0081953097  0.0740305784  0.0113457560 -0.0730162432  0.1859162379 #> Bdkrb1   -0.0035743200 -0.0133019427  0.0088635229 -0.0895456974 -0.0239729396 #> Traf4     0.0153475651 -0.0538373869 -0.0102294346  0.0182948930 -0.0006881794 #> Cx3cr1   -0.1152625193 -0.0196091336 -0.0274092428  0.1009393315 -0.0656781984 #> Anxa11    0.0306192051  0.0870956520  0.0036225158  0.0812796929  0.0263027989 #> Adgrb1   -0.0030309554  0.0031840676 -0.0374522760 -0.0153275825  0.0119889861 #> Lpar1     0.0476278263  0.0435928617  0.0020280490  0.0746232367  0.1298102224 #> Gpr17     0.0025401731  0.0005662896 -0.0009479047  0.0123481736  0.0224614597 #> Cxcl12    0.0259587751 -0.0803145670  0.2205790155 -0.0035209260  0.0561066541 #> Epha4     0.0184253750  0.0499462286  0.0336221642 -0.0186218203 -0.0147029244 #> Gpr182   -0.2534755411  0.0179822335  0.0373355099 -0.0495708868  0.0298790012 #> P2ry14   -0.0310073220  0.0288208597 -0.0417865789  0.0630527757  0.1301326691 #> Hcar1    -0.0470973355  0.0150505934  0.0450643238 -0.0254178679  0.0516577090 #> Ephb1     0.0127975795  0.0281064229  0.0253179143  0.0118765408 -0.0003328962 #> Grm3      0.0022015552  0.0155877839 -0.0300991692  0.0250237786  0.0006109857 #> P2ry1     0.0390721615 -0.0938427445  0.0562992587 -0.1027277123 -0.1332649744 #> Ptk7     -0.0409135357  0.0276891219  0.0199729404  0.1202901991  0.0149972077 #> Slco1a4  -0.0094815222 -0.0289233363 -0.1179435583 -0.0949682511 -0.1655249618 #> Insrr     0.0597817209  0.0218277702 -0.0786127688 -0.1992064243 -0.1614080209 #> Cmklr1    0.1632097386  0.0013436902  0.0207133275 -0.1653705027  0.0446512577 #> Fzd6      0.0265825012 -0.0466494382  0.1776002862 -0.0321665848  0.1161788872 #> S1pr5     0.0105981644  0.0057982787 -0.0104436839 -0.0055524275  0.0047167544 #> Pdgfrb   -0.0462453982  0.0160977721 -0.0875000320 -0.0833225399 -0.0444915005 #> Flt1      0.0976784033 -0.0651955465  0.2884047257  0.0587774703  0.1567360944 #> Adgrl4   -0.0719041934  0.0320504003 -0.0174235225  0.1958715886 -0.2212886929 #> Lpar6     0.0369442430  0.0307401746 -0.0111028141 -0.0539153396  0.1667735958 #> Epha6    -0.0328633984  0.0311962798  0.0146187070 -0.0304263515 -0.0399829420 #> Emcn      0.0112364215 -0.0608089652  0.1615072665 -0.0737648102 -0.0399875691 #> Cldn5     0.0204149877 -0.0300858866  0.0162360296 -0.2158661076  0.1110039257 #> P2ry12   -0.1206395661  0.0276429798  0.0376810063 -0.0170559281 -0.0297718489 #> Adgrf5   -0.0179361477 -0.0073426246  0.0599171739  0.0743399481  0.0156419340 #> P2yr13   -0.0498691742 -0.0053933251  0.0438090301 -0.0175744212 -0.0301115745 #> Adgre1   -0.0332917794  0.0027781318 -0.0273154560  0.0623990231 -0.0154906832 #> Cx3cl1   -0.0236891008 -0.0262808304  0.0387385874 -0.0014288352 -0.0200261274 #> Plxnb3    0.0162310820 -0.0063965561 -0.0740935139 -0.0770408568  0.1636894913 #> Flt4     -0.0689538869  0.0311083982 -0.1938909684 -0.0555589375 -0.0894329071 #> Slc17a7  -0.0289146155  0.0425722458  0.0701126970  0.0232735648 -0.0463168975 #> Cd300c2   0.0653548268 -0.0371744124  0.0205018905 -0.0473471820  0.0431594013 #> Tek       0.0428807066  0.0024981139 -0.0606809148 -0.1052841202 -0.0446033273 #> Kdr       0.0369765551  0.0102038582  0.0713548718  0.1320978867  0.1259427385 #> Kcnj8    -0.0791242779 -0.0248090798 -0.0486500116  0.0439075929 -0.0420799390 #> S1pr3     0.0856575460 -0.0040410964  0.0185821025  0.0508504153 -0.0878121111 #> Tie1      0.0573452707  0.0503492062 -0.1206172574  0.0162465182 -0.0191447684 #> Pdgfra   -0.0280317502  0.0103961741  0.0600223309 -0.0192693379  0.0591812252 #> Baiap2   -0.0210210933 -0.0056419399  0.0184234513  0.0248601112  0.0017755543 #> Calcrl   -0.0825650995 -0.0144141564 -0.0286974805 -0.0241529166 -0.0201910941 #> Adrb2     0.3360382142  0.2811331130 -0.1525094350  0.0074651216  0.2421735712 #> Ccr2      0.0584271039 -0.0631775439  0.0210749182 -0.0907168211  0.0473333600 #> Alk      -0.0043677754 -0.0080033500 -0.0526441239 -0.1444832842 -0.1703122653 #> Tacr3     0.1156308656 -0.5966789297 -0.2220151403  0.1309515316  0.1393855384 #> Erbb3     0.0123460118  0.0045883768  0.0145706220 -0.0080291113 -0.0093357840 #> Pcdh15   -0.0091755464 -0.0015889595 -0.0061804856 -0.0125474929  0.0124053132 #> Grm7     -0.0096265761  0.0150826953 -0.0066848793 -0.0249972776 -0.0299233315 #> F2r       0.0719919275 -0.0046989509  0.0245342557 -0.0381912211 -0.0784106718 #> Bdkrb2    0.2010754130  0.0474197417 -0.0581638144  0.1524579982 -0.0697287089 #> Adgrv1   -0.0160691881  0.0132584677  0.0307908039 -0.0093861950 -0.0214274700 #> Gprc5c    0.0740692169  0.0287902200 -0.0017672519  0.0517832804 -0.1127999995 #> Tbxa2r    0.1305016941  0.1503861452 -0.0737853764  0.1974737247  0.0954673505 #> Ackr1    -0.2657185417  0.0858147840 -0.3763377642 -0.1389111711  0.0075835804 #> Lpar2     0.1990541333 -0.0250342554  0.0278117992  0.0038384971 -0.0739159649 #> Myh11     0.3649418131  0.0889725133 -0.1321931539 -0.0430186219 -0.1498945525 #> Musk      0.1214191217 -0.4011116559 -0.1282297031  0.0941054269  0.0118160945 #> Cnr1     -0.0047298496 -0.0408812466 -0.0349508124 -0.0361086685  0.0486008767 #> C3ar1    -0.0117289562  0.0058619154 -0.0525103081  0.1120648053 -0.0385012289 #> S1pr4     0.1511210992  0.0484036098 -0.0919908814  0.0087802323 -0.0217401247 #> C5ar1     0.1443211662  0.0300653021 -0.0607538893  0.0750615740  0.0418080878 #> Fpr1      0.1421456315  0.0744722958 -0.0184353173  0.0521160088  0.0255547151 #> Sctr     -0.0330887728  0.0666106592 -0.0063804028 -0.0209689294  0.0298516721 #> Gpr158   -0.0023256167 -0.0625109056 -0.0336775163  0.0016981989  0.0051665279 #> Cxcr4    -0.0575271503  0.0787331352 -0.0303409285 -0.0114721046  0.0176789925 #> Hrh2      0.0005356513 -0.0148151194 -0.0057769739 -0.0029742509 -0.0092350390 #> Slc17a6  -0.0637812076  0.0811486979 -0.0520220567 -0.0420846588 -0.0016604208 #> Ppp1r3g   0.0174926413 -0.0332248554  0.0471978865  0.0042481764 -0.0125994109 #> Pln       0.3576715486  0.0543837430 -0.0668504524 -0.0935214247 -0.0945407711 #> Grin2b   -0.0037063454 -0.0072530994  0.0167725707  0.0079731903 -0.0081018447 #> Taar7e    0.0737504560 -0.3898461040 -0.1448294465  0.0772201013  0.0581309367 #> Ptger2   -0.0021096567 -0.0010385808 -0.0005894454  0.0127397014 -0.0048440244 #> Mc4r      0.0076238585 -0.1138043516 -0.0467649405  0.0685592598  0.0376308817 #> Ghsr     -0.0106874954  0.0422288348 -0.0115748420 -0.0062335690  0.0068787700 #> Nmbr      0.0034666140  0.0063363502  0.0274438556  0.0325759907 -0.0578854141 #>                 Dim.21        Dim.22        Dim.23        Dim.24       Dim.25 #> Mlc1      0.1915296127 -0.0775793281  1.188980e-01 -0.1047555231  0.039556093 #> Gprc5b   -0.0549817793  0.1054921539  7.393436e-02  0.0955792131 -0.013942117 #> Gfap      0.1922578511 -0.0645327114 -2.621349e-02 -0.0186868143  0.009780146 #> Ednrb    -0.0857139129  0.0753131208  6.767365e-02  0.1590247489 -0.027178242 #> Sox9      0.1795569333 -0.0475052367  4.654244e-02  0.0929118497  0.120863030 #> Aqp4     -0.1309970473  0.0693509209 -2.816152e-02 -0.0218622199 -0.068119575 #> Gjc3     -0.0646711374  0.0237506169  1.489202e-02  0.0248995659 -0.032100665 #> Sox8     -0.0693108081  0.0380768110  1.209124e-02  0.0080231226  0.004328523 #> Ntsr2    -0.3150781218  0.1608868117  2.892064e-02  0.0202361416 -0.074566497 #> Smo       0.0008163573  0.0220998235 -6.797454e-02 -0.0275337637 -0.006732909 #> C1qb     -0.0378975712  0.0022957083 -4.423654e-02 -0.0714302646 -0.035476834 #> Olig1    -0.0067851126  0.0669816723  3.649786e-02  0.0696325488 -0.032918211 #> C1qa     -0.0451707731  0.0255322639  7.364687e-03  0.1398990887  0.142937254 #> Pth1r    -0.1351896289 -0.0296428715 -4.989838e-03 -0.0501482100 -0.032546374 #> Gabbr2   -0.0269917135  0.0391783687 -3.499100e-03 -0.0081500785  0.002617412 #> Timp4    -0.0070541938 -0.0156677502  1.124549e-01  0.0377080530  0.042622457 #> Abcc9    -0.0196602900 -0.0014578050 -8.203687e-02  0.0599900089 -0.057177330 #> Csf1r     0.0310847863  0.0028615381 -5.470127e-03 -0.0234037359 -0.024221078 #> Ntrk2     0.1637291832 -0.0524484108 -3.886686e-02  0.0269026249  0.036738491 #> Adgrg1   -0.0071002039  0.0661790729  5.533680e-02 -0.0285386371  0.064969723 #> Ntrk3    -0.0894624038 -0.0293185716  6.636749e-02  0.0478123480  0.028125640 #> Erbb4    -0.0438301823  0.0505355260  6.982946e-02 -0.0051399622  0.011977923 #> Selplg   -0.0237587787 -0.1423122359  5.340832e-03  0.0240740011  0.053734175 #> Cspg5     0.2482102708 -0.1022354809 -1.241259e-01 -0.0929838030 -0.039540781 #> Dlk1     -0.1502080544 -0.0853319880 -8.517056e-02 -0.2127173934  0.041595810 #> Gpr37l1   0.0135719057  0.0291321546 -3.525957e-02  0.0001086977 -0.013996373 #> Fgfr3    -0.1721850307  0.0678645918 -1.516023e-02  0.0394986280 -0.059449655 #> Slc25a18  0.1097588989  0.0139540116  4.739821e-02  0.1313221098  0.071763583 #> Igf1r    -0.1319286762 -0.0155879648  1.086816e-01 -0.0845456483  0.049837506 #> S1pr1     0.0775983241 -0.0212825731 -1.812987e-02 -0.0295971476 -0.072389663 #> Grm5     -0.0578682216  0.0065440157  4.607397e-02 -0.0570421491  0.050593352 #> Axl      -0.0421322918 -0.2090089904 -1.189651e-02 -0.2001379200  0.101831406 #> Efemp1   -0.0308067445  0.0907488932 -2.116584e-03 -0.0754105592  0.021921933 #> Adgrb3   -0.0361829194 -0.0403740166 -2.195078e-02 -0.1325377403  0.076290144 #> Fn1      -0.0130333973  0.0418717859 -1.778008e-01 -0.0778997286  0.182133989 #> Mertk    -0.0065795361 -0.1505777324 -7.066423e-02 -0.2346000054  0.059578124 #> Adgrl2   -0.2394445015 -0.3259797433  6.379235e-02 -0.0258658395 -0.034654336 #> Fzd2     -0.0599796230 -0.0275748427 -2.405904e-02  0.0472897658  0.023335048 #> Aldh1l1   0.0292838084  0.0370187498  2.924074e-02  0.0246408159  0.019462586 #> Adgrg6    0.0655004840 -0.0256342471  2.808014e-02 -0.0639609223  0.006761307 #> Egfr     -0.0245010706 -0.0394974471  1.304427e-02  0.0507365135 -0.052561221 #> Kit      -0.1302903743  0.0561945445 -3.042602e-01 -0.1074716049 -0.116328470 #> Ptgdr     0.0475336332  0.0729000814  1.396272e-02 -0.0096917636 -0.017308596 #> Gad1      0.0351630056  0.0631986508  1.529795e-01 -0.0705984997  0.083019020 #> Tyro3    -0.0082839583  0.0191431291  4.284894e-03  0.0744030060 -0.019025913 #> Atp13a5   0.1680743403  0.1364207264  8.035783e-02 -0.0519511047  0.096049593 #> Ddr2     -0.0890726112 -0.0377890556 -5.113698e-02 -0.0178983854  0.012928557 #> Rspo3     0.0427108983  0.0620073040 -8.238892e-02 -0.0207517572 -0.005663147 #> Arhgap29 -0.0759247189 -0.1634788782  1.487002e-01  0.0215307366 -0.077727202 #> Fzd7     -0.0049434314  0.0478681321  3.197551e-02  0.0300620233  0.040444167 #> Slc47a1   0.0278350596 -0.0189630903  1.203786e-01  0.0805415257 -0.100325586 #> Ptger3    0.1821198247  0.0940800936  3.031294e-01 -0.0568593610 -0.171691783 #> Bdkrb1   -0.1705963809 -0.1837312611  1.690605e-01  0.1422144193 -0.029735535 #> Traf4    -0.0652595237 -0.1566988300  7.713567e-03  0.0098088611  0.003184511 #> Cx3cr1   -0.0523244863  0.1614972308  3.348895e-02  0.1108636180 -0.038719249 #> Anxa11    0.0235100249  0.1610749464  7.062493e-02 -0.1370160976 -0.152779570 #> Adgrb1   -0.1035804454  0.0239864016  2.194852e-02 -0.0111045282  0.010375879 #> Lpar1     0.0148901669  0.0871035222  5.238635e-02  0.0210393210  0.047568830 #> Gpr17     0.0142770197  0.0502802828 -1.561353e-02 -0.0838472507  0.025720278 #> Cxcl12   -0.0447495610  0.1839532946  4.570104e-02 -0.0229134805 -0.190689409 #> Epha4     0.0029347634  0.0520147048 -1.720780e-02 -0.0361172921  0.006550585 #> Gpr182    0.0330825785 -0.1028483534  1.811424e-01  0.1358389851  0.100979884 #> P2ry14    0.0274296820  0.0409666039  6.252702e-02 -0.0204289854 -0.126415668 #> Hcar1     0.0915852497 -0.0061217078  4.702383e-02  0.0388286949  0.007418826 #> Ephb1     0.0760060150 -0.0925606793 -3.482857e-02 -0.0854802709  0.068879785 #> Grm3     -0.0294356800 -0.0161372792 -1.016288e-01 -0.0571748475 -0.019593065 #> P2ry1     0.0658796707  0.2103749965 -5.493685e-02 -0.0613315566 -0.134045773 #> Ptk7     -0.1271409629  0.0022200278  6.260802e-02  0.0514920068  0.067134756 #> Slco1a4  -0.0581462781  0.2473115570  4.038462e-02 -0.1752912882  0.326081914 #> Insrr     0.0722906354 -0.1653379254  4.408181e-02  0.0576055048  0.053452613 #> Cmklr1    0.0816103928 -0.0748592653  7.695998e-03 -0.0870568740 -0.019758231 #> Fzd6      0.0061848117  0.0564681906 -8.512828e-02  0.0921004446  0.264314420 #> S1pr5    -0.0055743413 -0.0384014178 -1.825326e-02 -0.0331679302  0.009633422 #> Pdgfrb   -0.0473592278 -0.1456486559  1.494873e-02  0.0356618717 -0.027092292 #> Flt1     -0.1026684893 -0.0714492371 -1.135830e-01  0.1238304260 -0.196860521 #> Adgrl4   -0.0177759841 -0.0347506282  4.085207e-01 -0.2671020435 -0.164510243 #> Lpar6     0.1151728438  0.0633872370  9.056173e-02 -0.2518560138 -0.224137363 #> Epha6    -0.0517991009  0.0363953001 -1.383327e-02  0.0205771055 -0.014042106 #> Emcn     -0.0723361689  0.0307737319  1.605557e-01 -0.0804214354  0.112265716 #> Cldn5     0.0643915183  0.0570685391 -1.963390e-01  0.1222492732  0.093313284 #> P2ry12    0.0718742339 -0.0080271530 -1.016152e-02 -0.0225860937 -0.051489517 #> Adgrf5   -0.0604241979 -0.0071129981  4.124845e-02  0.0288662522  0.080089978 #> P2yr13    0.0103589697 -0.0666281028 -3.599000e-02  0.0737256473  0.074483339 #> Adgre1    0.0169277476  0.0940930525 -5.044943e-03  0.0160999981 -0.056368849 #> Cx3cl1    0.0282788378  0.0380254676 -2.730562e-02 -0.0428136299 -0.049911542 #> Plxnb3   -0.1039976175 -0.0452809544 -3.335290e-02 -0.1533483006  0.007199098 #> Flt4      0.0842881314  0.0794349639  5.076787e-02 -0.0713730767  0.022184847 #> Slc17a7   0.0529870744  0.0309162783 -8.536686e-02  0.0009543436 -0.054296954 #> Cd300c2  -0.0022153209 -0.0652456431 -4.496447e-02 -0.1782036297 -0.026796807 #> Tek       0.0349380048 -0.1041160462  9.621805e-03 -0.0632201723 -0.187130120 #> Kdr      -0.0001065728 -0.1522020960 -5.818851e-02  0.1216971770 -0.238345695 #> Kcnj8    -0.0373977761  0.0007711152 -7.692070e-02  0.0047830671 -0.014409797 #> S1pr3    -0.0179942689  0.0141945645  5.989462e-03 -0.0073935241  0.027838346 #> Tie1      0.0490415738 -0.0221670333 -6.525411e-02  0.0408185329 -0.190912656 #> Pdgfra    0.0568424442  0.0135379883 -2.578229e-02  0.0953814973 -0.094924247 #> Baiap2   -0.0229886967 -0.0334974481  8.064383e-05  0.0166931309  0.023302140 #> Calcrl    0.0146759878 -0.0506724135  1.157563e-02 -0.0664675326  0.015409180 #> Adrb2     0.1702886789 -0.0187340267  1.710123e-02  0.0419787429  0.106784215 #> Ccr2     -0.0163637115 -0.0921578924 -5.424001e-02 -0.1957791164 -0.059604232 #> Alk      -0.0091945410 -0.1207342981 -1.613326e-02  0.0259093232  0.015274026 #> Tacr3     0.1166453990 -0.1094358701  9.404744e-02 -0.0297390133  0.065286282 #> Erbb3     0.0504126446 -0.0813916892 -2.597030e-02 -0.0519744464  0.029246012 #> Pcdh15   -0.0137964915  0.0069633706  5.482266e-03 -0.0390587648  0.005226138 #> Grm7     -0.0789824401 -0.0387842261  3.279386e-02 -0.0034453666  0.054725745 #> F2r       0.0002731697  0.0850207656  6.741221e-02 -0.0681855080  0.122440116 #> Bdkrb2   -0.0293343803  0.1707003683 -2.598696e-01 -0.0629872847 -0.057508695 #> Adgrv1    0.0776992061 -0.0166361826 -3.535026e-02 -0.0723248882  0.068710615 #> Gprc5c   -0.0603997950 -0.0022632305 -5.038082e-02  0.0151884955 -0.014245735 #> Tbxa2r    0.0441911551  0.0700651325 -8.228275e-02  0.0202017055  0.154505812 #> Ackr1     0.2846627471 -0.0262780963 -1.053864e-01  0.1223092467 -0.094425835 #> Lpar2    -0.0299119081  0.1651707475  2.160898e-03 -0.0478955122 -0.083232676 #> Myh11     0.0548558494  0.0488557813  1.186295e-01  0.0534110707  0.027524435 #> Musk      0.0487086457  0.0284900644 -2.977132e-03 -0.0276613413 -0.027360978 #> Cnr1      0.0812875540 -0.1086635698 -8.253053e-02  0.2155287355 -0.120389805 #> C3ar1     0.0014665066  0.1555176354  7.966131e-02  0.0598280122 -0.130643545 #> S1pr4     0.0074997616  0.1078870436  8.636952e-02  0.0984612487  0.100035616 #> C5ar1    -0.0107388057 -0.0243464893  2.381740e-02  0.1464612196 -0.122396115 #> Fpr1     -0.0194940999  0.0407137532  1.569073e-01  0.1197729073  0.046365118 #> Sctr     -0.0498048556 -0.0484184472  6.695343e-03 -0.0508495242  0.055967438 #> Gpr158   -0.0306629755 -0.0284880958  3.781557e-03  0.0290347186  0.025185048 #> Cxcr4    -0.0208451388 -0.0238596036  1.731148e-02  0.0177518523  0.043120715 #> Hrh2     -0.0392549625  0.0034152926  9.768157e-03  0.0272326808  0.006284775 #> Slc17a6  -0.0685068391 -0.0232995367  7.812815e-03  0.0252356233  0.019338479 #> Ppp1r3g  -0.1146618589  0.0481419552  9.165347e-02  0.1199346583  0.067176668 #> Pln       0.0377710810  0.0214811455  9.177542e-02  0.0642456846  0.015404950 #> Grin2b   -0.0189247989 -0.0240678424  3.032638e-02 -0.0284279563  0.028220773 #> Taar7e    0.0746391677 -0.0467185618  4.526955e-02 -0.0025209992 -0.011327564 #> Ptger2   -0.0513065600 -0.0282519419 -2.183082e-03  0.0283308709  0.054729800 #> Mc4r      0.0040838607  0.0148713775  2.407896e-02  0.0473205192  0.062254269 #> Ghsr     -0.0429698126  0.0905348676 -7.673134e-03 -0.0353486070 -0.084151681 #> Nmbr      0.0007378491  0.0167915444  4.181913e-02 -0.1192725539  0.039587431 #>                 Dim.26       Dim.27       Dim.28        Dim.29        Dim.30 #> Mlc1      0.0878326009 -0.031554386 -0.052232152  0.0609383219 -4.327478e-02 #> Gprc5b    0.0266762043 -0.039531707 -0.049043569  0.1104838027 -6.467555e-02 #> Gfap     -0.0494719092 -0.017458645 -0.043128027  0.0081429937 -8.251075e-05 #> Ednrb    -0.0530457336 -0.148733210  0.065974757  0.0499350757  3.389917e-02 #> Sox9     -0.0672063613 -0.162932025  0.051151747 -0.1020523191  3.874905e-01 #> Aqp4      0.0592358591  0.030184146 -0.028689560  0.0506476477 -2.481883e-01 #> Gjc3      0.0357945574  0.003202220 -0.006444576  0.0485987561 -8.312943e-02 #> Sox8     -0.0188897330 -0.078855629  0.092491484 -0.0559746829  9.558878e-02 #> Ntsr2     0.0504637656 -0.176450341  0.055451770  0.0134966856  3.486750e-02 #> Smo       0.0453936042  0.023671510 -0.065132998 -0.2113907017 -4.484915e-02 #> C1qb     -0.0215946649 -0.101322647  0.085774897 -0.0819027638 -8.131109e-02 #> Olig1     0.0247423562 -0.085746692  0.076348594  0.0527235675 -3.159326e-02 #> C1qa      0.0590101044  0.032300526  0.020531352  0.0658019746  6.004304e-02 #> Pth1r     0.0793276583 -0.005238304  0.001428507  0.0212095978 -3.044433e-02 #> Gabbr2   -0.0305160056 -0.118445617 -0.067985257  0.0499118246  3.474506e-02 #> Timp4    -0.0493329144 -0.041776903  0.153002613 -0.0330770783  1.500863e-01 #> Abcc9    -0.0757869797  0.037515666 -0.055190640  0.0064512197  5.241319e-02 #> Csf1r    -0.0131894640  0.000217194 -0.077239650  0.1476638797 -4.309852e-02 #> Ntrk2     0.0163004913  0.055111531 -0.074643734 -0.0237210294 -7.040035e-02 #> Adgrg1   -0.0058308493  0.016603641  0.026238851 -0.0101407289 -2.807227e-02 #> Ntrk3     0.0943404860 -0.019256972  0.042941248 -0.0488731366  7.731345e-04 #> Erbb4    -0.0064517986 -0.010028324 -0.008534764  0.0249517081  4.463517e-02 #> Selplg   -0.0062924933 -0.075122971  0.056811882  0.0051738475 -2.786504e-02 #> Cspg5     0.0857373544  0.138007454 -0.148216221 -0.0310079249 -1.113713e-01 #> Dlk1      0.1781898410  0.314953528 -0.054369871 -0.0981283513  2.856689e-01 #> Gpr37l1  -0.0360816617  0.105188454  0.041953590  0.0340459382 -1.103544e-01 #> Fgfr3     0.0168849115 -0.054696630  0.010630278 -0.0264946717  5.159248e-02 #> Slc25a18 -0.0407008927 -0.066576135  0.063476504 -0.0941031416  1.169619e-01 #> Igf1r     0.0989874486  0.031592682  0.034262069 -0.0011935919 -6.570448e-02 #> S1pr1    -0.0067576752 -0.035319043  0.003840092  0.0147899280  1.971587e-02 #> Grm5      0.0668234244 -0.136042051 -0.100133227  0.0216725130  1.294152e-03 #> Axl      -0.1348052408 -0.124081403  0.168227653  0.0894831268 -6.117716e-02 #> Efemp1   -0.0152696437  0.045425742  0.004004264  0.2139556479  2.870743e-02 #> Adgrb3    0.0388614971  0.051592324 -0.149109419 -0.0429966570  3.560675e-03 #> Fn1       0.0335436994 -0.082264286  0.039691909  0.1343236923 -7.331423e-02 #> Mertk    -0.0369605346  0.115825408 -0.079525691  0.0823553238  1.518291e-01 #> Adgrl2   -0.3031091437  0.028781274 -0.207955907  0.0745953458 -6.911698e-02 #> Fzd2     -0.0196474015  0.018704715 -0.023720686 -0.0322295596 -3.000988e-02 #> Aldh1l1  -0.0263065087 -0.060703639 -0.018103907 -0.0417042691  1.716239e-01 #> Adgrg6    0.0361455668  0.003214755  0.047600691  0.0045602572  1.369179e-01 #> Egfr      0.0280105881 -0.011982193  0.016522429  0.0212010703  7.916745e-02 #> Kit       0.0972844998 -0.092067037 -0.034762412 -0.1832517095 -4.940600e-03 #> Ptgdr     0.1345251674 -0.000972766  0.051564822 -0.1181973448  7.937212e-03 #> Gad1      0.0024803734 -0.194092523 -0.192166030  0.0670521660  1.304732e-02 #> Tyro3    -0.0493684085 -0.050504987  0.023277967  0.0372930755 -1.383876e-01 #> Atp13a5   0.1102318274  0.024697697  0.009097302  0.2381686049  3.128646e-02 #> Ddr2     -0.1446549432 -0.027029968  0.068535023  0.1285995983  5.105404e-02 #> Rspo3     0.0383895382 -0.035471854  0.031994932 -0.0143180908  3.120201e-02 #> Arhgap29 -0.1331337804  0.019387670 -0.037186917 -0.0970775070 -1.215439e-02 #> Fzd7     -0.0528645423 -0.011210582 -0.099259268 -0.1107655688 -5.502641e-02 #> Slc47a1   0.0685560012  0.004504328 -0.049894809 -0.1428134117  1.662631e-02 #> Ptger3   -0.1149578447 -0.042873330  0.106208116 -0.3370559455 -9.293049e-02 #> Bdkrb1   -0.1680616312 -0.011605796 -0.161110710 -0.0197742199 -1.050297e-01 #> Traf4    -0.0630089584 -0.027047711 -0.017562959 -0.0463541917 -9.093199e-03 #> Cx3cr1    0.0366827055  0.108030351 -0.128763735 -0.0418743908  2.729474e-02 #> Anxa11   -0.0863467963 -0.041412179  0.061795794 -0.0759335373  4.787142e-02 #> Adgrb1    0.0549825835 -0.008844257  0.051408140 -0.0631193365  4.643709e-02 #> Lpar1     0.0137152954  0.055999299  0.061006148  0.0858385591  2.524876e-04 #> Gpr17    -0.0223114865  0.018027367  0.030622844 -0.0183894958  6.041809e-02 #> Cxcl12   -0.2963198493  0.043134523 -0.119446216  0.0622156948  1.554433e-01 #> Epha4     0.0111556311  0.027688422  0.003784837  0.0138894000 -6.321837e-03 #> Gpr182    0.2007643471  0.035824747 -0.036956261 -0.0773790951 -7.640493e-02 #> P2ry14   -0.2364683506 -0.019830170  0.038821070 -0.1339712090 -5.014946e-02 #> Hcar1     0.1225357064 -0.041110950  0.050346020 -0.1285632251 -4.310207e-02 #> Ephb1    -0.0236999760  0.021289044 -0.054030447 -0.0610688352  5.894711e-02 #> Grm3     -0.0782805813  0.086986043 -0.129667389 -0.0813163748 -6.732860e-02 #> P2ry1    -0.0511806935  0.045476010 -0.002367790  0.1490886369  1.694638e-01 #> Ptk7      0.0798616091  0.070500912  0.026882353 -0.1466074254  9.984724e-02 #> Slco1a4  -0.2864905757  0.101842785 -0.010535223 -0.0650067902 -6.822307e-02 #> Insrr     0.0601051358 -0.035821179  0.025679008  0.0488050424  5.633710e-02 #> Cmklr1    0.0107302382 -0.085659926  0.006279165 -0.0012097785 -1.436438e-02 #> Fzd6     -0.1425180046  0.061246515 -0.147816959 -0.1041921465 -2.410132e-02 #> S1pr5    -0.0506516216  0.017536520 -0.044307381 -0.0790472463  9.719188e-02 #> Pdgfrb    0.0125975243 -0.051232736 -0.086742556 -0.0484353510 -2.149450e-03 #> Flt1      0.1653240781 -0.075068582 -0.050347023  0.0651332978  1.794405e-02 #> Adgrl4    0.1435699479  0.078051246  0.158031934  0.0742145348 -1.074896e-03 #> Lpar6    -0.0222805323 -0.012269824 -0.008655777 -0.0573717230 -5.333696e-02 #> Epha6     0.0159374398 -0.032846947  0.072974666  0.0203934005 -1.367737e-02 #> Emcn      0.0952552735  0.040602359  0.097512203  0.1253907961  2.392048e-03 #> Cldn5     0.0082470676 -0.060041113 -0.053222653 -0.1486896343 -9.740433e-02 #> P2ry12   -0.0337505895 -0.064679455  0.033735272 -0.0276427592 -2.588625e-02 #> Adgrf5    0.0375343520  0.031342987  0.084864311 -0.0314227372  9.929285e-02 #> P2yr13   -0.0363893658 -0.079012939  0.090692759 -0.0009564144  3.512341e-02 #> Adgre1    0.0201581756  0.114743529 -0.058297038 -0.0811050654  3.813620e-02 #> Cx3cl1   -0.0533999581 -0.045979008 -0.044004851  0.0333713394 -8.758802e-03 #> Plxnb3    0.1341216837  0.171633978 -0.001815338 -0.1323667363  3.091820e-01 #> Flt4     -0.0561713369  0.015003327 -0.030172469 -0.0689513385 -6.067844e-02 #> Slc17a7  -0.1062673986 -0.029563099 -0.042975586  0.0216234961 -1.287816e-02 #> Cd300c2  -0.0379306242 -0.069730519  0.031819664 -0.1032123642  7.221290e-02 #> Tek       0.0483088968 -0.064006036  0.048860425  0.0906851316 -3.534582e-02 #> Kdr       0.0440265375 -0.062007461  0.004704177  0.0951282602  1.219989e-01 #> Kcnj8    -0.0753363763 -0.002278412 -0.070268701 -0.0531139703  3.043310e-02 #> S1pr3    -0.0288632831 -0.006001427 -0.021149635 -0.0336954404 -1.976000e-03 #> Tie1      0.0593750107 -0.066463298 -0.054573535  0.0039347637  1.054054e-02 #> Pdgfra    0.0966501397  0.072571474 -0.127076991  0.0151140353  1.331437e-02 #> Baiap2    0.0430865137 -0.068162152 -0.022952534  0.0028469305  3.222641e-02 #> Calcrl   -0.0183297629  0.032420069 -0.003017751  0.1557521916  6.885191e-02 #> Adrb2    -0.0497672651 -0.022470164  0.013146006  0.1804478675  1.209893e-02 #> Ccr2     -0.0538249124 -0.112410077  0.100603060 -0.0738814919 -8.365261e-02 #> Alk       0.0571780616  0.015428745 -0.001127190  0.0187479256  3.411386e-02 #> Tacr3     0.0581946328 -0.023971821 -0.076696685 -0.0818014747 -6.075309e-02 #> Erbb3    -0.0370666800 -0.006967861 -0.014557870 -0.0804474115  1.351229e-01 #> Pcdh15    0.0355974063 -0.032915103 -0.030134878 -0.0367493327  1.059245e-02 #> Grm7      0.0947724949  0.019858967  0.086543510  0.0362762156 -1.441902e-02 #> F2r      -0.0593552348  0.099757387 -0.041277910  0.0043312184  7.406235e-03 #> Bdkrb2    0.0414940104 -0.075858743  0.147780599 -0.0054418456 -3.582223e-02 #> Adgrv1    0.0349501476  0.018624239  0.002272959 -0.0354309548 -2.592842e-02 #> Gprc5c    0.0410839680  0.016269325 -0.026757826 -0.2465729600 -4.951070e-02 #> Tbxa2r    0.1527418870 -0.124352484  0.194509097 -0.1089740480 -9.541720e-02 #> Ackr1    -0.0717578364 -0.109322320 -0.057032195  0.0508922219  1.486985e-01 #> Lpar2    -0.0280515870  0.059642931 -0.037260877  0.1649670014  4.967281e-02 #> Myh11     0.0063646923  0.048941311 -0.050283091  0.0200373312  3.512964e-02 #> Musk     -0.0045792218  0.008050093  0.069816603  0.0292692270 -1.254557e-02 #> Cnr1     -0.1830336117  0.475317766  0.420329340 -0.0044069128 -8.615662e-02 #> C3ar1     0.0813728777  0.198159289 -0.255695077  0.0009797477 -1.036759e-02 #> S1pr4    -0.0203591492  0.096305901 -0.133002377 -0.0003491943 -2.967056e-02 #> C5ar1     0.1262845220  0.056913353 -0.109911244  0.0759594366  1.227053e-01 #> Fpr1      0.1051174552  0.054466506 -0.034666716 -0.0538367837 -9.876932e-02 #> Sctr      0.0298647435  0.013300436  0.027415609 -0.0095308161 -6.271336e-02 #> Gpr158    0.0027107531  0.011647145  0.087454663  0.0338829917 -7.746748e-03 #> Cxcr4     0.0033865260 -0.083185096  0.013639883  0.0035759456  2.864629e-02 #> Hrh2      0.0103471336  0.026383435  0.075884162  0.0206014597 -2.660904e-02 #> Slc17a6  -0.0008164387 -0.085923213  0.041082598 -0.0233140484 -1.242422e-02 #> Ppp1r3g  -0.1384504309 -0.099999760  0.036140294 -0.0796807691  2.628760e-01 #> Pln       0.0445109637 -0.014511131 -0.002485981  0.0051608577  4.888129e-02 #> Grin2b    0.0144133022 -0.030925128 -0.006750256  0.0361246426 -2.548812e-02 #> Taar7e   -0.0124750682 -0.031609189 -0.009036898 -0.0059682948  3.014806e-04 #> Ptger2    0.0764166989  0.093908008  0.112207441 -0.0096151290 -3.695083e-02 #> Mc4r      0.0472528642  0.072213711 -0.077193292 -0.0270830176  3.346141e-03 #> Ghsr      0.0052447572 -0.051142392  0.053817262 -0.1259749510  4.283643e-04 #> Nmbr      0.1145647537 -0.222794650 -0.228934077 -0.0086525620 -2.723308e-02 #>                Dim.31        Dim.32        Dim.33        Dim.34        Dim.35 #> Mlc1      0.046828468 -0.0598006726  2.728154e-02 -0.0447370101  0.0494032685 #> Gprc5b    0.043139566 -0.0645482478 -4.625959e-02 -0.1079741072 -0.0032662485 #> Gfap     -0.084451969  0.0189433844  7.755266e-02  0.0284905859  0.0887666941 #> Ednrb    -0.039601795  0.0165999322  1.015626e-02  0.0763068193  0.0267904621 #> Sox9     -0.006622427  0.0753248866  5.675914e-03 -0.1282415159 -0.0636306132 #> Aqp4      0.057116490 -0.0190713689 -5.925918e-02 -0.0139270737 -0.0245126799 #> Gjc3      0.013838298 -0.0216097008  2.018414e-02  0.0688803634 -0.0659016395 #> Sox8     -0.039792363  0.1001053422  4.248161e-02  0.0892288804  0.0159415039 #> Ntsr2     0.026916552  0.1789323057  8.604315e-02  0.1125314756 -0.1358046150 #> Smo      -0.019469457  0.0586247767  6.891104e-03 -0.0333074462  0.0279408821 #> C1qb      0.012424437 -0.0150347314 -7.047393e-02 -0.0418619337  0.0062502262 #> Olig1     0.066097899  0.0351040968 -8.447867e-03  0.0233609796  0.0013404769 #> C1qa      0.082729243 -0.1669126528 -7.458389e-03  0.1849357542 -0.0376629693 #> Pth1r     0.121885666  0.0380139862 -2.840862e-02 -0.0002658282 -0.0791146653 #> Gabbr2    0.090371961  0.0372215327 -1.220097e-01  0.0435938288 -0.0009317162 #> Timp4    -0.086464280  0.0933513361  4.923471e-02  0.0253984833  0.1920992832 #> Abcc9    -0.084384393 -0.0610777513  5.785971e-02  0.0807878971 -0.0338071616 #> Csf1r    -0.152633159  0.0473608548  4.269237e-02  0.1128218638 -0.0583104455 #> Ntrk2    -0.063591663 -0.1392178360 -4.827163e-02 -0.1001359086 -0.1637454518 #> Adgrg1    0.049207360 -0.1073650837 -8.895728e-02 -0.0377169187 -0.0318250457 #> Ntrk3    -0.111887148 -0.0711837646  4.267670e-02  0.0082900974 -0.1252205428 #> Erbb4     0.025227279 -0.0178451823 -1.220885e-02 -0.0374746419 -0.0142466855 #> Selplg    0.081529945 -0.0201341489 -1.323207e-02 -0.0154868793  0.0379776326 #> Cspg5     0.089496955 -0.0694036862  3.120273e-02 -0.0360626007  0.0188246325 #> Dlk1      0.149039116 -0.1877217986 -1.643182e-01 -0.0652078950 -0.0561248429 #> Gpr37l1  -0.024429701 -0.1005289171 -8.153428e-02 -0.0329499715  0.0363414821 #> Fgfr3     0.019317224 -0.0497822886  2.938358e-02  0.0011134531  0.0805321248 #> Slc25a18 -0.050743001 -0.0296061196  2.556011e-02 -0.0433518931 -0.2193483209 #> Igf1r    -0.076530319 -0.0062404586 -4.564518e-03 -0.0197511675 -0.0701019182 #> S1pr1    -0.021106526 -0.0134251511 -6.357475e-02 -0.0125899223  0.1420520110 #> Grm5     -0.234083083 -0.0954584451 -3.330167e-02  0.0028860124 -0.1660879724 #> Axl       0.044156482 -0.0599993938  1.419222e-02  0.0309315854 -0.1077802711 #> Efemp1   -0.063266484 -0.0088457345  9.670566e-02  0.0566883551  0.0119269021 #> Adgrb3   -0.153774463 -0.0635340697  9.247846e-03  0.1384534955  0.2085176516 #> Fn1      -0.021249829  0.1305903254  4.301929e-02 -0.1323524685 -0.1096978955 #> Mertk    -0.102921918  0.1281939202  1.623788e-01  0.2094871600  0.0207791043 #> Adgrl2   -0.007860873 -0.0021973300  5.234147e-02 -0.1777774342  0.0409187098 #> Fzd2      0.030239235  0.0124965190 -2.269772e-02 -0.1275234384  0.0133330593 #> Aldh1l1  -0.035923302  0.0644376425  1.734290e-02 -0.0587820633  0.0835981892 #> Adgrg6    0.069634243 -0.0587408715 -5.638447e-02  0.0099802747  0.0025818605 #> Egfr     -0.016326186 -0.0320479785 -6.859912e-05  0.1188884863  0.0085784392 #> Kit      -0.108737744  0.0852250667  9.599120e-02  0.1831727742 -0.1136392621 #> Ptgdr     0.019292896  0.0063555982 -4.826008e-02  0.0236474095  0.0269023481 #> Gad1      0.079657186 -0.0686074025 -4.335263e-02 -0.0771170862  0.0970554815 #> Tyro3     0.007539715 -0.0473039552 -3.568943e-02  0.0048044510  0.0286580500 #> Atp13a5  -0.006673755  0.0406455961  3.314240e-02 -0.2153231253  0.0201205947 #> Ddr2     -0.050036007 -0.0780244812  2.745486e-02  0.0928642216  0.1728063915 #> Rspo3     0.076118504  0.0238444237 -1.971699e-02  0.0677722837  0.0314639576 #> Arhgap29  0.012956082 -0.0694323961 -4.035540e-02  0.0135653452 -0.0120986106 #> Fzd7      0.014305674  0.1149147747  7.358168e-02  0.0346162309  0.0129175265 #> Slc47a1   0.012151578 -0.0831412240 -5.128258e-02  0.0155157148  0.0398152983 #> Ptger3   -0.058215780 -0.1489129512 -1.210736e-01  0.1115972400 -0.0120655440 #> Bdkrb1    0.067141336  0.0172753971 -1.802968e-02 -0.2273791512 -0.0992594890 #> Traf4    -0.011866296  0.0004981121 -4.951589e-03 -0.0912585027 -0.0355982296 #> Cx3cr1    0.024277900  0.0352343790 -1.212546e-03 -0.0963795964  0.0462792154 #> Anxa11   -0.002117323 -0.1968707311  1.251938e-01  0.0670237421 -0.1275454963 #> Adgrb1   -0.173912641 -0.1415132139  1.644371e-01 -0.1000261924 -0.1520951604 #> Lpar1     0.038127523 -0.2163020820 -9.496572e-02  0.0329034433  0.0638695741 #> Gpr17    -0.026323726  0.0388872221 -9.339464e-03 -0.0058489438  0.0379973241 #> Cxcl12    0.069416771  0.0506034263 -9.995949e-02  0.0425253996  0.0201389086 #> Epha4     0.056675874  0.0129259063  3.203585e-03  0.0179203115  0.0701734213 #> Gpr182    0.007513760  0.0845145986  9.137210e-02  0.0456192044  0.0147780005 #> P2ry14   -0.103551340 -0.1744112679 -5.322856e-02  0.1540049073  0.0163092480 #> Hcar1    -0.012512550  0.0870098305  2.631313e-03  0.0591000044 -0.0549805473 #> Ephb1    -0.064536802  0.0954271249  9.844991e-02  0.0572161968 -0.0388351299 #> Grm3     -0.035388021 -0.0259657636  2.541851e-04  0.0579422133  0.1305167588 #> P2ry1    -0.039865513 -0.0867544513 -1.093052e-02 -0.0094270283 -0.1347780920 #> Ptk7     -0.148622402 -0.0032059121 -7.716997e-02 -0.0435938209  0.1875523254 #> Slco1a4  -0.009672401 -0.0766497669 -5.563207e-02  0.0127129950  0.0216604487 #> Insrr     0.041762445 -0.0735588622 -1.072453e-02  0.0344998779  0.0853711705 #> Cmklr1   -0.073411183  0.0729766849  3.692986e-02  0.0334058808  0.0186064318 #> Fzd6      0.048545810  0.0841069983  4.021975e-02 -0.0765074943 -0.3001476592 #> S1pr5     0.003558514  0.0183656052  2.431260e-02 -0.0456651753 -0.0083827503 #> Pdgfrb    0.095926352  0.0462783166 -4.922459e-02 -0.1033001766  0.0362304442 #> Flt1     -0.012908200  0.0201207566  2.591138e-02 -0.0023468483 -0.0997050023 #> Adgrl4    0.109940514  0.1702367828  1.635577e-02 -0.0102367887 -0.1158632033 #> Lpar6    -0.176544128  0.2254068050  3.661908e-02 -0.1176513654 -0.0090381637 #> Epha6    -0.025988125 -0.0540053868  1.431176e-01 -0.1163527588  0.0928768639 #> Emcn      0.065982344  0.1227126807  6.668498e-02 -0.0217861866  0.0412138114 #> Cldn5    -0.069025765 -0.0435180826  2.949371e-02 -0.0016895091  0.1635148788 #> P2ry12   -0.023892123 -0.0160430920  1.215217e-02 -0.0679104842  0.0217107768 #> Adgrf5    0.065615569 -0.1000101407 -3.363524e-03  0.0902798957  0.0492302079 #> P2yr13    0.081844806 -0.1299638028 -5.584187e-02  0.0512208005 -0.0410498812 #> Adgre1    0.022579107 -0.0041167572  6.838308e-02 -0.1287046926  0.0487000771 #> Cx3cl1    0.220527393  0.0780650401 -1.431374e-02  0.0131880459  0.1633746357 #> Plxnb3    0.138582381  0.0010790332 -8.468542e-02 -0.0441258190 -0.0894258803 #> Flt4     -0.022974074  0.0076688861 -2.626752e-02 -0.0505514850 -0.0654974113 #> Slc17a7   0.300845666  0.1582499632  2.062201e-02  0.1066829830  0.0546577076 #> Cd300c2  -0.035958983  0.0981355804  8.655646e-03 -0.1665114222 -0.0190512954 #> Tek      -0.039842924  0.0342239248  1.347741e-03  0.0026123442  0.1472952488 #> Kdr      -0.020023374 -0.0874993765 -4.948848e-02  0.0556506639 -0.0064641496 #> Kcnj8    -0.059145594 -0.0433822437  6.304247e-03  0.0736169850 -0.0416797079 #> S1pr3    -0.008363763  0.0283323618  3.141338e-02  0.1134452541 -0.0397475771 #> Tie1     -0.019658018 -0.0394992963 -3.931671e-02  0.0194922677 -0.0953385382 #> Pdgfra   -0.040746646 -0.0797455783  1.714363e-02 -0.0865522199 -0.0509739034 #> Baiap2   -0.060755466 -0.0232509619  1.864062e-02 -0.0520752461  0.0255375312 #> Calcrl   -0.010114340 -0.1490642491  3.701947e-02  0.0965929504  0.0808241665 #> Adrb2    -0.042443886  0.0457706002  1.095481e-01  0.0394581013 -0.0804562647 #> Ccr2      0.052244168  0.0349708865 -6.291725e-02 -0.1560912744  0.0007372440 #> Alk       0.002457115  0.0193345489  6.111945e-02  0.0954399201  0.0496196240 #> Tacr3     0.063014434  0.0090085198  8.880871e-02  0.1086158422  0.0087241236 #> Erbb3    -0.035547031  0.0156821802  2.053372e-02 -0.1219785893 -0.0152604550 #> Pcdh15    0.015756330  0.0416455279 -3.092840e-02 -0.0184354526  0.0008065560 #> Grm7     -0.363749647 -0.0996376725 -7.967975e-02 -0.1242796748 -0.0816284023 #> F2r      -0.035856448 -0.0233279613  6.984108e-02  0.0959805202  0.0058801195 #> Bdkrb2    0.047983723 -0.0300023848 -1.814729e-01 -0.2887648702  0.1216281904 #> Adgrv1   -0.020518436  0.0127412933  4.092209e-02  0.0724540105  0.0447967700 #> Gprc5c    0.024902804  0.0877821129 -2.039111e-02  0.0615017823  0.0072692591 #> Tbxa2r    0.101752456  0.0637760717 -5.673629e-02  0.0118845179  0.0227262969 #> Ackr1    -0.064746410  0.0695407938 -1.187198e-02 -0.0904984610 -0.0710609276 #> Lpar2    -0.125029267  0.0204099466  3.052365e-02 -0.0438830232  0.0037824978 #> Myh11     0.091560936 -0.0414864920 -1.467731e-02 -0.0157910353 -0.0773840292 #> Musk     -0.014367541 -0.0698388453 -2.087723e-02 -0.1051635181  0.0750837693 #> Cnr1     -0.028825368  0.1360820946  8.153354e-02  0.0042860682 -0.0613969703 #> C3ar1    -0.107270182  0.1829165121  4.049878e-02 -0.0819728312  0.0598627527 #> S1pr4    -0.010424609  0.0573312489  3.275797e-02  0.0039531567 -0.0286053617 #> C5ar1     0.010422077 -0.0961241976  1.629990e-02  0.0317985102  0.0618174150 #> Fpr1     -0.016006759  0.1021449753  4.216517e-02  0.0487268964  0.0491982198 #> Sctr     -0.007395809 -0.0195678116  1.143698e-02  0.0155668037  0.0965021426 #> Gpr158   -0.116567139 -0.0108367875  3.243604e-02 -0.0712450487  0.0089005696 #> Cxcr4     0.013367688 -0.0067748190  2.585866e-02  0.0018319666 -0.0134507343 #> Hrh2     -0.139398040 -0.0291304104 -5.949163e-03 -0.0481852135 -0.0997687187 #> Slc17a6  -0.004612063  0.0630069893  3.650120e-02  0.0082822799  0.0213399951 #> Ppp1r3g  -0.080239074  0.1485934844 -8.515849e-03 -0.0923543880  0.1760423755 #> Pln       0.064400597 -0.0366968064 -2.027069e-02 -0.0219495922  0.0470307311 #> Grin2b   -0.048447452  0.0027897013 -8.976805e-02  0.0577922127 -0.0844752800 #> Taar7e   -0.008864837 -0.0358847537  2.822804e-02  0.0176690791 -0.0261339415 #> Ptger2   -0.254762975 -0.0129889699  8.403887e-03 -0.1382598346  0.3049073902 #> Mc4r      0.003322849  0.1230615140  6.443982e-02  0.1014378478  0.0310941899 #> Ghsr      0.215464544 -0.2932875291  7.425669e-01 -0.1957352497  0.0696802111 #> Nmbr     -0.106036672 -0.1269402661 -1.176558e-02  0.0450735836  0.0620510011 #>                 Dim.36       Dim.37        Dim.38        Dim.39        Dim.40 #> Mlc1     -0.0184651881 -0.030304498 -0.0160638709  0.0416501378  5.361885e-02 #> Gprc5b   -0.0939820092 -0.008529965  0.0350760268 -0.2553544395 -1.522452e-01 #> Gfap      0.0262586593  0.072650046  0.0113510685 -0.0715659259  9.849332e-02 #> Ednrb     0.0982531407 -0.104714980  0.0500510838 -0.1137377850 -1.269958e-01 #> Sox9     -0.0371162158 -0.151044779  0.1472019918 -0.0006830817 -1.397952e-01 #> Aqp4     -0.0390975216 -0.029896340 -0.0782866404  0.1162288178 -1.292995e-01 #> Gjc3      0.0468822349 -0.108358110 -0.1102798835  0.1361553064 -6.362949e-02 #> Sox8     -0.0601223808  0.060710974 -0.0614759031  0.1619193810  1.584736e-01 #> Ntsr2     0.1232741324  0.225969719  0.2488331589  0.0844487918  1.063193e-01 #> Smo      -0.0840642444  0.031353996  0.0023371307 -0.0484884572 -3.846325e-02 #> C1qb      0.0497127529  0.023999045 -0.0125238911 -0.0884486690  1.314621e-02 #> Olig1     0.0020762266 -0.047091326 -0.0503973505  0.0003963190 -6.083122e-02 #> C1qa      0.0754253599 -0.130997264  0.0978677252 -0.0278780722  2.200412e-02 #> Pth1r    -0.0030838041 -0.121727640  0.0059440802  0.0256618653 -3.905047e-02 #> Gabbr2    0.0808922385 -0.002790812  0.0233899836  0.0168918251  1.057552e-02 #> Timp4    -0.1270588590 -0.100894925 -0.1736479716 -0.0504274565  2.340758e-02 #> Abcc9     0.0187054444  0.011617286  0.0263868077 -0.0053857508 -1.218239e-01 #> Csf1r     0.1318275669 -0.163527135 -0.0838633215 -0.0052300633 -5.196351e-02 #> Ntrk2    -0.0398631515  0.085021496  0.0212158985  0.0415714242  4.249104e-02 #> Adgrg1   -0.0976986661 -0.012428502 -0.0988359397  0.1831834716 -4.760026e-02 #> Ntrk3    -0.0639744569  0.060570611  0.0078495448  0.0142525062  3.130265e-02 #> Erbb4    -0.0167264390 -0.016592544  0.0789511757  0.0093986326  7.037000e-02 #> Selplg   -0.0341170962  0.002527291 -0.0067316310  0.0186744185 -1.170480e-02 #> Cspg5     0.0680101482 -0.054979539  0.1151432372 -0.0593981661 -1.510112e-01 #> Dlk1     -0.0353745449 -0.218198801 -0.0375729362 -0.0670524620  3.335269e-02 #> Gpr37l1  -0.1523234693 -0.086291714 -0.2568447779  0.1904020485  5.128738e-02 #> Fgfr3     0.0642415927 -0.006308800 -0.0259544162 -0.1127973279  1.599982e-02 #> Slc25a18 -0.0465369947 -0.043853335  0.1848435107  0.1450936692  8.717011e-03 #> Igf1r     0.0399526150  0.026603673 -0.0788252706 -0.0306618990  7.775312e-02 #> S1pr1    -0.0325449201 -0.177263266 -0.2322677195 -0.1147150551  1.007809e-01 #> Grm5     -0.2516548488  0.018275587 -0.0514854108 -0.1098154125  2.549782e-02 #> Axl       0.0904061274 -0.078917037 -0.0569383991  0.0040041984  3.185887e-02 #> Efemp1   -0.0582386384 -0.020314725  0.0286624622  0.1112548354  6.487451e-02 #> Adgrb3    0.2126002272  0.018012550 -0.0611417626 -0.2114866671  1.160864e-01 #> Fn1       0.0234489932 -0.100600776 -0.0637769322 -0.0800411776  3.423702e-03 #> Mertk    -0.0220847008  0.048399868  0.0012613628 -0.0230931269 -5.811036e-02 #> Adgrl2   -0.1018121809 -0.039244339  0.1214987147  0.0966271918  6.848295e-04 #> Fzd2      0.0630975631  0.066823082 -0.0439847934 -0.0855735417 -6.062035e-05 #> Aldh1l1   0.0253316439 -0.035522819  0.0749115497 -0.0114900494 -6.626741e-02 #> Adgrg6    0.0537950862  0.241274154 -0.2195531775  0.0683674891 -2.408349e-01 #> Egfr     -0.0449813943 -0.010427737 -0.0072195101 -0.0074096746 -3.434149e-02 #> Kit      -0.0455521661 -0.084265229 -0.0346420438 -0.0145615556 -2.873945e-01 #> Ptgdr     0.0240254379  0.016648187 -0.0082421640  0.0044110074  7.595321e-02 #> Gad1      0.0795709522  0.028364256  0.0256205028  0.0613774902  6.682388e-02 #> Tyro3    -0.0722179570 -0.004041765 -0.0364148299 -0.1265511842 -7.153692e-03 #> Atp13a5  -0.0119193160  0.084586335  0.0006471908  0.0268182075 -7.756046e-02 #> Ddr2     -0.1338285901  0.025562956  0.1088641291  0.0549546481  6.355574e-02 #> Rspo3    -0.0044048184  0.011137614 -0.0138205060  0.0446353461 -2.149552e-03 #> Arhgap29 -0.0037139699 -0.011861371  0.0182434276  0.0652955305  4.654955e-02 #> Fzd7     -0.0502677342 -0.154618812  0.0863160473  0.0409111381 -2.471826e-02 #> Slc47a1   0.0224130779  0.003298689  0.0590472108 -0.0082628625 -4.528392e-02 #> Ptger3    0.0384768157 -0.049609578 -0.0071401496  0.0388993023  1.089749e-02 #> Bdkrb1    0.0270953361  0.009568066 -0.0759762411 -0.0072058860 -1.084141e-01 #> Traf4     0.0296824167 -0.016055322  0.0370464471  0.0136527758 -1.314091e-02 #> Cx3cr1   -0.1636810075  0.018512548  0.0386548891  0.1218234193  1.213436e-01 #> Anxa11    0.0508793245  0.023968906 -0.0667699889  0.0577319260  6.406210e-02 #> Adgrb1   -0.1725663835 -0.018179117 -0.0451824695 -0.0668524372  8.222429e-02 #> Lpar1    -0.0367472609 -0.116111132  0.1306757422 -0.1388211577 -1.317296e-01 #> Gpr17    -0.0297323810  0.028825072  0.0105482531 -0.0419610908  8.285689e-02 #> Cxcl12    0.0346060269  0.098685686 -0.1628733629  0.0578450895  4.298889e-02 #> Epha4     0.0135408213 -0.025926931  0.0254810852 -0.0050918601 -6.727591e-02 #> Gpr182   -0.0748048751  0.027327328  0.0835617206 -0.0064135173 -2.937942e-02 #> P2ry14   -0.0265676971 -0.174716836  0.1122414679  0.0567899290 -8.275995e-02 #> Hcar1     0.0165664308  0.050496632 -0.1165294466 -0.0351025722  8.169078e-02 #> Ephb1     0.0590708642  0.135181704  0.1128769853  0.0709783108  9.179299e-02 #> Grm3      0.0118479689  0.115666854  0.0235324871 -0.1569341816  1.927289e-01 #> P2ry1     0.1072456043  0.007266877 -0.0472425354  0.0838375817  1.468678e-01 #> Ptk7      0.0823052562  0.036186688 -0.0676373468 -0.0502177537 -3.600953e-03 #> Slco1a4   0.0077821794  0.032812009  0.0538668681 -0.0335722688  8.466779e-03 #> Insrr     0.0381300985  0.045587348  0.0321365280  0.0260483808  2.870478e-01 #> Cmklr1   -0.0740175255 -0.115472686 -0.0577966977  0.0792883802 -2.944634e-02 #> Fzd6      0.2070182469 -0.016673717 -0.2233819981  0.0178819476  3.697770e-02 #> S1pr5    -0.0033012816  0.061338714  0.0764305623  0.0413469057  2.639493e-02 #> Pdgfrb    0.0158029721  0.011404295 -0.1066469405  0.0148675119  1.414339e-01 #> Flt1      0.1009801665 -0.101288027  0.0191020162 -0.0815439050  6.693099e-02 #> Adgrl4    0.1272835024 -0.069567390  0.0804360659 -0.0866085252  1.376898e-02 #> Lpar6    -0.0586611705  0.080686514 -0.0012916598 -0.0274952559 -2.068817e-01 #> Epha6     0.0401898133 -0.015209634 -0.0283085247  0.1162029646 -9.925700e-02 #> Emcn     -0.1110714310  0.015489320 -0.0541160786 -0.0757955706  1.038678e-02 #> Cldn5    -0.1473402691 -0.003748776  0.1145678035  0.1063738699 -3.154296e-02 #> P2ry12    0.0087181022  0.152456837 -0.0246374030 -0.0501469131 -1.167572e-02 #> Adgrf5   -0.0731615024  0.251256309 -0.0753575003  0.1195170426 -2.033394e-01 #> P2yr13    0.0958447599  0.019205108  0.0086681309 -0.0262129339 -1.625402e-02 #> Adgre1   -0.1236192018  0.143904415  0.0104344192  0.0514115871 -5.733619e-02 #> Cx3cl1   -0.0111607015 -0.057099476  0.0367622389  0.0377961096 -1.014273e-01 #> Plxnb3   -0.0580301919 -0.177218373  0.0272946573  0.0619157127 -3.814762e-02 #> Flt4      0.1564807450 -0.049635448  0.0895078862 -0.1678011944  6.297056e-02 #> Slc17a7  -0.0626166295 -0.044459061  0.0484938798 -0.0097180309 -8.290817e-02 #> Cd300c2  -0.0527411828  0.113588822  0.0684308802  0.0530322867 -6.811482e-02 #> Tek      -0.1075037452 -0.181204847  0.1554732761  0.0277579229  9.678577e-02 #> Kdr      -0.0154287112  0.135188283 -0.1020429449  0.0387922063  5.634872e-02 #> Kcnj8     0.0160907110 -0.068873197  0.0285474299  0.0377063746 -5.337167e-02 #> S1pr3     0.0067908368 -0.025080717  0.0175108476 -0.0284456087  5.661047e-02 #> Tie1      0.1751761731 -0.003997850 -0.0373416228 -0.0754304033  3.054548e-02 #> Pdgfra    0.1216957063  0.063385337  0.1436888751 -0.1584631690 -1.639057e-01 #> Baiap2    0.1290711197 -0.037772225  0.0080747252  0.1325683913  9.908312e-03 #> Calcrl   -0.0783124314  0.087704244  0.0471934587  0.0327874872 -1.070924e-01 #> Adrb2    -0.0357940475  0.018562977 -0.0904828555 -0.0090089510 -1.300637e-01 #> Ccr2      0.0252828342  0.090584788 -0.0833943831 -0.0632729178 -1.630121e-02 #> Alk      -0.0492032970  0.019157148 -0.0264414335  0.0416550702  1.255275e-02 #> Tacr3    -0.0535589138  0.004730896 -0.0425153666 -0.0051265568 -9.853447e-03 #> Erbb3     0.0236258806  0.074459182  0.1138411718  0.0812697470 -1.703117e-02 #> Pcdh15   -0.0004332264 -0.035596986 -0.0727413870  0.1276550097  5.727905e-03 #> Grm7      0.0254595499 -0.032995583  0.0297535758  0.0594028503 -2.223731e-02 #> F2r      -0.0211161929  0.153332854  0.0863454750 -0.1951097109 -3.424781e-03 #> Bdkrb2   -0.0157341585  0.023271118  0.1367030101 -0.0248522751  1.484751e-01 #> Adgrv1   -0.0153838170 -0.003352800  0.0724944583 -0.0152677536  1.010589e-01 #> Gprc5c    0.0102780406  0.033180746 -0.0241477500 -0.0110264477  5.397094e-02 #> Tbxa2r   -0.0558196749  0.020794635 -0.0699801286  0.0518509430  7.055661e-02 #> Ackr1    -0.0213723098 -0.148936468 -0.0978936909 -0.0316796292  1.488596e-01 #> Lpar2    -0.0247879032 -0.122258220  0.0836873154  0.0514119058  3.079012e-02 #> Myh11     0.1154721096  0.085550607 -0.0590846312  0.0143622993 -2.695850e-02 #> Musk      0.0388165365 -0.041598096  0.0968544371 -0.0135082858 -4.084980e-02 #> Cnr1     -0.0214784697  0.016354044 -0.0680501854 -0.0844704614 -3.088668e-03 #> C3ar1    -0.0887895541 -0.056778803 -0.0517207885  0.0808060811  1.147404e-01 #> S1pr4     0.0471935318 -0.111264085  0.0106246804 -0.0247261562  2.333620e-02 #> C5ar1    -0.0122438345  0.267574304 -0.0509031489 -0.0755295187 -4.173971e-02 #> Fpr1     -0.0792090017 -0.123477018  0.0769766045  0.0049321412  2.671077e-02 #> Sctr     -0.0196127403 -0.024961104 -0.0077775181 -0.0198646814 -4.114963e-02 #> Gpr158    0.0503474194 -0.031459724  0.0166471130  0.0404700763  5.551943e-02 #> Cxcr4     0.0219997126  0.009940269  0.0754621830 -0.0315285395 -2.099672e-02 #> Hrh2     -0.1401452112  0.033707427 -0.0028436899 -0.1002431670 -3.916837e-02 #> Slc17a6  -0.0034701078  0.006230451  0.0148829739 -0.0309501901  1.716244e-03 #> Ppp1r3g  -0.0016334887 -0.089571735 -0.2226436240 -0.2746964147 -8.193983e-02 #> Pln      -0.0367428755 -0.002472797 -0.0022713359  0.0981751355 -2.531201e-02 #> Grin2b   -0.0899627373  0.035254581  0.0399758963 -0.0229135939  6.190592e-02 #> Taar7e    0.0301153876  0.028150223  0.0011443092 -0.0257971309  3.282681e-02 #> Ptger2    0.4568251485 -0.040841050  0.0250627486  0.2762322424 -1.432585e-01 #> Mc4r      0.1457895275 -0.080847123 -0.0888988041  0.2005187302 -1.070330e-02 #> Ghsr      0.0439222964 -0.091800363 -0.0993547255 -0.0464195668  7.397257e-02 #> Nmbr     -0.0646141507 -0.048184095 -0.2148970819  0.0432620435 -9.744349e-02 #>                 Dim.41       Dim.42       Dim.43        Dim.44        Dim.45 #> Mlc1      0.0643317341 -0.054764478 -0.174173415 -0.0923818740 -5.516297e-03 #> Gprc5b   -0.1021655180 -0.086213482 -0.105730502 -0.2534479133 -4.052155e-02 #> Gfap      0.0740504391 -0.041887867 -0.051935363 -0.0373155836 -2.432162e-03 #> Ednrb     0.0551232520  0.127999610  0.056461436  0.0579064124  2.568717e-02 #> Sox9     -0.0773481265  0.067782335  0.103099053 -0.0506625942 -7.112397e-02 #> Aqp4     -0.0516671195  0.097115387  0.142334263  0.1297990393 -1.181859e-02 #> Gjc3      0.0327259722  0.099922776  0.025632795 -0.0205891646  1.336047e-01 #> Sox8      0.0985313502 -0.112960344  0.025851437 -0.1551140998 -1.326157e-01 #> Ntsr2     0.0785200532 -0.114059990 -0.166204969  0.0204349901 -7.038725e-02 #> Smo      -0.0250814320 -0.038439680 -0.196627335  0.0452529613  1.820839e-01 #> C1qb      0.0212880572 -0.035488603 -0.015494208 -0.0330613409  6.395891e-02 #> Olig1     0.0253190839  0.017203247 -0.054599251 -0.0255273149  8.029054e-02 #> C1qa     -0.0135661511  0.037661404 -0.022047380  0.1568863111 -6.369763e-02 #> Pth1r    -0.0463781685  0.105152855 -0.007516537  0.0006439744 -3.570192e-02 #> Gabbr2   -0.0316439992  0.033223605  0.007232072  0.0014817700  2.633256e-02 #> Timp4     0.0588784958 -0.091471303  0.031377151  0.0583792125  1.494263e-02 #> Abcc9    -0.1109384449 -0.090681367 -0.073249093  0.0462842256  2.509298e-02 #> Csf1r    -0.0362950700  0.281248936  0.033717027 -0.1279655728 -5.613931e-02 #> Ntrk2    -0.1974515406 -0.034326054 -0.042678658 -0.0587749706  6.616282e-02 #> Adgrg1   -0.0383849797  0.048048074 -0.022739842  0.1498210432  1.316412e-01 #> Ntrk3    -0.0009595687 -0.032379267  0.158116075 -0.0451758739 -1.548037e-02 #> Erbb4    -0.0317971617  0.009962084  0.131608987 -0.1085651614  2.160674e-01 #> Selplg    0.0304610903 -0.117080780  0.020348523  0.0619208915  5.391372e-02 #> Cspg5     0.1009722957  0.016925344  0.037964084  0.0070723766 -4.276894e-03 #> Dlk1     -0.0381672000 -0.109022077 -0.006967999 -0.0488579536 -4.593968e-03 #> Gpr37l1  -0.0275785666 -0.019553809  0.254841214  0.0687479732  6.891691e-02 #> Fgfr3    -0.0005879796 -0.102328219  0.014884693  0.0545803003 -1.367574e-02 #> Slc25a18  0.0125550580  0.013679255 -0.208341235 -0.0364212544  1.823488e-01 #> Igf1r     0.1225668687  0.086411412 -0.063731591  0.1148387934 -1.373221e-02 #> S1pr1    -0.0633881381 -0.034127895  0.118770093  0.0579468371 -2.324412e-02 #> Grm5      0.0233830214 -0.001035762 -0.010456036  0.0124027827 -3.124437e-02 #> Axl       0.0074748291 -0.104766730 -0.017936965 -0.2031400035  1.936683e-02 #> Efemp1   -0.1488280631  0.027576071 -0.031953277  0.0145686118 -7.206308e-02 #> Adgrb3    0.2572227294  0.123914398 -0.067619456  0.0652661523  2.012681e-01 #> Fn1      -0.0255747186  0.034445417  0.094843573  0.0833642077 -7.105043e-02 #> Mertk     0.0767727788  0.138501387 -0.025807046 -0.1408189951 -1.005566e-01 #> Adgrl2   -0.0240220259  0.015997072  0.003344261 -0.1110349288 -3.838102e-02 #> Fzd2     -0.0606452445 -0.017963464 -0.007685615 -0.0237867403 -3.073157e-02 #> Aldh1l1  -0.0034666362  0.117546407  0.020814691  0.0322193967  3.682676e-02 #> Adgrg6    0.1414064016  0.140698465 -0.014073069 -0.1387687972  3.506657e-02 #> Egfr      0.0558185903  0.005256354  0.075116458  0.0199596118  8.231042e-02 #> Kit       0.0087070321 -0.178334333  0.046879683 -0.0640861680  7.038962e-02 #> Ptgdr     0.0736573806  0.131322670  0.025843988 -0.0216869608 -3.697933e-02 #> Gad1     -0.0396407508  0.036907797  0.051970643 -0.0149179111  2.973331e-02 #> Tyro3    -0.0064362358 -0.054881942 -0.047964494 -0.0228024468  8.213397e-02 #> Atp13a5   0.0384860186 -0.031310490 -0.020471104 -0.0543620856  1.208858e-02 #> Ddr2     -0.0626974873 -0.136709620 -0.007516952  0.0335426958  9.787339e-02 #> Rspo3    -0.0309039275  0.007325428  0.048003881 -0.0486419449 -8.835275e-03 #> Arhgap29  0.2237371425 -0.026624138  0.051350991  0.0419043496  1.204373e-01 #> Fzd7      0.1678221524  0.048668836 -0.007165167  0.1620989999  2.228624e-01 #> Slc47a1   0.0928683087 -0.025838626 -0.004168962 -0.0462685562  1.755251e-02 #> Ptger3    0.0249441519 -0.001156395  0.066937072 -0.1144621314 -1.752300e-01 #> Bdkrb1   -0.0085581111  0.002578463  0.047835175 -0.0263849742 -1.242401e-01 #> Traf4     0.0391640386  0.047990809 -0.009616797 -0.0261957322 -5.084471e-02 #> Cx3cr1    0.0938215373 -0.153063345 -0.019751679 -0.0025127260 -2.515914e-02 #> Anxa11   -0.0691047768  0.044786100  0.101128845 -0.0897481016 -1.890360e-01 #> Adgrb1   -0.0202667639  0.032484300 -0.038693140 -0.0397780956  1.208404e-01 #> Lpar1     0.0441309496 -0.067667745 -0.099856535 -0.0865986103 -6.077921e-02 #> Gpr17    -0.1071898757 -0.026963294 -0.017954576 -0.0075553221 -4.570432e-02 #> Cxcl12   -0.0585808077 -0.018787414 -0.162147952  0.1595591740  1.395589e-01 #> Epha4     0.0768834015  0.075467766 -0.019952318  0.0502040560  3.346546e-03 #> Gpr182   -0.0332409530  0.053377236  0.059545265  0.1059979898 -9.267929e-02 #> P2ry14    0.0726907181 -0.025061899  0.079530561  0.0112854547 -6.369785e-02 #> Hcar1    -0.1633868715 -0.097974787 -0.008102099  0.0059583586  3.634126e-02 #> Ephb1     0.0710242059  0.008265060 -0.011766185 -0.0336930429 -1.246034e-01 #> Grm3     -0.1163558580 -0.089911134 -0.009700036 -0.0040474147 -3.799352e-02 #> P2ry1     0.0427740614  0.043239623  0.078023330  0.0319931904  5.880956e-05 #> Ptk7     -0.1738777322  0.052519091 -0.042623964 -0.1358588876  1.645579e-02 #> Slco1a4  -0.1660790632  0.019009683 -0.082900310  0.1029068528  2.165118e-02 #> Insrr    -0.0928055497  0.163208850  0.022016892  0.0022208850 -6.100030e-02 #> Cmklr1   -0.0590268033  0.059089742 -0.037832479 -0.0261682465  1.021090e-01 #> Fzd6      0.0814355924 -0.003491441 -0.045973029 -0.0666552074 -5.901591e-02 #> S1pr5    -0.0598604617 -0.047335127  0.119767018  0.1640621887 -1.027682e-01 #> Pdgfrb    0.0465640210  0.066835296 -0.067035620 -0.0153185467  2.285277e-02 #> Flt1     -0.0092385127 -0.042416897  0.049647706 -0.0583126319 -7.909645e-02 #> Adgrl4    0.0069503370 -0.096620230 -0.027487525  0.0796945660  4.537073e-02 #> Lpar6    -0.1398854117  0.110902226 -0.026424475 -0.0157460599  5.261836e-02 #> Epha6    -0.0369973971 -0.164994019 -0.089436246  0.0168503290 -1.203159e-01 #> Emcn      0.2115045287 -0.121183948  0.179578346  0.0537757069  7.795342e-02 #> Cldn5     0.0613105591  0.076964392  0.040354729 -0.0988317227 -5.127217e-02 #> P2ry12   -0.0989624810 -0.040632207  0.020763570 -0.0522155059  2.673458e-02 #> Adgrf5    0.0828021697  0.089861284 -0.039354838 -0.0764565689  7.172751e-02 #> P2yr13   -0.0106891485 -0.017404493  0.001497426  0.0701777053  2.367790e-03 #> Adgre1    0.1001691670 -0.058688563 -0.013093919 -0.0098932845  2.375173e-02 #> Cx3cl1   -0.0555806187 -0.006286973 -0.022344697  0.0126028107 -9.688128e-04 #> Plxnb3   -0.0627204933 -0.088464068 -0.108271845  0.0101599412  3.946018e-03 #> Flt4     -0.2133975423 -0.125710608  0.052823970  0.0710389894 -3.312774e-02 #> Slc17a7  -0.0505456723 -0.044776726  0.019705770  0.0256305387 -5.015696e-02 #> Cd300c2   0.0100762109  0.050145541  0.092825455  0.1807528684 -5.933996e-02 #> Tek      -0.1690315426 -0.006420412 -0.059917126  0.0687387921 -8.067318e-04 #> Kdr      -0.0216746530 -0.057733516 -0.015496832  0.0194170503  5.277487e-02 #> Kcnj8     0.0048492597  0.047815100 -0.027415876 -0.0174393384  3.705245e-03 #> S1pr3    -0.0133622568 -0.032569877  0.067335411  0.0517770278  8.648706e-03 #> Tie1     -0.0813937966  0.042748703  0.003829562  0.0671889582  8.277435e-02 #> Pdgfra    0.0844983769 -0.052890325  0.115692019  0.1425262203  6.502142e-03 #> Baiap2   -0.0495186221 -0.105370594  0.095621026 -0.0877162658  1.251348e-01 #> Calcrl    0.0171005829 -0.033301150  0.063428463 -0.0668652827 -2.878973e-02 #> Adrb2    -0.0545787266 -0.210736922 -0.006614800  0.1604319958  1.237050e-01 #> Ccr2      0.0486999428 -0.098751510 -0.018711936 -0.0940158727  6.600146e-02 #> Alk      -0.1281344268  0.057304179 -0.058180620  0.0231666822 -3.856565e-02 #> Tacr3    -0.0624874037 -0.060614775  0.054495520 -0.0031829469  6.899449e-02 #> Erbb3    -0.0318475367  0.051369818  0.229836184  0.3004098202 -9.301888e-02 #> Pcdh15   -0.0430571176  0.103826398 -0.111215853  0.0970499275 -3.404765e-02 #> Grm7      0.0308857561  0.034880551  0.017555921  0.1518007948  6.885951e-02 #> F2r       0.0693665195 -0.201531214  0.345891709 -0.0454395100  3.700176e-02 #> Bdkrb2    0.2295575534  0.078549079  0.100648451 -0.0856030137 -7.896300e-02 #> Adgrv1   -0.0449550964  0.041159438 -0.198280336 -0.0178788815  6.412251e-02 #> Gprc5c   -0.0656708945  0.027526430 -0.007290792  0.0359554806  1.067112e-01 #> Tbxa2r   -0.1236270098  0.057306799  0.014556965  0.0090341568 -6.702018e-02 #> Ackr1     0.2019164143 -0.234676721 -0.032979505  0.0005812258  7.227304e-02 #> Lpar2     0.0495377903  0.079276116 -0.013536164 -0.1024118476 -2.978569e-02 #> Myh11     0.0322153722 -0.043370218 -0.015074004 -0.0240286296 -3.526565e-02 #> Musk      0.0990223092  0.094426541 -0.088036548  0.0163395110 -9.953970e-02 #> Cnr1      0.0785426673  0.023099311 -0.133322489  0.1013142557 -1.995846e-01 #> C3ar1     0.0089530762  0.046399448  0.032945168 -0.1216708792 -2.978944e-02 #> S1pr4     0.0300642851 -0.023770659 -0.059571937 -0.0696792762 -2.007499e-02 #> C5ar1    -0.2073652922  0.074308233  0.060042149  0.0687461017 -3.583460e-02 #> Fpr1     -0.0221856605 -0.022539129 -0.007247489 -0.0427372570 -1.640045e-02 #> Sctr      0.0235396431  0.041648525  0.033444745 -0.0225587535 -6.691755e-02 #> Gpr158    0.0329766739 -0.008530823 -0.040119471  0.0551543138  2.482754e-02 #> Cxcr4     0.0110892309  0.010852805  0.017564773 -0.0319806229  4.485823e-03 #> Hrh2     -0.0590743981 -0.010835017 -0.080590549 -0.1044074036 -1.246771e-02 #> Slc17a6  -0.0068493293 -0.018315494  0.012681583 -0.0238077598 -3.252311e-02 #> Ppp1r3g  -0.0526824261  0.107266646  0.015914684 -0.0064860291 -5.238345e-02 #> Pln       0.0109083191 -0.003322155 -0.101150780 -0.0431099968 -3.825230e-03 #> Grin2b   -0.0462492966  0.042369776  0.063174970  0.0331090631  3.820993e-02 #> Taar7e    0.0269635584  0.032332698 -0.042802051  0.0661121035  1.026312e-02 #> Ptger2   -0.0988007030 -0.224716974 -0.050034239 -0.0078701686  6.715279e-02 #> Mc4r     -0.0564594875 -0.179600625  0.228255492 -0.2039794284 -6.088343e-02 #> Ghsr     -0.0314799375  0.100300289 -0.012627397  0.0341753911  7.570183e-02 #> Nmbr      0.1466676367 -0.204003125 -0.254970016  0.2650677475 -4.621425e-01 #>                 Dim.46       Dim.47       Dim.48        Dim.49        Dim.50 #> Mlc1     -3.609612e-02 -0.066023377 -0.053245137 -0.0005666037  0.0005694164 #> Gprc5b   -8.469528e-02  0.156788151 -0.178225691 -0.0430244562 -0.0058373110 #> Gfap     -2.304603e-03 -0.008335894  0.027302635 -0.0095727295  0.0672685467 #> Ednrb    -7.193897e-02 -0.052959499  0.073387052  0.0868422292 -0.0074431370 #> Sox9     -4.431520e-02 -0.020581213 -0.079456079  0.0278801967 -0.0388738143 #> Aqp4      6.480487e-02  0.147580811 -0.036645535  0.0332258593 -0.0662155403 #> Gjc3      7.700075e-03 -0.151583195  0.045329570  0.1172799084 -0.0156182814 #> Sox8      4.742613e-02 -0.090087077  0.163979039 -0.0479065251 -0.1451686967 #> Ntsr2    -3.653848e-02 -0.018134522 -0.048345420 -0.0309826351  0.0105251743 #> Smo       1.877413e-01  0.196898790  0.114488102  0.0718535764  0.0856293831 #> C1qb      2.697623e-02  0.004236971  0.015446251 -0.0043411963 -0.0142665905 #> Olig1    -4.165291e-02  0.009604809 -0.131364599 -0.0439190482  0.1051083608 #> C1qa      4.377265e-02  0.083205303  0.071208712 -0.0013364060  0.1146369009 #> Pth1r    -1.575574e-01  0.096925470 -0.083282442  0.0997044510  0.0510609958 #> Gabbr2   -8.843364e-02 -0.161704077 -0.017095519 -0.0747410166 -0.0106345464 #> Timp4     1.148117e-01 -0.062397296  0.066438613 -0.0242846595  0.1555480638 #> Abcc9     1.094394e-01 -0.133622774  0.100885708 -0.0725002218  0.0606758793 #> Csf1r     1.529788e-01 -0.064328988 -0.086918057  0.0570521826 -0.1610032030 #> Ntrk2    -1.568100e-01  0.020994619 -0.007712980 -0.0071612051  0.0005229980 #> Adgrg1    2.388182e-02  0.017904895  0.008883993  0.0907701719 -0.1134864979 #> Ntrk3     1.106170e-01 -0.038423826  0.166696207 -0.0390014122 -0.0124688828 #> Erbb4     1.116445e-02 -0.011645203  0.009943270 -0.0056019374  0.0400326242 #> Selplg   -5.638070e-02  0.089465919  0.004589622 -0.0548685004 -0.0583841987 #> Cspg5     5.524470e-02  0.030915217 -0.133723908 -0.0156598612 -0.0056119573 #> Dlk1     -1.691182e-02 -0.128126549  0.010692953  0.0109357761 -0.0418994030 #> Gpr37l1   1.316078e-02 -0.070534856  0.139736417 -0.1249194281  0.0115320440 #> Fgfr3     8.364816e-02 -0.053370913  0.007261560  0.0221187734 -0.0028121421 #> Slc25a18 -7.118463e-02 -0.046701857  0.177465437  0.1952373504 -0.1292617254 #> Igf1r     1.026437e-01  0.110101990  0.081509743  0.1102287335 -0.0584441439 #> S1pr1     5.567532e-02 -0.010694832 -0.040164707 -0.0608230405  0.1521623432 #> Grm5      6.201133e-02  0.058192032 -0.034622390  0.0158311712  0.0945483831 #> Axl       1.313275e-01  0.001977299 -0.020392755 -0.0276729913 -0.0806823629 #> Efemp1   -1.022657e-01  0.036512620 -0.046267284 -0.1076514739 -0.0809859402 #> Adgrb3   -4.949285e-01 -0.022663479  0.200950151 -0.0393112140 -0.1533070751 #> Fn1      -1.143007e-01 -0.048965937  0.065166511  0.0948981952  0.0548166495 #> Mertk     7.734030e-02  0.029783392 -0.056683599  0.0415095697  0.2629019425 #> Adgrl2   -1.131086e-01  0.021964402  0.067595697  0.0198870424  0.0162037952 #> Fzd2      4.293113e-02 -0.088300269  0.087094340  0.0845049126 -0.0031670489 #> Aldh1l1   5.108596e-02  0.086922550 -0.065408401 -0.0866080823 -0.1793221836 #> Adgrg6    2.944860e-02  0.106268603  0.031681147 -0.1432775296  0.0241733100 #> Egfr     -9.949434e-02 -0.040076814 -0.003998721 -0.1417275200  0.0466602180 #> Kit      -9.576071e-02  0.049670300  0.011304211  0.0139331049 -0.0969204721 #> Ptgdr     2.987458e-02  0.046214553 -0.040824686 -0.0169567198  0.0861548332 #> Gad1      9.164643e-02  0.022376024  0.025937564  0.0174945240  0.0475197611 #> Tyro3    -1.012704e-01 -0.041053530  0.044575843 -0.0065171212  0.0870308019 #> Atp13a5   9.461724e-03  0.059848088  0.141217643 -0.1080931965 -0.1725735076 #> Ddr2     -3.336392e-03 -0.119776309 -0.100137104 -0.1072134262 -0.0186774712 #> Rspo3     1.431303e-01  0.120579759 -0.012950821  0.0869925988  0.0450280875 #> Arhgap29  1.097046e-01 -0.031582415 -0.231677106 -0.2123062495 -0.0144360578 #> Fzd7      4.812392e-02  0.045110462 -0.031251585  0.0528964049  0.0759748684 #> Slc47a1   2.689901e-02 -0.027593765  0.021204320  0.0133751215  0.0038773672 #> Ptger3   -1.217134e-01  0.107218245 -0.051536892  0.1308241241  0.0220483563 #> Bdkrb1   -1.237338e-01 -0.092245230  0.033552353  0.0570350297 -0.0516797543 #> Traf4     4.195331e-02 -0.053424190  0.019911588  0.0698559999 -0.0369034440 #> Cx3cr1   -1.374479e-01  0.115105459 -0.036614082 -0.0230737572  0.0243591138 #> Anxa11   -1.211922e-01  0.108175113 -0.116850119 -0.0307037486  0.0038767990 #> Adgrb1   -7.540231e-03  0.114818114  0.031592661 -0.0394018280  0.0064328615 #> Lpar1     6.743333e-02  0.036049384  0.130893921 -0.0154479875  0.0364291955 #> Gpr17    -3.424863e-02  0.099316050 -0.073836667 -0.0715334048 -0.0687982666 #> Cxcl12    7.118673e-03  0.078789436 -0.026506266 -0.0165250610  0.0276787455 #> Epha4    -1.077804e-01  0.005086550 -0.023424819 -0.0455338281 -0.0124169517 #> Gpr182   -5.127006e-03 -0.072255659  0.020643640 -0.0844610137  0.0384675086 #> P2ry14   -2.827262e-02 -0.017776785  0.069439084  0.0761260372 -0.0174479531 #> Hcar1     8.245219e-03 -0.169307515 -0.061136870  0.1048085002 -0.0125887689 #> Ephb1     7.933501e-02  0.009227109  0.043837704  0.0663940034  0.0013681269 #> Grm3      1.054366e-01  0.120671946  0.043812672 -0.0605719915 -0.0004615742 #> P2ry1    -1.241989e-01 -0.021344066 -0.015276009 -0.0891443634  0.1655238112 #> Ptk7      3.692229e-02  0.058365021  0.075297973 -0.0905807420 -0.2444265390 #> Slco1a4   3.960095e-02  0.012265630 -0.010000152  0.1347170749 -0.0790255671 #> Insrr     3.303288e-03 -0.056063168 -0.005658957  0.0366097474  0.0985863987 #> Cmklr1   -4.452884e-02 -0.079240285 -0.013233330  0.0314729793 -0.0262771918 #> Fzd6     -7.683884e-02  0.018953054  0.024373600  0.0324010441  0.1798808272 #> S1pr5     3.522360e-02  0.089564115  0.048410357 -0.0149731097 -0.0609867657 #> Pdgfrb    4.186066e-02  0.137317609 -0.149704384  0.1605377461  0.0292368222 #> Flt1     -4.515999e-02  0.079880039 -0.024935392 -0.1129170978 -0.0617926831 #> Adgrl4    2.230768e-02 -0.017956311  0.170414455 -0.1435166252  0.0963468776 #> Lpar6    -2.674174e-02 -0.176404229  0.100057704  0.0626369705  0.0749259054 #> Epha6     7.858181e-02 -0.092516939  0.004377653  0.0306614981 -0.0255877222 #> Emcn     -1.344921e-02  0.023755042 -0.207196493  0.2694192183 -0.0485825614 #> Cldn5    -1.662330e-02 -0.158216302 -0.053101664 -0.1886431748  0.0717726190 #> P2ry12   -1.238912e-02 -0.137329994  0.034529932  0.0091707142  0.0243161908 #> Adgrf5    2.284301e-02 -0.040937827 -0.021443237  0.0466198889 -0.0056802832 #> P2yr13   -1.113402e-02  0.014574959  0.014752478  0.0086699233  0.0154175081 #> Adgre1   -6.912791e-02 -0.026799727  0.018465152 -0.0136996215  0.0878366603 #> Cx3cl1   -2.685946e-02 -0.004512758 -0.013716984  0.0712291447  0.0486563910 #> Plxnb3   -6.405360e-02 -0.149172617 -0.090804014  0.0417755528  0.0114148640 #> Flt4      5.907203e-02 -0.165345418  0.065359515 -0.0580646987  0.0415148139 #> Slc17a7   2.502915e-02 -0.016152172 -0.011883352 -0.0275565058 -0.0649342280 #> Cd300c2  -9.178146e-02  0.146457911 -0.020980943 -0.0800686876  0.0117010951 #> Tek      -1.247060e-01  0.195125143  0.165550610  0.1597793441  0.0460309093 #> Kdr       1.436761e-02  0.013748201  0.043503363  0.2167032530 -0.0962465898 #> Kcnj8     3.780850e-02 -0.025929378  0.059541479 -0.0956904279  0.0526446523 #> S1pr3    -3.972054e-02 -0.086951394 -0.095395602  0.0551027782  0.0617825207 #> Tie1      1.494018e-01  0.104714932 -0.164364053 -0.0279915791 -0.2775782010 #> Pdgfra    3.014636e-02  0.051950432  0.165056354  0.0108871135  0.1149001052 #> Baiap2    8.481868e-02  0.054147008  0.064370961 -0.0088778323  0.0647071059 #> Calcrl   -1.175377e-01  0.074866839  0.063846494  0.2647417594  0.0094264784 #> Adrb2     1.369878e-02  0.028184139  0.007398724 -0.0849416283 -0.0538219816 #> Ccr2     -4.657241e-02 -0.079828485  0.017568886 -0.0839860010 -0.0314660612 #> Alk      -1.205000e-01  0.055750041 -0.031115226 -0.0926035406 -0.0500224877 #> Tacr3    -6.684064e-02  0.115898428  0.045611750 -0.0546322233 -0.0053085325 #> Erbb3    -1.296998e-02  0.129768155 -0.043497459 -0.0888212158 -0.0727856626 #> Pcdh15    2.671940e-02  0.001984140  0.036070622  0.0317228147  0.0873590711 #> Grm7      2.012896e-02 -0.010720198 -0.124076272 -0.0436772126 -0.0242379365 #> F2r      -2.145095e-02 -0.087422879 -0.200238742  0.2059786884 -0.1690432175 #> Bdkrb2    6.887812e-02 -0.011827868  0.124269712  0.1010077276  0.0610755412 #> Adgrv1    1.165612e-01  0.135440541 -0.059904482  0.0960754086 -0.1401058307 #> Gprc5c    6.391407e-02 -0.086733937 -0.080728177  0.0642973633  0.0895423161 #> Tbxa2r   -2.620424e-01 -0.032525551 -0.039874820 -0.0101757904 -0.0547843895 #> Ackr1    -2.547614e-02  0.053859953 -0.047158504  0.1347045621 -0.0575774110 #> Lpar2     3.800211e-02 -0.018605194  0.015109368  0.0438630718 -0.0062211486 #> Myh11     3.661799e-03  0.041543829 -0.011517432 -0.0810440828 -0.0120298574 #> Musk      1.254369e-01 -0.132897852 -0.085905798  0.0486926957 -0.0761179113 #> Cnr1     -6.078101e-02  0.029842763  0.020466309  0.0304315238 -0.0967712847 #> C3ar1     1.584089e-02 -0.146050154 -0.095446285  0.0278511398 -0.1640907807 #> S1pr4     4.631400e-02  0.010700759  0.011934261 -0.1105711788  0.0220394998 #> C5ar1    -1.782270e-02 -0.165383874  0.013860161  0.2538840182  0.1089257050 #> Fpr1     -1.089135e-02 -0.002540849 -0.030889116 -0.0527753640 -0.0560091472 #> Sctr      8.630072e-02  0.028219200  0.054964188 -0.0189475737 -0.0537832914 #> Gpr158    6.188227e-02 -0.055164521 -0.073148122  0.0714465893  0.1435800291 #> Cxcr4    -6.876068e-03 -0.035561742  0.011770111  0.0233199208  0.0643347245 #> Hrh2     -4.839773e-02  0.148475076 -0.203035365 -0.0343350389  0.2645500263 #> Slc17a6  -4.883941e-02 -0.009926849 -0.019351003 -0.0292647483 -0.0139834019 #> Ppp1r3g  -1.246256e-02  0.120582253  0.028793909  0.0059616133  0.0109484360 #> Pln      -4.313203e-03  0.053020230  0.050700097 -0.0391119953  0.0283814353 #> Grin2b   -2.498571e-02  0.016206301 -0.044238756  0.0074485686  0.0857301576 #> Taar7e   -4.859692e-02 -0.108048783 -0.108460696 -0.0561999077 -0.0196165702 #> Ptger2   -1.162974e-01  0.057366116 -0.249926227  0.0827042048  0.1736190167 #> Mc4r      1.149901e-02  0.245347709  0.239972113  0.0903362531  0.0432158993 #> Ghsr      1.223699e-02 -0.026448389 -0.008868179  0.0143234793 -0.0170332587 #> Nmbr     -3.516158e-05 -0.085034858 -0.006184928  0.0429620993 -0.0695392364 #>                 Dim.51        Dim.52       Dim.53        Dim.54        Dim.55 #> Mlc1      0.0864147797  0.0386775355 -0.133413111  0.0380473547 -0.1102939152 #> Gprc5b    0.0357622186  0.0512881874 -0.068807439 -0.0481835083 -0.0437332137 #> Gfap     -0.0217852383  0.0431115841  0.009178273 -0.0011945001  0.0040812457 #> Ednrb     0.1087725419 -0.0808638138 -0.071338394  0.0744174277 -0.0570105994 #> Sox9     -0.0176324689 -0.0826078232  0.152889225 -0.0917811558  0.0779147201 #> Aqp4     -0.0203445968 -0.0488174547 -0.016860661 -0.1032182345 -0.0363172386 #> Gjc3      0.1275113456 -0.0483121278 -0.019414639  0.1850497168  0.0011071938 #> Sox8     -0.1224535096 -0.1750904596  0.026583489  0.0173817150 -0.2252728971 #> Ntsr2     0.0140366587  0.0246952728  0.078319518 -0.0935201998  0.1169457543 #> Smo      -0.1031320026 -0.0359235598 -0.133693345  0.2038910383  0.1063444765 #> C1qb      0.0521542841  0.0094092029  0.002476313 -0.0246306159  0.0789103045 #> Olig1     0.0632934579  0.1449316489 -0.041198344  0.0611857623  0.0209697656 #> C1qa     -0.0656778650 -0.0254267826 -0.010955781 -0.0322721651  0.0374617121 #> Pth1r     0.0043895416 -0.0242733733  0.043880080 -0.0091430761 -0.0828741787 #> Gabbr2   -0.1374284613  0.1593460484 -0.059018276 -0.0275923685 -0.0399142930 #> Timp4    -0.0372242762  0.0271928268 -0.046978817  0.0956635701  0.0298385358 #> Abcc9    -0.0097259150  0.0314977534 -0.059431355  0.0274230190 -0.0052770571 #> Csf1r     0.0365952849 -0.0530367985 -0.072551262 -0.1872273090  0.0377306235 #> Ntrk2    -0.0194439843  0.0458547563 -0.048510111 -0.0597154606  0.0962834845 #> Adgrg1    0.0537804033  0.0166895477 -0.177489015  0.0122632813 -0.0093721989 #> Ntrk3    -0.0107225687  0.1100880625  0.014048952  0.0036945658  0.0791101853 #> Erbb4    -0.0440979329 -0.0123564634  0.039606601  0.0756432951 -0.0160496844 #> Selplg    0.0365344378 -0.0346125185 -0.132803428  0.1123293706 -0.0386259852 #> Cspg5     0.0517471169  0.0396240554  0.097696563  0.0373313387 -0.0593615155 #> Dlk1      0.0124225637 -0.0393928657  0.007115968 -0.0081002040  0.0062991755 #> Gpr37l1  -0.1375541205 -0.1426914677 -0.060408516  0.0049487567 -0.0002983586 #> Fgfr3     0.0704441310  0.0585355837 -0.005745559  0.1263525434 -0.1804427983 #> Slc25a18  0.1478459139 -0.0337286097 -0.052206896  0.0031981546  0.0202625142 #> Igf1r    -0.0676919148  0.2215479203  0.061604277 -0.1322078028 -0.0126485227 #> S1pr1     0.0217424181  0.0562988675  0.128672369 -0.0469290099 -0.0317916341 #> Grm5      0.1267232607 -0.1821298370  0.052846292  0.0424923720  0.0076355397 #> Axl      -0.0266549669 -0.0821029583  0.157901071  0.1279416129  0.0841713056 #> Efemp1    0.0433298740  0.0100590464  0.041090086  0.1147784825 -0.0637470063 #> Adgrb3    0.0340548251 -0.1994057731 -0.051887088 -0.0113294532 -0.0464800559 #> Fn1      -0.0349162454 -0.0401352883  0.048224773  0.0975955940  0.0997022949 #> Mertk    -0.1276267847  0.0775079185 -0.288190844  0.0569550685  0.0789090251 #> Adgrl2   -0.0241442306  0.0409112631 -0.096203450  0.1597259033  0.2413268814 #> Fzd2     -0.0419992850 -0.0180222553  0.022547760  0.0522350728 -0.1547725775 #> Aldh1l1   0.0422315537 -0.0231634494  0.034038794  0.1446442523  0.0158639102 #> Adgrg6   -0.0717403643 -0.0676177911  0.148759259 -0.0519620856  0.0842916639 #> Egfr      0.0284834388  0.0211036995  0.036558208 -0.1104781039  0.0106323406 #> Kit      -0.1765353989  0.0376083486  0.021545916 -0.0218771945 -0.0990823513 #> Ptgdr     0.0148796399 -0.0376569535  0.050108165  0.0071623126  0.1663118745 #> Gad1     -0.0541977029 -0.0163372119 -0.042973321 -0.0069105205  0.0047448288 #> Tyro3    -0.0569203364  0.0612726675  0.076203210 -0.0103244686  0.1607574988 #> Atp13a5   0.0113448248 -0.0653265478 -0.020052422  0.0191948702  0.0960118564 #> Ddr2      0.1681851656  0.0887515342 -0.052155085 -0.1562335324 -0.1977053642 #> Rspo3     0.0761000666  0.0035596410 -0.139773838  0.0350979016 -0.0044469695 #> Arhgap29  0.1667256161 -0.0773465523  0.093483749 -0.1120105349  0.0800865191 #> Fzd7      0.0391600922 -0.0131202374  0.180511473  0.0186110798 -0.0531900152 #> Slc47a1  -0.0121339774  0.0097956856 -0.055939685 -0.1478033048 -0.0290117398 #> Ptger3   -0.1227445202 -0.0024991875  0.030960076  0.1176523492  0.0523231574 #> Bdkrb1   -0.0563752401 -0.0242625363 -0.087956660 -0.0940087552 -0.0667586016 #> Traf4    -0.0111792112 -0.0426464501 -0.050267124 -0.0376267512 -0.0430799491 #> Cx3cr1   -0.1162055761 -0.0069438933 -0.028212431  0.2117797684 -0.0446537063 #> Anxa11    0.0353237978  0.1567190027 -0.054605970  0.1923689361 -0.0701103530 #> Adgrb1    0.0516243637 -0.0522654985  0.071080233 -0.0161336593  0.0100539573 #> Lpar1    -0.1384795678  0.0768995198 -0.144919035 -0.2200563502 -0.0663261050 #> Gpr17    -0.0746612602  0.0197536996  0.047348650 -0.1552907405 -0.0153074045 #> Cxcl12    0.0648913479 -0.0195018206 -0.026275858 -0.0723587833 -0.0564373482 #> Epha4    -0.0843040721 -0.0892352884  0.070502520 -0.0443669373 -0.0984616705 #> Gpr182   -0.0667528492  0.0433835251 -0.018812028 -0.0795079381  0.0061116662 #> P2ry14   -0.0449297426  0.0001195871  0.041216992 -0.0290320869 -0.0599709389 #> Hcar1    -0.1029181773 -0.1187874358 -0.146846265 -0.0006462698 -0.0039605024 #> Ephb1    -0.0616231277 -0.0751957167  0.035772510  0.0283280176 -0.1165143517 #> Grm3     -0.1007750989 -0.0433463680  0.135596165 -0.2009154012  0.1526114637 #> P2ry1     0.0233721854 -0.0638652285  0.016604629  0.0815173824  0.2315074879 #> Ptk7      0.0551579326  0.0445516383 -0.030319575  0.1172336511  0.0345609210 #> Slco1a4  -0.0087573577  0.0269395471  0.009395579 -0.1086067520  0.0605262607 #> Insrr     0.1270950449  0.0333949654  0.028659257  0.0734937210 -0.0372920581 #> Cmklr1    0.0344742592 -0.0113610834  0.013208863 -0.1708795430  0.0564534510 #> Fzd6     -0.0480376453  0.0350960455  0.126015787 -0.0412247023 -0.1663803009 #> S1pr5    -0.0582889903 -0.1316655993  0.012547598 -0.1397729434 -0.0412782701 #> Pdgfrb    0.0553378559  0.0080545505  0.112178670  0.0565945132 -0.1531415817 #> Flt1     -0.0775316321  0.0033952380 -0.061223744  0.0375820168 -0.0100047921 #> Adgrl4   -0.0081703643 -0.0834951982 -0.070501790 -0.0046751832 -0.0808977607 #> Lpar6     0.1223878463  0.0904897121  0.021726169 -0.1141456456 -0.0238123549 #> Epha6    -0.1143417531 -0.1650457045  0.038605281  0.0363261512  0.1822764977 #> Emcn     -0.0386266207  0.0852658395  0.038754419 -0.0403708596  0.0141791906 #> Cldn5     0.1123573616  0.0005760496 -0.018919683  0.0838494382 -0.0193509681 #> P2ry12    0.0229225179  0.0271101977  0.248601936 -0.0514222400 -0.0730620449 #> Adgrf5    0.0353231917 -0.0305784655 -0.012003946 -0.0538631125  0.0138152743 #> P2yr13    0.0270066085 -0.0380045514  0.070438540 -0.0439513987 -0.0244272732 #> Adgre1    0.0166776146  0.0691432729  0.067586534  0.0852109952 -0.0388432612 #> Cx3cl1   -0.0709108140 -0.1656054901 -0.005206945  0.0076716132  0.0551430461 #> Plxnb3    0.1009669067  0.0442974416  0.073272872 -0.0135246931  0.0790419632 #> Flt4      0.1086011493 -0.0605052837 -0.081719541  0.1028148958 -0.1342517212 #> Slc17a7   0.0808908105  0.0051317339  0.042305490  0.0567588205 -0.0031208272 #> Cd300c2   0.0183229148  0.0463674993 -0.252995102 -0.0309029261 -0.0998193754 #> Tek      -0.0551530251 -0.0582152041  0.233546927  0.0202078696  0.0123374170 #> Kdr      -0.1234118278 -0.0380859398 -0.039075774 -0.1609766667  0.1003331397 #> Kcnj8    -0.0103127285  0.0090620487  0.038700421 -0.0007958727 -0.0718108080 #> S1pr3    -0.0179677873  0.0380877212 -0.113772651  0.0039253432  0.0231778531 #> Tie1      0.0789047663 -0.1362516867 -0.039528137  0.1252079846  0.0525015330 #> Pdgfra    0.1019353138 -0.0312812942  0.003423582  0.0652608374  0.0743515118 #> Baiap2    0.1135912593  0.0219881411 -0.196006178 -0.1041168499 -0.0063890775 #> Calcrl   -0.0500724961 -0.0178709405  0.094389259  0.0691643926 -0.1170290672 #> Adrb2    -0.0595874908 -0.0390308949  0.144321534  0.1129875063 -0.0433099847 #> Ccr2      0.0654393950  0.0474509109  0.101245875 -0.0163764868 -0.0554918076 #> Alk       0.0442256589  0.0983084350 -0.040820285 -0.0361424587 -0.0345972165 #> Tacr3     0.1237807279  0.0658279984 -0.006089670 -0.0185418645  0.0645658705 #> Erbb3    -0.0340301323 -0.0390831253 -0.037639453 -0.0582994065 -0.0701854955 #> Pcdh15   -0.0374600639 -0.0224354030 -0.019501705 -0.0307194305  0.0861771739 #> Grm7     -0.1031227969  0.3295882376  0.118844898  0.0816743708 -0.1236703326 #> F2r       0.0931193789 -0.0836869052 -0.072068031  0.0333319191  0.1457884560 #> Bdkrb2    0.1627554070  0.0323463867 -0.054462392 -0.0971855631  0.0458285246 #> Adgrv1    0.0326083983  0.0377132153  0.037772805  0.0637532060 -0.1303758168 #> Gprc5c    0.0285250798 -0.0342096719 -0.056161499  0.0352883874  0.0546336930 #> Tbxa2r   -0.0233685859 -0.0140499300 -0.110105667 -0.0845488830  0.0240069920 #> Ackr1    -0.1012257854  0.1453868666 -0.204118822 -0.1431468391 -0.0383348973 #> Lpar2     0.0507513654  0.0161347153 -0.008616978 -0.0374190895 -0.0061587505 #> Myh11    -0.0155853017 -0.0046230824 -0.093167296  0.0473299380 -0.0628617684 #> Musk     -0.2221807449 -0.0659729925  0.022494216  0.0643440995 -0.1329958905 #> Cnr1      0.1975243417  0.0187672712 -0.018177801  0.0053602430  0.0616084661 #> C3ar1    -0.0381349950 -0.0744630426  0.069071944 -0.0494524922 -0.0451792090 #> S1pr4    -0.0419322910  0.0252769481  0.068791113 -0.0812493796  0.0012319352 #> C5ar1     0.0316802085  0.0356658521  0.122734759  0.0562466352 -0.0950808980 #> Fpr1     -0.0447367180 -0.0402554942  0.030249584 -0.0404073607  0.1518325236 #> Sctr      0.0005447204 -0.0305494889 -0.038582735  0.0843803157 -0.1776756301 #> Gpr158   -0.0341123742 -0.2321943439 -0.068175887 -0.0468304160 -0.0669802745 #> Cxcr4     0.0388084855 -0.0091183998  0.050108364  0.0228397673  0.0069202841 #> Hrh2      0.1102837536 -0.4622618107 -0.083352128 -0.1182196817 -0.2069093626 #> Slc17a6   0.0508423015 -0.0074970378  0.023322623 -0.0106506421  0.0541894186 #> Ppp1r3g  -0.0049939163  0.0635975777 -0.029785943  0.0447019980  0.0430259291 #> Pln      -0.0184412729 -0.0096171260  0.082225912 -0.0304172113 -0.1192326741 #> Grin2b    0.0246089221  0.0405930431 -0.005237479 -0.0605258111 -0.0156904103 #> Taar7e   -0.1608751357  0.0471814613  0.010069119  0.0267038913  0.0625994078 #> Ptger2   -0.0328753449 -0.0262785831  0.014433540 -0.0301211417  0.0668181404 #> Mc4r      0.3421843377  0.0888456847  0.074044448 -0.1326400789 -0.0619409513 #> Ghsr     -0.0176841854  0.0245916486 -0.038920106 -0.1558940969  0.0005784895 #> Nmbr      0.2825238073 -0.0171862648  0.014508438 -0.0115176735  0.1321641075 #>                 Dim.56        Dim.57        Dim.58        Dim.59       Dim.60 #> Mlc1      0.0125631175 -0.1258394688  0.0812768551 -0.0325152883  0.031562163 #> Gprc5b   -0.0305652385 -0.1085300649  0.1563698599  0.0231201457  0.070045161 #> Gfap      0.0021355509  0.0714058083  0.0763472244  0.0650322037  0.025693299 #> Ednrb     0.0584635092 -0.0767763288  0.0033938626  0.0378251709  0.066705871 #> Sox9      0.0805272566  0.0447301351 -0.0421526508 -0.1616761853 -0.159880316 #> Aqp4      0.0037243270 -0.0993403374 -0.2890032234 -0.0982454411  0.016497111 #> Gjc3      0.0101608573 -0.0619153596 -0.1513878036  0.0363212652 -0.110972943 #> Sox8     -0.0809782644 -0.2348320443  0.1566087641 -0.1970185600  0.009194735 #> Ntsr2     0.0389614486  0.1332368717  0.0042891304  0.0609521324 -0.016232585 #> Smo       0.1625453672 -0.0931763845  0.1032452338 -0.1873871441 -0.093587081 #> C1qb     -0.0288261215 -0.0201602299 -0.0335959487 -0.0114946500 -0.017538837 #> Olig1     0.0371927417  0.1044543073  0.0352491176 -0.0223503292 -0.049835683 #> C1qa      0.0184349063 -0.1299580747 -0.0968623043 -0.0704076438  0.102272300 #> Pth1r    -0.0190940473 -0.0458870239 -0.0230064508 -0.1267705292  0.025322508 #> Gabbr2    0.1279993443 -0.0819635234  0.0471205739  0.2377004740 -0.253864197 #> Timp4    -0.0103226545  0.0003300398  0.0331626903  0.1600166279  0.029633641 #> Abcc9     0.0127921714  0.1019249124  0.0798386143  0.1099444579 -0.047089993 #> Csf1r     0.0947957477  0.0616803037  0.0983375044 -0.0100382598 -0.024199670 #> Ntrk2     0.0540820596 -0.1076362312  0.0772730011 -0.1136272052 -0.090542287 #> Adgrg1   -0.2011991797  0.1105710216  0.1585851668  0.0814053222  0.002502263 #> Ntrk3     0.0342178396 -0.0922025185  0.0889694032 -0.0793067495 -0.040569347 #> Erbb4    -0.1127841244  0.1241517211  0.0243371267 -0.1387311268  0.003192089 #> Selplg    0.0056001049  0.0113088113  0.0617843140  0.0609322583  0.058498494 #> Cspg5    -0.1066170764  0.1051521321 -0.1719944945  0.0410005258  0.169845449 #> Dlk1     -0.0234520433 -0.0789734466  0.0812137717  0.0552190654  0.088636265 #> Gpr37l1   0.0115143322 -0.0563338750 -0.0050629521  0.0208197517 -0.103656551 #> Fgfr3     0.0512952728  0.0497756409  0.0732161680  0.0359611281  0.031370725 #> Slc25a18 -0.0364136515 -0.0352914382 -0.0115305289  0.1338703486  0.092329169 #> Igf1r    -0.1892876039 -0.0229877867  0.0257016685  0.1801316021 -0.016640364 #> S1pr1     0.1306441830  0.0018101914  0.0274789829 -0.0270158147  0.004429182 #> Grm5     -0.1368760458  0.1791687318 -0.1323974260 -0.1712051647  0.007993431 #> Axl       0.0080953078  0.1027457305 -0.0555705393  0.0558114128 -0.012201843 #> Efemp1   -0.0038693103 -0.0194672109 -0.0292948458  0.0015103619 -0.009499639 #> Adgrb3    0.0418865733  0.0876056078  0.0469282415 -0.0553319753 -0.028042824 #> Fn1      -0.0897428651 -0.0093729182  0.0532934136  0.1546065148  0.073347073 #> Mertk    -0.0428843560  0.0632799155  0.0225563024 -0.1080896706 -0.083921518 #> Adgrl2    0.0117531844 -0.1089285547 -0.0845206599 -0.0329888054  0.024433420 #> Fzd2      0.0156058562  0.2045668585 -0.0374698440 -0.0113486596  0.040327474 #> Aldh1l1  -0.2382201172  0.0128442191  0.0331049428 -0.0374622942 -0.003951492 #> Adgrg6    0.0474139284  0.0184103792 -0.0454821975  0.1156513958  0.066673811 #> Egfr     -0.1069417753 -0.0812671785 -0.0024913128 -0.0072973791 -0.122554489 #> Kit       0.0300642257 -0.0327735101  0.0267065298  0.1065209672  0.025192545 #> Ptgdr    -0.0125397577 -0.0361986382  0.0673530004 -0.0020460572 -0.115916877 #> Gad1      0.0284670439 -0.0464764177 -0.0098412840  0.0544587438  0.060824305 #> Tyro3    -0.1453580209  0.1799962090  0.0752516138 -0.1401475299 -0.025668316 #> Atp13a5   0.1384154615 -0.0586404260 -0.0577130317  0.0174343417  0.006329030 #> Ddr2      0.0155556273  0.0329578665 -0.1493021151 -0.0471333999 -0.006488838 #> Rspo3     0.1616813769  0.0365731059  0.0149345127 -0.0392573731  0.115983276 #> Arhgap29  0.1680927605  0.0079360302  0.1528593729 -0.0222403790 -0.130187594 #> Fzd7      0.0011474288 -0.3060422598  0.0584027983 -0.1677444767  0.022086315 #> Slc47a1  -0.0014693147  0.0327199581 -0.0303133683 -0.0562508697 -0.012478167 #> Ptger3    0.0025240676  0.0807933396 -0.0370147991  0.1870709440  0.026449610 #> Bdkrb1   -0.0054946102  0.0028979903  0.1049069710  0.0207177154  0.244792369 #> Traf4     0.0784828597 -0.0437363600 -0.0738189224  0.0091249010  0.034223995 #> Cx3cr1   -0.0070421751  0.1107192802 -0.0099338258  0.0906263805 -0.025540025 #> Anxa11    0.0279295400 -0.1257517021  0.0385773930 -0.0172069015  0.008509316 #> Adgrb1   -0.0997161699  0.0733953598 -0.1247643052 -0.0680026604  0.123040368 #> Lpar1     0.0024810195  0.0733857149  0.0980163593 -0.1670248625  0.025164236 #> Gpr17    -0.0281835976 -0.0070786767  0.1093938914 -0.0062593664  0.084807261 #> Cxcl12   -0.0205918367 -0.0186568854 -0.1313499570 -0.0362173683  0.065591407 #> Epha4    -0.0882998594  0.0214887514  0.0584114344 -0.0378809914  0.086296819 #> Gpr182   -0.2511028389 -0.1010533342  0.1584131767  0.0759866564 -0.118515215 #> P2ry14   -0.1699238060 -0.0311742208 -0.0810930931  0.0262569617 -0.004472930 #> Hcar1     0.1129573388  0.2409686412 -0.0272745259 -0.0412985034  0.161535440 #> Ephb1     0.0961312701 -0.1512075512 -0.1332085826  0.0929246304  0.091554560 #> Grm3     -0.0437337777 -0.1426346631 -0.0521254244  0.0830198376  0.220799293 #> P2ry1     0.0033777554 -0.0724721100  0.0975151749 -0.0683411033  0.172923042 #> Ptk7      0.0547041952  0.0288532318 -0.2986611777  0.0004828615 -0.155016303 #> Slco1a4  -0.0226297908  0.0337860563  0.0835626158  0.0552278139 -0.165459302 #> Insrr    -0.2437482602  0.0676910275 -0.0780102992  0.0981906440  0.028604828 #> Cmklr1    0.0027984760  0.0086719619  0.0829172848  0.0251346197  0.093161593 #> Fzd6      0.0008739310  0.0235940308  0.0248012771 -0.0825901102 -0.107852996 #> S1pr5     0.0242998373 -0.0273065472  0.0062585725  0.0563690282  0.087205293 #> Pdgfrb    0.0529741275  0.0550393462  0.1198278997 -0.0466095825 -0.029252266 #> Flt1     -0.0986397623 -0.0248673926 -0.1682185910 -0.0347979310 -0.138943493 #> Adgrl4   -0.0433109295  0.0117893302 -0.0717634707 -0.1129017096  0.090181666 #> Lpar6    -0.0659236459 -0.1430136329 -0.0293633463 -0.0277795373 -0.025439290 #> Epha6    -0.1939758161 -0.0343699315  0.0650277523 -0.0893479263 -0.061099359 #> Emcn      0.0495065102 -0.0647088550 -0.0845519180 -0.0093167166 -0.062814480 #> Cldn5     0.0112692681 -0.0160991141 -0.0005573598  0.0446081285  0.169515921 #> P2ry12   -0.0978875638 -0.0492236037 -0.1014475097 -0.0612664767 -0.027145536 #> Adgrf5    0.0752205862  0.0467587796 -0.0148236659 -0.0584500374  0.221630755 #> P2yr13    0.0933062122 -0.0537551669 -0.0219436226 -0.0060993427  0.015400181 #> Adgre1   -0.0099158210 -0.0356890146 -0.0483830547  0.0560885311  0.016669965 #> Cx3cl1   -0.1283467969  0.0980470576 -0.0157475082  0.0216342962 -0.103819901 #> Plxnb3   -0.0130991068 -0.0026998420 -0.0277201108  0.1244705153 -0.024357665 #> Flt4      0.0995414370  0.0028472668 -0.0282088913 -0.1313477633 -0.088914796 #> Slc17a7  -0.0230888467  0.0489992760 -0.0029864940  0.0032591073  0.100060779 #> Cd300c2  -0.0458736418  0.1020948329  0.0983767433 -0.0271564174 -0.043635012 #> Tek       0.2465059035  0.0394645247  0.0940994749  0.0396530885 -0.019712450 #> Kdr      -0.0649951747  0.0812261263 -0.0048572810  0.0271083938 -0.122392433 #> Kcnj8    -0.1014553427  0.0882397342  0.0366640333 -0.0348519591 -0.041307201 #> S1pr3    -0.0902119900 -0.0249242233 -0.0544814138  0.0771760642  0.053455368 #> Tie1     -0.1069020758 -0.0915140356  0.2578190970  0.0134750468  0.033993417 #> Pdgfra    0.0643018899  0.0281471252 -0.0739105961  0.2112805124 -0.041273586 #> Baiap2    0.1104616654 -0.1474351656 -0.0222166970  0.1386394947  0.020071104 #> Calcrl    0.1244032080  0.0365418755  0.0241490890 -0.0537304520 -0.171705872 #> Adrb2    -0.0485114356  0.0123821031  0.0490913193  0.1177803595  0.003030082 #> Ccr2     -0.0608178756 -0.0375105802 -0.0153748349  0.0297278426 -0.063357335 #> Alk      -0.0432839639 -0.0834115848 -0.0841439855 -0.0300399150 -0.027021944 #> Tacr3    -0.0427312328  0.0104073009  0.0184935125  0.0296168255 -0.029295753 #> Erbb3     0.0588699886  0.2054543319  0.0256636591 -0.0818830122 -0.070049261 #> Pcdh15    0.0006348089  0.0636586879 -0.1583186965  0.0142013211 -0.041341955 #> Grm7      0.1661827875  0.0744208850  0.0398764012 -0.0497191080  0.151582905 #> F2r      -0.0014730327 -0.0614655318 -0.0526321999 -0.0541502699  0.007806200 #> Bdkrb2   -0.0575874852 -0.0402068372  0.0397186042 -0.0078895207 -0.132682144 #> Adgrv1   -0.0951414401 -0.1127886005 -0.0350161915  0.0631818594 -0.052376734 #> Gprc5c    0.0047510536  0.0459720328 -0.0499402543 -0.1094925677  0.016724648 #> Tbxa2r    0.0666518978 -0.0522195564 -0.1106764446 -0.0737239887  0.111871445 #> Ackr1    -0.1044346039 -0.0377061386 -0.2082417510 -0.0568595862 -0.002542482 #> Lpar2    -0.0362003732  0.1112685866  0.0104502969  0.0225967070  0.131476991 #> Myh11    -0.0941300214 -0.0225495709 -0.0980065710 -0.0302217744 -0.105998619 #> Musk     -0.0211486737 -0.0259382155 -0.0295046770 -0.0114267884 -0.008274967 #> Cnr1      0.0632683129 -0.0035031760  0.0319345247 -0.0468717278 -0.048588307 #> C3ar1     0.0929069437  0.1297420031  0.0669043167  0.0787876501 -0.032815816 #> S1pr4     0.0128334673  0.0216923945 -0.1612809445  0.0144505534 -0.101883147 #> C5ar1    -0.0499523644 -0.1436311727  0.0870690367 -0.0836865760 -0.020422608 #> Fpr1      0.0791205054  0.0360995729 -0.0218960276  0.0328010364  0.015369955 #> Sctr     -0.0515800467  0.0467266061  0.0524115513  0.0469323465 -0.071430313 #> Gpr158   -0.0007208232 -0.0261546051  0.0082102851  0.0925688954  0.138652309 #> Cxcr4     0.0143479027  0.0340470151  0.0416501285 -0.0382331341  0.020915839 #> Hrh2     -0.0044647236 -0.0908611357 -0.0138365251  0.2488935041 -0.199251703 #> Slc17a6   0.0151548519  0.0369575062  0.0173631601  0.0034547619 -0.002517079 #> Ppp1r3g  -0.0405298481 -0.1222379604 -0.0346799352  0.0700405209  0.118079841 #> Pln       0.0748123078  0.0483826517 -0.0389908657 -0.0116775316 -0.005489177 #> Grin2b    0.0792476734 -0.0157385827 -0.0001124593  0.2310324967 -0.024981003 #> Taar7e    0.0644724481 -0.1096456877 -0.0059358117 -0.0317436310  0.013958289 #> Ptger2   -0.1258876980 -0.0501821138  0.0072855899 -0.0695578612  0.006726419 #> Mc4r     -0.0811609986  0.1272446124  0.1350917084 -0.0333871203  0.039833203 #> Ghsr      0.0876575950  0.0571697380 -0.0141473440  0.0578700676 -0.073276938 #> Nmbr      0.0750855237 -0.0243946563 -0.0134219369 -0.0729800023 -0.049924914 #>                 Dim.61        Dim.62        Dim.63       Dim.64        Dim.65 #> Mlc1     -0.0363434655 -0.1547949294  0.0690070544  0.120829101  2.312221e-01 #> Gprc5b    0.0362279509  0.0175050913  0.0905423914  0.014155961  8.418026e-02 #> Gfap     -0.0363755013 -0.0259665488 -0.0352573003  0.007087687 -4.463271e-02 #> Ednrb     0.0713049646  0.0933871364  0.0034181948  0.061534550 -7.867310e-03 #> Sox9      0.1701790493 -0.1457135747  0.1292493435 -0.161085744  2.435420e-02 #> Aqp4      0.0609575050  0.0622959430  0.0819136872 -0.087797690  1.548329e-01 #> Gjc3      0.0507582735 -0.0633504472 -0.0534559136  0.148344015  2.691779e-02 #> Sox8     -0.1511520915 -0.1050312649 -0.0178710295  0.023132844  2.683183e-02 #> Ntsr2    -0.0086247569 -0.0831650661 -0.0577663979  0.013954495  6.752734e-02 #> Smo      -0.0625214729 -0.0251252897  0.1275467246  0.138555843  2.784213e-02 #> C1qb     -0.0690887292 -0.0793736673  0.0510743038  0.150138335 -6.531145e-02 #> Olig1    -0.0369556045 -0.0069395097  0.0357138555 -0.140644311 -1.168722e-01 #> C1qa     -0.0187377855 -0.0244912115  0.0423976662 -0.051603049  6.670225e-04 #> Pth1r     0.0028351836  0.1058943534 -0.0409482964  0.036792352 -3.652917e-02 #> Gabbr2   -0.1162459705  0.1024793225  0.0029229914 -0.187797538  1.337037e-01 #> Timp4     0.0350464414  0.0329134652  0.0198732126  0.078165490  7.515997e-02 #> Abcc9     0.0761818642 -0.0410427203 -0.0113425588 -0.011964967  8.140403e-02 #> Csf1r    -0.1169059544  0.0771002961 -0.0225656742  0.054377017  1.765171e-01 #> Ntrk2    -0.0283888316  0.0484163434 -0.0428191822  0.088102580  2.805628e-02 #> Adgrg1    0.0392042591 -0.0906504241 -0.0653489655  0.042012621 -1.912321e-03 #> Ntrk3    -0.0013109246  0.0919907867 -0.1405054212 -0.071662132  7.280188e-02 #> Erbb4    -0.0132933634  0.0697890303  0.0512855728  0.104244028 -2.272039e-02 #> Selplg   -0.0885546636  0.0075408374  0.0268323459 -0.083826466  1.102152e-01 #> Cspg5     0.0145335597 -0.0522911210 -0.2276891360  0.027749113  7.355342e-03 #> Dlk1     -0.0585290783  0.1067931285 -0.0523287905  0.076587946 -8.788101e-02 #> Gpr37l1   0.0117530280  0.0567440375  0.1439278622 -0.088012784 -6.130192e-02 #> Fgfr3    -0.0702296226  0.0171812419  0.0581130944  0.066354233 -4.197903e-02 #> Slc25a18 -0.2102427413  0.2908783066  0.0928012716 -0.025961975 -1.695964e-01 #> Igf1r     0.0517043270 -0.1226090440  0.0168146348 -0.123404477 -1.077369e-01 #> S1pr1    -0.0816224861  0.0480052674 -0.0131399092 -0.037457685 -3.773583e-02 #> Grm5     -0.0300549804  0.0519683454  0.0575651156  0.050933926 -5.897599e-02 #> Axl       0.1635970644 -0.0978900111  0.0398933074  0.025567917 -5.145290e-02 #> Efemp1    0.0726508638  0.1016542543 -0.0614805003  0.014794407 -4.386747e-02 #> Adgrb3    0.1470858854 -0.0073336295 -0.0383271997 -0.065662739  8.932871e-02 #> Fn1      -0.1058294678 -0.0347351444  0.0207403748 -0.042515046  7.406163e-02 #> Mertk     0.0749844751  0.0571316367 -0.0171342954 -0.097561389 -1.733548e-01 #> Adgrl2   -0.0907134060 -0.1606302540 -0.0666785154 -0.038661246  3.070973e-02 #> Fzd2     -0.1395293382 -0.0559231309  0.0494726955 -0.135529819 -7.924828e-02 #> Aldh1l1  -0.0629451618 -0.1819791270 -0.3694097086  0.143497760 -3.546132e-02 #> Adgrg6   -0.1256371143  0.0360689842  0.1123032643  0.061291551 -1.050019e-01 #> Egfr     -0.0394857889  0.0288213323  0.1025090990  0.131267359 -1.798244e-01 #> Kit       0.0527135237  0.0296577131 -0.0724540051  0.017279987  1.479790e-02 #> Ptgdr     0.0084029918  0.0449752574  0.0094437808  0.081641587  6.026343e-02 #> Gad1      0.0045208390 -0.0203915408  0.0270705051 -0.063888453  3.795085e-02 #> Tyro3     0.0210221152  0.1052458845 -0.0150436166 -0.230928268 -3.541155e-02 #> Atp13a5   0.0446350024 -0.0906449940  0.0413781117 -0.008833788 -6.372984e-02 #> Ddr2      0.0546973860  0.1270878853  0.0054824872  0.088908891  2.441886e-02 #> Rspo3     0.1051182550  0.0320527931 -0.1020131912  0.049037703  6.075154e-02 #> Arhgap29  0.1589068947  0.1498024091 -0.0145526341  0.072643870 -4.978069e-02 #> Fzd7     -0.0185937818 -0.1644659693  0.0270833690 -0.061888287 -6.079709e-02 #> Slc47a1  -0.0508272483 -0.1030855685 -0.0060520438  0.017414978 -1.597815e-03 #> Ptger3   -0.0584433835  0.0294209687 -0.0817687826  0.011122160 -1.180247e-02 #> Bdkrb1    0.1816189771 -0.0094979873  0.1344661849  0.022435704 -1.301310e-01 #> Traf4     0.0665581800  0.0927689433 -0.0798955499  0.003978262  1.022135e-01 #> Cx3cr1    0.1233298588 -0.0202978330  0.0433191507  0.052033919 -2.997915e-02 #> Anxa11    0.0513003949  0.0323658764  0.0162963529 -0.009965616  3.153566e-02 #> Adgrb1   -0.0095715520  0.0601539994  0.0447904115 -0.055503417  1.346521e-01 #> Lpar1     0.0005013196  0.0181735025 -0.0536482226 -0.094870360 -1.450974e-01 #> Gpr17    -0.0467366713  0.0228362735  0.0797881897  0.018781938 -3.504827e-02 #> Cxcl12   -0.0804436914 -0.0525400551 -0.0031925270 -0.054069448  2.537165e-02 #> Epha4     0.1094037039 -0.1487513500  0.1270004458 -0.072452626 -3.484660e-02 #> Gpr182   -0.0033164079 -0.0149051188  0.0422184199  0.027191957  1.812753e-05 #> P2ry14    0.0077978961 -0.0339643140  0.0291564542 -0.053040744  1.054677e-01 #> Hcar1     0.1479011252 -0.0320484046  0.0354660553 -0.009629197  8.073636e-02 #> Ephb1     0.2143238400  0.0575415770  0.3121813814 -0.036390674 -9.131967e-02 #> Grm3     -0.0735233943 -0.0074907482 -0.0401411464  0.052211165  1.398112e-01 #> P2ry1     0.0419996193 -0.0555842984  0.0004363337 -0.056879141 -3.276266e-02 #> Ptk7     -0.2107969559 -0.0048060099  0.0123056527 -0.204726002 -8.022361e-02 #> Slco1a4   0.1147361423 -0.0756270772 -0.0436023380  0.096026886 -5.075217e-02 #> Insrr    -0.1172753250  0.0424788927  0.0820528921  0.023949188  1.144644e-01 #> Cmklr1   -0.0396041090  0.0136026580  0.0010788041  0.024602600  9.070060e-02 #> Fzd6     -0.1140211764  0.1530751429 -0.0697895657  0.113688375  9.875577e-02 #> S1pr5    -0.0660805937  0.1080812139  0.0046660077  0.030912316  1.341179e-02 #> Pdgfrb   -0.0732461491  0.1501492812 -0.0527445960 -0.047087757 -2.850070e-03 #> Flt1     -0.0155193272  0.0266518562  0.0673163402  0.094393292 -1.011798e-01 #> Adgrl4   -0.0346288260  0.0425105213 -0.0108792787 -0.009631311  1.770198e-01 #> Lpar6    -0.0588805058  0.0571018410  0.0483397106  0.050578808 -6.025791e-02 #> Epha6     0.1555536626  0.2430613926 -0.1852991630 -0.029631591  1.834738e-01 #> Emcn     -0.0305888355  0.0959423664 -0.1325424252 -0.123799242 -2.558188e-02 #> Cldn5    -0.0067321275  0.0122745704  0.0127934315 -0.085871309  5.538852e-02 #> P2ry12    0.1154826304 -0.0150175459 -0.0742144472  0.019093224 -1.626320e-01 #> Adgrf5   -0.0521902166  0.0320573870 -0.0207656274 -0.063117020  1.082515e-01 #> P2yr13    0.0339352881  0.0244972272 -0.0700270533 -0.145165307  8.854780e-02 #> Adgre1    0.1423820803  0.0869281922 -0.1034038317 -0.134396462 -4.992566e-02 #> Cx3cl1   -0.0546487691  0.1214932329  0.1470428951  0.172273146  4.498589e-02 #> Plxnb3    0.0549917780 -0.1360321683  0.0950419678 -0.066517875  1.400429e-01 #> Flt4      0.1198038368 -0.0217541494 -0.0295915995  0.003615632 -6.545003e-02 #> Slc17a7  -0.1040082909 -0.0544688558  0.1011107378  0.074855289 -3.432861e-02 #> Cd300c2  -0.0852420058  0.1236184937  0.0134183798 -0.021155570  2.728315e-02 #> Tek      -0.0482992317  0.0257313910 -0.0542945457 -0.037682356 -1.068850e-01 #> Kdr       0.1058664750 -0.1358585739  0.0403373051  0.181343131  3.036184e-02 #> Kcnj8    -0.0344877640  0.0163157234  0.0543891824  0.007888845  1.081797e-01 #> S1pr3    -0.0452942301 -0.0690724372  0.0166450601 -0.039199798 -1.201898e-01 #> Tie1      0.0844206796  0.0122081981  0.0943294026 -0.169360972 -1.482741e-01 #> Pdgfra   -0.0039157415  0.0876653809  0.0170881633  0.105164240  8.138765e-02 #> Baiap2    0.0334069736 -0.0659063688 -0.2514798559 -0.073928874 -1.306925e-01 #> Calcrl   -0.0795227061 -0.0702647992 -0.0283846237  0.160238947  5.060292e-02 #> Adrb2    -0.0608379472  0.0165235825 -0.0087501827 -0.043961970  6.355782e-02 #> Ccr2      0.0450320033  0.0201140813 -0.0817428718 -0.043632859 -2.042879e-02 #> Alk       0.0193764339  0.0129192361 -0.0440073469  0.082974022 -1.287248e-02 #> Tacr3     0.1332178273  0.0295397648  0.0777628377  0.026480596  3.395530e-02 #> Erbb3    -0.0567245023  0.0240321500 -0.0815180039 -0.006732310  9.438577e-03 #> Pcdh15    0.1906372756 -0.0610292243 -0.0448330055 -0.050284579  2.352267e-02 #> Grm7      0.0193440105 -0.2034341921  0.1329459106  0.191313159  1.325848e-01 #> F2r      -0.1506523811  0.0260753897  0.1440656235  0.033552726  2.891180e-02 #> Bdkrb2    0.1140806165 -0.0002623405  0.0836713590  0.060123821  1.249961e-01 #> Adgrv1    0.2284523889  0.2460625624  0.0494842467 -0.102673594  7.705142e-02 #> Gprc5c   -0.0565288608 -0.1142209865  0.0292548153 -0.118833458  2.911910e-04 #> Tbxa2r    0.0436121427 -0.0561700454 -0.0962430534  0.150360368 -1.478006e-01 #> Ackr1     0.0134996377 -0.0343470921 -0.0174875412 -0.050907786  4.855027e-02 #> Lpar2    -0.0112034563  0.0556131690  0.0485626116 -0.067900980 -2.298362e-02 #> Myh11     0.0794628081  0.0090021298 -0.0031261657  0.076100956 -9.440891e-04 #> Musk     -0.1132664810 -0.0160927527 -0.0139378836 -0.036576131 -4.239191e-02 #> Cnr1     -0.0066558292 -0.0366830708  0.0281410669 -0.004356620  2.028521e-02 #> C3ar1     0.0155008299  0.0166105274 -0.0245486781 -0.006759377  2.784848e-02 #> S1pr4    -0.0220906316  0.0033879640  0.0141870236  0.168667541 -6.699874e-02 #> C5ar1     0.0960111160 -0.0535007413 -0.0743741347 -0.072689203  2.516896e-02 #> Fpr1      0.0329341540  0.0321719135 -0.0596426659  0.006059747 -1.256468e-02 #> Sctr      0.0695576161 -0.0531381936  0.0921986957  0.011224008 -7.011426e-02 #> Gpr158    0.0015329909  0.0548280767 -0.2227016310  0.173174901 -2.903093e-01 #> Cxcr4    -0.0016786406  0.0219833075  0.0414682025 -0.003677807 -2.395059e-03 #> Hrh2     -0.0792255225 -0.2616825076 -0.0718836525 -0.161641011  1.007261e-01 #> Slc17a6  -0.0357243084 -0.0115859619 -0.0387670457  0.050875528  6.262938e-02 #> Ppp1r3g   0.1669086391  0.0811501547 -0.0286354384  0.145831306  8.553946e-02 #> Pln       0.0684256776  0.0694085860 -0.0522243887  0.065296752  5.266343e-02 #> Grin2b    0.0523079210  0.0052384402  0.0947439856  0.100807064 -1.024327e-01 #> Taar7e   -0.0738361372  0.0002086252 -0.0930331693 -0.020204480  5.401002e-02 #> Ptger2   -0.0667717302  0.0788384479  0.2038392132  0.004995610 -1.276164e-02 #> Mc4r      0.0333960736 -0.1396369222 -0.0106242395 -0.079133700  8.469524e-04 #> Ghsr     -0.0693555261 -0.0889129111  0.0880344797  0.014366345 -4.696204e-02 #> Nmbr     -0.0965961547  0.0039125312  0.0420587836 -0.020019142 -1.199213e-01 #>                 Dim.66        Dim.67       Dim.68        Dim.69        Dim.70 #> Mlc1     -2.180444e-02  0.0509485754  0.268830108  0.2073268570  0.1481951292 #> Gprc5b    5.735700e-02  0.2503791817 -0.106428827  0.1776642000 -0.0490134765 #> Gfap     -5.313815e-02 -0.0708074923  0.037384256  0.0016725497 -0.0362639411 #> Ednrb    -7.024608e-03  0.0946853285  0.034493813  0.0576949710 -0.2285982282 #> Sox9      1.807022e-01  0.0546773712  0.070783877 -0.0382300910 -0.1177357502 #> Aqp4      1.592885e-01  0.0329768358 -0.070395176 -0.0248747928  0.0970304244 #> Gjc3     -3.323623e-02 -0.0428932266 -0.097155096  0.0356396823 -0.0362664889 #> Sox8     -5.277059e-02 -0.0702069374 -0.067654032  0.0847521498 -0.1821537499 #> Ntsr2     1.688058e-02 -0.0855470970  0.027037766 -0.0228350509  0.0865575306 #> Smo       9.069631e-02 -0.0999477249  0.015316573 -0.1035136035 -0.0903782692 #> C1qb      6.431639e-02 -0.0236558233 -0.007937257 -0.0208539151 -0.0167829225 #> Olig1     8.167612e-02 -0.0768756932 -0.008059446 -0.0014557578  0.2081991701 #> C1qa     -7.250339e-02 -0.0610496153  0.041596122  0.0134164109  0.0697352462 #> Pth1r    -1.146547e-04  0.1146435822  0.027816673  0.0507767074 -0.0367906224 #> Gabbr2   -9.455405e-02  0.1017963300 -0.011819667 -0.1079435303 -0.0572648210 #> Timp4    -3.103154e-02 -0.0536642920 -0.075443225 -0.0680516985  0.1248819977 #> Abcc9     6.328993e-02  0.0068940021 -0.128888497  0.0248664545 -0.0376274956 #> Csf1r    -3.376456e-02 -0.1376937249  0.060473759  0.0179306420 -0.0185606207 #> Ntrk2    -6.184334e-02  0.0393200132  0.056932403 -0.0378919698  0.1476871517 #> Adgrg1   -5.671942e-02  0.0739760013 -0.056784189  0.0352210481 -0.0878511515 #> Ntrk3    -1.289265e-01  0.0926089226  0.014160283 -0.0855939359 -0.0864180736 #> Erbb4    -6.175009e-02 -0.0719833111  0.039687117 -0.0576475924  0.0276273570 #> Selplg    4.532071e-02 -0.0067639082 -0.069806173  0.0635047704  0.0003958421 #> Cspg5    -9.683195e-02 -0.1085274708 -0.156940211  0.0113932006 -0.1473729815 #> Dlk1     -9.038941e-02  0.0012696048  0.064229827 -0.0637610055 -0.0074678825 #> Gpr37l1   3.819727e-02  0.0278482987 -0.096895834 -0.0523089889  0.0574720748 #> Fgfr3    -1.543647e-01  0.0321129405  0.202431531 -0.0362069394 -0.0014650356 #> Slc25a18  3.852797e-02 -0.1596785085 -0.049197666 -0.0973583053 -0.0251660525 #> Igf1r     9.880276e-02 -0.0274912042  0.069245082  0.0646948662 -0.3308105369 #> S1pr1     3.196872e-02 -0.1341877696  0.182367895  0.0858929441 -0.0704561353 #> Grm5     -1.139508e-01 -0.0324040008 -0.062967961 -0.0596359471 -0.0422567204 #> Axl      -8.913474e-02  0.1042111503  0.096248942 -0.0570438354 -0.0892342835 #> Efemp1    2.237215e-02 -0.0352328527 -0.035873485 -0.0692725147  0.0478291537 #> Adgrb3    8.725996e-02 -0.0252023723  0.034915916 -0.0935292744  0.0627254945 #> Fn1      -1.163542e-01  0.0537656999  0.044686716  0.0810373760  0.0469238872 #> Mertk    -8.647904e-02  0.1210436145 -0.088566619  0.0573608159 -0.0006104242 #> Adgrl2   -2.064289e-03 -0.1157869316  0.047864879 -0.0746061721  0.0125967135 #> Fzd2      1.633771e-01 -0.1050816395 -0.005585715  0.1005945047 -0.0007038798 #> Aldh1l1  -4.863740e-02 -0.1081526474 -0.177888569 -0.0580112239  0.1650436979 #> Adgrg6    7.030933e-02 -0.0393976569  0.070051139 -0.0385737212  0.0380361790 #> Egfr     -1.122364e-01  0.0322319403 -0.014760206  0.1431062119 -0.0302216042 #> Kit      -5.858489e-02 -0.0252964268  0.025001497 -0.0119366782  0.0824318599 #> Ptgdr    -6.424682e-02  0.0878189159 -0.067495526  0.0076604962  0.0461745449 #> Gad1      4.734447e-02  0.0249047951 -0.067107862  0.0450866515  0.0022643001 #> Tyro3     9.807800e-02  0.0569549369  0.143174619 -0.2399856277 -0.0365760436 #> Atp13a5  -2.777914e-02 -0.0928380836  0.075681991 -0.0787949787 -0.0345953792 #> Ddr2      6.543896e-02 -0.0104007773  0.004722769  0.0426247739 -0.0748795891 #> Rspo3     4.291280e-02 -0.1178230258 -0.023212467 -0.2122770140 -0.0918374535 #> Arhgap29  5.550297e-02  0.0366830170 -0.167052644  0.0906459975 -0.0263857205 #> Fzd7      1.863546e-03  0.1070347570  0.115631709 -0.0591066088 -0.0776524979 #> Slc47a1   4.684035e-02 -0.0244283416  0.001303967  0.0608170870  0.0328530568 #> Ptger3   -6.286797e-02  0.0374204689  0.082281266  0.0563592703  0.0591123992 #> Bdkrb1   -9.511756e-02 -0.0942972014 -0.018464926 -0.0993888670  0.0237951108 #> Traf4    -1.149698e-01  0.0545923176  0.040503404 -0.1057209814 -0.0515894468 #> Cx3cr1    4.448548e-02  0.1501238920 -0.012641075 -0.0187385562 -0.0722349627 #> Anxa11    2.646427e-01 -0.2760280374 -0.061635376 -0.1054860528 -0.1362392279 #> Adgrb1   -4.789822e-02  0.0011749307 -0.040811845  0.3008067472  0.0414684839 #> Lpar1    -8.238595e-02 -0.1244296704 -0.063785151 -0.0347945122  0.0845929891 #> Gpr17     2.035282e-02  0.0203824417  0.028740057 -0.0610067861  0.0577816203 #> Cxcl12   -1.468419e-01 -0.0102809200  0.123691090  0.0417879960  0.0581991990 #> Epha4     1.010654e-01 -0.1343726689 -0.136827150  0.1453590870 -0.0766896454 #> Gpr182    5.702545e-02 -0.0369997088 -0.020969974 -0.0647287082  0.1126997056 #> P2ry14   -6.944200e-02  0.0533099636  0.051846358 -0.0416923965  0.1233763291 #> Hcar1    -3.004285e-02  0.0819482274 -0.069177994 -0.0250579826 -0.0863313712 #> Ephb1    -1.421088e-01 -0.0261027951 -0.071937626  0.1863365828  0.2779048367 #> Grm3      1.369024e-01  0.0029764265 -0.018496859 -0.0901648787 -0.0458559239 #> P2ry1    -7.449036e-02  0.0898084448 -0.039822891  0.0508188865 -0.0695922339 #> Ptk7     -8.549627e-02  0.0628703488 -0.062995763  0.1150675458  0.0603093544 #> Slco1a4  -8.244239e-02  0.0009620091 -0.053798546  0.1288775536  0.0187408190 #> Insrr     1.109964e-01  0.1194547260 -0.072473511 -0.0384624547 -0.0525173643 #> Cmklr1    8.287082e-02 -0.0535498217 -0.130034823 -0.0229776114  0.0500126685 #> Fzd6      1.321660e-01  0.0144199643 -0.208261844 -0.0206463307  0.1026324326 #> S1pr5    -3.306042e-02  0.0505443319  0.029651998 -0.0259124538 -0.1753439125 #> Pdgfrb   -9.453916e-02 -0.0430714491  0.038897726  0.0860887076  0.0148144960 #> Flt1      5.291115e-02 -0.0166497237  0.080254244 -0.0311409824  0.0428088617 #> Adgrl4   -2.415542e-05  0.0173469552 -0.082244419 -0.1429460622  0.0572207401 #> Lpar6     1.255938e-05  0.0679932436  0.070519629  0.0044468281 -0.0146509063 #> Epha6     1.158855e-01 -0.1942669820  0.234264801  0.2828944622  0.0425495209 #> Emcn     -9.433091e-02 -0.1458467574  0.005451370  0.0210588089  0.0322306084 #> Cldn5    -3.915228e-02 -0.0315559801  0.127931519 -0.0429383465 -0.0204878394 #> P2ry12   -3.373338e-02  0.0708821012  0.010509976 -0.0687328407  0.0139550011 #> Adgrf5    1.810203e-02  0.0732510684 -0.004878348 -0.0464582832 -0.0190382800 #> P2yr13   -6.614625e-02 -0.1078141268  0.001570643  0.0216281907  0.1539601742 #> Adgre1   -4.179230e-02 -0.0079797822 -0.050419779  0.0082445979  0.0229729075 #> Cx3cl1   -4.625971e-02 -0.0676084560  0.096315663  0.0050563932  0.0765853026 #> Plxnb3    1.749145e-01 -0.0455347819  0.001378771 -0.0049625043  0.0214533419 #> Flt4     -5.657952e-03 -0.0598560645 -0.072707446  0.0655366145 -0.0611033774 #> Slc17a7  -9.659451e-02  0.0985333693 -0.100712126 -0.0972843882  0.0283024070 #> Cd300c2   4.687387e-02  0.0491626576 -0.009755632  0.1019862691 -0.0398527218 #> Tek       3.057949e-02  0.0143083634 -0.267661650  0.1072584158  0.0635469833 #> Kdr      -2.662782e-02  0.0638379380 -0.090074157  0.0037730731 -0.0318037031 #> Kcnj8     2.719719e-02  0.0525318342 -0.027521016 -0.0557996198  0.0574561414 #> S1pr3     2.710308e-02 -0.0415936134  0.051371790  0.0304945807  0.0021683414 #> Tie1     -3.195196e-02  0.0023658947  0.045181223 -0.0131240363  0.1439546487 #> Pdgfra    1.664750e-02  0.0550685589  0.040726360  0.1454141458 -0.1236729211 #> Baiap2    1.802067e-01  0.1307522080 -0.014527508  0.1075417272  0.0841343417 #> Calcrl    1.208724e-01  0.0920428499  0.152312768  0.0113467312 -0.0543336788 #> Adrb2     7.526892e-02  0.0386791434 -0.014336466 -0.0221495165  0.0180708207 #> Ccr2      8.311026e-03  0.0216781648 -0.035463248 -0.0201927133  0.0268575194 #> Alk       8.424806e-02 -0.0171405303  0.037199497 -0.0337643015 -0.0291163607 #> Tacr3    -4.318870e-02 -0.1983578007  0.057655428  0.0561142818 -0.0235120459 #> Erbb3    -9.843728e-02  0.0121679417  0.201440315 -0.0553532446  0.0438030341 #> Pcdh15    1.998874e-02  0.0304796649  0.058526792 -0.0349101033  0.0521330978 #> Grm7     -3.338724e-02  0.0355627120  0.020473452 -0.1000911557  0.1716592555 #> F2r       1.549603e-01  0.0655745202 -0.086818368 -0.0692260393  0.1130852388 #> Bdkrb2   -4.415963e-02 -0.0588436381 -0.086076129 -0.0863462946  0.1205577456 #> Adgrv1   -1.323651e-02  0.1439844055  0.086699551 -0.2259830019 -0.0303825980 #> Gprc5c    8.620728e-02  0.0153277340  0.110902858  0.1075562888  0.0224857705 #> Tbxa2r   -8.235208e-02  0.0098698867  0.038334444  0.0345995030 -0.0854565427 #> Ackr1    -1.831774e-02 -0.0446091558 -0.049202852 -0.0186152904 -0.0066678322 #> Lpar2     3.916925e-02  0.0520418454  0.086949587 -0.0100194352  0.0013993009 #> Myh11    -1.734374e-02  0.0464736842  0.128354362 -0.0823989557  0.0091982929 #> Musk      1.420258e-01  0.1200756088 -0.088802771 -0.0528757769  0.0411670460 #> Cnr1      1.239605e-03  0.0222121304  0.033677847  0.0112741666  0.0032176017 #> C3ar1    -1.864165e-03 -0.0398766239  0.035853029 -0.0185812194 -0.0453215077 #> S1pr4     3.929798e-02 -0.0656080479  0.074751001 -0.0045482941 -0.0710797499 #> C5ar1    -6.574640e-02 -0.1134052895 -0.055974484 -0.0661784584  0.1015930800 #> Fpr1     -1.135557e-01  0.0649296347 -0.007038102 -0.0255501626  0.0423049175 #> Sctr      1.075215e-01 -0.0775023029  0.014688768 -0.0222430807  0.0228493694 #> Gpr158    3.210956e-01  0.1827852345  0.171148003 -0.0780930999  0.2047212526 #> Cxcr4    -2.404657e-02 -0.0181956487  0.031321822  0.0409752295 -0.0410268751 #> Hrh2     -1.481572e-01 -0.0915637868  0.004560917 -0.1947067988 -0.0511252540 #> Slc17a6   1.944781e-02 -0.0245591105 -0.064260286 -0.0088208413 -0.0154390916 #> Ppp1r3g   9.623146e-03  0.0108886993 -0.054879007 -0.0573771077  0.0462825739 #> Pln      -7.934541e-02  0.0241018518 -0.053936350 -0.0058742348  0.0062657235 #> Grin2b    8.801095e-03 -0.3010850306  0.078458310 -0.0510765245  0.0073081916 #> Taar7e   -7.515084e-02  0.0884732178 -0.050378275 -0.0004016495 -0.0794989187 #> Ptger2   -1.640076e-01 -0.0832545165 -0.128242094 -0.1058812083 -0.1898248819 #> Mc4r     -1.354755e-02  0.1309691658  0.074115489 -0.0553346191  0.0977042140 #> Ghsr     -1.043267e-01  0.0778342550 -0.039263466 -0.1128103024  0.0377625361 #> Nmbr      1.072201e-02  0.0774311468 -0.098071576 -0.1144985782  0.0181678188 #>                Dim.71       Dim.72        Dim.73       Dim.74        Dim.75 #> Mlc1     -0.060559691 -0.050950656  0.1022928436 -0.018755257 -0.1273852264 #> Gprc5b   -0.063104300  0.286250740 -0.0251856093 -0.038993956  0.0550875457 #> Gfap      0.065110279 -0.064439665 -0.0196306516  0.024552527  0.0119924509 #> Ednrb    -0.058516847  0.062645785 -0.0124203832 -0.038077283  0.0711736577 #> Sox9      0.082880214  0.035369083 -0.0739366722 -0.174569439 -0.0932799709 #> Aqp4     -0.032531480 -0.007643029 -0.0158767950 -0.113869475  0.0285774774 #> Gjc3      0.091675499 -0.039255337 -0.0040948021 -0.043561623 -0.0178024173 #> Sox8      0.116895229  0.066927753 -0.0972443985 -0.144672002  0.0168731617 #> Ntsr2    -0.015591112 -0.031524694 -0.0188671179  0.129121017 -0.0847018061 #> Smo      -0.224692032 -0.139799582 -0.1127574648 -0.013620345  0.0438908379 #> C1qb     -0.023277221 -0.083978585  0.0705403411 -0.162778227 -0.0148112351 #> Olig1    -0.053148196 -0.019962569 -0.0173464567 -0.072584330  0.0160094417 #> C1qa      0.039426648 -0.043254062  0.0631424835 -0.139113119  0.0205276659 #> Pth1r    -0.001187810  0.040533385 -0.0966006225  0.062951631 -0.1350839075 #> Gabbr2    0.046118872  0.012660744  0.0108177333 -0.044401072  0.0521251448 #> Timp4    -0.053006936 -0.110923467  0.1081139190  0.134769024 -0.0782112181 #> Abcc9    -0.007908647  0.014986630  0.0726891459 -0.066747179  0.1131103049 #> Csf1r     0.036190447 -0.008103598  0.0031644822  0.175836367  0.0805081945 #> Ntrk2     0.098648011  0.021707565  0.1659145137  0.147629244  0.0951983529 #> Adgrg1    0.024699669 -0.049958349  0.0173139360  0.002571492 -0.1207213763 #> Ntrk3    -0.057384905 -0.083562959 -0.0061604841 -0.179030823 -0.2691322738 #> Erbb4     0.010490645  0.047744514  0.1047638152 -0.028263450  0.0888599345 #> Selplg    0.042660938 -0.028439026 -0.0688687418  0.038770248  0.0401933829 #> Cspg5    -0.004519161 -0.055718106 -0.0271939542 -0.145355323  0.0468352442 #> Dlk1     -0.110660337  0.125386364  0.0777297668  0.069799658  0.0040221451 #> Gpr37l1  -0.078073292  0.110938679 -0.0595206938  0.040679380 -0.1031500316 #> Fgfr3    -0.088658454 -0.052835057  0.2319331029 -0.082535380  0.0624165765 #> Slc25a18 -0.065393512  0.038525963 -0.1580529219 -0.030167095  0.0821272433 #> Igf1r    -0.028591882  0.009023995  0.0770125327  0.056612838  0.0422655194 #> S1pr1     0.131751483 -0.178023590 -0.1113031726 -0.068278231  0.0293735256 #> Grm5      0.098687651  0.026115014  0.1762127827  0.039227284  0.0011007656 #> Axl       0.065805353  0.136747191 -0.0286514220  0.059956125  0.0617320661 #> Efemp1   -0.076220229 -0.129121931 -0.0562871224 -0.032787618  0.0289195308 #> Adgrb3    0.064041974  0.031469693 -0.0031008663 -0.157229323 -0.0410974684 #> Fn1       0.036286143  0.024180024 -0.0368936210 -0.078434365 -0.0193022541 #> Mertk     0.092169020  0.071722932 -0.0440574324 -0.010117281  0.0654870000 #> Adgrl2   -0.131856018 -0.028217458 -0.1340055799 -0.083751561  0.0149735164 #> Fzd2      0.115837403  0.094488379  0.0940590424  0.143806481  0.0211136055 #> Aldh1l1  -0.038335766  0.155998884  0.0142125899  0.031282719  0.0308590798 #> Adgrg6    0.055784075  0.070004096  0.0956388265 -0.059866370  0.0264481726 #> Egfr     -0.076453803 -0.064555290 -0.1362988360  0.046202873  0.1516301307 #> Kit       0.076757025 -0.048191096  0.0097628019 -0.015261147 -0.0029335677 #> Ptgdr    -0.029265026  0.002897508 -0.0690502261 -0.103131874  0.1510723175 #> Gad1     -0.047986395 -0.069248504 -0.0703758795  0.009887484 -0.0341162883 #> Tyro3    -0.030631130 -0.122470370  0.1276345734  0.079224103 -0.0248482228 #> Atp13a5   0.099169748 -0.077913932  0.0090822790  0.079108650  0.0275004530 #> Ddr2     -0.018975384 -0.058400662  0.0375447418  0.029753810 -0.0556353252 #> Rspo3     0.049313998  0.159672913  0.1039126727 -0.090252886 -0.2950482581 #> Arhgap29 -0.020959942 -0.107418816  0.0481068763  0.003069581  0.0944723651 #> Fzd7      0.101548628  0.111416672  0.2088554802  0.277222595  0.1188329761 #> Slc47a1   0.051708942  0.013968140  0.0593560566  0.084578114 -0.0629012098 #> Ptger3    0.051468349 -0.039737984 -0.0573526099 -0.049698682 -0.0162281929 #> Bdkrb1    0.127761941 -0.138731126  0.1608980963 -0.075051234  0.0590207919 #> Traf4    -0.063344704 -0.012534809  0.0203937363  0.144560887  0.0463399743 #> Cx3cr1    0.143654151  0.031789858 -0.0047925510  0.020867781  0.0621503244 #> Anxa11    0.009388242 -0.033943951  0.1442159699  0.105662335  0.0049519296 #> Adgrb1    0.150684850 -0.162891246 -0.2254326478  0.105044561 -0.0944318070 #> Lpar1    -0.058870535 -0.024864632 -0.1245706115  0.004371882 -0.1295023517 #> Gpr17     0.027053603  0.059960360  0.0420375037 -0.001731964  0.0365777244 #> Cxcl12    0.101076179  0.125139444 -0.0374556342 -0.257389544 -0.0221984599 #> Epha4    -0.294763563 -0.075414276 -0.0277372962  0.026642616  0.0518827275 #> Gpr182    0.133006977 -0.001128710 -0.0548371742 -0.011982830 -0.0443853979 #> P2ry14    0.026657020  0.076195817 -0.0076906024  0.117600171  0.0460448912 #> Hcar1    -0.059214971  0.039174103 -0.0936225281 -0.040445328  0.1625684908 #> Ephb1    -0.101019819 -0.046744247  0.1529176941  0.021629283 -0.1404678211 #> Grm3      0.109301186 -0.029724067 -0.1228539379  0.055711961  0.1192337728 #> P2ry1    -0.180612427 -0.026837031  0.0109558247  0.083601305  0.0408412516 #> Ptk7     -0.010507897 -0.064895990  0.1458587935  0.051389172  0.1265438662 #> Slco1a4   0.010247809 -0.082895546  0.0001276429 -0.027588189 -0.0934805234 #> Insrr    -0.082158744  0.037805907  0.0795378949 -0.008487538 -0.0445181066 #> Cmklr1   -0.004152000 -0.023137470  0.1257604252  0.003100938 -0.0263894946 #> Fzd6     -0.081008714 -0.025902064  0.0844757620  0.010606930  0.0006235811 #> S1pr5    -0.022733316  0.047537196 -0.0512570357  0.011060552 -0.0124225958 #> Pdgfrb    0.009121902  0.008915702 -0.1023114767 -0.176491732 -0.1017082329 #> Flt1      0.031452419 -0.013018861 -0.0501526701  0.009772905 -0.0350141819 #> Adgrl4   -0.005513909  0.087751651 -0.0044220610  0.009775016  0.0089576878 #> Lpar6    -0.009826361 -0.078178309  0.0020631523 -0.100706026 -0.0036210347 #> Epha6    -0.121894975  0.055095684  0.2062313111 -0.166419465  0.1678945872 #> Emcn      0.043449920 -0.028290495 -0.0304780762  0.005189266  0.1157880487 #> Cldn5     0.035189418  0.078680386 -0.0467720459 -0.017826302  0.0386936431 #> P2ry12   -0.178236825  0.093585603  0.0011242759 -0.081253246 -0.1264142502 #> Adgrf5   -0.077603642 -0.026613754 -0.0067177286  0.062230559  0.0813823346 #> P2yr13   -0.079648099  0.062733282 -0.1485847766  0.200841669 -0.0352454412 #> Adgre1    0.023379592  0.011143278 -0.0376802157  0.002915943  0.0124277978 #> Cx3cl1   -0.037397708  0.109724067 -0.0842579078  0.135686249  0.1131269610 #> Plxnb3    0.124569927 -0.183848448 -0.0120186075 -0.077876821  0.0107417823 #> Flt4      0.094907782 -0.032516940 -0.1425573097  0.070694990  0.1707816625 #> Slc17a7   0.104236653 -0.213271141  0.0138193008  0.074494125 -0.0968776258 #> Cd300c2   0.049152009 -0.018961612  0.0194293868  0.003806559  0.0687467162 #> Tek      -0.007670036  0.107529236  0.2391819060 -0.050292116  0.0018261780 #> Kdr      -0.019381754 -0.002021575  0.0451753736 -0.054807464  0.0224094181 #> Kcnj8    -0.005558235  0.012980134 -0.0277121970 -0.047229748 -0.1231623118 #> S1pr3    -0.127394091  0.021648696  0.0175628003 -0.017508824 -0.0248130574 #> Tie1      0.008215865 -0.146948617 -0.0485479008  0.039243866 -0.1254431631 #> Pdgfra   -0.090384602 -0.056379918  0.0331875230  0.073043289 -0.1358707139 #> Baiap2    0.103627350  0.164105029  0.0565464234  0.037955166 -0.0261337736 #> Calcrl   -0.030020670 -0.109678204 -0.1254510999  0.163198581 -0.0862017149 #> Adrb2     0.002161610  0.088005914 -0.0241958440 -0.025731530 -0.0285909318 #> Ccr2     -0.208463359  0.044159734 -0.1422987412  0.140113228 -0.1372275759 #> Alk      -0.084746657 -0.036533273  0.0464469251 -0.012244701 -0.0149087274 #> Tacr3     0.077760336  0.128150600  0.0022168409  0.036205854 -0.0953883249 #> Erbb3    -0.144530162  0.030135373  0.0767444070  0.037887542  0.0086161100 #> Pcdh15    0.014829554  0.007248258 -0.0211172492  0.112911203  0.0301431138 #> Grm7     -0.047209521  0.105826237 -0.1215784923 -0.089147272  0.1116265036 #> F2r      -0.030329587  0.028170487  0.0749223907 -0.112193761 -0.0218313770 #> Bdkrb2    0.137587609  0.033391732  0.0002635216 -0.029210482  0.0628804221 #> Adgrv1   -0.016049451 -0.027250083 -0.0180509832 -0.044595126  0.1089364143 #> Gprc5c   -0.114962935  0.215002898 -0.0340260345  0.044331893 -0.1009861606 #> Tbxa2r   -0.089298824 -0.111843703  0.0940002112  0.061147276  0.0245176681 #> Ackr1    -0.128625115 -0.022980789  0.0332587304  0.040003594  0.0439962906 #> Lpar2    -0.024285271  0.024547820  0.0321658867 -0.008548279 -0.0394970902 #> Myh11     0.050344685  0.010990289 -0.1060057159  0.047070393  0.0278885561 #> Musk     -0.125214290 -0.169802429  0.0001039446 -0.035932161  0.0812629584 #> Cnr1      0.038376210  0.116879598 -0.0127700809 -0.001983683 -0.0331605346 #> C3ar1    -0.125735276  0.069509768 -0.0910894863  0.174240351 -0.1569059637 #> S1pr4    -0.054025801  0.046655947  0.0790624390 -0.101284971 -0.1315372025 #> C5ar1     0.079675134  0.013193643 -0.0797084519  0.059000007  0.0752920821 #> Fpr1     -0.104878749 -0.017347497 -0.0208630069 -0.104059744 -0.0468103471 #> Sctr     -0.050468735  0.069985910 -0.0151862557 -0.022359392 -0.0080035183 #> Gpr158    0.131369538 -0.113953865 -0.1356260208 -0.041406388 -0.0023394918 #> Cxcr4    -0.008670854 -0.009210456 -0.0005997615 -0.007249846 -0.0286132290 #> Hrh2     -0.130491936 -0.119811469  0.1015890625 -0.039165314  0.0176380121 #> Slc17a6   0.060163594 -0.041283659 -0.0479424058  0.047416627  0.0093347458 #> Ppp1r3g  -0.066629853 -0.013792342 -0.0585162403  0.126508444 -0.0662379240 #> Pln       0.079018611 -0.028710834  0.0087757763 -0.005087685  0.1033973260 #> Grin2b   -0.111822627  0.243692045 -0.1578893097 -0.082824719  0.1513802580 #> Taar7e   -0.047234773 -0.035073135  0.0476735877 -0.050495762 -0.0040686524 #> Ptger2    0.106915541  0.010806603 -0.0462962406  0.062192881 -0.1690984676 #> Mc4r     -0.216306566 -0.155642589 -0.0712733495 -0.066852618  0.2659486098 #> Ghsr     -0.003243523  0.092192635 -0.0514766228 -0.050259131  0.0318545930 #> Nmbr     -0.030472123  0.138068709 -0.0914862322  0.021187606  0.0183807215 #>                 Dim.76        Dim.77        Dim.78        Dim.79        Dim.80 #> Mlc1     -0.0363355712 -0.0145850457  4.619688e-02 -0.0827422236 -0.2286119280 #> Gprc5b    0.0378449691  0.1408382865 -2.108614e-01  0.0589767365 -0.0211923850 #> Gfap     -0.0358361030 -0.0318860948 -3.667653e-02  0.0377614621  0.0083006782 #> Ednrb     0.0544582259 -0.0790516103 -1.767260e-01  0.0612266925 -0.0966505028 #> Sox9     -0.0423490415  0.1829919235  1.022337e-01 -0.0440008623  0.0249128488 #> Aqp4     -0.0490670917  0.0312792174  1.604871e-01 -0.0203047670 -0.0206999055 #> Gjc3      0.0040269543 -0.0118508993  2.115296e-03 -0.1311189707  0.1275781304 #> Sox8      0.0154296858  0.0921118891  1.099499e-01  0.2129670877  0.1750382804 #> Ntsr2     0.0555101521  0.0334074512 -8.656427e-02  0.0011841208  0.0452857527 #> Smo       0.0047894203  0.1232687312 -9.303399e-04 -0.0271568814  0.0253260703 #> C1qb      0.0478372170  0.0304290715  6.717821e-02 -0.0494929893  0.0201865056 #> Olig1     0.0494195615 -0.0382916207  2.342742e-02 -0.1271106990 -0.1839703352 #> C1qa      0.0611427730 -0.0092837490  6.203749e-02  0.0273246218 -0.0082114823 #> Pth1r    -0.1096084532 -0.0674148034  4.511431e-02 -0.0849483486  0.0447609778 #> Gabbr2   -0.1130569980  0.0846608280  1.968073e-01 -0.0555984294 -0.0731710691 #> Timp4     0.1263856775 -0.0030835233 -1.645243e-02  0.1049776872  0.0892833384 #> Abcc9     0.1826401727  0.1421652865 -7.319609e-02 -0.0560503173 -0.0030302058 #> Csf1r     0.0046355290  0.0641369775 -9.832798e-02 -0.0448371208 -0.0245870961 #> Ntrk2     0.2037201363  0.0217331969  2.091932e-02  0.0244895404  0.3759422328 #> Adgrg1   -0.0578984680 -0.0573947087  8.177562e-02  0.0470807182  0.1292144826 #> Ntrk3    -0.0710488939 -0.2061473876 -1.524915e-01 -0.0565253864 -0.0302339522 #> Erbb4    -0.0953303470  0.1293148032 -1.501850e-01 -0.1623917938  0.0463883134 #> Selplg   -0.2322851583  0.0297233284 -8.647665e-02  0.0434054587  0.0473792620 #> Cspg5    -0.1518318569  0.0900088395 -3.953102e-02  0.1227085636  0.0071160477 #> Dlk1      0.0625768921 -0.0003054694 -4.654048e-02 -0.0176091706 -0.0935692458 #> Gpr37l1   0.0264995083  0.0239750508 -1.288843e-01 -0.0690497219 -0.1208690615 #> Fgfr3     0.0465398498  0.1401291817  2.132495e-01  0.0372214881 -0.0861244140 #> Slc25a18 -0.0435888626 -0.1779055393 -4.778637e-02 -0.0052799722 -0.2224713545 #> Igf1r     0.0747048584  0.1654967803  1.210928e-01 -0.0715755555 -0.0604122390 #> S1pr1     0.0442306278 -0.1133540339 -1.197171e-01 -0.0932948193  0.0303706699 #> Grm5     -0.1338209139  0.2319024076 -3.959755e-02 -0.0485246500 -0.0323851915 #> Axl       0.0826296026 -0.1164918690 -8.938248e-03 -0.0857293880  0.0123623205 #> Efemp1    0.0316806632  0.0619865727  8.706941e-02  0.0998284791  0.0273842532 #> Adgrb3    0.0682007357  0.0325455170 -3.481689e-02 -0.0512028188 -0.0031584051 #> Fn1      -0.0038519258  0.0455066318  1.842734e-02  0.0248713324 -0.0198623485 #> Mertk    -0.0198082836 -0.1637886302 -1.210735e-02  0.0711536213 -0.0633425862 #> Adgrl2    0.0720700714  0.1563693141 -5.897087e-02 -0.0815778607 -0.0447727688 #> Fzd2     -0.0966759738 -0.0939515765 -1.197041e-02 -0.0813943337  0.1076128857 #> Aldh1l1  -0.0013086915 -0.1275540425  1.506279e-01 -0.0072982955 -0.0930111260 #> Adgrg6    0.0530038219 -0.0658479530 -1.388035e-01  0.1545743274  0.0585043790 #> Egfr     -0.2603799282  0.0468905204  8.295931e-02 -0.0641833853  0.0688460234 #> Kit       0.0450426937  0.0182436506  3.543153e-02 -0.0458470023 -0.0606077450 #> Ptgdr     0.0929971881  0.0886538028  3.662809e-02  0.1243810600 -0.1552982897 #> Gad1      0.0844120085 -0.1252449059  1.205522e-02  0.1359940178  0.0097745236 #> Tyro3    -0.1444913632 -0.0586614776  6.465287e-02  0.3048110683 -0.0540606896 #> Atp13a5  -0.0552501205 -0.0218025098 -2.288236e-02 -0.0035680573 -0.0627137145 #> Ddr2     -0.0508719870 -0.1007551405 -2.958171e-02 -0.1442772472  0.0556476249 #> Rspo3     0.0338330458 -0.0542197124 -6.765473e-02 -0.1873662386  0.0046042496 #> Arhgap29  0.0807445491 -0.0001153793  8.071399e-02  0.1030840002 -0.0644647035 #> Fzd7     -0.0436997161 -0.0548530561 -4.980433e-02 -0.0374893985 -0.0748534653 #> Slc47a1   0.0087582645 -0.0517938717 -5.079785e-03  0.0241306334 -0.0435709406 #> Ptger3    0.0368987806  0.0688256562 -5.803567e-02 -0.0936473395  0.0746865433 #> Bdkrb1    0.0329121080 -0.1000481608  5.177176e-02  0.0166607719 -0.0518769411 #> Traf4     0.0398456972  0.0330790356 -1.965694e-02  0.1185728816  0.0764863235 #> Cx3cr1   -0.0410060213 -0.1130256354  3.264678e-02 -0.0284754493  0.0344127890 #> Anxa11   -0.0414437162  0.0792399040 -4.027865e-02  0.0206615906 -0.1181902216 #> Adgrb1    0.2729268719 -0.0388388740  6.540292e-02  0.0576916634 -0.2010228841 #> Lpar1    -0.0415085486  0.0348881853  1.091373e-01  0.0553319100  0.1421372606 #> Gpr17     0.0032016089 -0.0198702249 -1.672234e-02 -0.2128814855 -0.0753817921 #> Cxcl12    0.0095354248  0.0284045785 -1.582160e-01  0.1804325939 -0.0054606697 #> Epha4     0.1978961841 -0.1485884850 -1.287429e-01 -0.2141727029  0.2116429636 #> Gpr182   -0.0162499074 -0.0161425738 -1.476342e-01 -0.1221477943 -0.0473299512 #> P2ry14   -0.0772437717 -0.0623492782 -1.124091e-02  0.0470685012  0.0023902668 #> Hcar1     0.0021060685 -0.0089962935  5.536445e-02 -0.0355671638 -0.1393775600 #> Ephb1    -0.1992170360  0.0780243628  7.084537e-04 -0.0410192452  0.0079085436 #> Grm3     -0.1316824466 -0.1233140069  1.505651e-01 -0.1331179247 -0.1339327576 #> P2ry1    -0.1007682917  0.0222584599  7.551530e-02 -0.0813933903 -0.0470920059 #> Ptk7     -0.0525628308  0.0512145288 -2.747049e-02 -0.0689726023  0.0315609010 #> Slco1a4  -0.0933132472  0.0471517140 -1.358988e-01 -0.0179708094 -0.1019919126 #> Insrr     0.0821974479 -0.0141710807  7.455271e-03  0.0085840246  0.0680143345 #> Cmklr1   -0.0432580214  0.0222173019  1.213038e-02  0.1202270029 -0.0410927874 #> Fzd6      0.0250430289 -0.0273719775  8.057744e-02 -0.0080968344  0.0002633071 #> S1pr5     0.1699856207  0.0151161592 -6.826067e-02  0.1135536878  0.0283736078 #> Pdgfrb   -0.0702083431 -0.0335570848  1.184078e-01 -0.0371727515  0.0370642654 #> Flt1      0.0410303616 -0.1623786561 -1.061110e-01  0.0929263722 -0.0335727245 #> Adgrl4   -0.0744578770  0.0643895826  2.897772e-02 -0.0423981794  0.0217017849 #> Lpar6     0.0578828676 -0.0697921425  3.960271e-02 -0.0172022802  0.0439216471 #> Epha6    -0.1740711124 -0.1260203832 -3.443853e-02  0.0245462517  0.0084451230 #> Emcn      0.1117072284  0.0748040016 -1.105911e-01  0.0015341114  0.0447229918 #> Cldn5     0.0158847440  0.0769490294  2.268918e-02 -0.0397490744  0.0291013802 #> P2ry12    0.1389404589 -0.0256037950  8.026131e-02 -0.0104299034 -0.0502138053 #> Adgrf5   -0.0142220032  0.0021463003  1.644623e-01 -0.0830476018  0.0576580532 #> P2yr13   -0.0096114960  0.1231481736 -1.506480e-01  0.0791215869 -0.0527619195 #> Adgre1    0.0339938167 -0.0827248192  1.140248e-02 -0.0704072565 -0.0600671676 #> Cx3cl1    0.1739816415 -0.0550031446  1.601526e-01 -0.0393460397 -0.0062745083 #> Plxnb3   -0.0539509892 -0.0451823625 -4.287604e-02  0.0847098335  0.0802834011 #> Flt4     -0.0012230056 -0.1052873187  6.401684e-02  0.0739900899 -0.0256397021 #> Slc17a7   0.0190030184  0.0388135682 -1.137889e-01  0.0583866880 -0.1111693785 #> Cd300c2  -0.0120538397 -0.0223582199 -5.733176e-02 -0.0143223030  0.0248971829 #> Tek      -0.0095093428 -0.0562624922 -1.506817e-02  0.0961611427  0.0091508760 #> Kdr      -0.1193318122 -0.0169945768 -6.778868e-02 -0.0663464302 -0.1384546129 #> Kcnj8    -0.0330823272  0.0377115301  4.100845e-02 -0.0309045506  0.0059744366 #> S1pr3     0.1257233369  0.0415924694 -3.368253e-02  0.0691431969  0.0985217164 #> Tie1     -0.0001737544 -0.0578651194  7.836068e-02 -0.0024042144  0.1279032672 #> Pdgfra   -0.0599125953  0.0539507418  2.392577e-02  0.0391562760  0.1095946997 #> Baiap2    0.0559107795 -0.0383318910  1.374346e-01  0.0043857533 -0.0629922296 #> Calcrl   -0.0064588693 -0.0931802310  1.298936e-01  0.0490509106 -0.0429053004 #> Adrb2     0.0108691063  0.0490653556  4.380074e-03 -0.0305979681  0.0101463145 #> Ccr2     -0.0578373929  0.1054229795 -4.599388e-02  0.0205562403 -0.0246245682 #> Alk       0.0116086383  0.0948584740 -7.040831e-02  0.1534694864 -0.0183842735 #> Tacr3     0.0711322798  0.0499749534  1.289962e-01  0.0737663570 -0.0121843993 #> Erbb3     0.0941613621 -0.0054133025 -1.042618e-02 -0.0885299818 -0.1220656048 #> Pcdh15   -0.0286616954 -0.0341530564  2.503556e-05  0.1763402366  0.0342324909 #> Grm7     -0.0547467637 -0.1627361311 -5.901421e-02  0.1642366139  0.0436076926 #> F2r       0.0004674493 -0.1074030976  7.598153e-02  0.1260301835  0.0188770088 #> Bdkrb2    0.0217584627 -0.0137170807 -6.977910e-02  0.0282272397  0.0050616562 #> Adgrv1    0.0494049139 -0.0389058136 -1.316207e-01  0.0057301486  0.1323432794 #> Gprc5c   -0.0443731621 -0.0687569505 -7.860086e-02  0.0994528214  0.0433155886 #> Tbxa2r   -0.0365319183 -0.0197471560 -2.088756e-02  0.1132764609 -0.0726937623 #> Ackr1     0.0800119932  0.0792421576  2.676663e-02 -0.0402310903  0.0087411884 #> Lpar2     0.1056304559 -0.0029641070  1.780869e-01 -0.0332162486  0.0793253784 #> Myh11     0.0144281911 -0.0464288788 -1.411834e-03 -0.0459868790 -0.0051649687 #> Musk      0.0656672619 -0.0476787296 -8.177055e-02 -0.0239648061 -0.0786758229 #> Cnr1     -0.0014192105  0.0035849168  9.162548e-02 -0.0276969549 -0.0279960472 #> C3ar1    -0.1311069797  0.0716111422 -6.570013e-02  0.1243819813 -0.0162806350 #> S1pr4     0.0319407828 -0.1083394571 -8.205955e-02  0.0475249731 -0.0523493951 #> C5ar1     0.0835207283  0.1059874838 -5.281588e-02 -0.0417692154 -0.0841209585 #> Fpr1      0.1169890643  0.0335406649  1.362155e-01 -0.0828701932  0.0543940443 #> Sctr      0.0197145876  0.0658662605  5.272389e-02  0.1860293442 -0.2439555775 #> Gpr158   -0.0886371498  0.3145306831 -9.340059e-02 -0.0316687474  0.0494743274 #> Cxcr4    -0.0703100779 -0.0429129596 -1.127758e-02 -0.0206795470 -0.0176666130 #> Hrh2     -0.0248799200 -0.1901193315  1.679709e-02 -0.0012646053 -0.0182938290 #> Slc17a6   0.0088166909 -0.0707498438 -4.748368e-02 -0.0799726348  0.1049215432 #> Ppp1r3g  -0.1641733705 -0.0507014230  8.750264e-02 -0.0354750424  0.0893140330 #> Pln       0.0002424275  0.0612874494 -2.284823e-03 -0.0627246611 -0.0895280165 #> Grin2b   -0.1601821140 -0.0397917030  1.420783e-01  0.0381312596  0.1261084076 #> Taar7e   -0.1158512547 -0.1101975798 -8.198578e-02 -0.0595354115  0.0256896070 #> Ptger2    0.0186546780  0.0693885108  1.935567e-02  0.0205028835 -0.0709532479 #> Mc4r     -0.0692233244 -0.0130575857 -1.383449e-01 -0.0001251354  0.0326516777 #> Ghsr     -0.1002845603  0.0157519532 -7.428544e-03  0.0214926474  0.1154889747 #> Nmbr      0.0116987931 -0.0560298097 -1.098731e-02 -0.0983196070  0.0451396033 #>                Dim.81        Dim.82        Dim.83        Dim.84        Dim.85 #> Mlc1     -0.093735387  0.1200973176 -0.0160785957  0.1336642551  0.0793526409 #> Gprc5b   -0.004330739  0.0230413421  0.0047498014  0.0884552400  0.0105176609 #> Gfap      0.051426761 -0.0628112513 -0.0209238625  0.0023613787  0.0108277007 #> Ednrb    -0.150908441 -0.0282064825  0.1678329384 -0.0291582135  0.2441313287 #> Sox9      0.070901568 -0.0612837992 -0.0745932300  0.0142183784 -0.0576132217 #> Aqp4     -0.078194229  0.2058795931 -0.0184833864 -0.0194567997 -0.0230407479 #> Gjc3      0.092813453 -0.0538281269  0.0600185714  0.0885473595 -0.1089634311 #> Sox8     -0.122443709  0.0952410306  0.1252869154  0.0398065303 -0.1503193599 #> Ntsr2    -0.014035892 -0.1323497662 -0.0533465028  0.0758342228 -0.0500524979 #> Smo      -0.165099942 -0.0210943075 -0.1108363230  0.2040286379  0.0990239405 #> C1qb     -0.059329219 -0.1098273049  0.0024608868 -0.1270682887 -0.0514775681 #> Olig1     0.074402136 -0.0806522540 -0.1521452273  0.0221041139 -0.0168247154 #> C1qa      0.008506292 -0.0303846703  0.0025777237  0.0729904963 -0.0705206723 #> Pth1r    -0.097529836 -0.0777161834  0.0593022443 -0.1261974022  0.0080101626 #> Gabbr2    0.050500647 -0.1376070838  0.1828769780  0.0042395710  0.0860778897 #> Timp4    -0.053985809 -0.0103088207 -0.0349899576 -0.0009470189  0.0785925946 #> Abcc9    -0.084000979  0.0481453110  0.0300460317 -0.0303041154 -0.0358995446 #> Csf1r    -0.023856999  0.0072382401 -0.0193290958 -0.0060316055  0.0270143678 #> Ntrk2     0.057003878  0.0271395619 -0.0373520180 -0.0591720512  0.0719077231 #> Adgrg1   -0.032633384  0.0523410286 -0.1092554370 -0.2119288979 -0.1244712114 #> Ntrk3     0.184167727 -0.0052183942 -0.0457542903  0.1335193784  0.1305230486 #> Erbb4     0.022719586  0.0403344003  0.0106936040  0.0114230827 -0.0931475983 #> Selplg    0.119420394  0.0019057928  0.0201809859 -0.0117402780 -0.0017012819 #> Cspg5    -0.055727227 -0.0341658044  0.1250707131  0.1442527391 -0.0420218035 #> Dlk1     -0.018414694 -0.0275189532 -0.0010024202 -0.0649090699 -0.1129470891 #> Gpr37l1  -0.068786541 -0.2576964841  0.0489630383  0.0434810435  0.0071331021 #> Fgfr3     0.132117015  0.1804626755  0.0093820869 -0.1255848657 -0.0741670774 #> Slc25a18  0.017735221  0.1511728119  0.0283768842 -0.1208252332  0.0110099331 #> Igf1r     0.122323547 -0.0220986197 -0.0153538013  0.0580046362 -0.1251907183 #> S1pr1     0.098165575  0.0717365792  0.0788429479  0.0464750260 -0.0898707564 #> Grm5      0.158893312 -0.0245137518  0.0598589637 -0.0420515081  0.2497392118 #> Axl      -0.098346838  0.0372442597 -0.0503337550 -0.0532898638  0.1678125967 #> Efemp1    0.068470705 -0.0804955997  0.0308911141  0.1443210531 -0.0128082459 #> Adgrb3   -0.113504658  0.0293691951 -0.0464523296  0.0478208033  0.0528604849 #> Fn1      -0.036487071  0.0489999345 -0.1096257886 -0.0575619377  0.0453148701 #> Mertk     0.029489096  0.0029953317  0.0426388017 -0.0288841273 -0.1268492175 #> Adgrl2    0.002953736 -0.1020826135  0.1090301988 -0.2094479581 -0.0557262594 #> Fzd2     -0.138129078 -0.0217151728  0.0256563905  0.0817216866 -0.0202232053 #> Aldh1l1   0.053356541 -0.0384042048 -0.0170205676  0.0409807696  0.0707628310 #> Adgrg6    0.004449662 -0.0505498312 -0.0829132231  0.0657147804 -0.0201166244 #> Egfr     -0.133535664 -0.1243481550 -0.4432832708 -0.0106905826  0.1482925886 #> Kit       0.026742829  0.0314906484 -0.0115530882 -0.0278371370 -0.0041457159 #> Ptgdr     0.005354746  0.1040894668  0.0141634041 -0.0576823501 -0.0605783251 #> Gad1     -0.056547558 -0.0361165158 -0.0132463950 -0.0237646789  0.0006399957 #> Tyro3    -0.076695541  0.1344567982  0.0465629212 -0.1483871063 -0.1150626940 #> Atp13a5   0.063483461 -0.0221045012  0.0630452534 -0.0553326727 -0.0812343112 #> Ddr2     -0.027766826 -0.0580709862  0.1198700458  0.0091584849  0.0144595563 #> Rspo3     0.113088557  0.2164508702 -0.0493329731 -0.0042624743  0.0401556101 #> Arhgap29  0.034794911  0.1340649463  0.0975341849 -0.0484821398 -0.0176624386 #> Fzd7      0.030534888 -0.0737895048  0.0298190523  0.0445103314 -0.0266417723 #> Slc47a1   0.002414622 -0.0116127627  0.1881597736 -0.0575984497  0.0338414335 #> Ptger3    0.020971315 -0.0858008902  0.0471187179 -0.0972593225  0.0115405388 #> Bdkrb1   -0.005632865  0.0015174666 -0.1083891291  0.3034279659 -0.0571970683 #> Traf4     0.127200387  0.0290749941 -0.2078394820  0.1385487525 -0.0061526142 #> Cx3cr1    0.073344614  0.0202269269 -0.0344100298  0.0327389794  0.1356894848 #> Anxa11   -0.205003102  0.0218770431 -0.1147588917 -0.0467618665 -0.0096104694 #> Adgrb1   -0.010245871 -0.0289001310 -0.0406959418  0.0850357347 -0.1399789458 #> Lpar1    -0.100519996 -0.0296181051 -0.0303608873  0.0284140963  0.1079446603 #> Gpr17    -0.037413183 -0.0409449419  0.1066698878 -0.0904712564 -0.0042850736 #> Cxcl12    0.166303218 -0.0741088720 -0.0987652140 -0.1045173035  0.0379263063 #> Epha4     0.236215472  0.1187559210 -0.1014044458 -0.2576374317 -0.0288992920 #> Gpr182   -0.007325424  0.1239147034  0.0567236821 -0.0303465614 -0.0172635204 #> P2ry14    0.026060228  0.0623355729 -0.1191555344  0.1284210156 -0.0615401150 #> Hcar1    -0.017866841 -0.0878042377 -0.0253030057  0.0218291965 -0.1156933762 #> Ephb1    -0.006609463  0.0556474977  0.0607459593 -0.1802441884  0.0067445497 #> Grm3      0.087976984 -0.0172607813 -0.0414884321 -0.0473811798  0.1605742802 #> P2ry1    -0.046186003  0.1353774255  0.0579385318  0.1446826680 -0.0586571090 #> Ptk7     -0.096323825  0.1641962315  0.0216347633  0.0616541843 -0.0307671660 #> Slco1a4  -0.092257226  0.0641209606  0.0799656090  0.1018008345 -0.0074273235 #> Insrr    -0.059080030 -0.0670002809 -0.0310309035  0.1380043199  0.0266727706 #> Cmklr1   -0.061271398 -0.0383254611 -0.0126749000 -0.1366653701 -0.0442663116 #> Fzd6      0.053287406 -0.1081961814  0.0797959776 -0.0092843009  0.0709059583 #> S1pr5    -0.101201473  0.0273667827  0.0480230199 -0.0692913512  0.1770706385 #> Pdgfrb   -0.051505924  0.0364359113 -0.1830693271 -0.0753629471  0.0507032542 #> Flt1     -0.038053300  0.0767461723  0.0208032046 -0.0537280068 -0.0615250878 #> Adgrl4    0.026253555 -0.0268851874 -0.0377383111 -0.0297586542  0.0100685614 #> Lpar6     0.071099049 -0.0220534155  0.0066036776  0.0916356476  0.0322774410 #> Epha6    -0.023285186 -0.1823371659 -0.0069725568 -0.0382722419  0.0177770319 #> Emcn     -0.185055908  0.0024771658  0.0003246873 -0.0001023792  0.1275890844 #> Cldn5    -0.005991687  0.0458753655 -0.1251857613 -0.0118347265  0.0297507920 #> P2ry12   -0.197614091  0.0387684568  0.0214227613 -0.0147775014  0.0438934561 #> Adgrf5    0.010745935 -0.1632673109  0.1081391279 -0.0029739122  0.0350290076 #> P2yr13    0.179447022  0.0572060389 -0.0278561314  0.1064854478 -0.1103962367 #> Adgre1   -0.052122112  0.0176002566  0.1360406511  0.1011271489  0.0047794617 #> Cx3cl1    0.098913594  0.0786969858  0.1179818711  0.1422956979 -0.0695686299 #> Plxnb3    0.002883744  0.0072856985  0.0137006839  0.0883121522  0.1875815346 #> Flt4      0.096013501 -0.0247383588 -0.1021594334 -0.1251698885 -0.0021921914 #> Slc17a7  -0.256499781 -0.0782267820 -0.0653459735 -0.0471411164 -0.0838828422 #> Cd300c2   0.015434046  0.0945279368  0.0423602416  0.0735319305 -0.0023573835 #> Tek       0.065209708 -0.0462791237  0.0200272894  0.1305409348 -0.0477164219 #> Kdr       0.004992421  0.0467759451 -0.0132908062  0.0838992391 -0.0444099964 #> Kcnj8    -0.006457918  0.0137809431  0.0077145057  0.0735818538 -0.0634035547 #> S1pr3     0.080031181  0.0215036975 -0.0091979488  0.1529445656  0.1258799645 #> Tie1     -0.009394909 -0.1332618374  0.2182733559  0.1134867086  0.1495459134 #> Pdgfra   -0.024210376 -0.1301655468 -0.0157326771 -0.1138978194 -0.0861137852 #> Baiap2   -0.086956494 -0.0217690733 -0.2253096697 -0.0436361141 -0.0404289886 #> Calcrl    0.095010135  0.0287122339  0.0330597124 -0.0030495130 -0.0184638459 #> Adrb2    -0.004960049  0.1767430408 -0.0227114221  0.0274593626 -0.0143647826 #> Ccr2      0.068857935  0.1079559698  0.0220579132  0.0950169039 -0.0317731027 #> Alk       0.115865387  0.0844081755  0.0250473222 -0.0431262849  0.0344749285 #> Tacr3    -0.051025366 -0.1259265507  0.0828404405 -0.0514782206 -0.0486880966 #> Erbb3    -0.150982847 -0.0644175904 -0.0784411207  0.0645418493 -0.0734840167 #> Pcdh15   -0.118717951  0.2693692684  0.0205868683 -0.0427408517  0.2768821344 #> Grm7     -0.092151484 -0.1024376606  0.1144558682 -0.1056192634 -0.0453776912 #> F2r       0.105792536  0.0144681129 -0.1002946522  0.0456532091 -0.0794064443 #> Bdkrb2    0.006001383 -0.0459385959  0.0088333126 -0.0305198133 -0.0526452216 #> Adgrv1   -0.026158465 -0.2056272141 -0.1198631418  0.0233466285 -0.2518471017 #> Gprc5c   -0.023790564 -0.0678341827  0.1192417349  0.0314452670 -0.0645376975 #> Tbxa2r    0.140387432 -0.1359503411  0.0385701747  0.0276742671  0.0093499153 #> Ackr1    -0.029065291 -0.0578602700  0.0755327226 -0.0082264946  0.0336118587 #> Lpar2    -0.062835829 -0.0388571222  0.0238483036  0.0313594088  0.0680303424 #> Myh11     0.024970701  0.0200975461  0.1009525960 -0.0326637175 -0.0211099112 #> Musk      0.063985092  0.0535659480 -0.0550955508 -0.0079134786  0.0937532730 #> Cnr1     -0.013906595 -0.0051928058 -0.0156992706  0.0061304241  0.0403338016 #> C3ar1     0.040076607  0.0062155089 -0.1244926028 -0.0492635936 -0.0471373831 #> S1pr4    -0.065958029 -0.0107962960 -0.0762538210  0.0620445279 -0.0655559389 #> C5ar1    -0.063637211 -0.0071225936 -0.0490415793 -0.1249847305  0.0498359527 #> Fpr1     -0.007449543  0.0349705591  0.0454274730 -0.0330372227  0.0021663403 #> Sctr      0.217948125 -0.2021586654 -0.0313647208 -0.0323918549  0.2127553516 #> Gpr158   -0.010826408  0.0262009227  0.0733116753  0.0279112388 -0.1041623031 #> Cxcr4    -0.076691016  0.0345196880  0.0775273150 -0.0060655988 -0.0866485357 #> Hrh2     -0.099014764 -0.0467100393  0.0278380198 -0.0417478197 -0.0970706786 #> Slc17a6  -0.082618502  0.0339428623 -0.0348717086  0.0473219326  0.0196922049 #> Ppp1r3g   0.013087120  0.0001441324  0.0678246439 -0.0276088484 -0.1342479581 #> Pln      -0.060753126 -0.0002540803 -0.0455250134  0.0102654582 -0.0195768585 #> Grin2b   -0.069454630  0.1341492975  0.0771539648  0.1749918653 -0.0473794907 #> Taar7e   -0.032709596  0.0944560187 -0.0695272893 -0.0133027666 -0.0999029114 #> Ptger2    0.044539693  0.0204023883 -0.0229346732  0.0242302762  0.0367794357 #> Mc4r      0.013592632  0.0278544767  0.0774813171  0.0160754232  0.0464084266 #> Ghsr      0.057581076  0.0104375508  0.0562762594 -0.0150781170  0.0521752668 #> Nmbr     -0.027601323 -0.0431472576 -0.0146725241  0.0152135724 -0.1101811620 #>                 Dim.86        Dim.87        Dim.88       Dim.89        Dim.90 #> Mlc1     -0.0446194521 -1.805083e-02  0.1484667185  0.078401733 -2.924862e-02 #> Gprc5b    0.0747662202 -4.475160e-02 -0.2115922857 -0.105664583 -5.921809e-02 #> Gfap      0.0155304162  1.903392e-02 -0.0666472414  0.066194824 -2.246512e-02 #> Ednrb     0.0512531207  3.987415e-03  0.2369214973  0.166821179 -2.950391e-02 #> Sox9     -0.0350224532  1.287844e-01  0.0315784750  0.088571993 -1.438889e-03 #> Aqp4     -0.0409703527 -7.632461e-02 -0.0185938481 -0.174663056  1.345998e-02 #> Gjc3      0.0253485452  7.446386e-02  0.1748230538  0.056229272  9.247124e-02 #> Sox8     -0.0600121991  7.987573e-02  0.0152099579 -0.044230580 -1.182730e-01 #> Ntsr2    -0.0328373691  5.558512e-02  0.0091378822  0.059867405  1.238556e-02 #> Smo       0.0026082270 -8.615144e-05  0.1097382639  0.004404282  9.167016e-02 #> C1qb     -0.0463971696 -7.029504e-02  0.0017497232  0.029113934  5.680070e-02 #> Olig1     0.0475466556 -2.586215e-02 -0.1024841085 -0.158382061 -6.533709e-02 #> C1qa      0.0327250841  7.903381e-02 -0.0883805004 -0.004993833 -1.239920e-04 #> Pth1r    -0.0340636713 -7.034020e-02  0.0232577748  0.073222547 -2.297609e-02 #> Gabbr2    0.2467788563 -2.335529e-01  0.1066481236  0.009390707  1.378517e-01 #> Timp4     0.0344405694 -2.093301e-01 -0.2507068893  0.093717686  4.694750e-02 #> Abcc9    -0.1654077683  1.239701e-02  0.0133393661 -0.106839592  8.088886e-02 #> Csf1r    -0.0911006034  6.607610e-02 -0.0175853355 -0.083767182 -2.424711e-02 #> Ntrk2     0.0909720851  1.162075e-01  0.2498873675 -0.060203665 -5.733222e-02 #> Adgrg1    0.1604057654 -7.367918e-02 -0.0786447060 -0.011826503  1.166184e-01 #> Ntrk3    -0.0702398451 -1.291608e-01  0.0514904569 -0.189859230 -2.138488e-01 #> Erbb4    -0.1204752552 -7.039966e-02 -0.0068576943  0.092890744  2.754632e-02 #> Selplg   -0.0754350766  6.230948e-02  0.1336268565  0.063006232 -6.318817e-02 #> Cspg5    -0.0887596276 -1.065305e-01 -0.0557288014  0.051694191 -2.038485e-02 #> Dlk1     -0.0114570157  1.415152e-01  0.0767420697 -0.054251363  6.092212e-02 #> Gpr37l1   0.0100927556  1.574754e-01 -0.0523048732  0.085128714 -4.366962e-02 #> Fgfr3    -0.1019314966 -5.537155e-02  0.0190798414 -0.033899780 -9.996322e-02 #> Slc25a18  0.0111218317  5.032591e-02 -0.0940290665 -0.121073844  5.010449e-02 #> Igf1r     0.2054869791  1.404098e-01  0.0338512596 -0.087277620 -2.845034e-02 #> S1pr1    -0.0150071577 -1.081918e-01 -0.0680190781 -0.125823251  8.775953e-02 #> Grm5     -0.0681448131  2.929161e-02 -0.0651909556 -0.098733711  1.579165e-01 #> Axl       0.0590108802 -1.080991e-01  0.0771046579  0.007894065 -5.397611e-02 #> Efemp1   -0.1154580606  7.907215e-03 -0.0424233822 -0.051372093  2.600285e-02 #> Adgrb3    0.0321149563  3.287189e-02 -0.1250068947 -0.125439970  1.612462e-02 #> Fn1      -0.0263861792  2.825983e-02  0.0102674758  0.053535815  5.371041e-02 #> Mertk     0.0636284756  7.375500e-02  0.0038191254  0.140573724  1.177747e-01 #> Adgrl2   -0.0228908889 -7.787807e-02 -0.0810190261 -0.055962182 -1.500475e-01 #> Fzd2     -0.0043931382  3.327012e-02 -0.0681692424 -0.068827869  7.152434e-02 #> Aldh1l1   0.0710862542 -7.769703e-02  0.0582722364 -0.140624588 -4.983157e-02 #> Adgrg6   -0.0118591507 -7.894166e-02  0.1372651343 -0.110852399 -7.310954e-02 #> Egfr      0.0322822638  8.828886e-02 -0.0575830224  0.045389255 -3.166876e-02 #> Kit      -0.0063283850  4.850125e-02  0.0058902801  0.006787918 -4.666146e-02 #> Ptgdr    -0.0033795743  7.205373e-02 -0.0338538620  0.010687341  2.218572e-02 #> Gad1      0.0649317004  1.052728e-01 -0.0169077529 -0.087712485 -4.638314e-02 #> Tyro3    -0.1936872100  8.286322e-02  0.0596594836  0.158670818 -1.697447e-01 #> Atp13a5   0.0536887501 -7.139742e-02 -0.0006019162  0.032278164  3.367556e-02 #> Ddr2     -0.0118138792  7.599040e-02  0.0981873588 -0.011273135 -5.016877e-02 #> Rspo3     0.1926614623  2.216777e-01 -0.1237669286  0.190032935 -1.532177e-01 #> Arhgap29  0.0512842017  9.375010e-02  0.0144832564 -0.055482717  7.913907e-04 #> Fzd7     -0.0348546237 -7.435300e-02 -0.1377184601 -0.034325478  6.582313e-02 #> Slc47a1   0.0337073209 -4.600745e-02  0.0360188574 -0.002719568  7.251633e-03 #> Ptger3   -0.1665172671  6.925160e-02  0.0112721993 -0.057882229  3.436207e-02 #> Bdkrb1   -0.0149827331  3.956890e-02  0.0256329102  0.080174603  1.338152e-01 #> Traf4     0.1010347149 -4.021194e-02 -0.1354731048  0.051532783 -1.349484e-02 #> Cx3cr1    0.0009525478 -1.017464e-01  0.0049169613 -0.031228771 -1.107590e-01 #> Anxa11    0.1317304674 -5.213404e-02 -0.0008196147  0.104542851  9.760599e-02 #> Adgrb1    0.0569615285 -1.567489e-01  0.1746398448  0.167423492  6.489188e-02 #> Lpar1     0.0635439589 -1.292604e-01  0.0833577119 -0.042971513  2.382378e-02 #> Gpr17    -0.0424124024 -4.348071e-02  0.0262955726  0.025745022  8.425356e-02 #> Cxcl12    0.0010679019  4.864325e-02  0.0606862789  0.094669791  1.066750e-01 #> Epha4    -0.0821875289 -9.604508e-02  0.0612775936  0.120227765 -9.518840e-02 #> Gpr182   -0.0479715697  5.451215e-02  0.0271839533  0.042579190  8.562556e-03 #> P2ry14    0.1085034671 -5.430043e-02 -0.0155609584  0.050346184 -1.591596e-01 #> Hcar1    -0.0067979095 -3.439027e-02 -0.0022340629 -0.100960193 -8.404609e-02 #> Ephb1     0.0371327572 -5.541361e-02 -0.0188839748 -0.140323806 -2.243897e-02 #> Grm3      0.0389587964  1.446795e-01  0.0760903847  0.065248793 -5.862115e-02 #> P2ry1     0.0009032442 -5.571599e-02 -0.0329558709 -0.078559184 -2.140956e-01 #> Ptk7      0.1021790718  3.947358e-02 -0.1292614587  0.205451999 -1.922064e-01 #> Slco1a4  -0.1230216987  1.620591e-02 -0.0164715384  0.075624971 -7.504246e-02 #> Insrr    -0.0618564389  7.917756e-02 -0.0133765712 -0.053179434 -6.474554e-03 #> Cmklr1    0.0876965432 -1.905926e-01  0.0410382644  0.036860903 -1.367721e-01 #> Fzd6     -0.0606310055 -4.110305e-02 -0.0606122265  0.085063856 -1.423208e-01 #> S1pr5    -0.0333697225 -1.651912e-01 -0.2398338827  0.079263455  9.648839e-02 #> Pdgfrb    0.0722589193  6.142832e-02 -0.0268860101  0.071009120 -4.138239e-02 #> Flt1      0.0094090193 -3.079724e-02  0.0182186890 -0.075639673  1.047349e-03 #> Adgrl4   -0.0209377846  3.113586e-03  0.0128197093  0.070877993  5.843472e-02 #> Lpar6    -0.0402961268  7.686132e-02 -0.1282588895  0.008005590 -1.463135e-01 #> Epha6     0.1305479186  1.104275e-01 -0.1029818180 -0.055884161  1.073548e-01 #> Emcn     -0.0470831763  7.510201e-02  0.0362258487 -0.038194179 -2.105266e-01 #> Cldn5     0.0565542902  2.510552e-02  0.0315876240 -0.009298534  7.189559e-02 #> P2ry12    0.1143582937 -3.988627e-02 -0.0035901726  0.001953338  8.302300e-02 #> Adgrf5   -0.0461115669 -2.655683e-02 -0.0344487892 -0.023655936 -4.777138e-02 #> P2yr13    0.0125318115  5.569178e-02 -0.0420937780 -0.015805057  4.400681e-02 #> Adgre1    0.0117089575  1.161404e-01  0.0513334851  0.058824367  6.150708e-02 #> Cx3cl1    0.0525073828  2.093352e-02 -0.0754721673  0.169348562 -1.571408e-01 #> Plxnb3   -0.0205279486 -7.604818e-02 -0.0924020758 -0.006464499 -9.795533e-02 #> Flt4      0.1073713796 -1.297346e-02 -0.0427496857 -0.127412189 -1.227490e-01 #> Slc17a7   0.0565152861  2.272088e-01  0.0271522871 -0.229408843 -4.701083e-02 #> Cd300c2   0.0274907928  1.143450e-02  0.0065890129 -0.130221505 -7.010812e-02 #> Tek       0.0560011841  4.294065e-02  0.1335633219 -0.014078586  4.149950e-02 #> Kdr      -0.0201259418 -6.527167e-02 -0.0735287909 -0.018974185 -7.516299e-02 #> Kcnj8     0.0372905862 -1.116525e-02 -0.0252264071  0.044301430 -6.266965e-05 #> S1pr3    -0.0299521998  1.025287e-01  0.0882538463 -0.159986219 -2.502918e-02 #> Tie1     -0.0717360114  2.639144e-02 -0.1375540330  0.157961502  1.553215e-04 #> Pdgfra    0.0233506937  8.200833e-02  0.0038740056  0.095441443 -9.966319e-02 #> Baiap2   -0.4645124859 -6.708663e-03 -0.0683163507  0.095760104  4.075181e-02 #> Calcrl   -0.0755337762  2.884843e-02 -0.1971094832 -0.147954534  1.646196e-01 #> Adrb2     0.0232551104  2.182670e-02  0.0442128864 -0.031119813  7.749773e-03 #> Ccr2      0.0187758578  1.423078e-01 -0.0401214290  0.009916639  1.618989e-01 #> Alk       0.0094736307 -2.479994e-02 -0.0290829866  0.131559455  7.399575e-02 #> Tacr3     0.0475557748  2.828127e-02 -0.0447900242 -0.074897727 -1.551180e-01 #> Erbb3    -0.0116597367 -7.930685e-02  0.1488984855 -0.011857314 -2.676202e-02 #> Pcdh15   -0.0269552105  5.885912e-02  0.1059472583 -0.106230546  6.587346e-02 #> Grm7      0.0826025860  2.463791e-01 -0.1404234949  0.082048046 -3.615954e-02 #> F2r       0.1026273597 -4.818283e-02  0.0852606440  0.082413081  1.522432e-01 #> Bdkrb2   -0.0542236247 -6.360083e-02  0.0038745014 -0.025688396  3.332960e-02 #> Adgrv1   -0.1021722586 -1.422461e-01  0.0437448145 -0.056937217 -5.939909e-02 #> Gprc5c    0.0495495077 -1.119429e-01  0.0529993738 -0.084594579  4.060084e-02 #> Tbxa2r   -0.0121577529  7.251028e-03 -0.0883168339  0.064150475 -3.959664e-03 #> Ackr1     0.0079071318  5.988393e-02  0.0151373969  0.031453858  8.095278e-03 #> Lpar2     0.0043291299  8.080011e-02 -0.0356883105 -0.054470181 -1.099391e-02 #> Myh11    -0.0567735403  7.492579e-02 -0.1033736082 -0.045153914  5.432581e-02 #> Musk     -0.0627212129  8.387976e-02  0.0950492391  0.076878746  6.558108e-02 #> Cnr1     -0.0356711740 -5.338342e-02  0.0150921884 -0.018300402 -7.110529e-03 #> C3ar1    -0.0302378107 -2.663406e-02  0.0970212512  0.013354996  1.387947e-02 #> S1pr4     0.0777441924 -8.961595e-02 -0.0089304346 -0.026649657 -5.290134e-02 #> C5ar1     0.0334688763 -9.575626e-02  0.0356289138  0.058512222 -5.330371e-02 #> Fpr1      0.0178616196  6.087678e-02 -0.0822492653  0.025762868  1.574356e-01 #> Sctr     -0.0927803997  2.562672e-02  0.1087190230  0.024505202 -1.272342e-01 #> Gpr158    0.2804129926 -1.019917e-01  0.0460595008  0.011958022 -1.576415e-01 #> Cxcr4    -0.0124775636 -1.470519e-02  0.0210273618  0.013932847 -5.098411e-02 #> Hrh2      0.0527114067  1.065130e-01 -0.0018334120 -0.032959941 -3.524109e-02 #> Slc17a6   0.0356926463 -1.842255e-02 -0.1074389264 -0.015823678  8.473616e-02 #> Ppp1r3g  -0.0880604154  7.780899e-02  0.1949952894 -0.178453914  5.251934e-02 #> Pln      -0.0454816248  5.586009e-02 -0.0074355584  0.082752732 -4.942930e-02 #> Grin2b   -0.1556732114 -1.328897e-01  0.0514727255  0.102723982  6.283657e-03 #> Taar7e   -0.0604679604 -4.507736e-02 -0.0121886825  0.016353812  1.261960e-01 #> Ptger2   -0.0399916191 -4.134145e-02  0.0832987494 -0.094119195  3.060327e-02 #> Mc4r      0.1444646087 -1.640418e-02  0.0906481710  0.043195372  1.538470e-01 #> Ghsr     -0.0199047909  4.445657e-02 -0.0162983411 -0.028989517 -2.208633e-02 #> Nmbr     -0.0466640465 -6.363597e-02  0.0567610241  0.083868530 -6.956039e-02 #>                 Dim.91        Dim.92        Dim.93        Dim.94       Dim.95 #> Mlc1      5.274630e-02  0.1119067244 -0.0058843186 -0.1260245979 -0.062133638 #> Gprc5b    7.451196e-02 -0.0725239516 -0.0177110790  0.0422678106 -0.071748323 #> Gfap     -5.426800e-03 -0.0009118004  0.0203838019  0.0130710924 -0.058933794 #> Ednrb     1.270626e-01  0.1975129564  0.0128232313 -0.0401348038  0.069795811 #> Sox9      5.300940e-02 -0.0635346464  0.0548853394  0.0165461293  0.159258768 #> Aqp4     -1.517101e-02  0.0242932969  0.0024132074  0.0041561978  0.106669459 #> Gjc3     -9.228729e-02  0.1188491227  0.1082725892  0.0010672864  0.038196259 #> Sox8      7.469424e-02 -0.0440096699 -0.0868163694 -0.0280494469 -0.032285235 #> Ntsr2    -7.869387e-02 -0.0087441775  0.0994052047 -0.0470564988 -0.144997227 #> Smo      -4.865835e-02  0.0229379884 -0.1074756153  0.0354601048  0.116596708 #> C1qb     -2.074106e-02 -0.2393448345  0.0478761536 -0.0007524227 -0.014477896 #> Olig1     2.768440e-02 -0.1600840106  0.0088878639 -0.0040873489  0.022958611 #> C1qa      1.876587e-02  0.0138978653 -0.1212664358 -0.0558055109 -0.142545337 #> Pth1r    -1.809017e-01 -0.0452984472  0.0533957458 -0.1415904704 -0.004328204 #> Gabbr2   -2.182466e-02 -0.1128847191 -0.2304138433  0.1243715447  0.033183363 #> Timp4    -7.359871e-02 -0.0360900616 -0.0049517074 -0.1501054501  0.090362088 #> Abcc9     8.776331e-02  0.0521360242 -0.0085283136  0.1391603416 -0.022712588 #> Csf1r     5.100531e-02  0.0336142928 -0.0756824900  0.0037381114  0.020710353 #> Ntrk2    -2.417711e-01 -0.0812715030 -0.0043631322 -0.0081213750 -0.056854403 #> Adgrg1    1.346017e-01  0.1223961668 -0.2295753563 -0.0956746527 -0.090149156 #> Ntrk3    -2.374724e-02  0.0825801855  0.0551206233 -0.0290736291 -0.130174134 #> Erbb4    -3.835613e-02  0.1237293510  0.0517807023  0.0236626175 -0.100207753 #> Selplg    1.132267e-02 -0.0604731000  0.0723855567  0.0915252382  0.056802808 #> Cspg5    -1.119734e-01 -0.0693898022 -0.0016051719  0.0264069705 -0.095290874 #> Dlk1      4.919871e-02 -0.1741299554  0.0699417797  0.0420140222 -0.008967707 #> Gpr37l1   9.515550e-02 -0.0730644077  0.0446836441 -0.1253609433  0.053643619 #> Fgfr3     8.425444e-02  0.0039412239  0.0165419726  0.1590987135  0.146860270 #> Slc25a18 -8.814109e-02 -0.0135399639  0.0272595990  0.1088374133  0.056437595 #> Igf1r    -4.728995e-02  0.1028665732  0.2451292333 -0.1436671287  0.033086226 #> S1pr1     3.220078e-02  0.1448388548  0.1727089120  0.1872601124 -0.065810688 #> Grm5      6.983273e-02  0.0348919967 -0.0362557012 -0.1906023454  0.076228672 #> Axl       1.282342e-02  0.0774643176 -0.0002670706  0.0420034959  0.065182132 #> Efemp1   -1.303980e-01  0.0291655882 -0.0676869394  0.1547113193  0.187009834 #> Adgrb3   -3.224509e-02 -0.0544250128  0.0636919755 -0.0352234089  0.030183741 #> Fn1       1.095986e-02  0.0106850902  0.0123097978 -0.0392558434 -0.059979499 #> Mertk    -2.603184e-02  0.0188830892 -0.0363736098  0.0531165931  0.065029966 #> Adgrl2    6.419857e-02  0.0192476777  0.0609166898 -0.0268072961 -0.085087072 #> Fzd2      8.308113e-02 -0.0315091534 -0.0327257804  0.1299755197 -0.034626714 #> Aldh1l1   1.701282e-01 -0.0218071514 -0.1163273732 -0.0991568679  0.113192050 #> Adgrg6   -1.381625e-02 -0.0163830487 -0.0108848847 -0.0801376177  0.093141983 #> Egfr      9.556956e-02  0.0637854932 -0.0820240368  0.1227685775 -0.234172750 #> Kit       1.397337e-02  0.0074008920 -0.0111842346 -0.0473228962  0.040086813 #> Ptgdr    -1.496378e-01  0.1521258459  0.0043817332  0.0317115304  0.022757113 #> Gad1     -8.320921e-03 -0.0205413619  0.0208210785  0.0027575052  0.052196651 #> Tyro3     4.202130e-02 -0.0118759845 -0.1515579464 -0.0986512932  0.016103211 #> Atp13a5   5.137613e-02  0.0122029177  0.0166656726 -0.0367414591 -0.098132582 #> Ddr2      1.067384e-03 -0.0715132707 -0.0892093482 -0.0760200095  0.057334832 #> Rspo3     3.153281e-02 -0.1485852682 -0.0797618400  0.1017012014 -0.126598079 #> Arhgap29  3.673274e-02 -0.0313719339 -0.0092522089 -0.1041883214 -0.098033034 #> Fzd7     -8.768548e-02 -0.0556027811 -0.0340580667  0.0854028316  0.011053845 #> Slc47a1  -1.049590e-02 -0.0380321766  0.1020534531 -0.0740588261  0.064150133 #> Ptger3    8.999965e-02  0.0201227608 -0.0866566116  0.0150350012  0.068411317 #> Bdkrb1   -3.517196e-03  0.0177256164 -0.1910225702 -0.0084693673 -0.002411413 #> Traf4    -3.597948e-02  0.0169164589  0.1174897496  0.0671280949  0.185864850 #> Cx3cr1   -5.266623e-02  0.0399290009  0.1858021886  0.0158711747  0.111509837 #> Anxa11    3.333925e-02 -0.0208656309  0.0301249996 -0.0459639935 -0.052587851 #> Adgrb1    9.867209e-02 -0.2357833506 -0.0256168656  0.1360881588 -0.015569375 #> Lpar1     2.985648e-02  0.1592898623  0.2317965357  0.0136643880  0.178270900 #> Gpr17    -1.592767e-01  0.2122786878 -0.0493877360 -0.0910875088 -0.004874026 #> Cxcl12    1.513376e-02 -0.0099646162  0.0797348008 -0.0463832317 -0.040245633 #> Epha4    -4.408341e-02  0.0771809879 -0.1840034099  0.1428032845  0.042768029 #> Gpr182    7.206805e-02 -0.0692460810  0.0941783248  0.0670536943  0.009681566 #> P2ry14   -1.366635e-01 -0.0484745097  0.0587505754  0.1375289381 -0.091776111 #> Hcar1    -1.679301e-01 -0.0291004491 -0.0604382372 -0.1695048047 -0.113575750 #> Ephb1     5.449130e-02 -0.0570568594  0.0088434925 -0.0410839852  0.062984098 #> Grm3      1.422796e-01  0.0382414120 -0.1080238100 -0.0181992123  0.132527789 #> P2ry1    -1.234986e-04  0.0352800912  0.0061337002  0.0148423810  0.040628383 #> Ptk7     -3.400042e-02  0.1043124267 -0.0023697917 -0.0434795872 -0.127352696 #> Slco1a4  -1.102402e-01 -0.0510245545 -0.0154378755  0.0652769290  0.127281908 #> Insrr    -1.279034e-01 -0.0198141057 -0.0402604398  0.0917762751  0.120392818 #> Cmklr1   -6.111989e-02  0.0239326991  0.1557921105 -0.0467046857 -0.031457352 #> Fzd6      2.392842e-01  0.1070139799  0.1032530179  0.0594508148 -0.117127669 #> S1pr5    -1.698502e-01  0.0064873071 -0.0314512754 -0.0047582822 -0.088842584 #> Pdgfrb   -8.903590e-02  0.0554026147  0.0112335976 -0.0554802232  0.097785036 #> Flt1     -8.397945e-02  0.1104478313 -0.1445429372 -0.0585623138  0.085627628 #> Adgrl4    5.147395e-02 -0.0077315055 -0.0228087263  0.1125072990  0.015768241 #> Lpar6     2.688989e-02  0.0025936378 -0.0909584982 -0.0205692378  0.023886774 #> Epha6    -8.426374e-02  0.0083902484  0.0610022002  0.0535833669  0.043927727 #> Emcn     -3.379956e-02 -0.1881030057 -0.1108758191  0.0219499761  0.040543646 #> Cldn5     5.164176e-03 -0.0582697060  0.0315810714 -0.0780171074 -0.009205243 #> P2ry12   -3.672288e-04  0.0195319771  0.0371205083  0.0553671931 -0.054466839 #> Adgrf5    3.637698e-02  0.0418984353  0.0651674492  0.1303545172 -0.023513050 #> P2yr13   -1.053792e-02  0.2155203696 -0.1715896097 -0.1840113796  0.026579646 #> Adgre1    1.579639e-02  0.1910967722 -0.0406083345 -0.0335323958 -0.060401049 #> Cx3cl1    1.264855e-01 -0.0212992628  0.1466435162 -0.1492039960  0.055354754 #> Plxnb3    2.288169e-02  0.1594962174 -0.1326319356 -0.1112995400 -0.008911806 #> Flt4      2.436691e-03 -0.0625747141  0.1160129047 -0.1579802723 -0.025707302 #> Slc17a7  -2.162611e-02  0.1501026508  0.1773487521  0.0284518061 -0.002662220 #> Cd300c2   9.373069e-03  0.0455778645  0.0651040413 -0.0580099884  0.013556195 #> Tek       1.179705e-01  0.0442479816 -0.0622206196  0.0017044543 -0.073825263 #> Kdr       2.954364e-02 -0.0778192837  0.0419985628  0.1193363711  0.012406760 #> Kcnj8    -1.139091e-01 -0.0112078354  0.0632968271 -0.0711670943 -0.025603391 #> S1pr3     1.651888e-01 -0.0941163033 -0.0543558259 -0.0878114038  0.060274450 #> Tie1      2.183940e-02 -0.0929299554  0.1221934973  0.0714904304 -0.035429824 #> Pdgfra    4.470313e-02 -0.0704080579 -0.0366466912 -0.0660518979  0.070267173 #> Baiap2   -5.007352e-02  0.0964096735  0.0653049088 -0.0439186303  0.099053514 #> Calcrl    5.086396e-02 -0.0443910277 -0.0632429601 -0.0755402623 -0.170827488 #> Adrb2    -8.531171e-02 -0.0235390834  0.0277281774 -0.0281566993 -0.012074353 #> Ccr2     -1.111422e-02  0.0798895460 -0.0142434512  0.0499987246  0.051588246 #> Alk       8.818340e-02 -0.0064481907  0.1489984479  0.0272100256 -0.002052568 #> Tacr3    -2.423263e-02  0.1858740584 -0.0864598644  0.1845241189  0.011070858 #> Erbb3     8.649665e-02  0.0403412424 -0.0080201021  0.0573785690 -0.067445700 #> Pcdh15    1.793187e-01 -0.0904384341  0.1222951706  0.2295291974 -0.205263012 #> Grm7      4.082372e-02  0.0645856989  0.0246271920  0.0779872938  0.118455276 #> F2r       2.593090e-02  0.1970133776  0.1180674408  0.1078030635 -0.035225472 #> Bdkrb2    4.564745e-02  0.0071894322 -0.0718710495  0.0627660964 -0.032027913 #> Adgrv1    3.446076e-01  0.0422527952  0.0312952274 -0.1030285349 -0.094754773 #> Gprc5c    2.988676e-03  0.0616420471 -0.0758919905  0.0202860957 -0.054501685 #> Tbxa2r    1.076748e-01 -0.0119957490  0.0666507185  0.0809035397  0.074280864 #> Ackr1    -9.688354e-03  0.1109129947 -0.0213916976  0.0203904193 -0.052891145 #> Lpar2    -1.743762e-02  0.0145641239  0.0126481211 -0.0354632132 -0.110595369 #> Myh11    -1.829092e-03 -0.0306573803 -0.0995110444  0.0341511540  0.001283886 #> Musk     -6.212793e-02 -0.0801629560  0.0638048127 -0.1806913031 -0.159469306 #> Cnr1      5.976242e-03 -0.0178971737 -0.0075423455 -0.0488774634  0.055390504 #> C3ar1     3.295826e-02  0.0129418092 -0.0200485611  0.0907133802  0.096648532 #> S1pr4    -3.719727e-02 -0.0622030391 -0.1293827367 -0.0283849392  0.078226450 #> C5ar1     1.801483e-03  0.0308498187  0.0473987344 -0.0730893051  0.069828518 #> Fpr1      7.931787e-02  0.0837330351  0.0236887889  0.0098323219 -0.135110079 #> Sctr     -2.198100e-01  0.0260801526 -0.0583525288  0.1126435113 -0.251303669 #> Gpr158    2.018869e-02  0.0735612563 -0.1174086930  0.1017593704 -0.026547291 #> Cxcr4     2.807854e-02 -0.0252815960 -0.0357495237  0.0205471203  0.064926506 #> Hrh2     -4.505155e-02  0.0547656474  0.0717706742  0.0838867644  0.014215480 #> Slc17a6   1.118016e-01  0.0334324949  0.0303828133 -0.0459640930  0.084925433 #> Ppp1r3g  -1.845598e-01 -0.0806323697  0.0278996958  0.0034614065 -0.203229312 #> Pln      -5.207526e-02 -0.0141919704  0.0136697737  0.0119358138  0.022949312 #> Grin2b    3.785940e-02 -0.0624963454  0.1174093742 -0.1673219285 -0.129418076 #> Taar7e    5.297093e-02 -0.1448636627  0.1009128563 -0.0668147619  0.087798126 #> Ptger2    6.293152e-02 -0.0018785182  0.0015214838 -0.0097059538 -0.053563140 #> Mc4r     -2.186995e-02 -0.1983943923 -0.0134706415 -0.1139875981  0.068989559 #> Ghsr      2.851065e-05  0.0086599489 -0.0222297196 -0.0583938753 -0.002155070 #> Nmbr     -3.243908e-02 -0.0140878731 -0.0506366406  0.0631695680 -0.002616482 #>                 Dim.96        Dim.97        Dim.98        Dim.99       Dim.100 #> Mlc1     -0.0443537762  0.0360484369  0.0819819508  1.260459e-01  0.0450089853 #> Gprc5b   -0.0510558926 -0.0167780274 -0.0765372383 -5.747994e-02  0.0109242827 #> Gfap     -0.0172649627 -0.0325150875 -0.1045522993  2.849920e-02 -0.0343928321 #> Ednrb     0.1799824844 -0.0266675468  0.0126936581  1.502550e-01  0.0914827465 #> Sox9     -0.0776139391 -0.1348317883  0.0272543567 -1.218634e-01  0.0578865312 #> Aqp4     -0.0108937623  0.1450361285  0.2153831763 -5.214377e-02  0.0292030131 #> Gjc3     -0.0711227766 -0.0237886291  0.0343921640 -8.717850e-02  0.0005867661 #> Sox8     -0.0219504626  0.1839473385 -0.0055640059  8.358220e-02 -0.0472305015 #> Ntsr2    -0.0632400181 -0.0132755552 -0.0229996979  1.290156e-02 -0.1622541807 #> Smo       0.0446726332  0.0240068066 -0.1061320550 -1.462967e-01 -0.0498647005 #> C1qb     -0.0711368702  0.0638066014  0.1014940176  7.417651e-02  0.2129650839 #> Olig1     0.1893899465 -0.0113085427  0.0271378206  7.785833e-02 -0.0509245967 #> C1qa     -0.0449503731 -0.0960650048 -0.0771657285  4.181065e-02 -0.0754157023 #> Pth1r    -0.0108889896  0.0968962403 -0.0397244781 -3.021003e-02  0.1744126574 #> Gabbr2   -0.1127715258  0.1773201109 -0.1029834145  1.209036e-01 -0.0706423471 #> Timp4    -0.0469308197 -0.0136558665  0.1427075714  7.442107e-02  0.2083804252 #> Abcc9    -0.0868392638  0.0548558733  0.1813730140 -9.282117e-02 -0.1516930779 #> Csf1r     0.0597065849 -0.0116122845  0.0336615327 -1.838982e-02 -0.0626278245 #> Ntrk2     0.0889879882  0.0814695626  0.0465132494  4.193621e-02  0.0532033928 #> Adgrg1   -0.0046413805 -0.1743434429 -0.1574148804 -2.932602e-01 -0.1899499941 #> Ntrk3    -0.0935254436 -0.2637648766  0.2785446170 -2.392332e-02 -0.0058407785 #> Erbb4    -0.1687700521 -0.0341593112 -0.2247057880  1.110902e-01  0.0796625842 #> Selplg    0.0437971895 -0.0463517396  0.0465568388  6.566697e-02 -0.0708426139 #> Cspg5    -0.0097326391  0.0375980393  0.1274219462  7.434923e-02 -0.0581365681 #> Dlk1     -0.0550064886 -0.1046811997  0.0624809226  3.654155e-02 -0.0024350514 #> Gpr37l1   0.0557102606 -0.0889941638 -0.1141913728  1.594975e-01 -0.0369676530 #> Fgfr3     0.0586096854 -0.0269485012 -0.0181944486 -6.419439e-02  0.1628006771 #> Slc25a18 -0.0754009255  0.1231508326  0.0387336149  4.379239e-02 -0.0008650515 #> Igf1r    -0.0071980557  0.1371319776  0.0010901707  1.028243e-01  0.1415628044 #> S1pr1    -0.0586984413  0.1770275465 -0.1479985976 -1.284361e-01 -0.1350629013 #> Grm5     -0.0112312693  0.1778657338 -0.0605667870  1.595176e-01 -0.1533531628 #> Axl       0.0868458539  0.0655911386 -0.0048398865 -1.126509e-01 -0.1559221555 #> Efemp1   -0.0309381034 -0.1439380354 -0.0925716241  7.542845e-02  0.0478113886 #> Adgrb3   -0.0560734659  0.0039267328 -0.0026751082 -1.309427e-01 -0.0333891198 #> Fn1      -0.0239286942 -0.0205363547  0.0211027429 -2.125365e-02 -0.0460118361 #> Mertk     0.0395005414  0.0640619585  0.1031300535 -5.733631e-02  0.1335469428 #> Adgrl2    0.0195788504  0.0789741627 -0.0008308767  2.853738e-03 -0.0062170128 #> Fzd2     -0.0065199766 -0.1310735935  0.1572681321  8.776131e-02  0.0552191702 #> Aldh1l1  -0.0224101512  0.0292154700 -0.0378982746 -9.869550e-03  0.1135695271 #> Adgrg6   -0.0555596044  0.0919334192 -0.0236862783  2.818611e-03 -0.0003815807 #> Egfr     -0.1078294613  0.1540900612  0.1981852096 -1.919934e-02  0.0780892047 #> Kit       0.0523865550 -0.0386807889  0.0162609700 -1.247745e-02  0.0111076131 #> Ptgdr     0.1490205337 -0.0648832054 -0.0358539783  1.555095e-01 -0.1691839548 #> Gad1      0.1130041785  0.0439577095  0.1340075342 -6.451207e-02 -0.0300128673 #> Tyro3     0.0373603761  0.1074132990  0.1054368777 -4.662024e-02 -0.0365530052 #> Atp13a5   0.0073141075  0.0294909094  0.0357624918  1.460249e-02  0.0689017805 #> Ddr2     -0.0841406286  0.1473669490 -0.0089520103 -1.673733e-01  0.0827914374 #> Rspo3     0.0742247994  0.2529983374 -0.0580867643 -6.847477e-03 -0.0299330728 #> Arhgap29 -0.0269153620 -0.1034054972 -0.0060879314  3.061664e-02 -0.0037196932 #> Fzd7      0.0826427421 -0.0354264650  0.1027051543 -8.486209e-02 -0.0869939679 #> Slc47a1   0.0377543892 -0.0122535769 -0.0236616772 -9.365409e-02 -0.0203153213 #> Ptger3   -0.0761078960  0.0401885677 -0.0211771590 -1.105876e-01  0.1265538944 #> Bdkrb1   -0.0360341989  0.0180912458 -0.0813510345  3.149664e-02 -0.0125204111 #> Traf4    -0.0841528360  0.0417908160 -0.0470187449 -5.853414e-03  0.0402492851 #> Cx3cr1    0.0121677778  0.0283883732  0.0090845478 -7.015568e-02 -0.0086359019 #> Anxa11   -0.1266526962 -0.0901204568  0.1300161597  4.910297e-02 -0.0988169775 #> Adgrb1    0.0715700958  0.0673534814 -0.0393200976 -1.013340e-01  0.0162896611 #> Lpar1    -0.0002344535  0.0775491634 -0.0357163481  7.684334e-02 -0.1244453280 #> Gpr17     0.0571312823 -0.0167074981  0.1165888236 -1.667889e-01 -0.0238835701 #> Cxcl12    0.1057562688  0.0050510973  0.1631412288  4.178168e-02 -0.0218110911 #> Epha4     0.0391504682  0.0103309385 -0.0521921360  2.497589e-01  0.0326497811 #> Gpr182    0.0126087893  0.1296180784  0.0151222552 -7.079531e-02  0.0402807391 #> P2ry14    0.1392576242  0.0009081532 -0.1124062478  9.233882e-02 -0.1015120121 #> Hcar1    -0.0067673809  0.0410951436 -0.0203082511  1.203454e-01  0.1064953338 #> Ephb1     0.0149729283 -0.0202305784 -0.0350631704 -3.970236e-02 -0.1435495491 #> Grm3     -0.0594710151 -0.1637695938 -0.1229371505  6.062457e-02  0.0349878895 #> P2ry1    -0.1005179917  0.1687439529 -0.0487013462 -9.843553e-02  0.0611132939 #> Ptk7      0.0957404922 -0.0178864154 -0.0425020642 -7.592525e-02  0.0114444663 #> Slco1a4  -0.0626315893  0.0201931781  0.0744170417  9.867970e-02 -0.0053665358 #> Insrr     0.0944776078  0.0335998295  0.0432814485 -5.041559e-02 -0.0815594033 #> Cmklr1   -0.0783381406  0.0509605751 -0.1146788289 -1.831444e-02 -0.0341116091 #> Fzd6      0.1052248180  0.0788448872 -0.0421288772 -1.087229e-01  0.0585974004 #> S1pr5    -0.0013298678  0.0368014566  0.0470516154 -8.905017e-02  0.0877678767 #> Pdgfrb   -0.1018702817 -0.0594929075  0.0011852843  9.373763e-02 -0.0681029985 #> Flt1     -0.0794881609 -0.0767376686 -0.0352270387  1.701944e-02 -0.0593478010 #> Adgrl4    0.0715719036 -0.0024930768 -0.0026283303 -7.695242e-02 -0.0081116497 #> Lpar6    -0.0338539052 -0.0699560815 -0.1013519424  1.572401e-02 -0.0209834505 #> Epha6     0.1292911044  0.0639261186 -0.0787368065 -7.881928e-02  0.0730507215 #> Emcn     -0.0630136885 -0.0387701346 -0.1296581708 -2.786186e-02 -0.0795758492 #> Cldn5     0.0089685139  0.0378101412  0.0372486792  5.591290e-03  0.0116931295 #> P2ry12    0.0407785955 -0.0067044142 -0.0493437175  1.554941e-02 -0.1460416692 #> Adgrf5    0.0356186631 -0.0929036549 -0.0431651800 -2.943058e-02 -0.0265416805 #> P2yr13   -0.1024577086  0.1104307839 -0.0186240317 -1.499583e-01  0.2366327278 #> Adgre1   -0.0207542755  0.1252825896 -0.0217732142  2.833754e-02 -0.0388424267 #> Cx3cl1   -0.3294128886  0.0023821356  0.2061062819 -2.316771e-02 -0.2453750441 #> Plxnb3    0.1697384800  0.1661675573 -0.0152867680  8.637727e-02 -0.0701051213 #> Flt4      0.0586426204  0.0176883428 -0.0125178126  3.461665e-02 -0.0392505043 #> Slc17a7   0.0828733051  0.0429671987 -0.1974277477 -6.446599e-02  0.1643070653 #> Cd300c2  -0.0481613197 -0.0563445727 -0.0710774534  7.344774e-03 -0.0100193949 #> Tek      -0.0089852611  0.0414927826  0.0590540015 -1.597511e-02  0.0268458258 #> Kdr       0.0779024612  0.0734437579 -0.0069344954  1.293320e-02  0.0015974350 #> Kcnj8     0.0818562748 -0.0584210918 -0.1080648007  7.424314e-02  0.1278848916 #> S1pr3     0.1318715326  0.0812680530 -0.0165760443 -8.612860e-02 -0.0265361090 #> Tie1      0.0033508741  0.1083100692 -0.0006694247  2.620638e-02  0.0579725541 #> Pdgfra   -0.0387369696  0.0588450248 -0.0787371045 -2.944948e-02 -0.1049359760 #> Baiap2   -0.0775217698  0.1349416427 -0.1636373601  1.108546e-01 -0.1079669366 #> Calcrl    0.1419570347  0.0208696070 -0.0293084541  1.669668e-01  0.0357484666 #> Adrb2    -0.0365630186 -0.0082632953 -0.0670394928  6.155158e-02  0.0227936987 #> Ccr2      0.0858909799 -0.0021885373  0.0625329152 -2.820142e-02  0.0099452840 #> Alk       0.0458290549 -0.0734565716 -0.1648546419  5.582668e-02 -0.0792551027 #> Tacr3     0.0265660569 -0.0436933519  0.0850627227  9.230092e-02  0.0687709599 #> Erbb3     0.1245836146  0.1412833680  0.0164346809  1.122492e-01 -0.0665527368 #> Pcdh15   -0.2529142945 -0.1004256139 -0.1432620596  1.004588e-01  0.2194278503 #> Grm7     -0.1397368781  0.1089594413  0.0379568219  1.443681e-02 -0.0322724861 #> F2r      -0.0423929786  0.0566388736 -0.0074588355  1.282994e-02  0.0393546109 #> Bdkrb2    0.0781244052  0.0162706420 -0.0392946792 -9.185904e-03  0.1108206463 #> Adgrv1   -0.0356076159  0.0738471856 -0.0006103067  9.597895e-02  0.0121626521 #> Gprc5c   -0.2042111942 -0.0003886170 -0.0891583759  8.981869e-02 -0.0085222955 #> Tbxa2r    0.0088643166  0.0266243067  0.0670353931 -7.072588e-02 -0.1360094300 #> Ackr1    -0.0123965578 -0.1484398276  0.0494395270 -4.358139e-02  0.0026337024 #> Lpar2    -0.0224920176 -0.1120428877 -0.0551356136 -3.575251e-02  0.0088337743 #> Myh11     0.0404946186  0.0164047386 -0.0386613025  2.024687e-02 -0.0207320428 #> Musk     -0.0524175931  0.0439845020 -0.0106651062 -9.185905e-02 -0.0704663974 #> Cnr1     -0.0508017667  0.0555751164 -0.0332689232  6.523213e-03 -0.0693199266 #> C3ar1     0.1046549965  0.0508510489  0.0800600990 -3.385654e-02 -0.0109808954 #> S1pr4    -0.0717778678  0.0565913811 -0.1038866351 -1.688067e-02  0.0660013158 #> C5ar1    -0.0336764016  0.0003741751 -0.0131256422 -9.364569e-02  0.0141209369 #> Fpr1      0.0418202715  0.1105538549  0.0453254973  3.427520e-02  0.0066593880 #> Sctr     -0.1433701071  0.0896402281 -0.1137159324 -2.522357e-01 -0.0207737837 #> Gpr158    0.0562321374 -0.0563950797  0.1171726660  4.753825e-02 -0.0126591675 #> Cxcr4     0.0118897498 -0.1273500733 -0.0736292578  9.587281e-05 -0.0497375321 #> Hrh2     -0.0696668100 -0.0344627831  0.0156450293 -1.724896e-02  0.0246493820 #> Slc17a6   0.0333474238  0.0239279656  0.0496821502  1.116024e-01 -0.0052144861 #> Ppp1r3g   0.0152166395  0.0842415215  0.0323072063  8.383231e-02 -0.2180193222 #> Pln       0.0560646403 -0.0693041040  0.0316120048 -3.325110e-02  0.0144415377 #> Grin2b    0.3086303995 -0.1369938155 -0.0702822115 -1.924546e-01  0.0952752006 #> Taar7e    0.0299564845  0.0113191149 -0.1575437408 -7.225802e-02 -0.0143840271 #> Ptger2    0.0687272492 -0.0360582887 -0.0043759260  1.268787e-02  0.0203538675 #> Mc4r     -0.0853855671  0.0217886780  0.0046874230 -3.175744e-02 -0.0417995305 #> Ghsr      0.0217415657  0.0229802934 -0.0204775738  2.456220e-02  0.0040153451 #> Nmbr     -0.0143240610 -0.0464849471 -0.0352151903 -1.932095e-02  0.0324894853 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":null,"dir":"Reference","previous_headings":"","what":"my_arowMeans — my_arowMeans","title":"my_arowMeans — my_arowMeans","text":"my_arowMeans","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"my_arowMeans — my_arowMeans","text":"","code":"my_arowMeans(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"my_arowMeans — my_arowMeans","text":"x data use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"my_arowMeans — my_arowMeans","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_arowMeans.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"my_arowMeans — my_arowMeans","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  my_arowMeans(m) #>  [1] -0.5417610 -0.2227548  0.1578376  0.2002051  0.1017837 -0.6461654 #>  [7]  0.8037910 -0.3705254 -0.4083799  0.4040291"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":null,"dir":"Reference","previous_headings":"","what":"my_growMeans — my_growMeans","title":"my_growMeans — my_growMeans","text":"my_growMeans","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"my_growMeans — my_growMeans","text":"","code":"my_growMeans(x, offset = 0.1)"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"my_growMeans — my_growMeans","text":"x data use offset offset","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"my_growMeans — my_growMeans","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_growMeans.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"my_growMeans — my_growMeans","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  my_growMeans(abs(m)) #>  [1] 0.4898760 0.5735737 0.6441830 0.5510774 0.7287629 0.7224097 0.4566198 #>  [8] 0.8709865 0.6379915 0.7580299"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":null,"dir":"Reference","previous_headings":"","what":"my_rowMeans — my_rowMeans","title":"my_rowMeans — my_rowMeans","text":"my_rowMeans","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"my_rowMeans — my_rowMeans","text":"","code":"my_rowMeans(x, method = c(\"arithmic\", \"geometric\"), offset = 0.1)"},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"my_rowMeans — my_rowMeans","text":"x data use method method either \"arithmic\" \"geometric\" offset offset","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"my_rowMeans — my_rowMeans","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/my_rowMeans.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"my_rowMeans — my_rowMeans","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  my_rowMeans(m) #>  [1] -0.11429801  0.06630945 -0.38510854 -0.38755999 -0.08956358  0.84401809 #>  [7] -0.06373938  0.25949145 -0.02899145  0.44829355"},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":null,"dir":"Reference","previous_headings":"","what":"nnDT_to_kNN — nnDT_to_kNN","title":"nnDT_to_kNN — nnDT_to_kNN","text":"Convert nearest network data.table kNN object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"nnDT_to_kNN — nnDT_to_kNN","text":"","code":"nnDT_to_kNN(nnDT)"},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"nnDT_to_kNN — nnDT_to_kNN","text":"nnDT nearest neighbor network data.table format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"nnDT_to_kNN — nnDT_to_kNN","text":"kNN object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnDT_to_kNN.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"nnDT_to_kNN — nnDT_to_kNN","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_nn <- getNearestNetwork(g, output = \"data.table\", name = \"custom_NN\") #> The NN network type was not specified, default to the #>  first: \"sNN\"  nnDT_to_kNN(g_nn) #> k-nearest neighbors for 624 objects (k=3). #> Distance metric:  #>  #> Available fields: dist, id, k, sort"},{"path":"https://drieslab.github.io/GiottoClass/reference/nnNetObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 nnNetObj — nnNetObj-class","title":"S4 nnNetObj — nnNetObj-class","text":"Framework store nearest neighbor network information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnNetObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 nnNetObj — nnNetObj-class","text":"nnNetObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnNetObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 nnNetObj — nnNetObj-class","text":"name name nnNetObj nn_type type nearest neighbor network igraph igraph object containing network information feat_type feature type data spat_unit spatial unit data provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/nnNetObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 nnNetObj — nnNetObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"nnNetObj\") #> An object of class nnNetObj : \"sNN.pca\" #> --| Contains nearest neighbor network generated with: sNN  #> ----| for feat_type: rna  #> ----|     spat_unit: aggregate  #> ----|     provenance: z0 z1  #>  #> IGRAPH 859f76e DNW- 462 3021 --  #> + attr: name (v/c), weight (e/n), distance (e/n), shared (e/n), rank #> | (e/n) #> + edges from 859f76e (vertex names): #> [1] 240649020551054330404932383065726870513->335295524680090725199231409883288198017 #> [2] 240649020551054330404932383065726870513->77151711298730578178892667721058396928  #> [3] 240649020551054330404932383065726870513->322879686187630160969459793861944841206 #> [4] 240649020551054330404932383065726870513->31072896077757820678000109671990674373  #> [5] 240649020551054330404932383065726870513->102184699197574201819246996094734116255 #> [6] 240649020551054330404932383065726870513->17685062374745280598492217386845129350  #> + ... omitted several edges #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto object history — objHistory","title":"Giotto object history — objHistory","text":"Print return giotto object history","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto object history — objHistory","text":"","code":"objHistory(object, summarized = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto object history — objHistory","text":"object giotto object summarized logical. whether print summarized","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto object history — objHistory","text":"list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objHistory.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto object history — objHistory","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  objHistory(g) #> Steps and parameters used: #> <0_normalize> #>   gobject           : mini_visium #>   expression_values : raw #>   norm_methods      : standard #>   library_size_norm : TRUE #>   scalefactor       : 6000 #>   log_norm          : TRUE #>   log_offset        : 1 #>   logbase           : 2 #>   scale_feats       : TRUE #>   scale_cells       : TRUE #>   scale_order       : first_feats #>   theta             : 100 #>   update_slot       : scaled #>   verbose           : T #> <1_subset> #>   gobject         : gobject #>   spat_unit       : spat_unit #>   feat_type       : feat_type #>   cell_ids        : selected_cell_ids #>   feat_ids        : selected_feat_ids #>   poly_info       : poly_info #>   spat_unit_fsub  : spat_unit_fsub #>   feat_type_ssub  : feat_type_ssub #>   verbose         : verbose #>   toplevel_params : 2 #> <2_filter> #>   gobject                : mini_visium #>   expression_values      : raw #>   expression_threshold   : 1 #>   feat_det_in_min_cells  : 5 #>   min_det_feats_per_cell : 20 #>   spat_unit_fsub         : :all: #>   feat_type_ssub         : :all: #>   tag_cells              : FALSE #>   tag_cell_name          : tag #>   tag_feats              : FALSE #>   tag_feats_name         : tag #>   verbose                : T #> <3_feat_stats> #>   gobject             : mini_visium #>   expression_values   : normalized #>   detection_threshold : 0 #>   return_gobject      : TRUE #>   verbose             : TRUE #> <4_cell_stats> #>   gobject             : mini_visium #>   expression_values   : normalized #>   detection_threshold : 0 #>   return_gobject      : TRUE #>   verbose             : TRUE #> <5_hvf> #>   gobject              : mini_visium #>   expression_values    : normalized #>   method               : cov_groups #>   reverse_log_scale    : FALSE #>   logbase              : 2 #>   expression_threshold : 0 #>   nr_expression_groups : 20 #>   zscore_threshold     : 1.5 #>   HVFname              : hvf #>   difference_in_cov    : 0.1 #>   var_threshold        : 1.5 #>   set_seed             : TRUE #>   seed_number          : 1234 #>   save_param           : list() #>   default_save_name    : HVFplot #>   return_gobject       : TRUE #>   verbose              : TRUE #> <6_pca> #>   gobject           : mini_visium #>   expression_values : normalized #>   reduction         : cells #>   return_gobject    : TRUE #>   center            : TRUE #>   scale_unit        : TRUE #>   ncp               : 100 #>   method            : irlba #>   method_params     : BiocParallel::SerialParam() #>   rev               : FALSE #>   set_seed          : TRUE #>   seed_number       : 1234 #>   verbose           : TRUE #>   ...               :  #> <7_umap> #>   gobject              : mini_visium #>   expression_values    : normalized #>   reduction            : cells #>   dim_reduction_to_use : pca #>   dimensions_to_use    : 1:10 #>   return_gobject       : TRUE #>   n_neighbors          : 40 #>   n_components         : 2 #>   n_epochs             : 400 #>   min_dist             : 0.01 #>   n_threads            : NA #>   spread               : 5 #>   set_seed             : TRUE #>   seed_number          : 1234 #>   verbose              : TRUE #>   toplevel_params      : 2 #>   ...                  :  #> <8_tsne> #>   gobject              : mini_visium #>   expression_values    : normalized #>   reduction            : cells #>   dim_reduction_to_use : pca #>   dimensions_to_use    : 1:10 #>   return_gobject       : TRUE #>   dims                 : 2 #>   perplexity           : 30 #>   theta                : 0.5 #>   do_PCA_first         : FALSE #>   set_seed             : TRUE #>   seed_number          : 1234 #>   verbose              : TRUE #>   ...                  :  #> <9_nn_network> #>   gobject              : mini_visium #>   type                 : sNN #>   dim_reduction_to_use : pca #>   dimensions_to_use    : 1:5 #>   expression_values    : normalized #>   return_gobject       : TRUE #>   k                    : 10 #>   minimum_shared       : 5 #>   top_shared           : 3 #>   verbose              : TRUE #>   ...                  :  #> <10_cluster> #>   gobject           : mini_visium #>   name              : leiden_clus #>   nn_network_to_use : sNN #>   network_name      : sNN.pca #>   resolution        : 0.1 #>   weight_col        : weight #>   partition_type    : RBConfigurationVertexPartition #>   n_iterations      : 1000 #>   return_gobject    : TRUE #>   set_seed          : TRUE #>   seed_number       : 1234 #> <11_delaunay_spatial_network> #>   dimensions used            : dimensions: sdimx and sdimy #>   method                     : deldir #>   maximum distance threshold : auto #>   name of spatial network    : Delaunay_network #> <12_spatial_network> #>   k neighbours               : 10 #>   dimensions used            : all #>   maximum distance threshold : 400 #>   name of spatial network    : spatial_network #> <13_create_metafeat> #>   gobject           : mini_visium #>   expression_values : normalized #>   feat_clusters     : cluster_genes #>   stat              : mean #>   name              : cluster_metagene #>   return_gobject    : TRUE #> <14_pca> #>   gobject           : mini_visium #>   expression_values : normalized #>   reduction         : cells #>   name              : custom_pca #>   feats_to_use      : my_spatial_genes #>   return_gobject    : TRUE #>   center            : TRUE #>   scale_unit        : TRUE #>   ncp               : 100 #>   method            : irlba #>   method_params     : BiocParallel::SerialParam() #>   rev               : FALSE #>   set_seed          : TRUE #>   seed_number       : 1234 #>   verbose           : TRUE #>   ...               :  #> <15_umap> #>   gobject              : mini_visium #>   expression_values    : normalized #>   reduction            : cells #>   dim_reduction_to_use : pca #>   dim_reduction_name   : custom_pca #>   dimensions_to_use    : 1:20 #>   name                 : custom_umap #>   return_gobject       : TRUE #>   n_neighbors          : 40 #>   n_components         : 2 #>   n_epochs             : 400 #>   min_dist             : 0.01 #>   n_threads            : NA #>   spread               : 5 #>   set_seed             : TRUE #>   seed_number          : 1234 #>   verbose              : TRUE #>   toplevel_params      : 2 #>   ...                  :  #> <16_nn_network> #>   gobject              : mini_visium #>   type                 : sNN #>   dim_reduction_to_use : pca #>   dim_reduction_name   : custom_pca #>   dimensions_to_use    : 1:20 #>   expression_values    : normalized #>   name                 : custom_NN #>   return_gobject       : TRUE #>   k                    : 5 #>   minimum_shared       : 5 #>   top_shared           : 3 #>   verbose              : TRUE #>   ...                  :  #> <17_cluster> #>   gobject           : mini_visium #>   name              : custom_leiden #>   nn_network_to_use : sNN #>   network_name      : custom_NN #>   resolution        : 0.15 #>   weight_col        : weight #>   partition_type    : RBConfigurationVertexPartition #>   n_iterations      : 1000 #>   return_gobject    : TRUE #>   set_seed          : TRUE #>   seed_number       : 1234 #> <18_spatial_deconvolution> #>   method used              : DWLS #>   deconvolution name       : DWLS #>   expression values        : normalized #>   logbase                  : 2 #>   cluster column used      : leiden_clus #>   number of cells per spot : 50 #>   used cut off             : 2 #> <19_spatial_deconvolution> #>   method used              : DWLS #>   deconvolution name       : DWLS #>   expression values        : normalized #>   logbase                  : 2 #>   cluster column used      : leiden_clus #>   number of cells per spot : 50 #>   used cut off             : 2 #> <20_spatial_deconvolution> #>   method used              : DWLS #>   deconvolution name       : DWLS #>   expression values        : normalized #>   logbase                  : 2 #>   cluster column used      : leiden_clus #>   number of cells per spot : 50 #>   used cut off             : 2 objHistory(g, summarized = TRUE) #> Processing steps: #> 0_normalize #> 1_subset #> 2_filter #> name info: tag tag #> 3_feat_stats #> 4_cell_stats #> 5_hvf #> name info: hvf HVFplot #> 6_pca #> 7_umap #> 8_tsne #> 9_nn_network #> 10_cluster #> name info: leiden_clus sNN.pca #> 11_delaunay_spatial_network #> name info: Delaunay_network #> 12_spatial_network #> name info: spatial_network #> 13_create_metafeat #> name info: cluster_metagene #> 14_pca #> name info: custom_pca #> 15_umap #> name info: custom_pca custom_umap #> 16_nn_network #> name info: custom_pca custom_NN #> 17_cluster #> name info: custom_leiden custom_NN #> 18_spatial_deconvolution #> name info: DWLS #> 19_spatial_deconvolution #> name info: DWLS #> 20_spatial_deconvolution #> name info: DWLS"},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto object name information — objName-generic","title":"Giotto object name information — objName-generic","text":"access set name slot fo S4 subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto object name information — objName-generic","text":"","code":"# S4 method for class 'ANY' objName(x)  # S4 method for class 'list' objName(x)  # S4 method for class 'nameData' objName(x)  # S4 method for class 'giottoPoints' objName(x)  # S4 method for class 'giottoLargeImage' objName(x)  # S4 method for class 'giottoImage' objName(x)  # S4 method for class 'list' objName(x) <- value  # S4 method for class 'nameData' objName(x) <- value  # S4 method for class 'giottoImage' objName(x) <- value  # S4 method for class 'giottoLargeImage' objName(x) <- value  # S4 method for class 'giottoPoints' objName(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto object name information — objName-generic","text":"x Giotto S4 class subobject name data value value set object name","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto object name information — objName-generic","text":"name slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Giotto object name information — objName-generic","text":"objName(nameData): Get name information objName(giottoPoints): Get name giottoPoints objName(giottoPoints) <- value: Set name giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objName-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto object name information — objName-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  objName(g) #> [1] \"normalized\""},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":null,"dir":"Reference","previous_headings":"","what":"Name wrangling for subobject lists — objectlist_name_utils","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"Name wrangling subobject lists","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"","code":"assign_objnames_2_list(obj_list, force_replace = FALSE)  assign_listnames_2_obj(obj_list)  .uniquify_dups(x, sep = \".\", what = \"\", verbose = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"obj_list list containing giotto subobjects force_replace logical. default = FALSE. Whether replace names objects name already name x character vector sep character. Separator used making names unique. Default \".\" character (optional). Description character vector input used printing verbose messages made unique verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/objectlist_name_utils.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Name wrangling for subobject lists — objectlist_name_utils","text":"","code":"if (FALSE) { # \\dontrun{ e <- new(\"exprObj\") a <- replicate(3L, e) # name the objects objName(a) <- letters[1:3]  # assign the object stored names to the list names(a) a <- assign_objnames_2_list(a) names(a)  # assign list names to the object b <- list(\"name_to_set\" = new(\"exprObj\"), \"name2\" = new(\"exprObj\")) objName(b) b <- assign_listnames_2_obj(b) objName(b)   # ensure that character values are unique input <- c(\"a\", \"b\", \"b\", \"c\", \"a\", \"a\", \"a\") .uniquify_dups(input, verbose = FALSE) } # }"},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read metadata of an ometif — ometif_metadata","title":"Read metadata of an ometif — ometif_metadata","text":"Use python package tifffile get XML metadata .ome.tif file. R package xml2 used work retrieve specific nodes xml data extract data.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read metadata of an ometif — ometif_metadata","text":"","code":"ometif_metadata(   path,   node = NULL,   output = c(\"data.frame\", \"xml\", \"list\", \"structure\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read metadata of an ometif — ometif_metadata","text":"path character. filepath .ome.tif image node character vector. Specific xml node get. terms can added get node specific hierarchy. output character. One \"data.frame\" return data.frame attributes information xml node, \"xmL\" xml2 representation node, \"list\" R native list (note many items list may overlapping names make indexing difficult), \"structure\" invisibly return NULL, print structure XML document node.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read metadata of an ometif — ometif_metadata","text":"list image metadata information","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_to_tif.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert ome.tif to tif — ometif_to_tif","title":"Convert ome.tif to tif — ometif_to_tif","text":"Simple converter .ome.tif .tif format. Utilizes python tifffile package. Performs image conversions one page time. Wrap loop lapply one image page.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_to_tif.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert ome.tif to tif — ometif_to_tif","text":"","code":"ometif_to_tif(   input_file,   output_dir = file.path(dirname(input_file), \"tif_exports\"),   page,   overwrite = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_to_tif.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert ome.tif to tif — ometif_to_tif","text":"input_file character. Filepath ome.tif convert output_dir character. Directory write .tif . Defaults new folder directory called \"tif_exports\" page numeric. page tif open (needed). provided, \"_%04d\" formatted suffix added output filename. overwrite logical. Default = FALSE. Whether overwrite filename already exists.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ometif_to_tif.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert ome.tif to tif — ometif_to_tif","text":"returns written filepath invisibly","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapImagesToMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"overlapImagesToMatrix — overlapImagesToMatrix","title":"overlapImagesToMatrix — overlapImagesToMatrix","text":"create count matrix based overlap results calculateOverlapPolygonImages","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapImagesToMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"overlapImagesToMatrix — overlapImagesToMatrix","text":"","code":"overlapImagesToMatrix(   gobject,   name = \"raw\",   poly_info = \"cell\",   feat_info = \"protein\",   name_overlap = \"images\",   aggr_function = \"sum\",   image_names = NULL,   spat_locs_name = \"raw\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapImagesToMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"overlapImagesToMatrix — overlapImagesToMatrix","text":"gobject giotto object name name overlap count matrix poly_info polygon information feat_info feature information name_overlap name overlap aggr_function function aggregate image information (default = sum) image_names names images used spat_locs_name name spatial centroids / locations associated matrix return_gobject return giotto object (default: TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapImagesToMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"overlapImagesToMatrix — overlapImagesToMatrix","text":"giotto object data.table aggregated information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"overlapToMatrix — overlapToMatrix","title":"overlapToMatrix — overlapToMatrix","text":"create count matrix based overlap results calculateOverlap","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"overlapToMatrix — overlapToMatrix","text":"","code":"# S4 method for class 'giotto' overlapToMatrix(   x,   name = \"raw\",   poly_info = NULL,   feat_info = NULL,   type = c(\"point\", \"intensity\"),   count_info_column = NULL,   aggr_function = \"sum\",   return_gobject = TRUE,   verbose = TRUE,   ... )  # S4 method for class 'giottoPolygon' overlapToMatrix(   x,   feat_info = \"rna\",   type = c(\"point\", \"intensity\"),   count_info_column = NULL,   output = c(\"Matrix\", \"data.table\"),   ... )  # S4 method for class 'SpatVector' overlapToMatrix(   x,   col_names = NULL,   row_names = NULL,   count_info_column = NULL,   output = c(\"Matrix\", \"data.table\"),   verbose = TRUE,   ... )  # S4 method for class 'data.table' overlapToMatrix(x, aggr_function = \"sum\", output = c(\"Matrix\", \"data.table\"))"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"overlapToMatrix — overlapToMatrix","text":"x object containing overlaps info. Can giotto object SpatVector points data.table overlaps generated calculateOverlap name name overlap count matrix poly_info character. Polygon information use feat_info character. Feature information use type character. Type overlap data (either 'point' 'intensity') count_info_column column count information aggr_function function aggregate image information (default = sum) return_gobject return giotto object (default: TRUE) verbose verbose ... additional params pass methods output data format/class return results col_names, row_names character vector. (optional) Set row col names expected exist. fixes dimensions matrix since overlaps information directly report rows cols values detected.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"overlapToMatrix — overlapToMatrix","text":"giotto object count matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"overlapToMatrix — overlapToMatrix","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" gpoly <- getPolygonInfo(g,     polygon_name = \"aggregate\",     return_giottoPolygon = TRUE ) gpoints <- getFeatureInfo(g, return_giottoPoints = TRUE)  # calculate all transcripts overlapped out_all <- calculateOverlap(gpoly, gpoints) #> 1. convert polygon to raster #> 2. overlap raster and points #> 3. add polygon information #> 4. add points information #> 5. create overlap polygon #>  information  overlapToMatrix(out_all) #> Warning: [overlapToMatrix] expected col_names and row_names #>  not provided together. Points aggregation Matrix output #>  may be missing some cols and rows where no detections #>  were found. #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>   [[ suppressing 33 column names ‘100210519278873141813371229408401071444’, ‘101161259912191124732236989250178928032’, ‘101488859781016188084173008420811094152’ ... ]] #>                                                                                 #> Abcc9      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ackr1      .  . . 3 . .  . 1  .  1  7  . 2 2 1 .  .  . .  .  . . 1  . . 5 . . . #> Ackr3      .  . 2 . . .  . .  .  1  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adcyap1r1  .  . 1 4 1 4  5 4  1  1  6  7 2 1 2 1  1  2 .  2  2 2 1  3 1 1 2 3 . #> Adgra1     .  . 1 1 1 .  . 1  .  .  .  . 1 . . .  .  . .  2  . . 1  . . . . . . #> Adgra2     1  . . . . .  . .  .  .  .  . . . . .  .  . 2  .  . . .  . . . . . . #> Adgra3     .  1 . . . .  2 1  1  .  .  2 . . 2 .  .  . .  .  . . .  . . . . . . #> Adgrb1     .  . . 3 . 1  . 3  .  6  6  1 2 . . 1  1  3 .  1  . 3 5  1 1 . 1 . . #> Adgrb3     .  . . . . 3  . 2  1  1  3  1 . 1 . .  .  . .  .  . . .  2 . 2 3 1 . #> Adgre1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . 1 . . #> Adgrf2     .  . . . . 1  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Adgrf4     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrf5     4  . . . 1 .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrg1     2  . . . 1 .  4 .  2  .  .  . . . . .  1  . .  1  . . .  . . . 1 . . #> Adgrg2     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrg4     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrg6     .  . . . . .  1 .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrl1     1  . 1 1 3 1  . 4  1  .  1  6 3 2 2 1  .  1 .  .  1 . 1  1 . 2 . . . #> Adgrl2     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrl3     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrl4     2  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adgrv1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . 1 . . #> Adora1     .  1 1 1 . .  . .  1  1  .  1 . . 1 .  4  2 .  .  1 . 1  . 1 . . 1 . #> Adora2a    .  . . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Adora2b    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adra1a     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adra1b     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adra1d     .  . . . . .  . 1  .  1  1  . . 1 . .  .  2 .  .  . . 2  1 . 1 . . . #> Adra2a     .  . . . . .  . 1  .  .  .  . . . . 1  .  . .  .  . . .  1 . . . . . #> Adra2b     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Adrb1      .  . . . . .  . .  .  1  2  . . . . .  .  . .  .  . . .  . . . . . . #> Adrb2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Agtr1a     .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Aldh1l1    .  . . . 1 .  1 .  1  1  .  . . . . .  .  . .  2  . . .  . . . . . . #> Alk        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Amigo2     1  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  1 . . . . . #> Anxa11     .  . . 1 . 1  . 1  .  1  2  . 1 . 1 .  .  . 1  .  1 . 1  . 2 . . . . #> Aplnr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Aqp4       .  1 . . . .  3 .  4  .  .  . . . . .  1  1 . 11  . . .  . . . 1 . . #> Arhgap29   2  . . . 1 .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Ascl1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Atp13a5    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Avpr2      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Axl        .  . . . . .  1 .  2  .  .  . . . . .  .  . 3  .  . . .  . . . . . . #> Baiap2     .  1 5 2 1 2  . 3  .  4  7  1 4 1 1 .  .  2 .  1  1 5 2  5 . . . 1 . #> Bdkrb1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Bdkrb2     .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Blank-104  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-127  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-128  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-139  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-145  .  . . . . .  . .  .  1  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-148  .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Blank-152  .  . . . . .  . .  .  .  .  . 1 . . .  .  . .  .  . . .  . . . . . . #> Blank-155  .  . . 1 . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-161  .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-45   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . 1 . . . #> Blank-57   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-69   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-80   .  . . . . .  . 1  .  .  .  . . . . 1  .  . .  .  . . .  . . . . . . #> Blank-83   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Blank-95   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Brs3       .  1 . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> C1qa       .  1 . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 3 #> C1qb       .  3 . . . .  . .  .  .  .  . . . . .  .  . .  .  . . 1  . . . . . 4 #> C3ar1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> C5ar1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> C5ar2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Calcrl     .  . . . . .  . .  1  .  .  . . . . .  .  . 2  .  . . .  . . . . . . #> Casr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . 1 . . . #> Cckbr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ccr1       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ccr10      .  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Ccr2       .  1 . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ccr9       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Cd300c2    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Celsr1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . 1 . . #> Celsr2     .  1 . 5 1 2  1 3  .  2  3  2 3 1 2 1  .  4 .  .  . . 2  3 . 1 1 1 . #> Celsr3     .  . . . . .  . 1  .  .  .  . 1 1 . .  .  . .  4  . 1 1  . . . . . . #> Cenpe      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Chrm1      .  . . 6 . 1  . 2  .  1  .  2 1 1 1 1  .  1 .  .  1 1 3  3 1 2 . . . #> Chrm3      .  . . . . .  . 1  .  1  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Chrm4      .  . 2 . . .  . .  .  .  .  . . 1 . .  .  . .  .  . . 1  . . . . 1 . #> Chrm5      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Cldn5      5  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Cmklr1     .  . . . . .  1 .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Cnr1       .  . . . . .  . .  .  1  .  1 . . . .  .  . .  .  1 . .  . . . . 2 1 #> Crhr1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Crhr2      .  . . . . .  . 1  .  .  1  . . . . .  .  . .  .  . . .  . . . . . . #> Csf1r      .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . . 1  . . . . . 7 #> Cspg5      .  . . . 5 1 12 .  9  .  3  2 1 1 . 1  .  . .  3  1 2 2  . . . 7 . . #> Cx3cl1     .  . 1 5 1 .  1 5  1  2  2  7 2 4 . 3  .  3 1  2  3 5 6  6 1 4 . 3 . #> Cx3cr1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 3 #> Cxcl12     3  . . . 2 .  . .  .  .  1  . 1 . . .  .  3 9  4  . . 1  . 1 3 . 1 . #> Cxcr4      .  . . . 1 .  . .  .  .  .  . . . . .  .  . .  3  . . .  . . . . . . #> Cysltr2    1  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ddr1       .  6 . . . 1  . .  3  .  2  . . 1 . .  2  . .  3  . . 1  . . . . . . #> Ddr2       .  . 1 . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Dlk1       .  . . . . .  . .  .  .  .  . . . . .  4  . .  .  . . .  . . . 1 1 . #> Drd1       .  . . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Drd2       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Drd5       .  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Ednra      .  . . . . .  . .  1  .  .  . . . . .  .  . .  1  . . .  1 . . . . . #> Ednrb      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Efemp1     .  . . . . .  . .  2  .  .  . . . . .  .  . 3  .  . . .  . . . . . . #> Egfr       .  . . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . 1 . #> Emcn       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Eomes      .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Epha1      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Epha10     .  1 1 1 . .  . .  .  .  2  . 2 . . .  .  . .  .  . . .  . . . . . . #> Epha2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Epha3      .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . 1 .  1 . . . . . #> Epha4      .  . 1 2 1 1  . 3  1  .  3  1 1 2 2 1  1  3 .  .  1 2 4  3 2 1 . 1 . #> Epha5      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  1 . . . . . #> Epha6      .  . 1 . . 1  . .  .  1  3  1 . 3 . 1  .  1 .  .  1 . 2  2 . . . 2 . #> Epha7      .  . 1 . . 1  . 2  .  2  2  5 . 2 3 3  .  . 2  .  2 3 .  2 . . . 1 . #> Epha8      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ephb1      .  2 . . 1 .  . 1  .  .  .  . . . . .  1  . .  .  . . .  . . . 2 . . #> Ephb2      .  . . 1 . .  . .  .  1  .  . . . 1 .  .  . .  .  . . .  . . 1 . . . #> Ephb3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  1 . . . . . #> Ephb6      .  . . . . .  . .  .  .  .  . . . . .  .  1 .  1  1 . 2  . . . . 1 1 #> Erbb2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Erbb3      .  1 . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Erbb4      .  . . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  1 . . . . . #> F2r        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> F2rl3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Fgfr2      .  6 . . . .  . .  1  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Fgfr3      .  . . . 1 .  3 .  3  .  .  . . . . .  .  . .  1  . . .  . . . 1 . . #> Fgfrl1     .  . . . 1 .  . .  4  .  .  . . . . .  .  . .  2  . . .  . . . . . . #> Flt1      10  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Flt3       .  . . . . .  . .  .  .  1  . . . . .  .  . .  .  . . .  1 . . . . . #> Flt4       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Fn1        1  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Fpr1       .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Fzd1       .  . . . . .  . .  2  .  .  . . . . .  .  . .  .  1 . .  . . . . . . #> Fzd10      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Fzd2       .  . . . . .  1 .  .  .  .  . . . . .  .  . 1  .  . . .  . . . 1 . . #> Fzd3       .  1 . 1 1 2  . 1  1  .  .  2 2 2 . 1  1  . 1  .  . 2 1  2 1 2 . 1 . #> Fzd4       1  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Fzd5       .  1 . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  1 . . . . . #> Fzd6       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . 1 . . #> Fzd7       .  . . . . .  . 1  .  1  .  . . . . .  .  . .  .  . . .  2 . . . . . #> Fzd8       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . 1 1 . . . #> Fzd9       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gabbr1     .  2 4 1 1 1  . 4  2  3 10  5 3 2 1 1  .  2 .  3  1 4 3  6 . 6 2 . 2 #> Gabbr2     .  . 3 2 . 1  . 1  .  .  3  1 3 1 3 2  .  2 .  .  2 2 2  1 1 5 . . 1 #> Gad1       .  . 2 1 . 2  . 3  1  1  .  . . . . 1  .  . .  .  1 . 2  2 . . . . . #> Galr1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . 1  . . . . . . #> Gcgr       .  . . . . .  . .  .  .  1  . . . . .  .  . .  .  . . .  . . . . . . #> Gfap       1 12 . . 6 .  . .  1  2  .  . 1 . . . 21  . . 13  . . .  . . . 1 . . #> Ghsr       .  . . . . .  . .  .  .  .  . . . . 1  .  . .  .  . . .  1 . . . . . #> Gipr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gjc3       . 15 . . . .  . .  .  .  .  . . . . .  6  . .  .  . . .  . . . . . . #> Glp2r      .  . . . . .  . .  .  2  5  2 2 . . .  .  1 .  .  . 2 1  2 1 . . 1 . #> Gpbar1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gper1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr1       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr101     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr135     .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . 1 .  . . . . . . #> Gpr139     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr146     .  . . . . .  . .  .  .  .  . 1 1 . .  .  . 1  .  . . .  . . . . . . #> Gpr153     .  1 . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Gpr156     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr157     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr158     .  . 4 . 1 2  . 1  .  .  1  . 1 . 2 .  .  . .  .  . . 1  1 . 1 . . . #> Gpr160     1  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr161     .  . . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr162     .  . 1 1 . 1  . 2  .  1  .  1 . 2 . .  .  3 .  1  . 2 .  . . . . . 1 #> Gpr17      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr173     .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Gpr176     .  . . . . .  . 1  .  .  1  . . . . .  .  1 .  .  . 1 .  . . . . 1 . #> Gpr182     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr183     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr20      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr21      .  . . . . .  . .  .  1  .  . . . . .  2  . .  .  . . .  . . 1 . . 1 #> Gpr22      .  . . 2 1 .  . 2  .  1  1  . 2 1 . .  .  1 .  .  . 2 2  1 . 1 . 1 . #> Gpr26      .  . 1 . . .  . .  .  2  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr27      .  . . . 1 .  . 1  .  .  .  1 . . . .  .  . .  1  1 . .  . . . . . . #> Gpr34      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr37      .  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Gpr37l1    .  . . . 1 . 10 .  9  .  .  . . . . .  .  . .  5  . 1 .  . . . 2 . . #> Gpr4       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr45      .  . . . . .  . .  .  .  2  . . 1 . .  .  . .  .  . . .  . . . . . . #> Gpr52      .  . . . . .  . 1  .  .  3  1 . . . .  .  . .  .  . . .  . . 1 . . . #> Gpr55      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr6       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr61      .  . 1 1 . .  . 1  .  .  1  . . . . .  .  . .  .  . . .  . . . . 1 . #> Gpr62      .  1 . . . .  . .  .  .  .  1 . . . .  1  . .  .  . . 1  1 . . . . . #> Gpr63      .  . . . . .  1 .  .  .  2  . . . . .  .  1 .  .  . . .  . . . . 1 . #> Gpr75      .  . . . 1 .  . .  .  .  1  . . . 1 .  .  . .  .  . 3 .  . . . . . . #> Gpr83      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gpr85      .  . . . . 2  . 1  .  .  .  3 1 . . .  .  1 .  .  . 2 2  . . . . . . #> Gprc5b     . 17 . . 2 .  1 1  4  .  5  . 1 . . .  7  1 .  1  . . 1  . . . 1 . . #> Gprc5c     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Gramd3     .  . . . . .  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Grin2b     .  . 3 5 2 2  . 4  .  1  5  3 2 . 1 .  .  1 .  .  . 2 5  1 . 1 . 2 . #> Grm1       .  . 1 . . .  . 2  .  2  4  1 . . 1 .  .  1 .  .  . . 1  . . 1 . . . #> Grm2       .  . . 1 . .  . 1  .  2  2  2 1 1 . .  .  . .  1  . . 2  1 . 1 . . . #> Grm3       1  6 . . . .  . .  2  .  .  . . . . .  3  . .  .  . . .  . . . 1 . . #> Grm4       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Grm5       .  . 1 5 2 3  . 2  .  5  7  1 3 . 2 1  .  2 1  .  . 1 1  3 . 1 . . . #> Grm7       .  . 3 1 1 2  . 2  .  3  4  4 2 . 1 .  1  2 .  .  2 . .  1 1 . . 2 . #> Grpr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Hcar1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Hcrtr2     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Hrh1       .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Hrh2       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Hrh3       .  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . 1 . . . #> Htr1a      .  . . . 1 1  . 1  .  .  .  . . 1 . 1  .  . .  .  . . .  . . . . . . #> Htr1b      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Htr2a      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Htr4       .  . . . . .  . .  .  .  3  1 . . . .  .  1 .  .  . . .  1 . . . . . #> Htr5a      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Htr5b      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Htr6       .  . . . . .  . .  .  .  1  . . . . .  .  . .  .  . . .  . . . . . . #> Htr7       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Igf1r      5  1 1 1 1 .  . 1  .  .  1  . . . . .  1  . 1  3  . . .  1 . . 1 1 1 #> Insr       .  1 1 . . .  . 1  .  2  3  1 3 . . 1  1  1 .  .  . . .  . 1 . . . . #> Insrr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Kcnj8      .  . . . 1 1  . .  .  1  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Kdr        4  . . . 1 .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Kiss1r     .  . . . . .  . .  .  .  .  . . . . 1  .  . .  .  . . .  . . . . . . #> Kit        .  . . . 1 .  . .  .  .  .  . . . . .  .  . 2  2  . . .  . . . . . . #> Lgr4       .  . . . 1 .  1 .  1  .  1  3 . . . .  .  . 3  1  . . .  . . . 1 1 . #> Lgr6       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Lhcgr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Lmod1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Lmtk2      .  . 2 1 . .  . .  .  .  2  1 2 3 . 3  .  3 .  .  . . .  2 . . . . . #> Lpar1      .  4 . . 1 .  . .  .  .  .  . . . . .  2  . 1  .  . . .  . . . . . . #> Lpar2      .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Lpar4      .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Lpar6      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Man1a      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Mas1       .  . 2 2 . 3  . .  .  1  .  . . . 1 .  .  . .  .  2 . .  . . 1 . 1 . #> Mc4r       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Mc5r       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Mchr1      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Mertk      .  . . . 2 .  2 .  3  .  .  . . . . .  .  . .  1  . . .  . . . 1 . 1 #> Mlc1       .  1 . . 1 .  2 .  .  .  .  . . . . .  .  . .  1  . . .  1 . . . . . #> Mrgpre     .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . . .  . . . . . . #> Mrgprf     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Musk       .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Myh11      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Nmbr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Npy1r      .  . 1 . . .  . 1  .  .  1  . . 1 1 .  .  . 1  .  1 . .  . . 1 . 1 . #> Npy2r      .  . . 1 . 2  . 2  .  1  1  1 . . 1 1  .  1 .  .  1 1 2  1 . 1 . 3 . #> Nrp1       .  . . . . 1  . 2  3  .  .  2 1 . . 2  .  . .  1  1 . 1  1 1 . . . 3 #> Nrp2       .  1 1 . . .  . 1  .  1  .  . 1 . 2 .  .  . .  1  1 . .  . . 2 1 . . #> Ntrk2      1  1 . 1 1 .  4 .  7  1  1  2 1 . . .  .  . .  9  . 1 .  . . . 2 . . #> Ntrk3      .  . 3 5 1 4  . 3  .  6  4  3 1 2 3 2  .  3 .  .  4 4 3  4 1 2 . 1 . #> Ntsr2      1  2 . . 1 .  3 . 10  .  .  . . . . .  1  . .  5  . . .  . . . 1 . . #> Olig1      . 15 . . . 1  . .  1  .  .  . . . . .  3  1 .  .  . . .  . 1 . . . . #> Opn3       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Opn5       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Oprm1      .  . . . . 1  . .  .  1  .  . . . . .  .  . .  .  . . .  . . . . . . #> Oxtr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> P2ry1      .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> P2ry12     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . 2  . . . . . 4 #> P2ry14     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> P2ry2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> P2ry4      .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . . .  . . . . . . #> P2ry6      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> P2yr13     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . 1  . . . . . 3 #> Pcdh15     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Pdgfra     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Pdgfrb     .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Peg10      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Pln        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Plxnb3     .  . . . . .  . .  .  .  .  . . . . .  2  . .  .  . . .  . . . . . . #> Ppp1r3g    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Prokr2     .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . 1  1 . . . . . #> Ptafr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptgdr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptger2     .  . 1 . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptger3     .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptger4     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptgfr      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Pth1r      .  . . . . .  . .  1  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ptk7       .  . . . . .  . .  .  1  1  . . . . .  .  . 1  1  . . .  . . . . . . #> Ret        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Rho        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ror1       .  . . 1 . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ror2       .  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Rrh        .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Rspo3      .  . 1 . . .  . .  .  .  .  . . . 1 1  .  1 .  .  2 . 1  . . . . . . #> Rxfp3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Ryk        .  . . 1 . .  . 1  1  .  3  1 . . 1 .  1  . .  1  . . .  . . . . . 2 #> S1pr1      1  . . . 1 .  3 .  3  .  .  . . . . .  .  . .  .  . . .  . . . 2 . . #> S1pr2      .  1 . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> S1pr3      .  . . . . .  . 1  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> S1pr4      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> S1pr5      .  3 . . . .  . .  .  .  .  . . . . .  2  . .  .  . . .  . . . . . . #> Sctr       .  . . . . .  . .  .  .  .  . . . . .  .  . .  1  . . .  . . . . . . #> Selplg     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 6 #> Sema4d     .  9 . 1 . .  . 1  .  .  2  2 2 . 1 .  .  . .  .  1 . .  . . 1 . 1 . #> Slc15a3    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Slc17a6    .  . . . . .  . .  .  .  .  . . . . .  .  . .  5  . . .  . . . . . . #> Slc17a7    .  . 7 7 4 4  3 7  . 10 25 11 8 7 7 4  . 11 .  1 10 7 7 11 2 5 . 5 . #> Slc17a8    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Slc25a18   .  . . . . .  1 1  1  .  .  . . . . .  1  . .  2  . . 1  . . . 4 . . #> Slc32a1    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Slc47a1    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Slco1a4    1  . . . . .  . .  .  .  .  . . . . .  .  . 1  .  . . .  . . . . . . #> Smo        .  . . 1 . .  . .  .  1  .  . . . . .  .  . .  .  . . .  1 . . . . . #> Sox8       .  3 . . . .  . 1  .  2  .  1 . 1 . .  2  . .  .  . . .  . 2 . . . . #> Sox9       .  . . . 6 .  1 1  .  1  .  . . . . .  1  . .  1  . . .  . . . . . . #> Sstr1      .  . . . . 1  . 3  .  2  .  1 3 . . 1  .  . .  .  1 2 .  2 . 1 . 1 . #> Sstr2      .  . . . . .  . 1  .  .  2  . . . . .  .  . .  .  . . 1  . . 1 . 1 . #> Sstr3      .  . . . . .  . .  .  .  1  . 1 . . .  .  . .  .  . 2 1  1 . . . . . #> Sstr4      .  . . . . 1  1 1  .  .  .  1 1 3 2 .  .  1 .  .  . 1 1  . . . . . . #> Syt4       .  . . 1 . .  . 1  .  .  .  . 1 . . .  .  1 .  .  . 1 1  2 . . . 1 . #> Taar2      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Taar3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . 1 . #> Taar6      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Taar7e     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tacr1      .  . . . . .  . .  .  .  .  . . . 1 .  .  . .  .  . . .  . . . . . . #> Tacr3      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tas1r1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tas1r3     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tas2r135   .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tbxa2r     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tek        2  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Tie1       2  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Timp4      .  1 . . . .  1 .  1  .  .  . . . . .  .  . .  2  . . .  . . . . . . #> Tjap1      .  . . . . 1  . .  .  .  .  . . . . .  1  . .  .  . . .  . . . . . . #> Tmem108    .  . . 2 . 3  . 4  .  1  5  3 1 1 2 .  .  . .  .  . 2 2  1 1 . . . . #> Traf4      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . 1 #> Trhr       .  . 2 1 . 1  . .  .  .  2  1 1 . 1 .  .  4 .  .  . . 1  1 . 1 . . . #> Tyro3      .  9 . . . .  1 .  .  .  .  . . 1 1 .  .  . .  .  . . .  . . . . . . #> Uts2r      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> V1ra8      .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Vipr1      .  . . . . .  . .  .  .  .  . 1 . . .  .  1 .  .  . . .  . . . . . . #> Vmn1r40    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Vmn1r43    .  . . . . .  . .  .  .  .  1 . . . .  .  . .  .  . . .  . . . . . . #> Vmn1r46    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Vmn1r50    .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #> Vmn2r1     .  . . . . .  . .  .  .  .  . . . . .  .  . .  .  . . .  . . . . . . #>                            #> Abcc9      .  . . . ...... #> Ackr1      .  . . . ...... #> Ackr3      .  . . . ...... #> Adcyap1r1  1  2 . 2 ...... #> Adgra1     .  2 . . ...... #> Adgra2     .  . . . ...... #> Adgra3     .  . 1 1 ...... #> Adgrb1     .  . . . ...... #> Adgrb3     3  1 . . ...... #> Adgre1     .  . . . ...... #> Adgrf2     .  . . . ...... #> Adgrf4     .  . . . ...... #> Adgrf5     .  . . . ...... #> Adgrg1     4  . . . ...... #> Adgrg2     .  . . . ...... #> Adgrg4     .  . . . ...... #> Adgrg6     .  . . . ...... #> Adgrl1     1  4 . . ...... #> Adgrl2     .  . . . ...... #> Adgrl3     .  . . . ...... #> Adgrl4     .  . . . ...... #> Adgrv1     .  . . . ...... #> Adora1     .  1 . 1 ...... #> Adora2a    .  . . . ...... #> Adora2b    .  . . . ...... #> Adra1a     .  . . . ...... #> Adra1b     .  . . . ...... #> Adra1d     .  1 . . ...... #> Adra2a     .  . . . ...... #> Adra2b     .  . . . ...... #> Adrb1      .  . . . ...... #> Adrb2      .  . . . ...... #> Agtr1a     .  1 . . ...... #> Aldh1l1    4  . . . ...... #> Alk        .  . . . ...... #> Amigo2     .  . . . ...... #> Anxa11     .  . . . ...... #> Aplnr      .  . . . ...... #> Aqp4       3  . . . ...... #> Arhgap29   .  1 . . ...... #> Ascl1      .  . . . ...... #> Atp13a5    1  . . . ...... #> Avpr2      .  . . . ...... #> Axl        2  . . . ...... #> Baiap2     .  1 . . ...... #> Bdkrb1     .  . . . ...... #> Bdkrb2     .  . . . ...... #> Blank-104  .  . . . ...... #> Blank-127  .  . . . ...... #> Blank-128  .  . . . ...... #> Blank-139  .  . . . ...... #> Blank-145  .  . . . ...... #> Blank-148  .  . . . ...... #> Blank-152  .  . . . ...... #> Blank-155  .  . . . ...... #> Blank-161  .  . . . ...... #> Blank-45   .  . . . ...... #> Blank-57   .  . . . ...... #> Blank-69   .  . . . ...... #> Blank-80   .  . . . ...... #> Blank-83   .  . . . ...... #> Blank-95   .  . . . ...... #> Brs3       .  . . . ...... #> C1qa       .  . 5 . ...... #> C1qb       .  . 6 . ...... #> C3ar1      .  . . . ...... #> C5ar1      .  . . . ...... #> C5ar2      .  . . . ...... #> Calcrl     .  . . . ...... #> Casr       .  . . . ...... #> Cckbr      .  . . . ...... #> Ccr1       .  . . . ...... #> Ccr10      .  . . . ...... #> Ccr2       .  . . . ...... #> Ccr9       .  . . . ...... #> Cd300c2    .  . . . ...... #> Celsr1     .  . . . ...... #> Celsr2     .  1 . . ...... #> Celsr3     .  1 . . ...... #> Cenpe      .  . . . ...... #> Chrm1      .  1 . . ...... #> Chrm3      .  . . . ...... #> Chrm4      .  . . . ...... #> Chrm5      .  . . . ...... #> Cldn5      .  . . . ...... #> Cmklr1     .  . . . ...... #> Cnr1       .  . . . ...... #> Crhr1      .  . . . ...... #> Crhr2      .  . . . ...... #> Csf1r      .  . 3 . ...... #> Cspg5      5  1 . . ...... #> Cx3cl1     .  3 . . ...... #> Cx3cr1     .  . 3 . ...... #> Cxcl12     .  . . . ...... #> Cxcr4      .  . . . ...... #> Cysltr2    .  . . . ...... #> Ddr1       .  2 . . ...... #> Ddr2       .  . . . ...... #> Dlk1       .  . . . ...... #> Drd1       .  . . . ...... #> Drd2       .  . . . ...... #> Drd5       .  . . . ...... #> Ednra      .  . . . ...... #> Ednrb      2  . . . ...... #> Efemp1     .  . . . ...... #> Egfr       .  1 . . ...... #> Emcn       .  . . . ...... #> Eomes      .  . . . ...... #> Epha1      .  . . . ...... #> Epha10     .  . . . ...... #> Epha2      .  . . . ...... #> Epha3      .  . . . ...... #> Epha4      .  1 . . ...... #> Epha5      .  . . . ...... #> Epha6      .  . . . ...... #> Epha7      .  1 . . ...... #> Epha8      .  . . . ...... #> Ephb1      .  1 . . ...... #> Ephb2      .  . . . ...... #> Ephb3      1  . . . ...... #> Ephb6      .  . 1 . ...... #> Erbb2      .  . . . ...... #> Erbb3      .  . . . ...... #> Erbb4      .  . . 1 ...... #> F2r        .  . . . ...... #> F2rl3      .  . . . ...... #> Fgfr2      1  . . . ...... #> Fgfr3      7  . 1 . ...... #> Fgfrl1     1  . . . ...... #> Flt1       .  1 . . ...... #> Flt3       .  1 . . ...... #> Flt4       .  . . . ...... #> Fn1        .  . . . ...... #> Fpr1       .  . . . ...... #> Fzd1       .  . . . ...... #> Fzd10      .  . . . ...... #> Fzd2       .  . . . ...... #> Fzd3       2  . . . ...... #> Fzd4       .  1 . . ...... #> Fzd5       .  . . . ...... #> Fzd6       .  . . . ...... #> Fzd7       .  . . . ...... #> Fzd8       .  . . . ...... #> Fzd9       .  . . . ...... #> Gabbr1     3  3 1 . ...... #> Gabbr2     .  2 . . ...... #> Gad1       1  . . . ...... #> Galr1      .  . . . ...... #> Gcgr       .  . . . ...... #> Gfap       1  . 2 2 ...... #> Ghsr       .  . . . ...... #> Gipr       .  . . . ...... #> Gjc3       .  . . . ...... #> Glp2r      .  . . . ...... #> Gpbar1     .  . . . ...... #> Gper1      .  . . . ...... #> Gpr1       .  . . . ...... #> Gpr101     .  . . . ...... #> Gpr135     .  . . . ...... #> Gpr139     .  . . . ...... #> Gpr146     1  . . . ...... #> Gpr153     .  . . . ...... #> Gpr156     .  . . . ...... #> Gpr157     .  . . . ...... #> Gpr158     .  . . . ...... #> Gpr160     .  . . . ...... #> Gpr161     .  . . . ...... #> Gpr162     1  . . . ...... #> Gpr17      .  . . . ...... #> Gpr173     .  . . . ...... #> Gpr176     .  . . . ...... #> Gpr182     .  . . . ...... #> Gpr183     .  . . . ...... #> Gpr20      .  . . . ...... #> Gpr21      .  . . . ...... #> Gpr22      .  . . . ...... #> Gpr26      .  . . . ...... #> Gpr27      .  . . . ...... #> Gpr34      .  . . . ...... #> Gpr37      .  . . . ...... #> Gpr37l1    6  . . . ...... #> Gpr4       .  . . . ...... #> Gpr45      .  1 . . ...... #> Gpr52      .  . . . ...... #> Gpr55      .  . . . ...... #> Gpr6       .  . . . ...... #> Gpr61      .  . . . ...... #> Gpr62      .  . . . ...... #> Gpr63      .  . . . ...... #> Gpr75      .  . . . ...... #> Gpr83      .  . . . ...... #> Gpr85      .  1 . . ...... #> Gprc5b     2  1 . . ...... #> Gprc5c     .  . . . ...... #> Gramd3     .  . . . ...... #> Grin2b     .  2 . . ...... #> Grm1       .  1 . . ...... #> Grm2       .  . . . ...... #> Grm3       4  . . . ...... #> Grm4       .  . . . ...... #> Grm5       .  2 . . ...... #> Grm7       .  3 . . ...... #> Grpr       .  . . . ...... #> Hcar1      .  . . . ...... #> Hcrtr2     .  . . . ...... #> Hrh1       .  . . . ...... #> Hrh2       .  . . . ...... #> Hrh3       .  . . . ...... #> Htr1a      .  . . . ...... #> Htr1b      .  . . . ...... #> Htr2a      .  . . . ...... #> Htr4       .  1 . . ...... #> Htr5a      .  . . . ...... #> Htr5b      .  . . . ...... #> Htr6       .  . . . ...... #> Htr7       .  . . . ...... #> Igf1r      2  1 . . ...... #> Insr       3  1 . . ...... #> Insrr      .  . . . ...... #> Kcnj8      .  . . . ...... #> Kdr        .  1 . . ...... #> Kiss1r     .  . . . ...... #> Kit        .  . . . ...... #> Lgr4       2  . 1 . ...... #> Lgr6       .  . . . ...... #> Lhcgr      .  . . . ...... #> Lmod1      .  . . . ...... #> Lmtk2      .  2 1 . ...... #> Lpar1      .  . . . ...... #> Lpar2      .  . . . ...... #> Lpar4      .  1 . . ...... #> Lpar6      .  . . . ...... #> Man1a      .  . . . ...... #> Mas1       .  . . . ...... #> Mc4r       .  . . . ...... #> Mc5r       .  . . . ...... #> Mchr1      .  . . . ...... #> Mertk      3  . . . ...... #> Mlc1       1  . . . ...... #> Mrgpre     .  . . . ...... #> Mrgprf     .  . . . ...... #> Musk       .  . . . ...... #> Myh11      .  . . . ...... #> Nmbr       .  . . . ...... #> Npy1r      .  . . . ...... #> Npy2r      .  1 . . ...... #> Nrp1       .  3 . . ...... #> Nrp2       .  . . . ...... #> Ntrk2      3  . . 1 ...... #> Ntrk3      .  . 1 . ...... #> Ntsr2     13  . . . ...... #> Olig1      .  . . . ...... #> Opn3       .  . . . ...... #> Opn5       .  . . . ...... #> Oprm1      .  . . . ...... #> Oxtr       .  . . . ...... #> P2ry1      .  . . . ...... #> P2ry12     .  . 5 . ...... #> P2ry14     .  . . . ...... #> P2ry2      .  . . . ...... #> P2ry4      .  . . . ...... #> P2ry6      .  . . . ...... #> P2yr13     .  . 1 1 ...... #> Pcdh15     .  . . . ...... #> Pdgfra     .  . . . ...... #> Pdgfrb     1  . . . ...... #> Peg10      .  . . . ...... #> Pln        .  . . . ...... #> Plxnb3     .  . . . ...... #> Ppp1r3g    .  . . . ...... #> Prokr2     .  . . . ...... #> Ptafr      .  . . . ...... #> Ptgdr      .  . . . ...... #> Ptger2     .  . . . ...... #> Ptger3     .  . . . ...... #> Ptger4     .  . . . ...... #> Ptgfr      .  . . . ...... #> Pth1r      .  . . . ...... #> Ptk7       .  1 . . ...... #> Ret        .  . . . ...... #> Rho        .  . . . ...... #> Ror1       .  . . . ...... #> Ror2       .  . . . ...... #> Rrh        .  . . . ...... #> Rspo3      .  . . . ...... #> Rxfp3      .  . . . ...... #> Ryk        .  1 . . ...... #> S1pr1      3  . . . ...... #> S1pr2      .  . . . ...... #> S1pr3      .  . . . ...... #> S1pr4      .  . . . ...... #> S1pr5      .  . . . ...... #> Sctr       .  . . . ...... #> Selplg     .  . 2 . ...... #> Sema4d     .  1 . . ...... #> Slc15a3    .  . 1 . ...... #> Slc17a6    .  . . . ...... #> Slc17a7    . 16 1 . ...... #> Slc17a8    .  . . . ...... #> Slc25a18   1  . . . ...... #> Slc32a1    .  . . . ...... #> Slc47a1    .  . . . ...... #> Slco1a4    .  . . . ...... #> Smo        .  . . . ...... #> Sox8       1  . . . ...... #> Sox9       1  . 2 1 ...... #> Sstr1      .  1 . . ...... #> Sstr2      .  . . . ...... #> Sstr3      .  1 . . ...... #> Sstr4      .  1 . . ...... #> Syt4       .  2 . . ...... #> Taar2      .  . . . ...... #> Taar3      .  . . . ...... #> Taar6      .  . . . ...... #> Taar7e     .  . . . ...... #> Tacr1      .  . . . ...... #> Tacr3      .  . . . ...... #> Tas1r1     .  . . . ...... #> Tas1r3     .  . . . ...... #> Tas2r135   .  . . . ...... #> Tbxa2r     .  . . . ...... #> Tek        .  . . . ...... #> Tie1       .  . . . ...... #> Timp4      .  . . . ...... #> Tjap1      .  . . . ...... #> Tmem108    .  1 . . ...... #> Traf4      .  . . . ...... #> Trhr       .  1 . . ...... #> Tyro3      .  . . . ...... #> Uts2r      .  . . . ...... #> V1ra8      .  . . . ...... #> Vipr1      .  . . . ...... #> Vmn1r40    .  . . . ...... #> Vmn1r43    .  . . . ...... #> Vmn1r46    .  . . . ...... #> Vmn1r50    .  . . . ...... #> Vmn2r1     .  . . . ...... #>  #>  .....suppressing 429 columns in show(); maybe adjust options(max.print=, width=) #>  .............................."},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":null,"dir":"Reference","previous_headings":"","what":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"create count matrix based overlap results calculateOverlapRaster, calculateOverlapSerial, calculateOverlapParallel aggregate information multiple polygon layers (e.g. z-stacks) together","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"","code":"overlapToMatrixMultiPoly(   gobject,   name = \"raw\",   poly_info = \"cell\",   feat_info = \"rna\",   new_poly_info = \"multi\",   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"gobject giotto object name name overlap count matrix poly_info vector polygon information feat_info feature information new_poly_info name new aggregated polygon information return_gobject return giotto object (default: TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"giotto object count matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlapToMatrixMultiPoly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"overlapToMatrixMultiPoly — overlapToMatrixMultiPoly","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  overlapToMatrixMultiPoly(g, poly_info = \"z0\") #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #>   [multi][rna] raw #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"overlaps-generic — overlaps-generic","title":"overlaps-generic — overlaps-generic","text":"Access list overlaps information object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"overlaps-generic — overlaps-generic","text":"","code":"# S4 method for class 'giottoPolygon' overlaps(x, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"overlaps-generic — overlaps-generic","text":"x object name (optional) name overlaps information retrieve","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"overlaps-generic — overlaps-generic","text":"list overlaps object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"overlaps-generic — overlaps-generic","text":"overlaps(giottoPolygon): Get overlaps information giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/overlaps-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"overlaps-generic — overlaps-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  overlaps(g) #> $rna #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 32071, 4  (geometries, attributes) #>  extent      : 6400.441, 6900.032, -5149.827, -4699.984  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID feat_ID feat_ID_uniq stack #>  type        :                     <chr>   <chr>        <int> <int> #>  values      : 323754550002953984063006~  Selplg           87     1 #>                323754550002953984063006~   Fgfr3          122     1 #>                323754550002953984063006~    Gfap          138     1 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":null,"dir":"Reference","previous_headings":"","what":"pDataDT — pDataDT","title":"pDataDT — pDataDT","text":"show cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"pDataDT — pDataDT","text":"","code":"pDataDT(gobject, spat_unit = NULL, feat_type = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"pDataDT — pDataDT","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"pDataDT — pDataDT","text":"data.table cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/pDataDT.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"pDataDT — pDataDT","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  pDataDT(g) #>                 cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                  <char>     <int>    <int>      <num>      <num>       <num> #>   1: AACTCGATGGCGCAGT-1         1      265   41.79811  1057.9308           2 #>   2: GGCTGGCTAGCTTAAA-1         1      279   44.00631  1064.7493           5 #>   3: GACGCCTGTTGCAGGG-1         1      219   34.54259   964.9294           2 #>   4: GAGGGCATCGCGTATC-1         1      294   46.37224  1142.7664           2 #>   5: TCAACACATTGGGTAA-1         1      261   41.16719  1063.3517           2 #>  ---                                                                         #> 620: GGTAGTGCTCGCACCA-1         1      179   28.23344   768.4749           5 #> 621: AAGCTCGTGCCAAGTC-1         1      195   30.75710   756.0675           5 #> 622: TATTCAATTCTAATCC-1         1      247   38.95899   921.8264           5 #> 623: TTCAAAGTCTCTAGCC-1         1      384   60.56782   916.5929           6 #> 624: TTGAATATGGACTTTC-1         1      380   59.93691   912.3051           6 #>      custom_leiden #>              <num> #>   1:             4 #>   2:             3 #>   3:             3 #>   4:             3 #>   5:             3 #>  ---               #> 620:             4 #> 621:             4 #> 622:             4 #> 623:             7 #> 624:             4"},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Preview a Giotto spatial object — plot-generic","title":"Preview a Giotto spatial object — plot-generic","text":"S4 generic previewing Giotto's image subcellular objects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Preview a Giotto spatial object — plot-generic","text":"","code":"# S4 method for class 'giottoImage,missing' plot(x, y, ...)  # S4 method for class 'giottoLargeImage,missing' plot(   x,   y,   col,   max_intensity,   mar,   asRGB = FALSE,   legend = FALSE,   axes = TRUE,   maxcell = 5e+05,   smooth = TRUE,   ... )  # S4 method for class 'giottoAffineImage,missing' plot(x, y, ...)  # S4 method for class 'giottoPolygon,missing' plot(   x,   point_size = 0.6,   type = c(\"poly\", \"centroid\"),   max_poly = getOption(\"giotto.plot_max_poly\", 1e+06),   ... )  # S4 method for class 'giottoPoints,missing' plot(x, point_size = 0, feats = NULL, raster = TRUE, raster_size = 600, ...)  # S4 method for class 'spatLocsObj,missing' plot(x, y, ...)  # S4 method for class 'dimObj,missing' plot(x, dims = c(1, 2), ...)  # S4 method for class 'spatialNetworkObj,missing' plot(x, y, ...)  # S4 method for class 'affine2d,missing' plot(x, y, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Preview a Giotto spatial object — plot-generic","text":"x giotto image, giottoPolygon, giottoPoints object y used. ... additional parameters pass col character. Colors. default grDevices::grey.colors(n = 256, start = 0, end = 1, gamma = 1) max_intensity (optional) value treat maximum intensity color scale mar numeric vector length 4 set margins plot (make space legend). default (3, 5, 1.5, 1) asRGB (optional) logical. Force RGB plotting automatically detected legend logical character. FALSE legend drawn. character value can used indicate legend drawn. example \"topright\" \"bottomleft\" axes logical. Draw axes? maxcell positive integer. Maximum number cells use plot smooth logical. TRUE cell values smoothed point_size size points plotting giottoPoints type plot: either 'poly' (default) polygon 'centroid' max_poly numeric. type specified, maximum number polygons plot automatically switching centroids plotting. Default 1e4. value settable using options(\"giotto.plot_max_poly\") feats specific features plot within giottoPoints object (defaults NULL, meaning available features) raster default = TRUE, whether plot points rasterized plot size based raster_size param. See details. FALSE, plots via terra::plot() raster_size Default 600. used raster TRUE dims dimensions plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Preview a Giotto spatial object — plot-generic","text":"plot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Preview a Giotto spatial object — plot-generic","text":"[giottoPoints raster plotting] Fast plotting points information rasterizing information using terra::rasterize(). terra SpatVectors, faster scattermore plotting. plotting raster, col colors map whole image level, opposed mapping individual points, raster = FALSE Allows following additional params plotting specific feats input: force_size logical. raster_size param caps 1:1 spatial extent, also minimum resulting px dim 100. ignore constraints, set force_size = FALSE dens logical. Show point density using count statistic per rasterized cell. (Default = FALSE). param affects col param defaults. TRUE, col grDevices::hcl.colors(256). FALSE, \"black\" \"white\" used. background (optional) background color. Usually used col color mapping sufficient. Note col param base::plot() graphical params available ...","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Preview a Giotto spatial object — plot-generic","text":"plot(x = giottoImage, y = missing): Plot magick-based giottoImage object. ... param passes .plot_giottoimage_mg plot(x = giottoLargeImage, y = missing): Plot terra-based giottoLargeImage object. ... param passes .plot_giottolargeimage plot(x = giottoPolygon, y = missing): Plot terra-based giottoPolygon object. ... param passes plot plot(x = giottoPoints, y = missing): terra-based giottoPoint object. ... param passes plot plot(x = spatLocsObj, y = missing): Plot spatLocsObj plot(x = dimObj, y = missing): Plot dimObj plot(x = spatialNetworkObj, y = missing): Plot spatialNetworkObj plot(x = affine2d, y = missing): Plot affine2d. blue start, red end","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Preview a Giotto spatial object — plot-generic","text":"","code":"######### giottoLargeImage plotting ######### if (FALSE) { # \\dontrun{ gimg <- GiottoData::loadSubObjectMini(\"giottoLargeImage\") gimg <- GiottoClass:::.update_giotto_image(gimg) # only needed if out of date plot(gimg) plot(gimg, col = grDevices::hcl.colors(256)) plot(gimg, max_intensity = 100) } # }  ######### giottoPolygon plotting ######### gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") plot(gpoly)  plot(gpoly, type = \"centroid\")   ######### giottoPoints plotting ######### gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  # ----- rasterized plotting ----- # # plot points binary plot(gpoints)  # plotting all features maps colors on an image level plot(gpoints, col = grDevices::hcl.colors(n = 256)) # only 2 colors are used  plot(gpoints, col = \"green\", background = \"purple\")   # plot points density (by count) plot(gpoints, dens = TRUE, raster_size = 300)   # force_size = TRUE to ignore default constraints on too big or too small # (see details) plot(gpoints, dens = TRUE, raster_size = 80, force_size = TRUE)   # plot specific feature(s) plot(gpoints, feats = featIDs(gpoints)[seq_len(4)])   # ----- vector plotting ----- # # non-rasterized plotting (slower, but higher quality) plot(gpoints, raster = FALSE)   # vector plotting maps colors to transcripts plot(gpoints, raster = FALSE, col = grDevices::rainbow(nrow(gpoints)))   # plot specific feature(s) plot(gpoints, feats = featIDs(gpoints)[seq_len(4)], raster = FALSE)   ######### spatLocsObj plotting ######### sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\") plot(sl)   ######### dimObj plotting ######### d <- GiottoData::loadSubObjectMini(\"dimObj\") plot(d)  plot(d, dims = c(3, 5))"},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot a giotto image object — plotGiottoImage","title":"Plot a giotto image object — plotGiottoImage","text":"Display giotto image viewer panel. Image object plot can specified providing giotto object containing image (gobject), image object name (image_name), image object type (image_type). Alternatively, image objects can directly plotted respective associated params.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot a giotto image object — plotGiottoImage","text":"","code":"plotGiottoImage(   gobject = NULL,   image_name = NULL,   image_type = NULL,   giottoImage = NULL,   giottoLargeImage = NULL,   largeImage_crop_params_list = NULL,   largeImage_max_intensity = NULL,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot a giotto image object — plotGiottoImage","text":"gobject gobject containing giotto image object image_name name giotto image object image_type type giotto image object plot giottoImage giottoImage object plot directly giottoLargeImage giottoLargeImage object plot directly largeImage_crop_params_list (optional) named list params focusing specified region giottoLargeImage. largeImage_max_intensity (optional) assign override value treat maximum intensity color scale plotting giottoLargeImage ... additional params pass image object specific plotting functions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot a giotto image object — plotGiottoImage","text":"image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"largeimage-specific-additional-params","dir":"Reference","previous_headings":"","what":"largeImage-specific additional params","title":"Plot a giotto image object — plotGiottoImage","text":"largeImage_crop_params_list accepts named list following possible params define region interest (ROI) plot either terra extent object x y min max bounds given numerics: crop_extent – terra extent object define crop ROI xmax_crop – x max ROI xmin_crop – x min ROI ymax_crop – y max ROI ymin_crop – y min ROI largeImage_max_intensity accepts numeric value set max value plotting color scale. Can used case high outlier intensity values image preview alternative color scaling desired.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/plotGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot a giotto image object — plotGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  plotGiottoImage(g,     image_type = \"largeImage\", image_name = \"dapi_z0\",     largeImage_max_intensity = 200 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial polygons stamp — polyStamp","title":"Spatial polygons stamp — polyStamp","text":"Takes given stamp polygon places spatial location provided.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial polygons stamp — polyStamp","text":"","code":"polyStamp(   stamp_dt,   spatlocs,   id_col = \"cell_ID\",   x_col = \"sdimx\",   y_col = \"sdimy\",   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial polygons stamp — polyStamp","text":"stamp_dt data.table x y vertices polygon stamped. Column names expected 'x' 'y' respectively spatlocs spatial locations x y coordinates polygons stamped. Column names 'cell_ID', 'sdimx' 'sdimy' default id_col column spatlocs use IDs (default 'cell_ID') x_col column spatlocs use x locations (default 'sdimx') y_col column spatlocs use y locations (default 'sdimy') verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial polygons stamp — polyStamp","text":"data.table polygon vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/polyStamp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial polygons stamp — polyStamp","text":"","code":"# stamp shapes hex <- hexVertices(radius = 1) spatlocs <- data.table::data.table(     sdimx = rnorm(10, mean = 5, sd = 20),     sdimy = rnorm(10, mean = 5, sd = 20),     cell_ID = paste0(\"spot_\", seq_len(10)) ) random_hex <- polyStamp(hex, spatlocs) #> 10 polygons generated random_hex_poly <- createGiottoPolygon(random_hex) #>   Selecting col \"poly_ID\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(random_hex_poly)   # make a grid of shapes e <- c(0, 1000, 0, 1000) tg <- triGrid(extent = e, ccd = 100, id_prefix = \"bin_\")  r <- rectVertices(dims = c(x = 60, y = 50))  rect_grid_dt <- polyStamp(stamp_dt = r, spatlocs = tg) #> 104 polygons generated rect_poly <- createGiottoPolygon(rect_grid_dt) #>   Selecting col \"poly_ID\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively plot(rect_poly)"},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert polygon to raster — polygon_to_raster","title":"Convert polygon to raster — polygon_to_raster","text":"convert polygon raster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert polygon to raster — polygon_to_raster","text":"","code":"polygon_to_raster(polygon, field = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert polygon to raster — polygon_to_raster","text":"polygon SpatVector polygon rasterize field character. Name attribute polygon used rasterizing assign values. Passing NULL uses first attribute.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert polygon to raster — polygon_to_raster","text":"list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert polygon to raster — polygon_to_raster","text":"","code":"df <- data.frame(x = 1:5, y = c(1, 4, 4, 3, 1)) d <- data.frame(id = 1, name = \"polygon_1\") my_polygon <- terra::vect(as.matrix(df), type = \"polygons\", atts = d)  polygon_to_raster(my_polygon) #> $raster #> class       : SpatRaster  #> dimensions  : 3, 4, 1  (nrow, ncol, nlyr) #> resolution  : 1, 1  (x, y) #> extent      : 1, 5, 1, 4  (xmin, xmax, ymin, ymax) #> coord. ref. :   #> source(s)   : memory #> name        : poly_i  #> min value   :      1  #> max value   :      1  #>  #> $ID_vector #> 1  #> 1  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Provenance information — prov-generic","title":"Provenance information — prov-generic","text":"access set provenance slot S4 subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Provenance information — prov-generic","text":"","code":"# S4 method for class 'provData' prov(x)  # S4 method for class 'provData' prov(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Provenance information — prov-generic","text":"x Giotto S4 class subobject value value set provenance","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Provenance information — prov-generic","text":"provenance slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Provenance information — prov-generic","text":"prov(provData): Get provenance information prov(provData) <- value: Set provenance information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/prov-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Provenance information — prov-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  prov(g) #> [1] \"z0\" \"z1\""},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":null,"dir":"Reference","previous_headings":"","what":"R spatial conversions — r_spatial_conversions","title":"R spatial conversions — r_spatial_conversions","text":"R spatial conversions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"R spatial conversions — r_spatial_conversions","text":"","code":"# S4 method for class 'sf' as.sp(x)  # S4 method for class 'SpatVector' as.sp(x)  # S4 method for class 'stars' as.sp(x)  # S4 method for class 'Spatial' as.sp(x)  # S4 method for class 'giottoPolygon' as.sp(x, drop = TRUE)  # S4 method for class 'giottoPoints' as.sp(x, drop = TRUE)  # S4 method for class 'SpatVector' as.sf(x)  # S4 method for class 'Spatial' as.sf(x)  # S4 method for class 'stars' as.sf(x)  # S4 method for class 'sf' as.sf(x)  # S4 method for class 'giottoPolygon' as.sf(x, drop = TRUE)  # S4 method for class 'giottoPoints' as.sf(x, drop = TRUE)  # S4 method for class 'SpatVector' as.stars(x)  # S4 method for class 'sf' as.stars(x)  # S4 method for class 'Spatial' as.stars(x)  # S4 method for class 'stars' as.stars(x)  # S4 method for class 'giottoPolygon' as.stars(x, drop = TRUE)  # S4 method for class 'giottoPoints' as.stars(x, drop = TRUE)  # S4 method for class 'SpatVector' as.terra(x)  # S4 method for class 'sf' as.terra(x)  # S4 method for class 'stars' as.terra(x, type = c(\"vector\", \"raster\"))  # S4 method for class 'Spatial' as.terra(x)  # S4 method for class 'giottoPolygon' as.terra(x, drop = TRUE)  # S4 method for class 'giottoPoints' as.terra(x, drop = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"R spatial conversions — r_spatial_conversions","text":"x object coerce drop TRUE, returned object desired object type instead wrapped giottoPoints giottoPolygon object type whether data 'vector' 'raster'","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"R spatial conversions — r_spatial_conversions","text":"sf, sp, stars terra","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/r_spatial_conversions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"R spatial conversions — r_spatial_conversions","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  as.sf(g) #> Simple feature collection with 79761 features and 3 fields #> Geometry type: POINT #> Dimension:     XY #> Bounding box:  xmin: 6400.037 ymin: -5149.983 xmax: 6900.032 ymax: -4699.978 #> CRS:           NA #> First 10 features: #>    feat_ID global_z feat_ID_uniq                   geometry #> 1     Mlc1        0            1 POINT (6400.037 -4966.651) #> 2   Gprc5b        0            2 POINT (6400.041 -4965.377) #> 3     Gfap        0            3 POINT (6400.078 -5081.453) #> 4     Gfap        0            4 POINT (6400.084 -5038.288) #> 5    Ednrb        0            5 POINT (6400.172 -4816.516) #> 6     Gfap        0            6 POINT (6400.172 -5077.041) #> 7     Gfap        0            7 POINT (6400.189 -5080.815) #> 8     Sox9        0            8 POINT (6400.228 -4770.126) #> 9     Gfap        0            9 POINT (6400.246 -5096.167) #> 10  Gprc5b        0           10 POINT (6400.278 -4928.655)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine objects by rows (Giotto-related) — rbind-generic","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"row bind two objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"","code":"# S4 method for class 'cellMetaObj,cellMetaObj' rbind2(x, y, ...)  # S4 method for class 'featMetaObj,featMetaObj' rbind2(x, y, ...)  # S4 method for class 'spatLocsObj,spatLocsObj' rbind2(x, y, ...)  # S4 method for class 'giottoPolygon,giottoPolygon' rbind2(x, y, add_list_ID = TRUE, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"x item 1 rbind y item 2 rbind ... additional params pass methods add_list_ID whether generate list_ID column giottoPolygons append different names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"object appended rows","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"rbind2(x = giottoPolygon, y = giottoPolygon): Append giottoPolygon objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine objects by rows (Giotto-related) — rbind-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  rbind2(g, g) #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 924, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    :"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_hetero.html","id":null,"dir":"Reference","previous_headings":"","what":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","title":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","text":"Append two giotto polygons together different names Performed recursively rbind2 rbind. Generates additional list_ID attribute based original names. object name also becomes combination previous names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_hetero.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","text":"","code":"rbind2_giotto_polygon_hetero(x, y, new_name, add_list_ID = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_hetero.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","text":"x giottoPolygon 1 y giottoPolygon 2 add_list_ID whether include name origin giottoPolygons new 'list_ID' attribute","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_hetero.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Append giotto polygons of different names — rbind2_giotto_polygon_hetero","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_homo.html","id":null,"dir":"Reference","previous_headings":"","what":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","title":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","text":"Append two giotto polygons together name. Performed recursively rbind2 rbind","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_homo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","text":"","code":"rbind2_giotto_polygon_homo(x, y)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_homo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","text":"x giottoPolygon 1 y giottoPolygon 2","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rbind2_giotto_polygon_homo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Append giotto polygons of the same name — rbind2_giotto_polygon_homo","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read cell metadata — readCellMetadata","title":"Read cell metadata — readCellMetadata","text":"read cell metadata list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read cell metadata — readCellMetadata","text":"","code":"readCellMetadata(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read cell metadata — readCellMetadata","text":"data_list nested list cell metadata information default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read cell metadata — readCellMetadata","text":"cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read cell metadata — readCellMetadata","text":"","code":"df <- data.frame(     cell_ID = c(\"cell_1\", \"cell_2\", \"cell_3\"),     annotation = c(\"cell_type_1\", \"cell_type_1\", \"cell_type_2\") ) temporal_dir <- tempdir() write.csv(df, paste0(temporal_dir, \"/metadata.csv\"), row.names = FALSE)  readCellMetadata(paste0(temporal_dir, \"/metadata.csv\")) #>  #> List item [1]: #>  spat_unit: cell #>  feat_type: rna #> [[1]] #> An object of class cellMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #> dimensions: 3 2  #>  #>    cell_ID  annotation #>     <char>      <char> #> 1:  cell_1 cell_type_1 #> 2:  cell_2 cell_type_1 #> 3:  cell_3 cell_type_2 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read dimensional reduction data — readDimReducData","title":"Read dimensional reduction data — readDimReducData","text":"read dimension reduction results list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read dimensional reduction data — readDimReducData","text":"","code":"readDimReducData(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   reduction = c(\"cells\", \"feats\"),   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read dimensional reduction data — readDimReducData","text":"data_list (nested) list dimension reduction input data default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use reduction whether dim reduction performed 'cels' 'feats' provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read dimensional reduction data — readDimReducData","text":"dimObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readDimReducData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read dimensional reduction data — readDimReducData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"dimObj\")  readDimReducData(x) #> [[1]] #> An object of class dimObj : \"pca\" #> --| Contains dimension reduction generated with: pca  #> ----| for feat_type: rna  #> ----|     spat_unit: aggregate  #>  #>    100 dimensions for 462 data points #>  #> Additional included info: #> [1] \"eigenvalues\" \"loadings\"    #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read expression data — readExprData","title":"Read expression data — readExprData","text":"Read nested list expression data inputs order generate list giotto-native exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read expression data — readExprData","text":"","code":"readExprData(   data_list,   sparse = TRUE,   cores = determine_cores(),   default_feat_type = NULL,   verbose = TRUE,   provenance = NULL,   expression_matrix_class = c(\"dgCMatrix\", \"DelayedArray\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read expression data — readExprData","text":"data_list (nested) list expression input data sparse (boolean, default = TRUE) read matrix data sparse manner cores number cores use default_feat_type (optional) default feat_type use verbose verbose provenance (optional) provenance information expression_matrix_class class expression matrix use (e.g. 'dgCMatrix', 'DelayedArray')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read expression data — readExprData","text":"exprObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read expression data — readExprData","text":"mylistA = list('' = matrix(seq(5)), 'b' = matrix(seq(5))) depth(mylistA) mylistB = list(= list('' = matrix(seq(5)), 'b' = matrix(seq(5))), B = list('c' = matrix(seq(5)),'d' = matrix(seq(5)))) depth(mylistB) mylistC = list('RNA' = list('RAW' = list('cell' = matrix(seq(5)), 'nucleus' = matrix(seq(6,10))), 'NORM' = list('cell' = matrix(seq(11,15)), 'nucleus' = matrix(seq(20,25)))), 'PROT' = list('RAW' = list('cell' = matrix(seq(16,20))))) depth(mylistC) mymatD = matrix(data = seq(4))","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read expression data — readExprData","text":"","code":"x <- matrix(seq_len(100), nrow = 10) temporal_dir <- tempdir() write.csv(x, paste0(temporal_dir, \"/mymatrix.csv\"))  readExprData(paste0(temporal_dir, \"/mymatrix.csv\")) #> list depth of 1 #>  #> List item [1]: #>  spat_unit: cell #>  feat_type: rna #>  name: raw #> [[1]] #> An object of class exprObj : \"raw\" #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #>  #> contains: #> 10 x 10 sparse Matrix of class \"dgCMatrix\" #>                                #> 1 1 11 21 31 41 51 61 71 81 91 #> 2 2 12 22 32 42 52 62 72 82 92 #> 3 3 13 23 33 43 53 63 73 83 93 #> 4 4 14 24 34 44 54 64 74 84 94 #>  #>  ........suppressing 2 rows in show(); maybe adjust options(max.print=, width=) #>                                   #> 7   7 17 27 37 47 57 67 77 87  97 #> 8   8 18 28 38 48 58 68 78 88  98 #> 9   9 19 29 39 49 59 69 79 89  99 #> 10 10 20 30 40 50 60 70 80 90 100 #>  #>  First four colnames: #>  V1 V2 V3 V4  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":null,"dir":"Reference","previous_headings":"","what":"Read expression matrix — readExprMatrix","title":"Read expression matrix — readExprMatrix","text":"Function read expression matrix sparse matrix.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read expression matrix — readExprMatrix","text":"","code":"readExprMatrix(   path,   cores = determine_cores(),   transpose = FALSE,   feat_type = \"rna\",   expression_matrix_class = c(\"dgCMatrix\", \"DelayedArray\") )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read expression matrix — readExprMatrix","text":"path path expression matrix cores number cores use transpose transpose matrix feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") expression_matrix_class class expression matrix use (e.g. 'dgCMatrix', 'DelayedArray')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read expression matrix — readExprMatrix","text":"sparse matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read expression matrix — readExprMatrix","text":"expression matrix needs unique column names row names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readExprMatrix.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read expression matrix — readExprMatrix","text":"","code":"x <- matrix(seq_len(100), nrow = 10) temporal_dir <- tempdir() write.csv(x, paste0(temporal_dir, \"/mymatrix.csv\"))  readExprMatrix(paste0(temporal_dir, \"/mymatrix.csv\")) #> 10 x 10 sparse Matrix of class \"dgCMatrix\" #>   [[ suppressing 10 column names ‘V1’, ‘V2’, ‘V3’ ... ]] #>                                   #> 1   1 11 21 31 41 51 61 71 81  91 #> 2   2 12 22 32 42 52 62 72 82  92 #> 3   3 13 23 33 43 53 63 73 83  93 #> 4   4 14 24 34 44 54 64 74 84  94 #> 5   5 15 25 35 45 55 65 75 85  95 #> 6   6 16 26 36 46 56 66 76 86  96 #> 7   7 17 27 37 47 57 67 77 87  97 #> 8   8 18 28 38 48 58 68 78 88  98 #> 9   9 19 29 39 49 59 69 79 89  99 #> 10 10 20 30 40 50 60 70 80 90 100"},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read feature information — readFeatData","title":"Read feature information — readFeatData","text":"Function read lists feature information data output list generated giottoPoints objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read feature information — readFeatData","text":"","code":"readFeatData(data_list, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read feature information — readFeatData","text":"data_list (nested) list input data read verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read feature information — readFeatData","text":"list giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read feature information — readFeatData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"giottoPoints\")  readFeatData(list(x)) #> pointslist is a list without names #> [ rna ] Process point info... #> $rna #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3 #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read feature metadata — readFeatMetadata","title":"Read feature metadata — readFeatMetadata","text":"read feature metadata listt","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read feature metadata — readFeatMetadata","text":"","code":"readFeatMetadata(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read feature metadata — readFeatMetadata","text":"data_list nested list feature metadata information default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read feature metadata — readFeatMetadata","text":"featMetadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readFeatMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read feature metadata — readFeatMetadata","text":"","code":"df <- data.frame(     feat_ID = c(\"feat_1\", \"feat_2\", \"feat_3\"),     geneID = c(\"gene_1\", \"gene_1\", \"gene_2\") ) temporal_dir <- tempdir() write.csv(df, paste0(temporal_dir, \"/metadata.csv\"), row.names = FALSE)  readFeatMetadata(paste0(temporal_dir, \"/metadata.csv\")) #> list depth of 2 #>  #> List item [1]: #>  spat_unit: cell #>  feat_type: rna #> [[1]] #> An object of class featMetaObj  #> spat_unit : \"cell\" #> feat_type : \"rna\" #> provenance: cell  #>  #>    feat_ID geneID #>     <char> <char> #> 1:  feat_1 gene_1 #> 2:  feat_2 gene_1 #> 3:  feat_3 gene_2 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — readGiottoInstructions","title":"deprecated — readGiottoInstructions","text":"Retrieves instruction associated provided parameter","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — readGiottoInstructions","text":"","code":"readGiottoInstructions(giotto_instructions, param = NULL, default)"},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — readGiottoInstructions","text":"giotto_instructions giotto object result createGiottoInstructions() param parameter retrieve default default object return parameter retrieve exist","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — readGiottoInstructions","text":"specific parameter","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readGiottoInstructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"deprecated — readGiottoInstructions","text":"","code":"readGiottoInstructions(     giotto_instructions = createGiottoInstructions(),     param = \"show_plot\" ) #> Warning: `readGiottoInstructions()` was deprecated in GiottoClass 0.3.5. #> ℹ Please use `instructions()` instead. #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> [1] TRUE"},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read nearest neighbor network data — readNearestNetData","title":"Read nearest neighbor network data — readNearestNetData","text":"read nearest network results list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read nearest neighbor network data — readNearestNetData","text":"","code":"readNearestNetData(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read nearest neighbor network data — readNearestNetData","text":"data_list (nested) list input data read default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read nearest neighbor network data — readNearestNetData","text":"nnNetObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readNearestNetData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read nearest neighbor network data — readNearestNetData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"nnNetObj\")  readNearestNetData(x) #> [[1]] #> An object of class nnNetObj : \"sNN.pca\" #> --| Contains nearest neighbor network generated with: sNN  #> ----| for feat_type: rna  #> ----|     spat_unit: aggregate  #> ----|     provenance: z0 z1  #>  #> IGRAPH 859f76e DNW- 462 3021 --  #> + attr: name (v/c), weight (e/n), distance (e/n), shared (e/n), rank #> | (e/n) #> + edges from 859f76e (vertex names): #> [1] 240649020551054330404932383065726870513->335295524680090725199231409883288198017 #> [2] 240649020551054330404932383065726870513->77151711298730578178892667721058396928  #> [3] 240649020551054330404932383065726870513->322879686187630160969459793861944841206 #> [4] 240649020551054330404932383065726870513->31072896077757820678000109671990674373  #> [5] 240649020551054330404932383065726870513->102184699197574201819246996094734116255 #> [6] 240649020551054330404932383065726870513->17685062374745280598492217386845129350  #> + ... omitted several edges #>  #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read list of polygons information — readPolygonData","title":"Read list of polygons information — readPolygonData","text":"Function extract list polygons given raw input either mask tabular data. Calls respective createGiottoPolygons functions.  giottoPolygon object passed edits made updating name slot list named.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read list of polygons information — readPolygonData","text":"","code":"readPolygonData(   data_list,   default_name = \"cell\",   input = \"guess\",   polygon_mask_list_params = NULL,   polygon_dfr_list_params = NULL,   calc_centroids = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read list of polygons information — readPolygonData","text":"data_list read polygon results list default_name default name assign polygonlist list. polygonlist unnamed list default_name used part template generating indexed default names. input type input used. set 'guess', uses 'mask' polygonlist type character 'table' polygonlist dataframe-like polygon_mask_list_params parameters using 'mask' workflow polygon_dfr_list_params parameters using 'table' workflow calc_centroids whether centroids calculated polygon creation verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read list of polygons information — readPolygonData","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readPolygonData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read list of polygons information — readPolygonData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  readPolygonData(x) #> polygonlist is not a list #> [ cell ] Process polygon info... #> $aggregate #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    : rna #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read spatial enrichment — readSpatEnrichData","title":"Read spatial enrichment — readSpatEnrichData","text":"read spatial enrichment results list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read spatial enrichment — readSpatEnrichData","text":"","code":"readSpatEnrichData(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read spatial enrichment — readSpatEnrichData","text":"data_list (nested) list spatial enrichment input data default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read spatial enrichment — readSpatEnrichData","text":"spatEnrObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatEnrichData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read spatial enrichment — readSpatEnrichData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatEnrObj\")  readSpatEnrichData(x) #> [[1]] #> An object of class spatEnrObj : \"cluster_metagene\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>    ------------------------ #>  #> preview: #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #>  #> ...first 20 remaining colnames: #>  #>    #>  #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read spatial location data — readSpatLocsData","title":"Read spatial location data — readSpatLocsData","text":"read spatial locations/coordinates nested list generate list Giotto spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read spatial location data — readSpatLocsData","text":"","code":"readSpatLocsData(   data_list,   default_spat_unit = NULL,   provenance = NULL,   cores = determine_cores(),   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read spatial location data — readSpatLocsData","text":"data_list (nested) list spatial locations input data default_spat_unit (optional) default spat_unit use provenance (optional) provenance information cores many cores use verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read spatial location data — readSpatLocsData","text":"list spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatLocsData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read spatial location data — readSpatLocsData","text":"","code":"df <- data.frame(     feat_ID = c(\"feat_1\", \"feat_2\", \"feat_3\"),     sdimx = c(1, 2, 3), sdimy = c(1, 2, 1) ) temporal_dir <- tempdir() write.csv(df, paste0(temporal_dir, \"/spatlocs.csv\"), row.names = FALSE)  readSpatLocsData(paste0(temporal_dir, \"/spatlocs.csv\")) #> list depth of 1 #>  #> List item [1]: #>  spat_unit: cell #>  name: raw #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> [[1]] #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"cell\" #> provenance: cell  #> dimensions: 3 3  #> preview   : #>    sdimx sdimy cell_ID #>    <int> <int>  <char> #> 1:     1     1  feat_1 #> 2:     2     2  feat_2 #> 3:     3     1  feat_3 #>  #> ranges: #>      sdimx sdimy #> [1,]     1     1 #> [2,]     3     2 #>  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":null,"dir":"Reference","previous_headings":"","what":"Read spatial networks — readSpatNetData","title":"Read spatial networks — readSpatNetData","text":"read spatial networks data list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read spatial networks — readSpatNetData","text":"","code":"readSpatNetData(   data_list,   default_spat_unit = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read spatial networks — readSpatNetData","text":"data_list (nested) list spatial network input data default_spat_unit (optional) default spat_unit use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read spatial networks — readSpatNetData","text":"spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/readSpatNetData.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Read spatial networks — readSpatNetData","text":"","code":"x <- GiottoData::loadSubObjectMini(\"spatialNetworkObj\", idx = 2)  readSpatNetData(x) #> [[1]] #> An object of class spatialNetworkObj : \"kNN_network\" #> Contains spatial network generated with: dbscan  #> spat_unit : \"aggregate\" #> provenance: z0 z1  #>    2211 connections (filtered) #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/read_data_params.html","id":null,"dir":"Reference","previous_headings":"","what":"read_data_params — read_data_params","title":"read_data_params — read_data_params","text":"read_data_params","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/read_data_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"read_data_params — read_data_params","text":"data_list (nested) list input data read default_spat_unit (optional) default spat_unit use default_feat_type (optional) default feat_type use provenance (optional) provenance information verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/read_data_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"read_data_params — read_data_params","text":"data params","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":null,"dir":"Reference","previous_headings":"","what":"Reconnect a GiottoClass object — reconnect","title":"Reconnect a GiottoClass object — reconnect","text":"Reconnect GiottoClass object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reconnect a GiottoClass object — reconnect","text":"","code":"# S4 method for class 'giottoLargeImage' reconnect(x, path = NULL, ...)  # S4 method for class 'giottoImage' reconnect(x, path = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reconnect a GiottoClass object — reconnect","text":"x object reconnect path character. (optional) New filepath associate object. needed filepath normally carried object path changed. ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reconnect a GiottoClass object — reconnect","text":"GiottoClass object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reconnect a GiottoClass object — reconnect","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  reconnect(g_image) #> An object of class giottoLargeImage : \"alignment\" #> Image extent            : 2364.5, 6522.5, -5425.25, -2620.75 (xmin, xmax, ymin, ymax) #> Original image extent   : 2364.5, 6522.5, -5425.25, -2620.75 (xmin, xmax, ymin, ymax) #> Scale factor            : 13.2420382165605, 13.2287735849057 (x, y) #> Resolution              : 0.0755170755170755, 0.0755927972900695 (x, y) #> Layers                  : 4  #> Estimated max intensity : 174  #> Estimated min intensity : 0  #> Values                  : integers #> File path               : '/home/runner/work/_temp/Library/GiottoData/Mini_datasets/Visium/VisiumObject/Images/alignment_spatRaster'"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Reconnect images with dead pointers — reconnectGiottoImage","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"reconnect gobject's dead image pointers using filepaths original source image files","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"","code":"reconnectGiottoImage(   gobject,   auto_reconnect = TRUE,   reconnect_type = c(\"all\", \"image\", \"largeImage\"),   image_name = NULL,   largeImage_name = NULL,   image_path = NULL,   largeImage_path = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"gobject giotto object auto_reconnect automatically reconnect images TRUE. manual FALSE reconnect_type type image reconnect auto_reconnect = TRUE image_name names images reconnect largeImage_name name large images reconnect image_path named list paths images reconnect giottoImages largeImage_path named list paths images reconnect giottoLargeImages verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"giotto object updated image pointer","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"Inputs can either given image name (image_name/largeImage_name) filepath (image_path/largeImage_path) args named list filepath argument alone. auto_reconnect = TRUE additional params need supplied. long giotto image objects directly created using filepaths, filepaths stored within image objects referenced reconnection. Issues arise giotto image objects created directly underlying image handling package objects (magick raster objects) image files moved since giotto image object generated. cases, use manual reconnection setting auto_reconnect = FALSE.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnectGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Reconnect images with dead pointers — reconnectGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  reconnectGiottoImage(g, reconnect_type = \"largeImage\") #> Attempting automatic reconnection... #> largeImage(s) discovered... #> --> alignment : filepath found #>  #> --> image : filepath found #>  #>  #> done #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoImage_MG.html","id":null,"dir":"Reference","previous_headings":"","what":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","title":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","text":"reconnect giottoImage image pointer broken","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoImage_MG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","text":"","code":"reconnect_giottoImage_MG(giottoImage, image_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoImage_MG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","text":"giottoImage giottoImage reconnect image_path path source file giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoImage_MG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reconnect_giottoImage_MG — reconnect_giottoImage_MG","text":"reconnected giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","title":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","text":"reconnect giottoLargeImage image pointer broken","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","text":"","code":"reconnect_giottoLargeImage(giottoLargeImage, image_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","text":"giottoLargeImage giottoLargeImage reconnect image_path path source file giottoLargeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_giottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reconnect_giottoLargeImage — reconnect_giottoLargeImage","text":"reconnected giottoLargeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":null,"dir":"Reference","previous_headings":"","what":"reconnect_image_object — reconnect_image_object","title":"reconnect_image_object — reconnect_image_object","text":"Reconnect giotto image object dead image pointer using filepath original image source","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"reconnect_image_object — reconnect_image_object","text":"","code":"reconnect_image_object(image_object, image_type, image_path)"},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"reconnect_image_object — reconnect_image_object","text":"image_object giotto image object image_type type giotto image object image_path path image source reconnect image object ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"reconnect_image_object — reconnect_image_object","text":"reconnected image_object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reconnect_image_object.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"reconnect_image_object — reconnect_image_object","text":"simple wrapper function image object-specific reconnection functions include functionality find specific image objects giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":null,"dir":"Reference","previous_headings":"","what":"Generate rectangular polygon vertices — rectVertices","title":"Generate rectangular polygon vertices — rectVertices","text":"Generates vertex coordinates rectangle dimensions given dims param.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generate rectangular polygon vertices — rectVertices","text":"","code":"rectVertices(dims)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generate rectangular polygon vertices — rectVertices","text":"dims named vector style c(x = numeric, y = numeric) defines width (x) height (y) generated rectangle polygon.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Generate rectangular polygon vertices — rectVertices","text":"data.table rectangle vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/rectVertices.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Generate rectangular polygon vertices — rectVertices","text":"","code":"rectVertices(c(x = 1, y = 2)) #>        x     y #>    <num> <num> #> 1:     0     0 #> 2:     0     2 #> 3:     1     2 #> 4:     1     0"},{"path":"https://drieslab.github.io/GiottoClass/reference/reexports.html","id":null,"dir":"Reference","previous_headings":"","what":"Objects exported from other packages — reexports","title":"Objects exported from other packages — reexports","text":"objects imported packages. Follow links see documentation. GiottoUtils getDistinctColors, getMonochromeColors, getRainbowColors","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reexports.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Objects exported from other packages — reexports","text":"character vector hexadecimal distinct colors","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/reexports.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Objects exported from other packages — reexports","text":"","code":"getDistinctColors(n = 5) #> [1] \"#377EB8\" \"#4DAF4A\" \"#A65628\" \"#BC80BD\" \"#FFED6F\""},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial relationships between geometries — relate","title":"Spatial relationships between geometries — relate","text":"relate() returns logical matrix indicating presence absence specific spatial relationships geometries x y.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial relationships between geometries — relate","text":"","code":"# S4 method for class 'giottoSpatial,giottoSpatial' relate(   x,   y,   relation,   pairs = TRUE,   na.rm = TRUE,   output = c(\"data.table\", \"matrix\"),   use_names = TRUE,   ... )  # S4 method for class 'giotto,giottoSpatial' relate(   x,   y,   ...,   what = c(\"polygon\", \"spatlocs\", \"points\"),   spat_unit = NULL,   feat_type = NULL,   spat_locs_name = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial relationships between geometries — relate","text":"x spatial object records test y spatial object records test relations relation character. One \"intersects\", \"touches\", \"crosses\", \"overlaps\", \"within\", \"contains\", \"covers\", \"coveredby\", \"disjoint\". \"DE-9IM\" string \"FF*FF****\". See wikipedia geotools doc pairs logical. TRUE two-column matrix returned indices cases requested relation TRUE. especially helpful dealing many geometries returned value generally much smaller na.rm logical. TRUE pairs=TRUE, geometries x related geometry y omitted output character. \"data.table\" \"matrix\". \"data.table\" possible pairs=TRUE use_names logical. TRUE, pairs=TRUE, output=\"data.table\" IDs geometries used. ... additional args pass character. type spatial data giotto object relate. One \"polygon\", \"spatlocs\", \"points\" spat_unit spatial unit feat_type feature type spat_locs_name name spatlocs use = \"spatlocs\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial relationships between geometries — relate","text":"data.table output=\"data.table\". matrix output=\"matrix\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/relate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial relationships between geometries — relate","text":"","code":"g <- GiottoData::loadGiottoMini(\"viz\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" activeSpatUnit(g) <- \"aggregate\" sl <- g[[\"spatial_locs\"]][[1]] gpoints <- g[[\"feat_info\"]][[1]] gpoly <- g[[\"spatial_info\"]][[1]]  res1 <- relate(gpoints, gpoly, relation = \"intersects\") res2 <- relate(gpoints, gpoly, relation = \"intersects\", use_names = FALSE)  selection <- system.file(\"extdata/viz_interactive_select.csv\",     package = \"GiottoClass\" ) select_polys <- createGiottoPolygon(data.table::fread(selection)) #>   Selecting col \"name\" as poly_ID column #>   Selecting cols \"x\" and \"y\" as x and y respectively res <- relate(g, select_polys, relation = \"intersects\") g[,res[y == \"polygon1\", x]] #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 25 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used g[,res[y == \"polygon2\", x]] #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 90 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used g[,res[y == \"polygon3\", x]] #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 245 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove cell annotation — removeCellAnnotation","title":"Remove cell annotation — removeCellAnnotation","text":"Removes cell annotation Giotto object specific feature modality (default = 'rna')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove cell annotation — removeCellAnnotation","text":"","code":"removeCellAnnotation(   gobject,   spat_unit = NULL,   feat_type = NULL,   columns = NULL,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove cell annotation — removeCellAnnotation","text":"gobject giotto object spat_unit spatial unit feat_type feature type columns names columns remove return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove cell annotation — removeCellAnnotation","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Remove cell annotation — removeCellAnnotation","text":"return_gobject = FALSE, return cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeCellAnnotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove cell annotation — removeCellAnnotation","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  annotation <- c(     \"1\" = \"cell_type_1\",     \"2\" = \"cell_type_2\",     \"3\" = \"cell_type_3\",     \"4\" = \"cell_type_4\",     \"5\" = \"cell_type_5\",     \"6\" = \"cell_type_6\",     \"7\" = \"cell_type_7\",     \"8\" = \"cell_type_8\" )  g <- annotateGiotto(g,     annotation_vector = annotation,     cluster_column = \"leiden_clus\" )  g <- removeCellAnnotation(g, columns = \"cell_types\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove feature annotation — removeFeatAnnotation","title":"Remove feature annotation — removeFeatAnnotation","text":"Removes feature annotation Giotto object specific feature modality","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove feature annotation — removeFeatAnnotation","text":"","code":"removeFeatAnnotation(   gobject,   spat_unit = NULL,   feat_type = NULL,   columns = NULL,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove feature annotation — removeFeatAnnotation","text":"gobject giotto object spat_unit spatial unit feat_type feature type columns names columns remove return_gobject boolean: return giotto object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove feature annotation — removeFeatAnnotation","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Remove feature annotation — removeFeatAnnotation","text":"return_gobject = FALSE, return gene metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeFeatAnnotation.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove feature annotation — removeFeatAnnotation","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  g <- removeFeatAnnotation(g, columns = \"hvf\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — replaceGiottoInstructions","title":"deprecated — replaceGiottoInstructions","text":"Function replace instructions giotto object. call initialize giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — replaceGiottoInstructions","text":"","code":"replaceGiottoInstructions(gobject, instructions = NULL, init_gobject = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — replaceGiottoInstructions","text":"gobject giotto object instructions new instructions (e.g. result createGiottoInstructions) init_gobject (boolean, default = TRUE) initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — replaceGiottoInstructions","text":"giotto object replaces instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"deprecated — replaceGiottoInstructions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  replaceGiottoInstructions(     gobject = g,     instructions = createGiottoInstructions() ) #> Warning: `replaceGiottoInstructions()` was deprecated in GiottoClass 0.3.5. #> ℹ Please use `instructions()` instead. #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace part of an object with [<- — replace_bracket","title":"Replace part of an object with [<- — replace_bracket","text":"Replace values Giotto Classes. Providing empty brackets x[] <- value usually replace entire contained data representation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace part of an object with [<- — replace_bracket","text":"","code":"# S4 method for class 'coordDataDT,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'metaData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'dimObj,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'exprData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'spatNetData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'nnData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'enrData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'spatGridData,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'giottoPoints,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'giottoPolygon,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'giottoLargeImage,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'giottoImage,missing,missing,ANY' x[i, j] <- value  # S4 method for class 'affine2d,missing,missing,ANY' x[i, j] <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace part of an object with [<- — replace_bracket","text":"x Giotto S4 object replace information , j indices specifying elements replace. Indices numeric character vectors empty value values(s) set","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replace part of an object with [<- — replace_bracket","text":"x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"-lt-methods","dir":"Reference","previous_headings":"","what":"`[<-` methods","title":"Replace part of an object with [<- — replace_bracket","text":"Assign coordinates slot giotto S4 Assign metaDT slot giotto S4 Assign coordinates slot giotto S4 dimObj Assign exprMat slot giotto S4 Assign networkDT slot giotto S4 Assign igraph slot giotto S4 Assign enrichDT slot giotto S4 Assign gridDT slot giotto S4 Assign spatVector slot giotto S4 Assign spatVector slot giottoPolygon Assign affine slot affine2d","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_bracket.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Replace part of an object with [<- — replace_bracket","text":"","code":"gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  gpoints[] <- gpoints[]"},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace part of an object with $<- — replace_dollar","title":"Replace part of an object with $<- — replace_dollar","text":"Replace values Giotto Classes using $<- operator.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Replace part of an object with $<- — replace_dollar","text":"","code":"# S4 method for class 'giotto' x$name <- value  # S4 method for class 'coordDataDT' x$name <- value  # S4 method for class 'spatEnrObj' x$name <- value  # S4 method for class 'dimObj' x$name <- value  # S4 method for class 'metaData' x$name <- value  # S4 method for class 'terraVectData' x$name <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Replace part of an object with $<- — replace_dollar","text":"x Giotto S4 object replace columns name literal character string (possibly backtick quoted). normally matched colnames. value values(s) set column","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Replace part of an object with $<- — replace_dollar","text":"x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"-lt-methods","dir":"Reference","previous_headings":"","what":"`$<-` methods","title":"Replace part of an object with $<- — replace_dollar","text":"Set values colname giotto S4 data.table coordinates slot. Works via data.table methods Set values colname giotto S4 spatEnrObj. Set entries misc slot giotto S4 dimObj. Set values colname giotto S4 data.table metaDT slot. Works via data.table methods Set values colname giotto S4 spatVector slot.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/replace_dollar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Replace part of an object with $<- — replace_dollar","text":"","code":"gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  gpoints$new_col <- sprintf(\"feat_%d\", seq(nrow(gpoints)))"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":null,"dir":"Reference","previous_headings":"","what":"Rescale an object — rescale","title":"Rescale an object — rescale","text":"Rescale object spatially. Z dimension scaling supported types subobjects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rescale an object — rescale","text":"","code":"# S4 method for class 'giotto' rescale(   x,   fx = 1,   fy = fx,   x0,   y0,   spat_unit = \":all:\",   feat_type = \":all:\",   images = \":all:\" )  # S4 method for class 'spatLocsObj' rescale(x, fx = 1, fy = fx, fz = fx, x0, y0, z0)  # S4 method for class 'data.frame' rescale(   x,   fx = 1,   fy = fx,   fz = fx,   x0,   y0,   z0,   geom = c(\"sdimx\", \"sdimy\", \"sdimz\") )  # S4 method for class 'giottoPolygon' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'giottoPoints' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'giottoImage' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'giottoLargeImage' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'giottoAffineImage' rescale(x, fx = 1, fy = fx, x0, y0)  # S4 method for class 'affine2d' rescale(x, fx = 1, fy = fx, x0, y0)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rescale an object — rescale","text":"x object fx numeric > 0. horizontal scaling factor fy numeric > 0. vertical scaling factor x0 numeric. x-coordinate center rescaling. missing, center extent x used y0 numeric. y-coordinate center rescaling. missing, center extent x used spat_unit character vector. spatial units affect feat_type character vector. feature types affect images character vector. Images affect fz numeric > 0. z scaling factor (supported objects) z0 numeric. z-coordinate center rescaling. missing, center extent x used (supported objects) geom character. Named vector colnames x, y, (z) coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Rescale an object — rescale","text":"re-scaled object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Rescale an object — rescale","text":"giotto object, \"::\" token can passed spat_unit, feat_type, images arguments affect available items.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Rescale an object — rescale","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  rescale(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"rescalePolygons — rescalePolygons","title":"rescalePolygons — rescalePolygons","text":"Rescale individual polygons x y factor","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rescalePolygons — rescalePolygons","text":"","code":"rescalePolygons(   gobject,   poly_info = \"cell\",   name = \"rescaled_cell\",   fx = 0.5,   fy = 0.5,   calculate_centroids = TRUE,   return_gobject = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rescalePolygons — rescalePolygons","text":"gobject giotto object poly_info polygon information name name name new polygon layer fx x-scaling factor fy y-scaling factor calculate_centroids calculate centroids return_gobject return giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rescalePolygons — rescalePolygons","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescalePolygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"rescalePolygons — rescalePolygons","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  rescalePolygons(g, poly_info = \"aggregate\") #> Setting polygon info [rescaled_cell] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate rescaled_cell  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Row and column names — row-plus-colnames-generic","title":"Row and column names — row-plus-colnames-generic","text":"Retrieve set row column names object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Row and column names — row-plus-colnames-generic","text":"","code":"# S4 method for class 'giotto' colnames(x)  # S4 method for class 'exprObj' colnames(x)  # S4 method for class 'cellMetaObj' colnames(x)  # S4 method for class 'featMetaObj' colnames(x)  # S4 method for class 'spatEnrObj' colnames(x)  # S4 method for class 'spatLocsObj' colnames(x)  # S4 method for class 'dimObj' colnames(x)  # S4 method for class 'giotto' rownames(x)  # S4 method for class 'exprObj' rownames(x)  # S4 method for class 'dimObj' rownames(x)  # S4 method for class 'metaData' rownames(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Row and column names — row-plus-colnames-generic","text":"x object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Row and column names — row-plus-colnames-generic","text":"character vector row col names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/row-plus-colnames-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Row and column names — row-plus-colnames-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"exprObj\")  colnames(g) #>                                         2  #> \"240649020551054330404932383065726870513\"  #>                                         3  #> \"274176126496863898679934791272921588227\"  #>                                         4  #> \"323754550002953984063006506310071917306\"  #>                                         5  #>  \"87260224659312905497866017323180367450\"  #>                                         6  #>  \"17817477728742691260808256980746537959\"  #>                                         7  #> \"182132384503107798660396708280285136358\"  #>                                         9  #> \"316289522368890354495930310222776908199\"  #>                                        10  #> \"318995879282318989627235045690211636294\"  #>                                        11  #> \"104570855383158731814075192607294301741\"  #>                                        12  #> \"115370283894795045523368609208878185314\"  #>                                        13  #> \"123860671559578247432410194986927758864\"  #>                                        14  #> \"126981423897188762239468136959275655616\"  #>                                        15  #> \"134398773695365619188678200952912609063\"  #>                                        16  #>  \"15242486364109501724975900940581726845\"  #>                                        17  #> \"152684748256642370929802439227360458069\"  #>                                        18  #> \"153751792203577791006158581642177087065\"  #>                                        19  #>  \"16326589507615554063401897357427439030\"  #>                                        20  #> \"165786478473465185470745991122188406667\"  #>                                        21  #> \"167710327060928309829388429279250508392\"  #>                                        22  #> \"172181421897607556322673704318102678295\"  #>                                        23  #> \"176844289786228093052039491926955764947\"  #>                                        24  #> \"182235958169292445695483205478317795477\"  #>                                        25  #> \"183227745956657225549068107012033843521\"  #>                                        26  #> \"186988931894710833920932112634285943415\"  #>                                        27  #> \"190687643154627893064711601675234362640\"  #>                                        28  #>  \"20548793658722995878220914240286086757\"  #>                                        29  #> \"206702762285684421190019779213421380201\"  #>                                        30  #> \"216701996099683814512199402223708471323\"  #>                                        31  #>  \"21934936165997373583174173761929761438\"  #>                                        32  #> \"230344318208995342827768566280706457626\"  #>                                        33  #> \"251905496166492083168644493421091558216\"  #>                                        34  #> \"262996653580953175020435707363716649390\"  #>                                        35  #>  \"27666206735695437393204421885258583706\"  #>                                        37  #> \"286906689872367261752702769926754066848\"  #>                                        38  #> \"288822108801800165318171357739905375883\"  #>                                        39  #> \"301054712356664458042996323827909441002\"  #>                                        40  #> \"304842190541754537761816256358565562302\"  #>                                        41  #> \"318439340668767417720582355350205310941\"  #>                                        42  #> \"335295524680090725199231409883288198017\"  #>                                        43  #>  \"35118346554513854436644695033199584696\"  #>                                        44  #>  \"41054036480225512911591384807281320971\"  #>                                        45  #>  \"43731708947199618294982749003938483862\"  #>                                        46  #>  \"48024672048124996997588408479044670509\"  #>                                        47  #>  \"51348907619842676963078202479438175138\"  #>                                        49  #>  \"67532821514617092397935003422482443295\"  #>                                        50  #>  \"77151711298730578178892667721058396928\"  #>                                        51  #>  \"77782228870577724567477221255169934206\"  #>                                        52  #>   \"8777587181320516093160667806451882030\"  #>                                        53  #>  \"95838678880751873613229512065975406368\"  #>                                        54  #>  \"95947958963963707263153541936375959179\"  #>                                        55  #>   \"9668748337336721830701975018211142813\"  #>                                        56  #>  \"97411078642927912684859796714759494710\"  #>                                        57  #> \"101161259912191124732236989250178928032\"  #>                                        58  #> \"110615983935499449765434338770904504245\"  #>                                        59  #> \"110858042010405247711695373195937122852\"  #>                                        60  #> \"110900719814678261966908552089216814729\"  #>                                        61  #>  \"12925323527075390484710711277617599454\"  #>                                        63  #> \"137348923180371322628727011975895485209\"  #>                                        64  #> \"138859376429590720661963324654447571708\"  #>                                        65  #> \"140543565961583233746802451796981444137\"  #>                                        66  #> \"143386081176260440019925196855300710659\"  #>                                        67  #> \"143408196806895889016075556052288734233\"  #>                                        68  #> \"145421744145915784890159499930205641713\"  #>                                        69  #> \"148336156782096202859532636956126767457\"  #>                                        70  #> \"150082699777048696177232440639953146354\"  #>                                        71  #>  \"15247055772869406897093633424720409278\"  #>                                        72  #>  \"15834776842182822801451197571763335013\"  #>                                        73  #> \"170833460535439412738579124041592991444\"  #>                                        74  #> \"173780780834031059819946658163431921979\"  #>                                        75  #> \"174306823762889142173283452439684229948\"  #>                                        76  #> \"175540604452034099044348476236813150837\"  #>                                        77  #> \"177757177666889772027017950398587309639\"  #>                                        78  #>  \"17868848607867654301368031294266874310\"  #>                                        79  #> \"180947508370750255585892730777436680945\"  #>                                        80  #> \"187952627468949069447188707715308813657\"  #>                                        81  #>   \"1900302715660571356090444774019116326\"  #>                                        82  #> \"203192161403397797138670022274582721699\"  #>                                        83  #> \"206016050634629330546630679047044021073\"  #>                                        85  #> \"214394514156259228118188949454902817376\"  #>                                        86  #> \"221669638772738575000116137509912039310\"  #>                                        87  #> \"224458376429228506642398057779371677646\"  #>                                        88  #> \"226912346807310637711937183879196326571\"  #>                                        89  #> \"227232155811404089141823608874580791245\"  #>                                        91  #> \"236677629222667262221261861475728542818\"  #>                                        93  #> \"244015124549889909957742476033146111487\"  #>                                        94  #> \"244247765904337326625465691380839405459\"  #>                                        95  #> \"244448312826260498647079278647004353269\"  #>                                        96  #> \"244840145612854293464477850603474951260\"  #>                                        97  #> \"262797098003740683881650619022037793005\"  #>                                        98  #> \"265185306239991354232232246957204545228\"  #>                                        99  #> \"266413162898429280572455841453688616870\"  #>                                       101  #> \"275784684664527332374777211328350223506\"  #>                                       102  #> \"277057315125198906319398446608128392905\"  #>                                       104  #> \"291975341311453330406711526698967834209\"  #>                                       105  #> \"295193149306421749943849825086053455411\"  #>                                       106  #>  \"30222355550742125173065032035537805062\"  #>                                       107  #> \"304560432600831995659079356647103974886\"  #>                                       108  #>  \"30571638947438619177947320407779261750\"  #>                                       109  #> \"306415949245581212081161219410047325001\"  #>                                       110  #> \"311565496674213535805029947713320284697\"  #>                                       111  #> \"314397389362641167108869069386457433770\"  #>                                       112  #>   \"3188909098022617910378369321966273882\"  #>                                       113  #> \"322879686187630160969459793861944841206\"  #>                                       114  #> \"330850389163886577071114668277958486114\"  #>                                       115  #> \"334199301045926627171760429217123408914\"  #>                                       116  #> \"339814056401091912617621500767389941735\"  #>                                       117  #>  \"36648998424868029072860674954666559763\"  #>                                       118  #>  \"39033692777509843205319060807429911979\"  #>                                       119  #>   \"3942785923272820952395109293003259310\"  #>                                       120  #>  \"47275912178029130797780898068213599096\"  #>                                       121  #>  \"56815638009315000170441964570512336625\"  #>                                       122  #>  \"57203625626451579261315887898923502046\"  #>                                       123  #>  \"62669443199671326763841071380380779477\"  #>                                       124  #>  \"64228015236811922665804882776457047292\"  #>                                       126  #>  \"68418314542386876178693610244900595267\"  #>                                       127  #>  \"70219882915166469874938407731799217344\"  #>                                       128  #>  \"75660428514717127988983246148828583482\"  #>                                       129  #>  \"75682347267697870039469591993208007445\"  #>                                       130  #>  \"87903363874776475366779322866396664731\"  #>                                       131  #>  \"88743795534206169429467675642537392511\"  #>                                       133  #>   \"9538866320245722231901445225545432644\"  #>                                       134  #>  \"96091484747656303270745913028146994621\"  #>                                       135  #> \"116860147088450350976374609398998546737\"  #>                                       136  #> \"133061403473432310288273623600023558748\"  #>                                       137  #> \"137154375879163008723188861204335796821\"  #>                                       138  #> \"185903314401459366597627436588666236388\"  #>                                       139  #> \"217996462208701069168232210617040322639\"  #>                                       140  #> \"226667648171626631993624597360362535576\"  #>                                       141  #> \"254829253202043893331055483138743800247\"  #>                                       142  #> \"271967915636064836314881508293335292245\"  #>                                       143  #> \"273673567134859598195435250950149370161\"  #>                                       144  #> \"305306955532868686456926844192964831687\"  #>                                       145  #> \"307030440204593378842812081935039092344\"  #>                                       146  #> \"311587331826654155209560142756469108973\"  #>                                       147  #>  \"44197902970141946871502798467323259089\"  #>                                       148  #>  \"44721220002773982161418195292536576043\"  #>                                       150  #>  \"65855854848879329159292019718060662708\"  #>                                       151  #>  \"76322781861215450124167009829890606622\"  #>                                       152  #>  \"11065258297873257226330942251431244138\"  #>                                       153  #> \"118071411587380747913796380721014165557\"  #>                                       154  #> \"123540785709544435621019288242840920053\"  #>                                       156  #> \"130428604684362047522418850101908720496\"  #>                                       157  #> \"134509424346276649608483685115101376571\"  #>                                       158  #> \"136341171141277731884608634279863298546\"  #>                                       160  #> \"137356600627014280700323828086313714576\"  #>                                       161  #> \"151798130004305208790801168757831384604\"  #>                                       162  #> \"162684318525520950869468479178769741207\"  #>                                       163  #> \"164424478098970510930576318421517316799\"  #>                                       164  #> \"166456955228473064319115194076209471689\"  #>                                       165  #> \"168376325588102040437463621554621047372\"  #>                                       166  #> \"179297712006471333306826676970515917851\"  #>                                       167  #>  \"19311588976622944909682910864587104989\"  #>                                       168  #> \"204611834270911643022584999768859598082\"  #>                                       169  #> \"212501669348639182111017279862555064555\"  #>                                       171  #> \"222047855782557501653245982274520432658\"  #>                                       173  #> \"231212643322278795528005770495251497705\"  #>                                       174  #> \"233229703476821612486041386363745481186\"  #>                                       175  #>  \"23470744401352443589618734383441183930\"  #>                                       176  #> \"234988593327199604253479621078255555503\"  #>                                       177  #> \"250481714349085757816071122854700489348\"  #>                                       178  #> \"254538897036257180617662178141894962698\"  #>                                       179  #> \"257184545464839903394564555141875300987\"  #>                                       180  #> \"266246243070401825856501948379131507953\"  #>                                       181  #> \"280661554698226730422771895627995747059\"  #>                                       182  #> \"283821893476134729825893155000887153128\"  #>                                       183  #> \"286146294981380023269011675378975275188\"  #>                                       184  #> \"292254379263157279159966458654907155929\"  #>                                       185  #> \"293900582929631255788566880963197704396\"  #>                                       186  #> \"296019945099320175547230863498668480924\"  #>                                       187  #> \"307915098305811968258082436904262060268\"  #>                                       188  #>  \"31072896077757820678000109671990674373\"  #>                                       189  #> \"324637742389179243201282186318588452049\"  #>                                       190  #> \"324877467507432389063800715005904969237\"  #>                                       191  #>  \"32535304551014256860916796345005841454\"  #>                                       192  #> \"325896428237586114830946437310469001833\"  #>                                       193  #>  \"32944790627105381861829233020285020883\"  #>                                       194  #> \"331580323004945087311483453179965743309\"  #>                                       195  #> \"331675815801204232182324913632094035806\"  #>                                       196  #> \"334356931858742201981142004419227940530\"  #>                                       198  #>  \"42056064196611141769700924475836317519\"  #>                                       199  #>  \"59141517931138845718061638546803837463\"  #>                                       200  #>  \"77541886028463256801311974652160917274\"  #>                                       201  #>  \"79668971589879493465166271739355011800\"  #>                                       202  #>  \"90740652120142025598838838824737408007\"  #>                                       203  #>  \"93766399603521973873598911761678204002\"  #>                                       204  #>  \"94915957193797412218079317943892351685\"  #>                                       205  #> \"101488859781016188084173008420811094152\"  #>                                       206  #> \"102184699197574201819246996094734116255\"  #>                                       207  #> \"107393799088150693125543893285009932508\"  #>                                       208  #> \"111687473021757662663527126267334037424\"  #>                                       209  #> \"112201175467804501210529603201546927780\"  #>                                       210  #> \"115235047525370533075441381313256765131\"  #>                                       211  #> \"119102272531447353986749088457842353881\"  #>                                       212  #> \"121108122402850896937802185181656711412\"  #>                                       213  #> \"122906612256038341059239630042273244949\"  #>                                       214  #> \"126809950897128716226739975254707226975\"  #>                                       215  #> \"126827073040370531574124290326181150621\"  #>                                       216  #> \"129220219089532886548658463773454811807\"  #>                                       217  #> \"130416595705865355812306620146726096256\"  #>                                       218  #> \"130720172120660644879676230721263100142\"  #>                                       219  #> \"134503679556257538045105223616434677584\"  #>                                       220  #> \"134512816139291924739198129882869576276\"  #>                                       222  #>  \"14225193593112604305545027950864785906\"  #>                                       223  #>  \"14615917600474753437497051666515185188\"  #>                                       224  #> \"146715357009983465209963560859286180117\"  #>                                       225  #> \"147103070941083943163952951858791268261\"  #>                                       226  #> \"150338819641781846748929553541898461633\"  #>                                       227  #> \"160318430812610433362422897343020317434\"  #>                                       228  #> \"166788256632929614638779193211391658357\"  #>                                       229  #> \"167818783196654344295653476753505898360\"  #>                                       230  #> \"185055418446250460085953045917995887188\"  #>                                       231  #> \"186404099358317212811882499608798243906\"  #>                                       232  #> \"188179457167181317036865075745680501410\"  #>                                       233  #> 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rowMeans_flex","text":"rowMeans_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowMeans_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rowMeans_flex — rowMeans_flex","text":"","code":"rowMeans_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rowMeans_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rowMeans_flex — rowMeans_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowMeans_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rowMeans_flex — rowMeans_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowMeans_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"rowMeans_flex — rowMeans_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  rowMeans_flex(m) #>  [1]  0.08871945 -0.29999737  0.47536178 -0.66005505 -0.03974135 -0.45622412 #>  [7] -0.14340232 -0.50460708  0.45589154 -0.04022921"},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"rowSums_flex — rowSums_flex","title":"rowSums_flex — rowSums_flex","text":"rowSums_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"rowSums_flex — rowSums_flex","text":"","code":"rowSums_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"rowSums_flex — rowSums_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"rowSums_flex — rowSums_flex","text":"numeric","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rowSums_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"rowSums_flex — rowSums_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  rowSums_flex(m) #>  [1] -4.7180057  3.5983422 -1.4346828  2.0426869  2.0530418 -4.1031143 #>  [7] -3.5399338  1.3677829  9.0450398 -0.2253641"},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"saveGiotto — saveGiotto","title":"saveGiotto — saveGiotto","text":"Saves Giotto object specific folder structure","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"saveGiotto — saveGiotto","text":"","code":"saveGiotto(   gobject,   foldername = \"saveGiottoDir\",   dir = getwd(),   method = c(\"RDS\", \"qs\"),   method_params = list(),   overwrite = FALSE,   image_filetype = \"PNG\",   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"saveGiotto — saveGiotto","text":"gobject Giotto object foldername Folder name dir Directory create folder method method save main object method_params additional method parameters RDS qs overwrite Overwrite existing folders image_filetype image filetype use, see writeRaster. Default \"PNG\". TIFF outputs, try \"COG\" verbose verbose ... additional parameters writeRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"saveGiotto — saveGiotto","text":"Creates directory Giotto object information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"saveGiotto — saveGiotto","text":"Works together loadGiotto save re-load Giotto objects. Additional method_params need provided list go saveRDS qsave","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/saveGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"saveGiotto — saveGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  saveGiotto(gobject = g, dir = tempdir(), overwrite = TRUE) #> Folder already exist and overwrite = TRUE, #>  overwrite folder #> 1. Start writing feature information #> 2. Start writing spatial information #> For spatial information: cell #> 3. Start writing image information #> For image information: alignment #> For image information: image #> [1] TRUE"},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cell metadata — setCellMetadata","title":"Set cell metadata — setCellMetadata","text":"Function set cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cell metadata — setCellMetadata","text":"","code":"setCellMetadata(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cell metadata — setCellMetadata","text":"gobject giotto object x cellMetaObj list cellMetaObj set. Passing NULL reset specified set cell metadata giotto object. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cell metadata — setCellMetadata","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set cell metadata — setCellMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" m1 <- getCellMetadata(g, output = \"data.table\") m2 <- data.frame(     cell_ID = m1$cell_ID,     new_column = sample(letters, 624, replace = TRUE) )  setCellMetadata(gobject = g, x = createCellMetaObj(m2)) #> > Cell metadata for spat_unit \" cell \" and feat_type \" rna \" already exists and #>  will be replaced with new metadata. #> Setting cell metadata [cell][rna] #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":null,"dir":"Reference","previous_headings":"","what":"Set dimension reduction data — setDimReduction","title":"Set dimension reduction data — setDimReduction","text":"Function dimension reduction information Giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set dimension reduction data — setDimReduction","text":"","code":"setDimReduction(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   name = \"pca\",   reduction = c(\"cells\", \"feats\"),   reduction_method = c(\"pca\", \"umap\", \"tsne\"),   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set dimension reduction data — setDimReduction","text":"gobject giotto object x dimObj list dimObj set. Passing NULL remove specified set dimension reduction information gobject spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name reduction results reduction reduction cells features reduction_method reduction method (e.g. \"pca\") provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set dimension reduction data — setDimReduction","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setDimReduction.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set dimension reduction data — setDimReduction","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" dimred <- getDimReduction(g)  setDimReduction(gobject = g, x = dimred) #> > pca already exists and will be replaced with #>  new dimension reduction object #> Setting dimension reduction [cell][rna] pca #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":null,"dir":"Reference","previous_headings":"","what":"Set expression data — setExpression","title":"Set expression data — setExpression","text":"Function set expression values giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set expression data — setExpression","text":"","code":"setExpression(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   name = \"raw\",   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set expression data — setExpression","text":"gobject giotto object x exprObj list exprObj set. Passing NULL remove specified set expression data giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name expression information provenance provenance information (optional) information giotto object. Pass NULL remove expression object verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set expression data — setExpression","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setExpression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set expression data — setExpression","text":"","code":"g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" m <- matrix(rnorm(100), nrow = 10) colnames(m) <- paste0(\"cell_\", seq_len(10)) rownames(m) <- paste0(\"feat_\", seq_len(10))  g <- setExpression(gobject = g, x = createExprObj(m, name = \"raw\")) #> Setting expression [cell][rna] raw"},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feature info — setFeatureInfo","title":"Set feature info — setFeatureInfo","text":"Set giotto polygon spatVector features","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feature info — setFeatureInfo","text":"","code":"setFeatureInfo(   gobject,   x,   feat_type = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feature info — setFeatureInfo","text":"gobject giotto object x giottoPoints object list giottoPoints set. Passing NULL remove specified giottoPoints object giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feature info — setFeatureInfo","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set feature info — setFeatureInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" featinfo <- getFeatureInfo(g, return_giottoPoints = TRUE)  setFeatureInfo(gobject = g, x = featinfo) #> > \" rna \" already exists and will be #>  replaced with new giotto points #> Setting feature info [rna] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feature metadata — setFeatureMetadata","title":"Set feature metadata — setFeatureMetadata","text":"Function set feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feature metadata — setFeatureMetadata","text":"","code":"setFeatureMetadata(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feature metadata — setFeatureMetadata","text":"gobject giotto object x featMetaObj list featMetaObj set. Passing NULL reset specified set feature metadata giotto object. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feature metadata — setFeatureMetadata","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setFeatureMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set feature metadata — setFeatureMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" m1 <- getFeatureMetadata(g, output = \"data.table\") m2 <- data.frame(     feat_ID = m1$feat_ID,     new_column = paste0(\"gene_\", m1$feat_ID) )  setFeatureMetadata(gobject = g, x = createFeatMetaObj(m2)) #> Setting feature metadata [cell][rna] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Set giotto subobjects into giotto object — setGiotto","title":"Set giotto subobjects into giotto object — setGiotto","text":"Set giotto subobjects giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set giotto subobjects into giotto object — setGiotto","text":"","code":"# S4 method for class 'giotto,list' setGiotto(gobject, x, verbose = TRUE, ...)  # S4 method for class 'giotto,cellMetaObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,featMetaObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,exprObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,giottoPoints' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,giottoPolygon' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,dimObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,spatLocsObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,spatEnrObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,nnNetObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,spatialNetworkObj' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,giottoLargeImage' setGiotto(gobject, x, ...)  # S4 method for class 'giotto,giottoImage' setGiotto(gobject, x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set giotto subobjects into giotto object — setGiotto","text":"gobject giotto object x giottoSubobject set verbose verbose ... additional params pass specific Giotto setter functions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set giotto subobjects into giotto object — setGiotto","text":"giottoSubobject","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set giotto subobjects into giotto object — setGiotto","text":"","code":"g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_expression <- GiottoData::loadSubObjectMini(\"exprObj\")  setGiotto(gobject = g, x = g_expression) #> Setting expression [aggregate][rna] normalized #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 462 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [aggregate][rna] normalized #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Set giotto image object — setGiottoImage","title":"Set giotto image object — setGiottoImage","text":"Directly attach giotto image giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set giotto image object — setGiottoImage","text":"","code":"setGiottoImage(gobject, image, image_type = NULL, name = NULL, verbose = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set giotto image object — setGiottoImage","text":"gobject giotto object image giotto image object attached without modification giotto object image_type deprecated name name giotto image object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set giotto image object — setGiottoImage","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set giotto image object — setGiottoImage","text":"Use care! function directly attaches giotto image objects gobject without modifications spatial positioning values within image object generally needed order plot correct location relative modalities spatial data.  general-purpose method attaching image objects, see addGiottoImage","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set giotto image object — setGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" gimg <- getGiottoImage(gobject = g)  setGiottoImage(g, NULL, name = objName(gimg)) #> NULL passed to `image` param #>  removing specified image #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : dapi_z1 polyT_z0 polyT_z1  #>  #>  #> Use objHistory() to see steps and params used setGiottoImage(gobject = g, image = gimg) #> > image 'dapi_z0' already exists and will be replaced #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set multiomics integration results — setMultiomics","title":"Set multiomics integration results — setMultiomics","text":"Set multiomics integration result Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set multiomics integration results — setMultiomics","text":"","code":"setMultiomics(   gobject = NULL,   result,   spat_unit = NULL,   feat_type = NULL,   integration_method = \"WNN\",   result_name = \"theta_weighted_matrix\",   verbose = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set multiomics integration results — setMultiomics","text":"gobject Giotto object result matrix result multiomics integration (e.g. theta weighted values runWNN) spat_unit spatial unit (e.g. 'cell') feat_type (e.g. 'rna_protein') integration_method multiomics integration method used. Default = 'WNN' result_name Default = 'theta_weighted_matrix' verbose verbose ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set multiomics integration results — setMultiomics","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setMultiomics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set multiomics integration results — setMultiomics","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  setMultiomics(     gobject = g, result = matrix(rnorm(100), nrow = 10),     spat_unit = \"cell\", feat_type = \"rna_protein\" ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Set nearest neighbor network — setNearestNetwork","title":"Set nearest neighbor network — setNearestNetwork","text":"Set NN-network Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set nearest neighbor network — setNearestNetwork","text":"","code":"setNearestNetwork(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   nn_type = \"sNN\",   name = \"sNN.pca\",   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set nearest neighbor network — setNearestNetwork","text":"gobject giotto object x nnNetObj list nnNetObj. Passing NULL remove specified set nearest neighbor network information gobject spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_type \"kNN\" \"sNN\" name name NN network used yet supported. provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set nearest neighbor network — setNearestNetwork","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setNearestNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set nearest neighbor network — setNearestNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" dimred <- getNearestNetwork(gobject = g) #> The NN network type was not specified, default to the #>  first: \"sNN\" #> The NN network name was not specified, default to the #>  first: \"sNN.pca\"  setNearestNetwork(gobject = g, x = dimred) #> > 'sNN.pca' already exists and will be replaced with #>  new nearest neighbor network #> Setting nearest neighbor network [cell][rna] sNN.pca #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"Set polygon info — setPolygonInfo","title":"Set polygon info — setPolygonInfo","text":"Set polygon information Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set polygon info — setPolygonInfo","text":"","code":"setPolygonInfo(   gobject,   x,   name = \"cell\",   centroids_to_spatlocs = FALSE,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set polygon info — setPolygonInfo","text":"gobject giotto object x single object named list objects set polygon information (see details) name (optional, character) name assign polygon spatial unit polygon might define. used single giottoPolygon objects. Names taken named list multiple polygons. centroids_to_spatlocs centroid information discovered, whether additionally set set spatial locations (default = FALSE) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set polygon info — setPolygonInfo","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set polygon info — setPolygonInfo","text":"Inputs can provided either single objects named lists objects. list named, generic name template 'cell_i' applied.  input character string, assumed filepath.  required formatting reading tabular data objects, see createGiottoPolygonsFromDfr details.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setPolygonInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set polygon info — setPolygonInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" polyinfo <- getPolygonInfo(g, return_giottoPolygon = TRUE)  setPolygonInfo(gobject = g, x = polyinfo) #> > \" z0 \" already exists and will be replaced #>  with new giotto polygon #> Setting polygon info [z0] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial enrichment — setSpatialEnrichment","title":"Set spatial enrichment — setSpatialEnrichment","text":"Function set spatial enrichment slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial enrichment — setSpatialEnrichment","text":"","code":"setSpatialEnrichment(   gobject,   x,   spat_unit = NULL,   feat_type = NULL,   name = \"enrichment\",   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial enrichment — setSpatialEnrichment","text":"gobject giotto object x spatEnrObj list spatEnrObj set. Passing NULL remove specified set spatial enrichment information gobject. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name spatial enrichment results. Default \"DWLS\" provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial enrichment — setSpatialEnrichment","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialEnrichment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set spatial enrichment — setSpatialEnrichment","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spatenrich <- GiottoData::loadSubObjectMini(\"spatEnrObj\")  g <- setSpatialEnrichment(g, spatenrich) #> > \" cluster_metagene \" already exists and will be replaced with new spatial #>  enrichment results #> Setting spatial enrichment [aggregate][rna] cluster_metagene"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial grid — setSpatialGrid","title":"Set spatial grid — setSpatialGrid","text":"Function set spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial grid — setSpatialGrid","text":"","code":"setSpatialGrid(   gobject,   spatial_grid,   spat_unit = NULL,   feat_type = NULL,   name = NULL,   verbose = TRUE,   set_defaults = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial grid — setSpatialGrid","text":"gobject giotto object spatial_grid spatial grid object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name spatial grid verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial grid — setSpatialGrid","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialGrid.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set spatial grid — setSpatialGrid","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5) sg <- getSpatialGrid(g, return_grid_Obj = TRUE) #> The grid name was not specified, default to the first: \"spatial_grid\"  setSpatialGrid(gobject = g, spatial_grid = sg) #> > \" spatial_grid \" already exists and will be replaced with new spatial grid #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial locations — setSpatialLocations","title":"Set spatial locations — setSpatialLocations","text":"Function set spatial location slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial locations — setSpatialLocations","text":"","code":"setSpatialLocations(   gobject,   x,   spat_unit = NULL,   name = \"raw\",   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial locations — setSpatialLocations","text":"gobject giotto object x spatLocsObj list spatLocsObj. Passing NULL remove specified set spatial locations data. spat_unit spatial unit (e.g. \"cell\") name name spatial locations, default \"raw\" provenance provenance information (optional) verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial locations — setSpatialLocations","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set spatial locations — setSpatialLocations","text":"Spatial information set nested location described tagged spat_unit name information. alternative location can also specified respective params function.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialLocations.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set spatial locations — setSpatialLocations","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" x <- getSpatialLocations(g, output = \"data.table\") sl <- data.frame(cell_ID = x$cell_ID, sdimx = rnorm(624), sdimy = rnorm(624))  setSpatialLocations(gobject = g, x = createSpatLocsObj(sl, name = \"raw\")) #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> > raw already exists and will be replaced with new spatial #>  locations #> Setting spatial locations [cell] raw #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial network — setSpatialNetwork","title":"Set spatial network — setSpatialNetwork","text":"Function set spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial network — setSpatialNetwork","text":"","code":"setSpatialNetwork(   gobject,   x,   spat_unit = NULL,   name = NULL,   provenance = NULL,   verbose = TRUE,   initialize = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial network — setSpatialNetwork","text":"gobject giotto object x spatialNetworkObj list spatialNetworkObj set. Passing NULL removes specified set spatial network information gobject. spat_unit spatial unit (e.g. \"cell\") name name spatial network provenance provenance name verbose verbose initialize (default = FALSE) whether initialize gobject returning ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial network — setSpatialNetwork","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/setSpatialNetwork.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set spatial network — setSpatialNetwork","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spatnet <- getSpatialNetwork(g)  setSpatialNetwork(gobject = g, x = spatnet) #> > \" Delaunay_network \" already exists and will be replaced with new spatial #>  network #> Setting spatial network [cell] Delaunay_network #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":null,"dir":"Reference","previous_headings":"","what":"set_default_feat_type — set_default_feat_type","title":"set_default_feat_type — set_default_feat_type","text":"Function guess default feature type. Also see activeFeatType() methods-instructions.R way manually assign default","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"set_default_feat_type — set_default_feat_type","text":"","code":"set_default_feat_type(gobject, feat_type = NULL, spat_unit)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"set_default_feat_type — set_default_feat_type","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") spat_unit spatial unit (e.g. \"cell\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"set_default_feat_type — set_default_feat_type","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"set_default_feat_type — set_default_feat_type","text":"","code":"g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  set_default_feat_type(gobject = g, spat_unit = \"cell\", feat_type = \"rna\") #> [1] \"rna\""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":null,"dir":"Reference","previous_headings":"","what":"set_default_spat_unit — set_default_spat_unit","title":"set_default_spat_unit — set_default_spat_unit","text":"Function guess default spatial unit. Also see activeSpatUnit() methods-instructions.R way manually assign default","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"set_default_spat_unit — set_default_spat_unit","text":"","code":"set_default_spat_unit(gobject, spat_unit = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"set_default_spat_unit — set_default_spat_unit","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"set_default_spat_unit — set_default_spat_unit","text":"character","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"set_default_spat_unit — set_default_spat_unit","text":"","code":"g <- createGiottoObject() #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  set_default_spat_unit(gobject = g, spat_unit = \"cell\") #> [1] \"cell\""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":null,"dir":"Reference","previous_headings":"","what":"Set multiomics integration results — set_multiomics","title":"Set multiomics integration results — set_multiomics","text":"Set multiomics integration result Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set multiomics integration results — set_multiomics","text":"","code":"set_multiomics(   gobject,   result,   spat_unit = NULL,   feat_type = NULL,   integration_method = \"WNN\",   result_name = \"theta_weighted_matrix\",   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set multiomics integration results — set_multiomics","text":"gobject Giotto object result matrix result multiomics integration (e.g. theta weighted values runWNN) spat_unit spatial unit (e.g. 'cell') feat_type (e.g. 'rna_protein') integration_method multiomics integration method used. Default = 'WNN' result_name Default = 'theta_weighted_matrix' verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set multiomics integration results — set_multiomics","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_multiomics.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Set multiomics integration results — set_multiomics","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  set_multiomics(     gobject = g, result = matrix(rnorm(100), nrow = 10),     spat_unit = \"cell\", feat_type = \"rna_protein\" ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/settleGeom.html","id":null,"dir":"Reference","previous_headings":"","what":"Settle polygon bounds — settleGeom","title":"Settle polygon bounds — settleGeom","text":"Settle boundaries polygons overlap splitting point touch. Works intersection voronoi centroids.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/settleGeom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Settle polygon bounds — settleGeom","text":"","code":"# S4 method for class 'giottoPolygon' settleGeom(x)  # S4 method for class 'SpatVector' settleGeom(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/settleGeom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Settle polygon bounds — settleGeom","text":"x SpatVector type \"polygons\" object inheriting giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/settleGeom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Settle polygon bounds — settleGeom","text":"class x, contained polygons borders settled relation .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/settleGeom.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Settle polygon bounds — settleGeom","text":"","code":"svp <- GiottoData::loadSubObjectMini(\"giottoPolygon\")[] svp <- buffer(svp, 5) plot(svp)  svp <- settleGeom(svp) plot(svp)"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Deprecated — seuratToGiotto","title":"Deprecated — seuratToGiotto","text":"Deprecated. Please use either seuratToGiottoV4 seuratToGiottoV5","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Deprecated — seuratToGiotto","text":"","code":"seuratToGiotto(   sobject,   spatial_assay = \"Spatial\",   dim_reduction = c(\"pca\", \"umap\"),   subcellular_assay = \"Vizgen\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Deprecated — seuratToGiotto","text":"sobject Input Seurat object convert Giotto object spatial_assay Specify name spatial assay slot Seurat. Default \"Spatial\". dim_reduction Specify dimensional reduction computations fetch subcellular_assay Specify name subcellular assay input object. Default \"Vizgen\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Deprecated — seuratToGiotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"Convert Seurat V4 object Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"","code":"seuratToGiottoV4(   sobject,   spatial_assay = \"Spatial\",   dim_reduction = c(\"pca\", \"umap\"),   subcellular_assay = \"Vizgen\",   sp_network = NULL,   nn_network = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"sobject Input Seurat object convert Giotto object spatial_assay Specify name spatial assay slot Seurat. Default \"Spatial\". dim_reduction Specify dimensional reduction computations fetch input Seurat object. Default \"c('pca', 'umap')\". subcellular_assay Specify name subcellular assay input sp_network sp_network nn_network nn_network verbose logical. Default TRUE object. Default \"Vizgen\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"Giotto object converted Seurat object computations stored .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert a Seurat V4 object to a Giotto object — seuratToGiottoV4","text":"","code":"m_expression <- Matrix::Matrix(rnorm(100), nrow = 10, sparse = TRUE) s <- Seurat::CreateSeuratObject(counts = m_expression)  seuratToGiottoV5(s, spatial_assay = \"RNA\") #> Warning: data layer is not found and counts layer is used #> Images for RNA assay not found in the data. #>                         Skipping image processing. #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" #> There are non numeric or integer columns for the spatial location #>  input at column position(s): 1 #>  The first non-numeric column will be considered as a cell ID #>  to test for consistency with the expression matrix #>  Other non numeric columns will be removed #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 10, 10 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized #> spatial locations ---------------- #>   [cell] raw #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV5.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","title":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","text":"Convert Seurat V5 object Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV5.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","text":"","code":"seuratToGiottoV5(   sobject,   spatial_assay = \"Spatial\",   dim_reduction = c(\"pca\", \"umap\"),   subcellular_assay = \"SCT\",   sp_network = NULL,   nn_network = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV5.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","text":"sobject Input Seurat object convert Giotto object spatial_assay Specify name spatial assay slot Seurat. Default \"Spatial\". dim_reduction Specify dimensional reduction computations fetch input Seurat object. Default \"c('pca', 'umap')\". subcellular_assay Specify name subcellular assay input sp_network sp_network nn_network nn_network verbose logical. Default TRUE object. Default \"Vizgen\".","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV5.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert a Seurat V5 object to a Giotto object — seuratToGiottoV5","text":"Giotto object converted Seurat object computations stored .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply a shear tranform — shear","title":"Apply a shear tranform — shear","text":"Apply shear transformation spatial object. Currently works 2D transforms. implementation applies shear along one axis adding value axis multiplicative factor fx fy applied.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply a shear tranform — shear","text":"","code":"# S4 method for class 'spatLocsObj' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'SpatVector' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'giottoPoints' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'giottoPolygon' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'giottoLargeImage' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'giottoAffineImage' shear(x, fx = 0, fy = 0, x0, y0, ...)  # S4 method for class 'affine2d' shear(x, fx = 0, fy = 0, x0, y0, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply a shear tranform — shear","text":"x object fx numeric. x shear fy numeric. y shear x0 numeric. x-origin shear y0 numeric. y-origin shear ... additional args pass (none implemented)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply a shear tranform — shear","text":"shear transformed object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/shear.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply a shear tranform — shear","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  plot(shear(sl, fx = 2))   # equivalent affine transform shear_m <- diag(rep(1, 3)) shear_m[2, 1] <- 2 plot(affine(sl, shear_m))  plot(shear(sl, fx = 2, x0 = 0, y0 = 0))"},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":null,"dir":"Reference","previous_headings":"","what":"Show methods for Giotto classes — show","title":"Show methods for Giotto classes — show","text":"Show methods Giotto classes","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show methods for Giotto classes — show","text":"","code":"# S4 method for class 'giotto' show(object)  # S4 method for class 'packedGiotto' show(object)  # S4 method for class 'exprObj' show(object)  # S4 method for class 'cellMetaObj' show(object)  # S4 method for class 'featMetaObj' show(object)  # S4 method for class 'dimObj' show(object)  # S4 method for class 'nnNetObj' show(object)  # S4 method for class 'spatLocsObj' show(object)  # S4 method for class 'spatialNetworkObj' show(object)  # S4 method for class 'spatialGridObj' show(object)  # S4 method for class 'spatEnrObj' show(object)  # S4 method for class 'giottoPolygon' show(object)  # S4 method for class 'packedGiottoPolygon' show(object)  # S4 method for class 'giottoPoints' show(object)  # S4 method for class 'packedGiottoPoints' show(object)  # S4 method for class 'giottoImage' show(object)  # S4 method for class 'giottoLargeImage' show(object)  # S4 method for class 'affine2d' show(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show methods for Giotto classes — show","text":"object object show","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show methods for Giotto classes — show","text":"giotto slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/show.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Show methods for Giotto classes — show","text":"","code":"sl <- data.frame(seq(10), seq(10), letters[seq(10)]) |>     createSpatLocsObj(verbose = FALSE) show(sl) #> An object of class spatLocsObj : \"test\" #> spat_unit : \"cell\" #> dimensions: 10 3  #> preview   : #>    sdimx sdimy cell_ID #>    <int> <int>  <char> #> 1:     1     1       a #> 2:     2     2       b #> 3:     3     3       c #>  #> ranges: #>      sdimx sdimy #> [1,]     1     1 #> [2,]    10    10 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoCellMetadata — showGiottoCellMetadata","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"shows available cell metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"","code":"showGiottoCellMetadata(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"gobject giotto object nrows number rows print metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"prints name small subset available metadata","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoCellMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoCellMetadata — showGiottoCellMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoCellMetadata(g) #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>          An object of class cellMetaObj  #>          spat_unit : \"cell\" #>          feat_type : \"rna\" #>          provenance: cell  #>          dimensions: 4 7  #>           #>                        cell_ID in_tissue nr_feats perc_feats total_expr leiden_clus #>                         <char>     <int>    <int>      <num>      <num>       <num> #>          1: AACTCGATGGCGCAGT-1         1      265   41.79811  1057.9308           2 #>          2: GGCTGGCTAGCTTAAA-1         1      279   44.00631  1064.7493           5 #>          3: GACGCCTGTTGCAGGG-1         1      219   34.54259   964.9294           2 #>             custom_leiden #>                     <num> #>          1:             4 #>          2:             3 #>          3:             3 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoDimRed — showGiottoDimRed","title":"showGiottoDimRed — showGiottoDimRed","text":"shows available dimension reductions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoDimRed — showGiottoDimRed","text":"","code":"showGiottoDimRed(gobject, nrows = 3, ncols = 2)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoDimRed — showGiottoDimRed","text":"gobject giotto object nrows number coordinates rows print ncols number coordinates columns print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoDimRed — showGiottoDimRed","text":"prints name small subset available dimension reduction coordinates","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoDimRed.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoDimRed — showGiottoDimRed","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoDimRed(g) #> Dim reduction on cells: #>  -------------------------  #>  #> . #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>       ├──Dim reduction type \"pca\" #>       │  ├──S4 dimObj \"pca\" coordinates:   (624 rows 100 cols) #>       │  │                            Dim.1      Dim.2 #>       │  │     AAAGGGATGTAGCAAG-1  0.801127   2.874369 #>       │  │     AAATGGCATGTCTTGT-1  6.995542  -2.010611 #>       │  │     AAATGGTCAATGTGCC-1 -7.813633 -12.305266 #>       │  │   #>       │  └──S4 dimObj \"custom_pca\" coordinates:   (624 rows 100 cols) #>       │                                Dim.1     Dim.2 #>       │        AAAGGGATGTAGCAAG-1 -0.4547083  3.383001 #>       │        AAATGGCATGTCTTGT-1 -6.2679882  1.503456 #>       │        AAATGGTCAATGTGCC-1 10.2690789 -7.006071 #>       │      #>       ├──Dim reduction type \"umap\" #>       │  ├──S4 dimObj \"umap\" coordinates:   (624 rows 2 cols) #>       │  │                             Dim.1      Dim.2 #>       │  │     AAAGGGATGTAGCAAG-1  -3.975629   4.401250 #>       │  │     AAATGGCATGTCTTGT-1 -16.788569 -20.950487 #>       │  │     AAATGGTCAATGTGCC-1  27.206731  -9.034316 #>       │  │   #>       │  └──S4 dimObj \"custom_umap\" coordinates:   (624 rows 2 cols) #>       │                                Dim.1      Dim.2 #>       │        AAAGGGATGTAGCAAG-1  -3.731145  -3.665592 #>       │        AAATGGCATGTCTTGT-1 -14.201382 -23.566582 #>       │        AAATGGTCAATGTGCC-1  29.736043   6.478635 #>       │      #>       └──Dim reduction type \"tsne\" #>          └──S4 dimObj \"tsne\" coordinates:   (624 rows 2 cols) #>                                        Dim.1      Dim.2 #>                AAAGGGATGTAGCAAG-1 -3.4389554  -1.690378 #>                AAATGGCATGTCTTGT-1  0.4290782 -18.060330 #>                AAATGGTCAATGTGCC-1 17.8533998  12.975694 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoExpression — showGiottoExpression","title":"showGiottoExpression — showGiottoExpression","text":"shows available matrices","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoExpression — showGiottoExpression","text":"","code":"showGiottoExpression(gobject, nrows = 4, ncols = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoExpression — showGiottoExpression","text":"gobject giotto object nrows number rows print matrix (ignored sparse matrices) ncols number columns print matrix (ignored sparse matrices)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoExpression — showGiottoExpression","text":"prints name small subset available matrices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoExpression.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoExpression — showGiottoExpression","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoExpression(g) #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>       ├──Expression data \"raw\" values: #>       │     An object of class exprObj : \"raw\" #>       │     spat_unit : \"cell\" #>       │     feat_type : \"rna\" #>       │     provenance: cell  #>       │      #>       │     contains: #>       │     634 x 624 sparse Matrix of class \"dgCMatrix\" #>       │                                              #>       │     Gna12  1 2 1 1 9 1 3 5 3 . . 10 7 ...... #>       │     Ccnd2  . 1 1 . . 1 . 1 1 . .  . 3 ...... #>       │     Btbd17 . 1 1 1 . . 2 . . . .  . . ...... #>       │      #>       │      ........suppressing 611 columns and 628 rows in show(); maybe adjust options(max.print=, width=) #>       │                                                    #>       │     Gm19935       . 1 . . . . . . . . 1 . . ...... #>       │     9630013A20Rik . . . . . . . . . . 1 . . ...... #>       │     2900040C04Rik 1 . . . . . . . . 1 . . . ...... #>       │      #>       │      First four colnames: #>       │      AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 #>       │      AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  #>       │   #>       ├──Expression data \"normalized\" values: #>       │     An object of class exprObj : \"normalized\" #>       │     spat_unit : \"cell\" #>       │     feat_type : \"rna\" #>       │     provenance: cell  #>       │      #>       │     contains: #>       │     634 x 624 sparse Matrix of class \"dgCMatrix\" #>       │                                                                                                 #>       │     Gna12  3.783033 3.929306 3.213481 3.625522 5.749157 2.399595 4.127923 4.693522 5.299374 . . #>       │     Ccnd2  .        3.021024 3.213481 .        .        2.399595 .        2.578969 3.785883 . . #>       │     Btbd17 .        3.021024 3.213481 3.625522 .        .        3.583641 .        .        . . #>       │                                     #>       │     Gna12  5.683074 5.036423 ...... #>       │     Ccnd2  .        3.871485 ...... #>       │     Btbd17 .        .        ...... #>       │      #>       │      ........suppressing 611 columns and 628 rows in show(); maybe adjust options(max.print=, width=) #>       │                                                                                #>       │     Gm19935       .        3.021024 . . . . . . . .        3.103487 . . ...... #>       │     9630013A20Rik .        .        . . . . . . . .        3.103487 . . ...... #>       │     2900040C04Rik 3.783033 .        . . . . . . . 3.488189 .        . . ...... #>       │      #>       │      First four colnames: #>       │      AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 #>       │      AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  #>       │   #>       └──Expression data \"scaled\" values: #>             An object of class exprObj  #>             for spatial unit: \"cell\" and feature type: \"rna\" #>               Provenance: cell #>              #>             contains: #>             634 x 624 dense matrix of class \"dgeMatrix\" #>              #>                          [,1]       [,2]        [,3]       [,4] #>             Gna12   0.3648960  0.3883749  0.02397458  0.2635371 #>             Ccnd2  -0.9726302  0.5135323  0.59882469 -0.8883955 #>             Btbd17 -0.6902939  1.0914525  1.12309944  1.3267401 #>             Sox9   -0.8344595 -1.0154377 -0.84282003 -0.7614102 #>              #>              First four colnames: #>              AAAGGGATGTAGCAAG-1 AAATGGCATGTCTTGT-1 #>              AAATGGTCAATGTGCC-1 AAATTAACGGGTAGCT-1  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoFeatInfo — showGiottoFeatInfo","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"show available giotto spatial feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"","code":"showGiottoFeatInfo(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"SpatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoFeatInfo — showGiottoFeatInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoFeatInfo(g) #> For Feature info:  rna  #>  #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  source      : rna_feature_spatVector.shp #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3 #>  #> ----------------------------- #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoFeatMetadata — showGiottoFeatMetadata","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"shows available feature metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"","code":"showGiottoFeatMetadata(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"gobject giotto object nrows number rows print metadata","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"prints name small subset available metadata","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoFeatMetadata.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoFeatMetadata — showGiottoFeatMetadata","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoFeatMetadata(g) #> ├──Spatial unit \"z0\" #> │  └──Feature type \"rna\" #> │        An object of class featMetaObj  #> │        spat_unit : \"z0\" #> │        feat_type : \"rna\" #> │        provenance: z0  #> │         #> │           feat_ID #> │            <char> #> │        1:    Mlc1 #> │        2:  Gprc5b #> │        3:    Gfap #> │      #> ├──Spatial unit \"z1\" #> │  └──Feature type \"rna\" #> │        An object of class featMetaObj  #> │        spat_unit : \"z1\" #> │        feat_type : \"rna\" #> │        provenance: z1  #> │         #> │           feat_ID #> │            <char> #> │        1:    Mlc1 #> │        2:  Gprc5b #> │        3:    Gfap #> │      #> └──Spatial unit \"aggregate\" #>    └──Feature type \"rna\" #>          An object of class featMetaObj  #>          spat_unit : \"aggregate\" #>          feat_type : \"rna\" #>          provenance: z0 z1  #>           #>             feat_ID nr_cells perc_cells total_expr mean_expr mean_expr_det hvg_orig #>              <char>    <int>      <num>      <num>     <num>         <num>   <char> #>          1:    Mlc1       80   17.31602   526.5915  1.139808      6.582394       no #>          2:  Gprc5b      138   29.87013   944.0153  2.043323      6.840690       no #>          3:    Gfap      151   32.68398  1229.1943  2.660594      8.140359      yes #>                   var    hvf #>                 <num> <char> #>          1:  1.815718    yes #>          2:  2.388911    yes #>          3: 12.899599    yes #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoImageNames — showGiottoImageNames","title":"showGiottoImageNames — showGiottoImageNames","text":"Prints available giotto images attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoImageNames — showGiottoImageNames","text":"","code":"showGiottoImageNames(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoImageNames — showGiottoImageNames","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoImageNames — showGiottoImageNames","text":"prints names available giotto image objects","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoImageNames.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoImageNames — showGiottoImageNames","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoImageNames(g) #> Image type: largeImage  #>  #> --> Name: dapi_z0  #> --> Name: dapi_z1  #> --> Name: polyT_z0  #> --> Name: polyT_z1  #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — showGiottoInstructions","title":"deprecated — showGiottoInstructions","text":"Function display instructions giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — showGiottoInstructions","text":"","code":"showGiottoInstructions(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — showGiottoInstructions","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — showGiottoInstructions","text":"named vector giotto instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"deprecated — showGiottoInstructions","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoInstructions(g) #> Warning: `showGiottoInstructions()` was deprecated in GiottoClass 0.3.5. #> ℹ Please use `instructions()` instead. #> <giottoInstructions> #> python_path      : /usr/share/miniconda/envs/giotto_env/bin/python #> show_plot        : TRUE #> return_plot      : FALSE #> save_plot        : FALSE #> save_dir         : NA #> plot_format      : png #> dpi              : 300 #> units            : in #> height           : 9 #> width            : 9 #> is_docker        : FALSE #> active_spat_unit : cell #> active_feat_type : rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoNearestNetworks — showGiottoNearestNetworks","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"shows available nearest neighbor networks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"","code":"showGiottoNearestNetworks(gobject, nrows = 3)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"gobject giotto object nrows number network rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"prints name small subset available nearest neighbor network info","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoNearestNetworks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoNearestNetworks — showGiottoNearestNetworks","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoNearestNetworks(g) #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>       └──NN network type \"sNN\" #>          ├──S4 nnNetObj \"sNN.pca\"   (3748 rows) #>          │                      from                 to    weight distance shared  rank #>          │                    <char>             <char>     <num>    <num>  <int> <int> #>          │     1: AAAGGGATGTAGCAAG-1 CAGTGTCCGCAGAATG-1 0.3777898 1.646975      9     1 #>          │     2: AAAGGGATGTAGCAAG-1 ACGTAGATTGCTGATG-1 0.2318818 3.312541      6     2 #>          │     3: AAAGGGATGTAGCAAG-1 CGTACCTGATAGGCCT-1 0.3122768 2.202287      6     3 #>          │   #>          └──S4 nnNetObj \"custom_NN\"   (1872 rows) #>                                 from                 to    weight distance shared  rank #>                               <char>             <char>     <num>    <num>  <int> <int> #>                1: AAAGGGATGTAGCAAG-1 AACTGGGTCCCGACGT-1 0.1492788 5.698874      2     1 #>                2: AAAGGGATGTAGCAAG-1 CAGCTCGTGCTTGTGT-1 0.1507539 5.633328      1     2 #>                3: AAAGGGATGTAGCAAG-1 CGTACCTGATAGGCCT-1 0.1566434 5.383926      1     3 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"shows available spatial enrichment results","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"","code":"showGiottoSpatEnrichments(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"gobject giotto object nrows number rows print spatial enrichment data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"prints name small subset available data.table","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatEnrichments.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatEnrichments — showGiottoSpatEnrichments","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoSpatEnrichments(g) #> Spatial unit:  aggregate   #>  #> --> Feature type:  rna   #>  #> ----> Name  cluster_metagene :  #>           1         2         3         4     5 #>       <num>     <num>     <num>     <num> <num> #> 1: 1.014837 0.0000000 0.3160792 0.0000000     0 #> 2: 3.207415 0.9579716 0.6728505 0.2132677     0 #> 3: 3.953661 0.4604975 0.0000000 0.2302488     0 #> 4: 4.093622 0.5886051 0.1962017 0.5886051     0 #>                                    cell_ID #>                                     <char> #> 1: 240649020551054330404932383065726870513 #> 2: 274176126496863898679934791272921588227 #> 3: 323754550002953984063006506310071917306 #> 4:  87260224659312905497866017323180367450"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatGrids — showGiottoSpatGrids","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"Prints available spatial grids attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"","code":"showGiottoSpatGrids(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"gobject giotto object nrows number rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"prints name available spatial grids","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatGrids.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatGrids — showGiottoSpatGrids","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g <- createSpatialGrid(g, sdimx_stepsize = 5, sdimy_stepsize = 5)  showGiottoSpatGrids(g) #> └──Spatial unit \"cell\" #>    └──Feature type \"rna\" #>       └──S4 spatialGridObj \"spatial_grid\"   (388800 rows) #>                x_start y_start  x_end y_end gr_name gr_x_name gr_y_name #>                  <num>   <num>  <num> <num>  <char>    <char>    <char> #>             1:  3067.5   -5445 3072.5 -5440    gr_1    gr_x_1    gr_y_1 #>             2:  3072.5   -5445 3077.5 -5440    gr_2    gr_x_2    gr_y_1 #>             3:  3077.5   -5445 3082.5 -5440    gr_3    gr_x_3    gr_y_1 #>             4:  3082.5   -5445 3087.5 -5440    gr_4    gr_x_4    gr_y_1 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatLocs — showGiottoSpatLocs","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"shows available spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"","code":"showGiottoSpatLocs(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"gobject giotto object nrows number rows print spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"prints name small subset available data.table","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatLocs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatLocs — showGiottoSpatLocs","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoSpatLocs(g) #> └──Spatial unit \"cell\" #>    └──S4 spatLocsObj \"raw\" coordinates:   (624 rows) #>          An object of class spatLocsObj  #>          provenance: cell #>              ------------------------ #>             sdimx sdimy            cell_ID #>             <int> <int>             <char> #>          1:  5477 -4125 AAAGGGATGTAGCAAG-1 #>          2:  5959 -2808 AAATGGCATGTCTTGT-1 #>          3:  4720 -5202 AAATGGTCAATGTGCC-1 #>          4:  5202 -5322 AAATTAACGGGTAGCT-1 #>           #>          ranges: #>               sdimx sdimy #>          [1,]  3069 -5442 #>          [2,]  6441 -2568 #>           #>           #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatNetworks — showGiottoSpatNetworks","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"Prints available spatial networks attached Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"","code":"showGiottoSpatNetworks(gobject, nrows = 4)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"gobject giotto object nrows number rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"prints names small subset available spatial network info","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatNetworks.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatNetworks — showGiottoSpatNetworks","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoSpatNetworks(g) #> └──Spatial unit \"cell\" #>    ├──S4 spatialNetworkObj \"Delaunay_network\"   (1770 rows) #>    │                      from                 to sdimx_begin sdimy_begin sdimx_end #>    │                    <char>             <char>       <num>       <num>     <num> #>    │     1: AAAGGGATGTAGCAAG-1 TCAAACAACCGCGTCG-1        5477       -4125      5340 #>    │     2: AAAGGGATGTAGCAAG-1 ACGATCATACATAGAG-1        5477       -4125      5546 #>    │     3: AAAGGGATGTAGCAAG-1 TATGCTCCCTACTTAC-1        5477       -4125      5408 #>    │     4: AAAGGGATGTAGCAAG-1 TTGTTCAGTGTGCTAC-1        5477       -4125      5615 #>    │        sdimy_end distance      weight #>    │            <num>    <num>       <num> #>    │     1:     -4125 137.0000 0.007299270 #>    │     2:     -4244 137.5573 0.007269700 #>    │     3:     -4244 137.5573 0.007269700 #>    │     4:     -4125 138.0000 0.007246377 #>    │   #>    └──S4 spatialNetworkObj \"spatial_network\"   (3288 rows) #>                           from                 to sdimx_begin sdimy_begin sdimx_end #>                         <char>             <char>       <int>       <int>     <int> #>          1: AAAGGGATGTAGCAAG-1 TCAAACAACCGCGTCG-1        5477       -4125      5340 #>          2: AAAGGGATGTAGCAAG-1 ACGATCATACATAGAG-1        5477       -4125      5546 #>          3: AAAGGGATGTAGCAAG-1 TATGCTCCCTACTTAC-1        5477       -4125      5408 #>          4: AAAGGGATGTAGCAAG-1 TTGTTCAGTGTGCTAC-1        5477       -4125      5615 #>             sdimy_end distance      weight #>                 <int>    <num>       <num> #>          1:     -4125 137.0000 0.007246377 #>          2:     -4244 137.5573 0.007217233 #>          3:     -4244 137.5573 0.007217233 #>          4:     -4125 138.0000 0.007194245 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"showGiottoSpatialInfo — showGiottoSpatialInfo","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"show available giotto spatial polygon information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"","code":"showGiottoSpatialInfo(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"SpatVector","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoSpatialInfo.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showGiottoSpatialInfo — showGiottoSpatialInfo","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showGiottoSpatialInfo(g) #> For Spatial info:  z0  #>  #> An object of class giottoPolygon #> spat_unit : \"z0\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 498, 1  (geometries, attributes) #>  extent      : 6399.244, 6903.243, -5152.39, -4694.868  (xmin, xmax, ymin, ymax) #>  source      : z0_spatInfo_spatVector.shp #>  coord. ref. :   #>  names       :                                 poly_ID #>  type        :                                   <chr> #>  values      :  40951783403982682273285375368232495429 #>                240649020551054330404932383065726870513 #>                274176126496863898679934791272921588227 #>  centroids   : calculated #>  overlaps    : rna #> ----------------------------- #>   #> For Spatial info:  z1  #>  #> An object of class giottoPolygon #> spat_unit : \"z1\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 504, 1  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.873  (xmin, xmax, ymin, ymax) #>  source      : z1_spatInfo_spatVector.shp #>  coord. ref. :   #>  names       :                                 poly_ID #>  type        :                                   <chr> #>  values      :  40951783403982682273285375368232495429 #>                 17685062374745280598492217386845129350 #>                223553142498364321238189328942498473503 #>  centroids   : calculated #>  overlaps    : rna #> ----------------------------- #>   #> For Spatial info:  aggregate  #>  #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  source      : aggregate_spatInfo_spatVector.shp #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    : rna #> ----------------------------- #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGrids.html","id":null,"dir":"Reference","previous_headings":"","what":"Show Spatial Grids — showGrids","title":"Show Spatial Grids — showGrids","text":"Show Spatial Grids","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGrids.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show Spatial Grids — showGrids","text":"","code":"showGrids(...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGrids.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show Spatial Grids — showGrids","text":"... Arguments passed showGiottoSpatGrids gobject giotto object nrows number rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGrids.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show Spatial Grids — showGrids","text":"prints name available spatial grids","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showNetworks.html","id":null,"dir":"Reference","previous_headings":"","what":"Show networks — showNetworks","title":"Show networks — showNetworks","text":"Show networks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showNetworks.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Show networks — showNetworks","text":"","code":"showNetworks(...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showNetworks.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show networks — showNetworks","text":"... Arguments passed showGiottoSpatNetworks gobject giotto object nrows number rows print","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showNetworks.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show networks — showNetworks","text":"prints names small subset available spatial network info","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":null,"dir":"Reference","previous_headings":"","what":"showProcessingSteps — showProcessingSteps","title":"showProcessingSteps — showProcessingSteps","text":"shows sequential processing steps performed Giotto object summarized format","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"showProcessingSteps — showProcessingSteps","text":"","code":"showProcessingSteps(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"showProcessingSteps — showProcessingSteps","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"showProcessingSteps — showProcessingSteps","text":"list processing steps names","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showProcessingSteps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"showProcessingSteps — showProcessingSteps","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  showProcessingSteps(g) #> Warning: `showProcessingSteps()` was deprecated in GiottoClass 0.4.0. #> ℹ Please use `objHistory()` instead. #> ℹ objHistory with arg `summarized = TRUE` replaces this functionality #> Processing steps: #> 0_normalize #> 1_subset #> 2_filter #> name info: tag tag #> 3_feat_stats #> 4_cell_stats #> 5_hvf #> name info: hvf HVFplot #> 6_pca #> 7_umap #> 8_tsne #> 9_nn_network #> 10_cluster #> name info: leiden_clus sNN.pca #> 11_delaunay_spatial_network #> name info: Delaunay_network #> 12_spatial_network #> name info: spatial_network #> 13_create_metafeat #> name info: cluster_metagene #> 14_pca #> name info: custom_pca #> 15_umap #> name info: custom_pca custom_umap #> 16_nn_network #> name info: custom_pca custom_NN #> 17_cluster #> name info: custom_leiden custom_NN #> 18_spatial_deconvolution #> name info: DWLS #> 19_spatial_deconvolution #> name info: DWLS #> 20_spatial_deconvolution #> name info: DWLS"},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Slice giotto object by spat_unit and feat_type — sliceGiotto","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"Extract specific spatial units feature types giotto object independent giotto objects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"","code":"sliceGiotto(gobject, spat_unit = \":all:\", feat_type = \":all:\", verbose = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"gobject giotto object spat_unit character vector. Spatial units slice . \"::\" means keeping output feat_type character vector. Feature types slice . \"::\" means keeping output verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/sliceGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Slice giotto object by spat_unit and feat_type — sliceGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" res <- sliceGiotto(g, spat_unit = \"aggregate\") force(res) #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 462 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"smoothGiottoPolygons — smoothGiottoPolygons","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"Smooths Giotto polygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"","code":"smoothGiottoPolygons(   gpolygon,   vertices = 20,   k = 3,   set_neg_to_zero = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"gpolygon giotto polygon object vertices number vertices k k set_neg_to_zero set negative values zero (default: TRUE) ... additional params pass spline","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"Smoothed Giotto polygon object reduced vertices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/smoothGiottoPolygons.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"smoothGiottoPolygons — smoothGiottoPolygons","text":"","code":"gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  smoothGiottoPolygons(gpolygon = gpoly) #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6391.72, 6903.433, 0, 0  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    : NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatEnrObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 spatEnrObj Class — spatEnrObj-class","title":"S4 spatEnrObj Class — spatEnrObj-class","text":"Framework store spatial enrichment results","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatEnrObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 spatEnrObj Class — spatEnrObj-class","text":"spatEnrObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatEnrObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 spatEnrObj Class — spatEnrObj-class","text":"name name enrichment object method method used perform spatial enrichment enrichDT spatial enrichment data.table spat_unit spatial unit feat_type feature type provenance provenance information misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatEnrObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 spatEnrObj Class — spatEnrObj-class","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatEnrObj\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial and feature IDs — spatIDs-generic","title":"Spatial and feature IDs — spatIDs-generic","text":"Get cell IDs (termed spatial IDs better reflect single-cell level) feature IDs giotto object subobject. [giotto object specific] applied giotto object, functions pull cell_ID feat_ID slots. values within slots updated whenever object data changed , importantly, whenever active spat_unit feat_type set (see activeSpatUnit() activeFeatType()). New values slots specific active spat_unit feat_type detected either subcellular level (giottoPolygon giottoPoints) aggregate level (expression matrix) data, preference latter exists. aware current behavior, values returned byspatIDs() featIDs() regarded minimal set expected IDs within giotto slots, always exact set ordering.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial and feature IDs — spatIDs-generic","text":"","code":"# S4 method for class 'giotto' spatIDs(x, spat_unit = NULL, subset, negate = FALSE, quote = TRUE, ...)  # S4 method for class 'exprObj' spatIDs(x, ...)  # S4 method for class 'spatLocsObj' spatIDs(x, ...)  # S4 method for class 'cellMetaObj' spatIDs(x, ...)  # S4 method for class 'spatialNetworkObj' spatIDs(x, ...)  # S4 method for class 'dimObj' spatIDs(x, ...)  # S4 method for class 'giottoPolygon' spatIDs(x, use_cache = TRUE, uniques = TRUE, ...)  # S4 method for class 'spatEnrObj' spatIDs(x, ...)  # S4 method for class 'nnNetObj' spatIDs(x, ...)  # S4 method for class 'giotto' featIDs(x, feat_type = NULL, subset, negate = FALSE, quote = TRUE, ...)  # S4 method for class 'exprObj' featIDs(x, ...)  # S4 method for class 'featMetaObj' featIDs(x, ...)  # S4 method for class 'giottoPoints' featIDs(x, use_cache = TRUE, uniques = TRUE, ...)  # S4 method for class 'spatEnrObj' featIDs(x, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial and feature IDs — spatIDs-generic","text":"x object spat_unit (optional) specify spatial unit subset logical expression find subset features. negate logical. TRUE IDs subset selected quote logical. TRUE, subset param quoted substitute(). Set FALSE calling function, although may recommended since NSE output can unexpected used interactively. ... additional params pass used subset param. spatID(), pass spatValues(). featID(), currently pass fDataDT(). use_cache use cached IDs available (gpoly gpoints ) uniques return unique ID values (currently gpoly gpoints ) feat_type (optional) specify feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial and feature IDs — spatIDs-generic","text":"character vector cell/spatial IDs feature IDs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatIDs-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial and feature IDs — spatIDs-generic","text":"","code":"g <- GiottoData::loadGiottoMini(\"vis\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" spatIDs(g) #>   [1] \"AAAGGGATGTAGCAAG-1\" \"AAATGGCATGTCTTGT-1\" \"AAATGGTCAATGTGCC-1\" #>   [4] \"AAATTAACGGGTAGCT-1\" \"AACAACTGGTAGTTGC-1\" \"AACAGGAAATCGAATA-1\" #>   [7] \"AACAGGATGGGCCGCG-1\" \"AACCATGGGATCGCTA-1\" \"AACCCAGAGACGGAGA-1\" #>  [10] \"AACCGAGCTTGGTCAT-1\" \"AACCGTTGTGTTTGCT-1\" \"AACGATAGAAGGGCCG-1\" #>  [13] \"AACGATATGTCAACTG-1\" \"AACGCGGTCTCCAGCC-1\" \"AACGTCAGACTAGTGG-1\" #>  [16] \"AACTCGATGGCGCAGT-1\" \"AACTGATATTAGGCCT-1\" \"AACTGGGTCCCGACGT-1\" #>  [19] \"AACTTGCCCGTATGCA-1\" \"AAGAGATGAATCGGTA-1\" \"AAGCTCGTGCCAAGTC-1\" #>  [22] \"AAGGAGCGGTTGGTGC-1\" \"AAGGCGCGTAAAGCTT-1\" \"AAGGCTGTGCTCATCG-1\" #>  [25] \"AAGTAGAAGACCGGGT-1\" \"AAGTAGTGACGCGAGG-1\" \"AATCCAAGGGCCTGAG-1\" #>  [28] \"AATGACTGTCAGCCGG-1\" \"AATGCAACCGGGTACC-1\" \"AATGGTTCTCACAAGC-1\" #>  [31] \"AATTTGGTTCCAAAGA-1\" \"ACAACAGCATGAGCTA-1\" \"ACAACGGTCCCTGCGA-1\" #>  [34] \"ACAAGGACAAGAGGTT-1\" \"ACACAAAGACGGGTGG-1\" \"ACACACTTTCTACACG-1\" #>  [37] \"ACACCCAGCATGCAGC-1\" \"ACACCCGAGAAATCCG-1\" \"ACACCTTAAGTAGGGC-1\" #>  [40] \"ACACGAGACTCCTTCT-1\" \"ACACGGGAACTTAGGG-1\" \"ACATAATAAGGCGGTG-1\" #>  [43] \"ACCAAGAACGCGTGTC-1\" \"ACCACAAGTTTCTATC-1\" \"ACCCTTCATCTGCGAA-1\" #>  [46] \"ACCGACTGAGTCCCAC-1\" \"ACCTAATCGACTTCCT-1\" \"ACGATCATACATAGAG-1\" #>  [49] \"ACGCATTCGTGAGTAC-1\" \"ACGCCAGATGATTTCT-1\" \"ACGCGGGCCAAGGACA-1\" #>  [52] \"ACGGAATTTAGCAAAT-1\" \"ACGTAGATTGCTGATG-1\" \"ACGTGCGCCTCGTGCA-1\" #>  [55] \"ACGTTTAGTTGTGATC-1\" \"ACTACCAGCTCTCTGG-1\" \"ACTATTCGTCCGTGGT-1\" #>  [58] \"ACTCAATAAAGGCACG-1\" \"ACTGCCGTCGTAACTC-1\" \"ACTGTAGCACTTTGGA-1\" #>  [61] \"ACTGTCCAGGATTATA-1\" \"ACTGTCTTCTTTAGAA-1\" \"ACTGTGCTAGTAGATC-1\" #>  [64] \"ACTTAGTACGACAAGA-1\" \"ACTTCGCCATACGCAC-1\" \"ACTTGGGACCCGGTGG-1\" #>  [67] \"ACTTTCCTATAGCTTC-1\" \"AGAACGTGGTACATTC-1\" \"AGACCATGGGATACAA-1\" #>  [70] \"AGACCCGCCCTCCTCG-1\" \"AGACTAGCCTTCCAGA-1\" \"AGAGCGGGCTAATCAT-1\" #>  [73] \"AGAGCGTACAAGCTCG-1\" \"AGATAACTTCAGGGCC-1\" \"AGATACGACTTCATAT-1\" #>  [76] \"AGATCTCAGGTGTGAT-1\" \"AGATGACTCGCCCACG-1\" \"AGCACCAGTACTCACG-1\" #>  [79] \"AGCACTTAAGGACGCC-1\" \"AGCATCGTCGATAATT-1\" \"AGCCCTAAGCGAAGTT-1\" #>  [82] \"AGCGACATCCCATTCA-1\" \"AGCGACCAACGATATT-1\" \"AGCGGGAAGGGTCCAT-1\" #>  [85] \"AGCTATTTAATCCAAC-1\" \"AGGACATCGCACGTCG-1\" \"AGGCCACCCGTTATGA-1\" #>  [88] \"AGGCCCATTGTACAGG-1\" \"AGGCTATGGTTAGCTT-1\" \"AGGGCGTGATCGGCTA-1\" #>  [91] \"AGGGCTGCAGTTACAG-1\" \"AGGGTTTAGTTCGGGA-1\" \"AGGTAACCTCCTATTC-1\" #>  [94] \"AGGTACGATATTGCCA-1\" \"AGGTAGGTACAAAGCT-1\" \"AGGTTGAGGCACGCTT-1\" #>  [97] \"AGTAATGTCTTGCCGC-1\" \"AGTAGGTAACATACAT-1\" \"AGTATAATACTAGGCA-1\" #> [100] \"AGTCAGCCACCGCCTG-1\" \"AGTCGGCCCAAACGAC-1\" \"AGTCTTCTCCTCAAAT-1\" #> [103] \"AGTTCCTACAGAATTA-1\" \"AGTTTCGCAGGTCGGA-1\" \"ATAAAGGCTCGGTCGT-1\" #> [106] \"ATAACGGAGTCCAACG-1\" \"ATAATAGTGTAGGGAC-1\" \"ATACCACGGGCAACTT-1\" #> [109] \"ATACTAGCATGACCCT-1\" \"ATAGACGAAGAGAAAG-1\" \"ATAGAGTACTGGGACA-1\" #> [112] \"ATAGGGATATCCTTGA-1\" \"ATAGGTTGGGCAGATG-1\" \"ATATCTTAGGGCCTTC-1\" #> [115] \"ATATTCCCACAGGTCA-1\" \"ATATTGCTGTCAAAGT-1\" \"ATATTTAACCCTCAAG-1\" #> [118] \"ATCAATCTGGGCTGCA-1\" \"ATCACTTCATCCTCGC-1\" \"ATCCAACGCAGTCATA-1\" #> [121] \"ATCGACTCTTTCCGTT-1\" \"ATCGCACGCCGGGAGA-1\" \"ATCTCCCTGCAATCTA-1\" #> [124] \"ATCTGGTTAAGACTGT-1\" \"ATCTGTAATTGTACCC-1\" \"ATCTTGACCTGCAACG-1\" #> [127] \"ATGAAGCCAAGGAGCC-1\" \"ATGACGCCGGCTCTAA-1\" \"ATGAGGAGTGTTAATC-1\" #> [130] \"ATGATCGGGAATAGAC-1\" \"ATGCACTACCGCATTG-1\" \"ATGCATGATCCAGGAT-1\" #> [133] \"ATGCCGGTCTTGCATA-1\" \"ATGCGACAGTCCCATT-1\" \"ATGCTCAGTGTTGCAT-1\" #> [136] \"ATGGATTGACCAAACG-1\" \"ATGTGCATCCGACGCA-1\" \"ATGTTACGAGCAATAC-1\" #> [139] \"ATTAATACTACGCGGG-1\" \"ATTAATTCGGTCACTC-1\" \"ATTACTAGCCTCTTGC-1\" #> [142] \"ATTAGATTGATAGCGG-1\" \"ATTATGCCATAGGGAG-1\" \"ATTCCTCCGCCAGTGC-1\" #> [145] \"ATTCTCGTCTCTTTAG-1\" \"ATTGAAGATCTTAGTG-1\" \"ATTGCTGCTCCTCCAT-1\" #> [148] \"ATTGGGAATATCTTGG-1\" \"ATTTAACTCGTATTAC-1\" \"ATTTACAGTTTACTGG-1\" #> [151] \"ATTTGTTCCAGGGCTC-1\" \"CAAACGGTCGCACTTT-1\" \"CAAACTATTGAGCTTC-1\" #> [154] \"CAAATTGTCAGCAAGC-1\" \"CAACGACCCGTTTACA-1\" \"CAACGGTTCTTGATAC-1\" #> [157] \"CAACTCCTTGATCCCG-1\" \"CAAGCAACGTCGGAGT-1\" \"CAAGCACCAAATGCCT-1\" #> [160] \"CAATAAACCTTGGCCC-1\" \"CAATTAAGGGTGATGA-1\" \"CACACAGGGATAGATT-1\" #> [163] \"CACAGCACCCACGGCA-1\" \"CACAGCTAGGGAGTGA-1\" \"CACCATCGGAGGAGAC-1\" #> [166] \"CACCCACACGTCACCC-1\" \"CACCGCCAGAAGGTTT-1\" \"CACCTAATCAGTTTAC-1\" #> [169] \"CACCTCGATGGTGGAC-1\" \"CACGAAAGTTAGTCCC-1\" \"CACGCACAGCGCAGCT-1\" #> [172] \"CACGCAGCGAGGCTTT-1\" \"CACTAAAGTTGCCTAT-1\" \"CACTCAGCTCTTGAGG-1\" #> [175] \"CACTGTCCAAGTGAGA-1\" \"CACTTAATCAGACGGA-1\" \"CACTTCGCCACAGGCT-1\" #> [178] \"CAGAGCATGAGCTTGC-1\" \"CAGATACTAACATAGT-1\" \"CAGCTCACTGAGACAT-1\" #> [181] \"CAGCTCGTGCTTGTGT-1\" \"CAGCTTAGTAGGTAGC-1\" \"CAGTGTCCGCAGAATG-1\" #> [184] \"CAGTTCAAATTGACAC-1\" \"CATACAAAGCCGAACC-1\" \"CATAGTAGCATAGTAG-1\" #> [187] \"CATCATCTACCCGGAC-1\" \"CATCGCCCGCGGCCAA-1\" \"CATGAACCGACATTTG-1\" #> [190] \"CATGATGCACAATTCT-1\" \"CATGCGTTAGACAGAA-1\" \"CATGCTGGCTCCAATT-1\" #> [193] \"CATGGCAGGAAGATCG-1\" \"CATGGTCTAGATACCG-1\" \"CATTACGTCGGCCCGT-1\" #> [196] \"CATTATGCTTGTTGTG-1\" \"CCAAACAGAACCCTCG-1\" \"CCAACGATGCACTGAT-1\" #> [199] \"CCAAGACTTCTGCGAA-1\" \"CCAAGCGTAACTCGTA-1\" \"CCAAGGAACAGAGAGG-1\" #> [202] \"CCAATAGTGCCGTCGA-1\" \"CCAATTGAATGTTAAT-1\" \"CCACGAGAAGAGAATC-1\" #> [205] \"CCAGGGACGTGGCCTC-1\" \"CCATAAACAACCCGAC-1\" \"CCATAGGTTGGCGTGG-1\" #> [208] \"CCATCCATACCAAGTC-1\" \"CCATGCCTGTTTAGTA-1\" \"CCATGCTCTGCAGGAA-1\" #> [211] \"CCATTAGCGATAATCC-1\" \"CCATTCCCTGCCCACA-1\" \"CCCGACCATAGTCCGC-1\" #> [214] \"CCCGCCATGCTCCCGT-1\" \"CCCGTCAGCGTCTGAC-1\" \"CCCTCATTCTGGAATT-1\" #> [217] \"CCCTGAAATGAGTTGA-1\" \"CCGAAAGTGGTGAGCA-1\" \"CCGCCGGTCAACACAC-1\" #> [220] \"CCGGAATGGTTTCAGT-1\" \"CCGGCGCATATTGGAT-1\" \"CCGGGACCCGCAGAGA-1\" #> [223] \"CCGGGCGGTCTCGTCA-1\" \"CCGTACCCAAGCGCCA-1\" \"CCGTGCCCATGACGGC-1\" #> [226] \"CCTACGGCTCAGTCGA-1\" \"CCTACTGCTTACACTT-1\" \"CCTAGTTAGTCGCATG-1\" #> [229] \"CCTATGGGTTACCGTC-1\" \"CCTCACCAATCTTGAC-1\" \"CCTCCGACAATTCAAG-1\" #> [232] \"CCTCGAAGTGGACGGG-1\" \"CCTCGCCAGCAAATTA-1\" \"CCTCTAATCTGCCAAG-1\" #> [235] \"CCTCTCTCCCATCTAG-1\" \"CCTCTGGCCTAGACGG-1\" \"CCTGAATATTTACATA-1\" #> [238] \"CCTGCTATTTGAGAAG-1\" \"CCTGGCTAGACCCGCC-1\" \"CCTGTCACCCGGGCTC-1\" #> [241] \"CCTTCTTGATCCAGTG-1\" \"CGAACGCCCAGTGCCG-1\" \"CGAAGTTGCTCTGTGT-1\" #> [244] \"CGAGAGATGTGAACCT-1\" \"CGAGCGTTGATCAGCC-1\" \"CGAGCTGGGCTTTAGG-1\" #> [247] \"CGAGGCTAAATATGGC-1\" \"CGCAAACACGAGTTAC-1\" \"CGCAATTACTTTCGGT-1\" #> [250] \"CGCAATTAGGGTAATA-1\" \"CGCAATTCTACAATAA-1\" \"CGCATTAGCTAATAGG-1\" #> [253] \"CGCGCCCGACTTAATA-1\" \"CGCGTTCATGAAATAC-1\" \"CGCTATACCGCCCACT-1\" #> [256] \"CGCTATTCAATGTATG-1\" \"CGCTCGACATAATGAT-1\" \"CGCTCTCCGTAGATTA-1\" #> [259] \"CGCTGTGACGCCGCAC-1\" \"CGCTTCCACTGAAATC-1\" \"CGCTTTCATACCGGTG-1\" #> [262] \"CGGAGTTTGAGAGACA-1\" \"CGGCACTCAAGAAAGT-1\" \"CGGCCACGCACAAAGT-1\" #> [265] \"CGGGATCAATGTAAGA-1\" \"CGGGCAGCTAAACCGC-1\" \"CGGTGTACTTGATCCC-1\" #> [268] \"CGTACCTGATAGGCCT-1\" \"CGTAGCGAATTGTCAG-1\" \"CGTATTAAGAGATCTA-1\" #> [271] \"CGTCAGTGCGCACAAG-1\" \"CGTCTGGAAGGGCCCG-1\" \"CGTGTCCCATTCGCGA-1\" #> [274] \"CGTTGTTTCAATTCCC-1\" \"CGTTTAAGCGGAGCAC-1\" \"CGTTTCGCTCATTACA-1\" #> [277] \"CTAATTCGCACGCGCT-1\" \"CTAATTTCAACAACAC-1\" \"CTACGCACGGAGTACC-1\" #> [280] \"CTACTGCCACCTGACC-1\" \"CTAGCATAGTATAATG-1\" \"CTAGTGAAGGACAGGA-1\" #> [283] \"CTAGTTGGGCCCGGTA-1\" \"CTATCGGGTCTCAACA-1\" \"CTATGTCACTAGCCCA-1\" #> [286] \"CTATGTCTATTGAAAC-1\" \"CTCAGGACTCACCTGT-1\" \"CTCATGGCTCACAATC-1\" #> [289] \"CTCATTTGATGGGCGG-1\" \"CTCCGGCCTAATATGC-1\" \"CTCCTAAGTTATGTCT-1\" #> [292] \"CTCGAGGTCGAACAGT-1\" \"CTCGCACCTATATAGT-1\" \"CTCGGTCCGTAGCCTG-1\" #> [295] \"CTCTCACAATCGATGA-1\" \"CTCTGCGAAGCAAGCA-1\" \"CTCTGGACGCCTGGTG-1\" #> [298] \"CTCTGTTTGAGGATTC-1\" \"CTGAAAGAGATCCGAC-1\" \"CTGCACCTGGAACCGC-1\" #> [301] \"CTGGAAATGGATGCTT-1\" \"CTGTATGGTGTAGAAA-1\" \"CTGTTCACTGCCTGTG-1\" #> [304] \"CTGTTCATCTCACGGG-1\" \"CTTAACTTCGAAGTAC-1\" \"CTTACACGGTATTCCA-1\" #> [307] \"CTTACACTGGGAAATA-1\" \"CTTATGTTGACTACCA-1\" \"CTTCATAGCTCAAGAA-1\" #> [310] \"CTTCTTACGTCGTATA-1\" \"CTTGTACTTGTTGACT-1\" \"CTTGTTTATGTAGCCA-1\" #> [313] \"CTTTAACTTTCAAAGG-1\" \"CTTTGGCTTTAGTAAA-1\" \"GAAACAGCCATGCAGT-1\" #> [316] \"GAAACTCTAATGAAGG-1\" \"GAAAGTGACTAACTGC-1\" \"GAAATCGCGCGCAACT-1\" #> [319] \"GAAATGGCGGTGTTAG-1\" \"GAAATTCACATCGCTG-1\" \"GAACACACATCAACCA-1\" #> [322] \"GAACGACCGAATGATA-1\" \"GAAGAACGGTGCAGGT-1\" \"GAAGCGTGAGGAATTT-1\" #> [325] \"GAAGCTTGCTGACCGC-1\" \"GAAGTGCTGGATAGCT-1\" \"GAATCGACATGGTCAC-1\" #> [328] \"GAATCGCCGGACACGG-1\" \"GAATGTTGGGTAATCT-1\" \"GAATTATAGTGAAAGG-1\" #> [331] \"GAATTTCTCGCTGCAG-1\" \"GACAACGCAGCTTACG-1\" \"GACACAAGGGAAGAAA-1\" #> [334] \"GACCAGAGCCCTGTAG-1\" \"GACGCCTGTTGCAGGG-1\" \"GACGTGTAGGGATTAT-1\" #> [337] \"GACTAAGATCATGCAC-1\" \"GACTAAGTAGGCTCAC-1\" \"GAGACTGATGGGTAGA-1\" #> [340] \"GAGATCTGCTTGGCAT-1\" \"GAGATCTGTCACTCCG-1\" \"GAGCATCATCCCTGGG-1\" #> [343] \"GAGCGAGGGAGTACCG-1\" \"GAGCTCTCGGACCTAA-1\" \"GAGGAATGGAGAGGTT-1\" #> [346] \"GAGGCTATCAAAGTCG-1\" \"GAGGGCATCGCGTATC-1\" \"GAGGTACATCCATCTT-1\" #> [349] \"GAGTACGGGTATACAA-1\" \"GATAAATCGGTGGATG-1\" \"GATATCTCATGCAATA-1\" #> [352] \"GATCATTCCAAACATT-1\" \"GATCCCTTTATACTGC-1\" \"GATCGACACTATCTGA-1\" #> [355] \"GATCGGTGGCCATAAC-1\" \"GATGCTACAAGCGCCT-1\" \"GATGGCGCACACATTA-1\" #> [358] \"GATGTTTGTGCGAGAT-1\" \"GATTCCCTTGTCGCAG-1\" \"GATTCCGCGTTTCCGT-1\" #> [361] \"GCAAATATTACGCTTT-1\" \"GCAAGTGCACAGAGAA-1\" \"GCACTAGTCGCGCTAT-1\" #> [364] \"GCAGGACTATAGAATA-1\" \"GCATCCCTAACTTTGA-1\" \"GCCCACCAAGGCTGTC-1\" #> [367] \"GCCCAGTTGGTATGCC-1\" \"GCCCGCGCGTTTGACA-1\" \"GCCGAAATTCCTACGT-1\" #> [370] \"GCCTAGCGATCTGACC-1\" \"GCCTATTCCGATATAG-1\" \"GCCTTCAGCCCTACCG-1\" #> [373] \"GCGAAGCCATACCCGT-1\" \"GCGAGTTCTGCAAAGA-1\" \"GCGCTAATTGAATAGA-1\" #> [376] \"GCGGGAACCAGGCCCT-1\" \"GCGGTCCCTAGACGCA-1\" \"GCGTCGAAATGTCGGT-1\" #> [379] \"GCTAATACCGAATGCC-1\" \"GCTAGTTTCATTGAGG-1\" \"GCTCTAAACCCTGACG-1\" #> [382] \"GCTCTATGTTACGTGC-1\" \"GCTCTCGGGTACCGAA-1\" \"GCTGCTCTCCGGACAC-1\" #> [385] \"GCTGGCATATTCACCT-1\" \"GCTTGATGATAATCAG-1\" \"GGAGAAGTCATTGGCA-1\" #> [388] \"GGAGTGCCGCCCTGGA-1\" \"GGATTCAGTACGGTGG-1\" \"GGCAATAGTCAATGAG-1\" #> [391] \"GGCACTCCACTGGGCA-1\" \"GGCATACAGGTAGCGG-1\" \"GGCGGAGTAATATTAG-1\" #> [394] \"GGCGGTAGGATCATTG-1\" \"GGCGTCCTATCCGCTG-1\" \"GGCTATTAAGTTGTAT-1\" #> [397] \"GGCTCGTGCCACCAGC-1\" \"GGCTCTGCTCCAACGC-1\" \"GGCTGGCTAGCTTAAA-1\" #> [400] \"GGGACTGCATAGATAG-1\" \"GGGAGAACTCACAGTA-1\" \"GGGAGTTAATGAGGCG-1\" #> [403] \"GGGCGATATGTGTGAA-1\" \"GGGCGGTCCTATTGTC-1\" \"GGGCGTACATTTATAT-1\" #> [406] \"GGGCTGCCTAGGGCGA-1\" \"GGGCTGGTTAGTCGCG-1\" \"GGGTATGTATGCACTT-1\" #> [409] \"GGGTCACCGTGACGGT-1\" \"GGGTGTTTCAGCTATG-1\" \"GGTAACTATGTATCTG-1\" #> [412] \"GGTAGTGCTCGCACCA-1\" \"GGTATTGCCGAGTTTA-1\" \"GGTCGGTAATTAGACA-1\" #> [415] \"GGTGAGATGCAGATAA-1\" \"GGTGCGGATAAGTGGC-1\" \"GGTTAGGCTTGGAGAA-1\" #> [418] \"GGTTTACAATCTCAAT-1\" \"GGTTTGAGTGCTGGAA-1\" \"GTAAGCGGGCAGTCAG-1\" #> [421] \"GTAAGTAGGGTATACC-1\" \"GTACGAGATTGCGACA-1\" \"GTACTAAGATTTGGAG-1\" #> [424] \"GTACTGAGGTCGTAAC-1\" \"GTACTGCATGAAGCGT-1\" \"GTACTTGGGCACTTCT-1\" #> [427] \"GTAGACGTCGTTACAT-1\" \"GTATAGGACTCAGTAG-1\" \"GTATCAGCTTGGGTTC-1\" #> [430] \"GTCAAAGTTTACATAG-1\" \"GTCACTCTCCAAATCT-1\" \"GTCAGAATAGTCTATG-1\" #> [433] \"GTCATGCACCTCCGTT-1\" \"GTCATGGACATGACTA-1\" \"GTCCCAACGTAAAGTA-1\" #> [436] \"GTCCGGCTGAATTGCG-1\" \"GTCGGATATCTCAGAC-1\" \"GTCGTCAATTATAAGG-1\" #> [439] \"GTGAAACGTGCTCCAC-1\" \"GTGCAACAAATGTGGC-1\" \"GTGCACGAAAGTGACT-1\" #> [442] \"GTGCGGGTCTCCAAAT-1\" \"GTGCTCAAGTACTGTC-1\" \"GTGGACGTGCTGAGAC-1\" #> [445] \"GTGGGCTTAGACACAC-1\" \"GTTCACAGGAGTCTAG-1\" \"GTTCCAGTCTGACCAT-1\" #> [448] \"GTTCTTCCCTCGATGT-1\" \"GTTGCACGGAGTTTCG-1\" \"GTTGTCGTGTTAGTTG-1\" #> [451] \"GTTTCCTGGAGGGTGA-1\" \"GTTTGACCAAATCCTA-1\" \"GTTTGGCCGCTCAGCG-1\" #> [454] \"TAAATGAATCCGTTTC-1\" \"TAACAAAGGGAGAAGC-1\" \"TAACGCTTTGAGAGCG-1\" #> [457] \"TAACTATCGAAGGTCC-1\" \"TAACTCCATGGAGGCT-1\" \"TAAGGAACTTGTGGGA-1\" #> [460] \"TAAGGCAACATAAGAT-1\" \"TAATACACAGTAGTAT-1\" \"TAATATTGAAATTCGC-1\" #> [463] \"TACAAGTCTCGTGCAT-1\" \"TACCAGCTAGGTTTAA-1\" \"TACCTCACGCTTGTAC-1\" #> [466] \"TACGAACACGACTTCA-1\" \"TACGAGAACTTCACGT-1\" \"TACGATGTTGATCATC-1\" #> [469] \"TACGTGCACTATGCTG-1\" \"TAGAGCTACGAAGAAC-1\" \"TAGAGTCTAAGCGAAC-1\" #> [472] \"TAGCTAAGTCCGGGAG-1\" \"TAGGGTGTTTCAAGAG-1\" \"TAGGTGAGCCCTACTC-1\" #> [475] \"TAGGTTCGAGTTCGTC-1\" \"TAGTGCCCTCCAGAGT-1\" \"TAGTTTATTCTTGCTT-1\" #> [478] \"TATAAATCCACAAGCT-1\" \"TATAAGTGAGGATAGC-1\" \"TATACACGCAAAGTAT-1\" #> [481] \"TATCCATATCATGCGA-1\" \"TATCCTGCATGGGAAT-1\" \"TATCGATGATTAAACG-1\" #> [484] \"TATGCTCCCTACTTAC-1\" \"TATGGATGTGCTACGC-1\" \"TATGGCCCGGCCTCGC-1\" #> [487] \"TATGGGTACGTATCGT-1\" \"TATTCAATTCTAATCC-1\" \"TATTCGTGCCAGAATA-1\" #> [490] \"TATTTAGTCTAGATCG-1\" \"TATTTGTTACCCTTTA-1\" \"TCAAACAACCGCGTCG-1\" #> [493] \"TCAAACTTAGATTGTT-1\" \"TCAACACATTGGGTAA-1\" \"TCAACCATGTTCGGGC-1\" #> [496] \"TCACAGGTTATTGGGC-1\" \"TCACGCATTGTAGATC-1\" \"TCACGGTCATCGCACA-1\" #> [499] \"TCAGCAAATGCATCTC-1\" \"TCAGGGTGTAACGTAA-1\" \"TCAGGTTCTTTGAGAA-1\" #> [502] \"TCAGTACTGACCCGCG-1\" \"TCATCACTCGAGCTCG-1\" \"TCATCCCAGAGGGTGG-1\" #> [505] \"TCCACAATGGTTTACG-1\" \"TCCAGGCGAGTACGGT-1\" \"TCCCAAAGACGAAGGA-1\" #> [508] \"TCCCAGCTTTAGTCTG-1\" \"TCCCAGGCTTAGCTAA-1\" \"TCCCGCGTACTCCTGG-1\" #> [511] \"TCCCGGGTGTGCTGCT-1\" \"TCCCGTCAGTCCCGCA-1\" \"TCCCTGGCTCGCTGGA-1\" #> [514] \"TCCGATAATTGCCATA-1\" \"TCCGATGACTGAGCTC-1\" \"TCCGATGGTGCGACAT-1\" #> [517] \"TCCGATTACATTGCCG-1\" \"TCCTCTACGAGATGGC-1\" \"TCCTTCAGTGGTCGAA-1\" #> [520] \"TCCTTTCTTACGCTTA-1\" \"TCGAAATTTAGGACCA-1\" \"TCGCATCCCTAAGTGT-1\" #> [523] \"TCGCCGGTCGATCCGT-1\" \"TCGCGTCCAGAAGGTC-1\" \"TCGCTCGATATATTCC-1\" #> [526] \"TCGCTGGGCGGATTGT-1\" \"TCGCTGTGCGTAAATC-1\" \"TCGGAATGCGCTCTGA-1\" #> [529] \"TCGGAGTACATGAGTA-1\" \"TCGTATAGTGCAATTA-1\" \"TCGTCCGCTGGCGTCT-1\" #> [532] \"TCTACCGTCCACAAGC-1\" \"TCTAGCATCTTCGATG-1\" \"TCTAGTTATCAGAAGA-1\" #> [535] \"TCTATCATGCAGTTAC-1\" \"TCTATCGGTCGCAACA-1\" \"TCTATTACGCTGGCGA-1\" #> [538] \"TCTCTAATAGCTGGTA-1\" \"TCTGAACCGGTCGGCT-1\" \"TCTTACAGAGGTACCG-1\" #> [541] \"TCTTACGGCATCCGAC-1\" \"TCTTCGATACCAATAA-1\" \"TCTTGATGCGTAGCGA-1\" #> [544] \"TCTTGGTAACACCAAA-1\" \"TGAAACTTATGCAAGC-1\" \"TGACCCACGTTAGACA-1\" #> [547] \"TGAGAATGCTTTACCG-1\" \"TGATCGGTTTGACCCT-1\" \"TGATCTCCGGCGCCAG-1\" #> [550] \"TGATTCGTCTATCACT-1\" \"TGATTTCCTCCTGACG-1\" \"TGCAAGAATGACGTAA-1\" #> [553] \"TGCAGGATCGGCAAAG-1\" \"TGCATGGATCGGATCT-1\" \"TGCCACCTGGCGAAAC-1\" #> [556] \"TGCCTGATCAAACGAT-1\" \"TGCGCAAAGCATTTGG-1\" \"TGCGCGATTAACGGAG-1\" #> [559] \"TGCGGAGTAAAGGTGC-1\" \"TGCGGCATAGTTCAAC-1\" \"TGCGGTGAAATTTCAT-1\" #> [562] \"TGCTGGTTGGACAATT-1\" \"TGGAAGACGAACACCA-1\" \"TGGAAGGATAAAGATG-1\" #> [565] \"TGGAGTGATGCGATGA-1\" \"TGGCCAAACTGAAGTA-1\" \"TGGCCGTATATTGACC-1\" #> [568] \"TGGCTTTGGGTAGACA-1\" \"TGGGAAATGCCTTTCC-1\" \"TGGGCACGTTCTATGG-1\" #> [571] \"TGGGCCACAAGAGCGC-1\" \"TGGTTCGTAGCAAAGG-1\" \"TGTAGTGATCTATAAT-1\" #> [574] \"TGTCCCGACATAGCAC-1\" \"TGTCCTAAGTCACCGC-1\" \"TGTCTACAGTTTCTGT-1\" #> [577] \"TGTGACTACGCCAGTC-1\" \"TGTGTCGCGAGTTGCA-1\" \"TGTTCTTCCATTGACT-1\" #> [580] \"TGTTTCGGTACTTCTC-1\" \"TTAACCAACCCTCCCT-1\" \"TTAAGCGCCTGACCCA-1\" #> [583] \"TTAATCAGTACGTCAG-1\" \"TTAATGTAGACCAGGT-1\" \"TTAATTTCAGACGCGG-1\" #> [586] \"TTACAACTACGCATCC-1\" \"TTACATCGTGGCCTGG-1\" \"TTACCATTGATTACCC-1\" #> [589] \"TTAGCAACATGGATGT-1\" \"TTATATTTGGCAATCC-1\" \"TTATCCAATCGAACTC-1\" #> [592] \"TTATCTGTATCATAAC-1\" \"TTATGACAAACTGGAT-1\" \"TTATTAGGGAAGCATC-1\" #> [595] \"TTCAAAGTCTCTAGCC-1\" \"TTCAACGACCCGACCG-1\" \"TTCAAGCCGAGCTGAG-1\" #> [598] \"TTCATGGCGCAACAGG-1\" \"TTCCTCGAGGGTGTCT-1\" \"TTCGACGGGAAGGGCG-1\" #> [601] \"TTCGCACTCGCGTGCT-1\" \"TTCGTACTCCAGAACG-1\" \"TTCTACTTGCGAGGGC-1\" #> [604] \"TTCTAGGCCAATTGTG-1\" \"TTCTTAGTGAACGGTG-1\" \"TTCTTAGTGGCTCAGA-1\" #> [607] \"TTCTTGTAACCTAATG-1\" \"TTGAAGAATTCCCAGG-1\" \"TTGAATATGGACTTTC-1\" #> [610] \"TTGATCTAACTTTGTC-1\" \"TTGATTATGCAGATGA-1\" \"TTGCACGGAGCAGCAC-1\" #> [613] \"TTGCTCCCATACCGGA-1\" \"TTGCTGAAGGAACCAC-1\" \"TTGCTGATCATGTTCG-1\" #> [616] \"TTGGATTGGGTACCAC-1\" \"TTGGCTCGCATGAGAC-1\" \"TTGGGACACTGCCCGC-1\" #> [619] \"TTGGGCGGCGGTTGCC-1\" \"TTGTAATCCGTACTCG-1\" \"TTGTATCACACAGAAT-1\" #> [622] \"TTGTCGTTCAGTTACC-1\" \"TTGTGGCCCTGACAGT-1\" \"TTGTTCAGTGTGCTAC-1\" spatIDs(g, subset = nr_feats <= 200) #>  [1] \"GTCGTCAATTATAAGG-1\" \"TCGTATAGTGCAATTA-1\" \"GAGTACGGGTATACAA-1\" #>  [4] \"TCTTACAGAGGTACCG-1\" \"GTTGTCGTGTTAGTTG-1\" \"GTACTTGGGCACTTCT-1\" #>  [7] \"CGCTATTCAATGTATG-1\" \"AATGGTTCTCACAAGC-1\" \"CTTCATAGCTCAAGAA-1\" #> [10] \"CAACGGTTCTTGATAC-1\" \"ACACCCGAGAAATCCG-1\" \"CACTGTCCAAGTGAGA-1\" #> [13] \"CATAGTAGCATAGTAG-1\" \"CAACTCCTTGATCCCG-1\" \"AAGTAGAAGACCGGGT-1\" #> [16] \"TACGTGCACTATGCTG-1\" \"GTATCAGCTTGGGTTC-1\" \"TAACAAAGGGAGAAGC-1\" #> [19] \"TTACATCGTGGCCTGG-1\" \"TCTGAACCGGTCGGCT-1\" \"TATAAGTGAGGATAGC-1\" #> [22] \"TGCTGGTTGGACAATT-1\" \"TATAAATCCACAAGCT-1\" \"CGCTCGACATAATGAT-1\" #> [25] \"TTCAACGACCCGACCG-1\" \"GTCACTCTCCAAATCT-1\" \"TTCTACTTGCGAGGGC-1\" #> [28] \"CTGTTCATCTCACGGG-1\" \"TTCTTGTAACCTAATG-1\" \"GCTTGATGATAATCAG-1\" #> [31] \"TTGGCTCGCATGAGAC-1\" \"GCCCAGTTGGTATGCC-1\" \"TCGTCCGCTGGCGTCT-1\" #> [34] \"TTCTAGGCCAATTGTG-1\" \"ATGAAGCCAAGGAGCC-1\" \"CCCGTCAGCGTCTGAC-1\" #> [37] \"GACTAAGATCATGCAC-1\" \"TGGTTCGTAGCAAAGG-1\" \"CTGTTCACTGCCTGTG-1\" #> [40] \"CGTACCTGATAGGCCT-1\" \"GAATGTTGGGTAATCT-1\" \"CACACAGGGATAGATT-1\" #> [43] \"TAACTATCGAAGGTCC-1\" \"GGGCGTACATTTATAT-1\" \"ATCGCACGCCGGGAGA-1\" #> [46] \"TATGCTCCCTACTTAC-1\" \"TCCTCTACGAGATGGC-1\" \"TTGATTATGCAGATGA-1\" #> [49] \"GTAAGTAGGGTATACC-1\" \"CGCAAACACGAGTTAC-1\" \"TGGCCGTATATTGACC-1\" #> [52] \"ACTGTAGCACTTTGGA-1\" \"GCTCTCGGGTACCGAA-1\" \"CACCGCCAGAAGGTTT-1\" #> [55] \"TCCCAAAGACGAAGGA-1\" \"TTATATTTGGCAATCC-1\" \"AGCACCAGTACTCACG-1\" #> [58] \"CGTGTCCCATTCGCGA-1\" \"GATCCCTTTATACTGC-1\" \"ATAGGTTGGGCAGATG-1\" #> [61] \"CAATTAAGGGTGATGA-1\" \"TCGCGTCCAGAAGGTC-1\" \"GGCGTCCTATCCGCTG-1\" #> [64] \"TCAGCAAATGCATCTC-1\" \"GAGATCTGTCACTCCG-1\" \"CAGCTTAGTAGGTAGC-1\" #> [67] \"CGAAGTTGCTCTGTGT-1\" \"CTCTGGACGCCTGGTG-1\" \"AGGGTTTAGTTCGGGA-1\" #> [70] \"CTCTCACAATCGATGA-1\" \"TCGGAGTACATGAGTA-1\" \"TTACCATTGATTACCC-1\" #> [73] \"CCTCTCTCCCATCTAG-1\" \"GCGCTAATTGAATAGA-1\" \"GGTAGTGCTCGCACCA-1\" #> [76] \"AAGCTCGTGCCAAGTC-1\" spatIDs(g, subset = Dim.1 > 25, dim_reduction_to_use = \"umap\") #>  [1] \"AAATGGTCAATGTGCC-1\" \"AAATTAACGGGTAGCT-1\" \"AAGGCTGTGCTCATCG-1\" #>  [4] \"ACCACAAGTTTCTATC-1\" \"ACCTAATCGACTTCCT-1\" \"ACTTGGGACCCGGTGG-1\" #>  [7] \"AGTTCCTACAGAATTA-1\" \"ATATTTAACCCTCAAG-1\" \"ATTGAAGATCTTAGTG-1\" #> [10] \"CAAACGGTCGCACTTT-1\" \"CAGCTCACTGAGACAT-1\" \"CCAACGATGCACTGAT-1\" #> [13] \"CCATTCCCTGCCCACA-1\" \"CCTCCGACAATTCAAG-1\" \"CGAAGTTGCTCTGTGT-1\" #> [16] \"CGCTCTCCGTAGATTA-1\" \"CGGGCAGCTAAACCGC-1\" \"CGTTTCGCTCATTACA-1\" #> [19] \"CTTACACGGTATTCCA-1\" \"CTTTGGCTTTAGTAAA-1\" \"GAAATGGCGGTGTTAG-1\" #> [22] \"GAAGCTTGCTGACCGC-1\" \"GCAGGACTATAGAATA-1\" \"GGCACTCCACTGGGCA-1\" #> [25] \"GGGCTGGTTAGTCGCG-1\" \"GTTCACAGGAGTCTAG-1\" \"TACGAACACGACTTCA-1\" #> [28] \"TACGAGAACTTCACGT-1\" \"TATGGGTACGTATCGT-1\" \"TCCAGGCGAGTACGGT-1\" #> [31] \"TCCCAGCTTTAGTCTG-1\" \"TCGAAATTTAGGACCA-1\" \"TTGATCTAACTTTGTC-1\"  featIDs(g) #>   [1] \"Gna12\"         \"Ccnd2\"         \"Btbd17\"        \"Sox9\"          #>   [5] \"Sez6\"          \"Serpinf1\"      \"S100a6\"        \"Col1a1\"        #>   [9] \"Vwf\"           \"Esam\"          \"Npas1\"         \"Tiam1\"         #>  [13] \"Bcam\"          \"Hmgn2\"         \"Rab3b\"         \"Inmt\"          #>  [17] \"Ddr1\"          \"Homer3\"        \"Cp\"            \"Calb2\"         #>  [21] \"Man1a\"         \"Efnb3\"         \"Hlf\"           \"Gstm7\"         #>  [25] \"Cavin1\"        \"Sst\"           \"Hapln2\"        \"Hspb1\"         #>  [29] \"Ndrg1\"         \"Nid1\"          \"Kit\"           \"Pvalb\"         #>  [33] \"Tmbim1\"        \"Crip1\"         \"Tek\"           \"Elovl1\"        #>  [37] \"Cyba\"          \"Itih3\"         \"Cnp\"           \"Hap1\"          #>  [41] \"Clic1\"         \"Stx1a\"         \"Arpp19\"        \"Dio2\"          #>  [45] \"Id3\"           \"Crlf1\"         \"Ttc9b\"         \"Carhsp1\"       #>  [49] \"Cabp7\"         \"Fam163b\"       \"Rarres2\"       \"Syn2\"          #>  [53] \"Ick\"           \"Prox1\"         \"Adssl1\"        \"Vipr2\"         #>  [57] \"Gltp\"          \"Amotl1\"        \"Bcas1\"         \"Aldh1a2\"       #>  [61] \"Tppp3\"         \"Sirt2\"         \"Lpl\"           \"Cers2\"         #>  [65] \"Qdpr\"          \"Stk32c\"        \"Lbp\"           \"Hsd11b1\"       #>  [69] \"Vtn\"           \"Stac2\"         \"Plxdc1\"        \"Igfbp4\"        #>  [73] \"Dbndd2\"        \"Pltp\"          \"Slc12a4\"       \"Cadps2\"        #>  [77] \"Erbb3\"         \"Pmp22\"         \"Kcnab3\"        \"Myh11\"         #>  [81] \"Plod1\"         \"Etnppl\"        \"Arhgef25\"      \"Rcn3\"          #>  [85] \"Vip\"           \"Utrn\"          \"Grm1\"          \"Reep3\"         #>  [89] \"Fabp7\"         \"Dcn\"           \"Slc17a8\"       \"Dusp6\"         #>  [93] \"Kitl\"          \"Ccn2\"          \"Timp3\"         \"Ascl1\"         #>  [97] \"Unc5b\"         \"Vsir\"          \"Gamt\"          \"Ptprb\"         #> [101] \"Csrp2\"         \"Adarb1\"        \"Rnf130\"        \"Nefh\"          #> [105] \"Aebp1\"         \"Sept4\"         \"Gria1\"         \"Sypl\"          #> [109] \"Arsg\"          \"Cacng4\"        \"Rab37\"         \"Itgb4\"         #> [113] \"Aspa\"          \"Cygb\"          \"Rflnb\"         \"Doc2b\"         #> [117] \"Gfap\"          \"Npas3\"         \"Serpina3n\"     \"Clmn\"          #> [121] \"Prkch\"         \"Fbln5\"         \"Akr1c18\"       \"Gng4\"          #> [125] \"Sema4d\"        \"Cxcl14\"        \"Hexb\"          \"Iqgap2\"        #> [129] \"Crhbp\"         \"Rab3c\"         \"Thbs4\"         \"Serinc5\"       #> [133] \"Erbin\"         \"Prkcd\"         \"Pdlim2\"        \"Ednrb\"         #> [137] \"Cpne6\"         \"Sema5a\"        \"Matn2\"         \"Nptxr\"         #> [141] \"Enpp2\"         \"Efcab6\"        \"Ppp1r1a\"       \"Litaf\"         #> [145] \"Il1rap\"        \"Apod\"          \"Cpox\"          \"Grik1\"         #> [149] \"Clic6\"         \"Nr4a1\"         \"Igfbp6\"        \"Sncg\"          #> [153] \"Gzma\"          \"Grm2\"          \"Prph\"          \"Rsph1\"         #> [157] \"Sox8\"          \"Fam234a\"       \"Lims2\"         \"Aqp4\"          #> [161] \"Slc12a2\"       \"Cd74\"          \"Pdgfrb\"        \"Csf1r\"         #> [165] \"Cbln2\"         \"Frmd8\"         \"Gldc\"          \"Tcf7l2\"        #> [169] \"Bhlhe22\"       \"Kcnip2\"        \"Alas2\"         \"Gdf11\"         #> [173] \"Baiap2\"        \"Ifitm3\"        \"Phkg1\"         \"Nptx1\"         #> [177] \"Pde8a\"         \"Itih5\"         \"Homer2\"        \"Fam20c\"        #> [181] \"Cplx2\"         \"Myo5b\"         \"Snca\"          \"Col3a1\"        #> [185] \"Ecrg4\"         \"Map4k4\"        \"2010300C02Rik\" \"Ogfrl1\"        #> [189] \"Fn1\"           \"Efhd1\"         \"Ngef\"          \"Bok\"           #> [193] \"Tmem163\"       \"Lct\"           \"Cfh\"           \"Ptpn4\"         #> [197] \"Tnni1\"         \"Csrp1\"         \"Nfasc\"         \"Syt2\"          #> [201] \"Atp2b4\"        \"Rgs16\"         \"Ncf2\"          \"Cnih3\"         #> [205] \"Tmem63a\"       \"Cfap126\"       \"Meig1\"         \"Ccdc3\"         #> [209] \"Rgs5\"          \"Enkur\"         \"Myoc\"          \"Vim\"           #> [213] \"Prkcq\"         \"Gad2\"          \"Lcn2\"          \"Nr4a2\"         #> [217] \"Ermn\"          \"Fibcd1\"        \"Gsn\"           \"Grb14\"         #> [221] \"Notch1\"        \"Ube2l6\"        \"Gatm\"          \"Cd82\"          #> [225] \"Mdk\"           \"Lamp5\"         \"Itpka\"         \"Chgb\"          #> [229] \"Mal\"           \"Pdyn\"          \"Nkx2-2\"        \"Edn3\"          #> [233] \"Car2\"          \"Col9a3\"        \"Chrna4\"        \"Gss\"           #> [237] \"Slc7a11\"       \"Tm4sf1\"        \"Kcnab1\"        \"Shox2\"         #> [241] \"Serpini1\"      \"Tspan2\"        \"S100a11\"       \"Vcam1\"         #> [245] \"Lef1\"          \"Npy2r\"         \"F3\"            \"Calb1\"         #> [249] \"Epha7\"         \"Slc44a1\"       \"1110017D15Rik\" \"Tpm2\"          #> [253] \"Slc6a9\"        \"Laptm5\"        \"Sema3c\"        \"Hpca\"          #> [257] \"Padi2\"         \"Slc4a2\"        \"Gabrd\"         \"Rgs12\"         #> [261] \"Slc30a3\"       \"Emilin1\"       \"1700001C02Rik\" \"Gabra4\"        #> [265] \"Pdgfra\"        \"Epha5\"         \"Tesc\"          \"Pitpnm2\"       #> [269] \"Mmp17\"         \"Cit\"           \"Foxp2\"         \"Arpc1b\"        #> [273] \"Col1a2\"        \"Eln\"           \"Pcolce\"        \"Tsc22d4\"       #> [277] \"Cald1\"         \"Ccdc136\"       \"Npy\"           \"Slc13a4\"       #> [281] \"Gkn3\"          \"Slc6a13\"       \"Mgp\"           \"Lmo3\"          #> [285] \"Slco1c1\"       \"Cpne9\"         \"Itpr2\"         \"Slc6a11\"       #> [289] \"Vamp1\"         \"Cd9\"           \"Pglyrp1\"       \"Slc17a6\"       #> [293] \"Sipa1l3\"       \"Sh3gl3\"        \"Plekhb1\"       \"Nupr1\"         #> [297] \"Dkk3\"          \"Cox6a2\"        \"Dkkl1\"         \"Fgfr2\"         #> [301] \"Crym\"          \"Slc38a5\"       \"Flna\"          \"Bgn\"           #> [305] \"Col4a1\"        \"Plat\"          \"Nr3c2\"         \"Cbln1\"         #> [309] \"Gab1\"          \"Pllp\"          \"Necab2\"        \"Dbndd1\"        #> [313] \"Agt\"           \"Cryab\"         \"Tagln\"         \"Mcam\"          #> [317] \"Olfm2\"         \"Icam5\"         \"Anxa2\"         \"Rora\"          #> [321] \"Calml4\"        \"Htr3a\"         \"Paqr5\"         \"Rasgrf1\"       #> [325] \"Zic1\"          \"Mobp\"          \"Hhatl\"         \"Trf\"           #> [329] \"Cpne4\"         \"Cdhr4\"         \"Cd59a\"         \"Gng11\"         #> [333] \"Chrm1\"         \"Prr5l\"         \"Ugt8a\"         \"Rims3\"         #> [337] \"Sgpp2\"         \"Camkv\"         \"Sox10\"         \"Micall1\"       #> [341] \"Tie1\"          \"Fa2h\"          \"Ucp2\"          \"Vav3\"          #> [345] \"Ccp110\"        \"Gria2\"         \"Rasl10a\"       \"Foxj1\"         #> [349] \"Trim59\"        \"Dynlrb2\"       \"Gjc1\"          \"Neurod1\"       #> [353] \"Ttyh2\"         \"Cpne7\"         \"Nrip3\"         \"Tbr1\"          #> [357] \"Lcat\"          \"Tmem98\"        \"Myo1d\"         \"Prdm8\"         #> [361] \"Tgfbi\"         \"Kcnc2\"         \"Thrsp\"         \"Isg15\"         #> [365] \"Acta2\"         \"H2-Q4\"         \"Dock4\"         \"Myrf\"          #> [369] \"Lmo1\"          \"Igfbp7\"        \"P2ry12\"        \"Pcdh8\"         #> [373] \"Lgi4\"          \"Fxyd1\"         \"Fxyd7\"         \"Mag\"           #> [377] \"Zcchc12\"       \"Anln\"          \"Wnt4\"          \"C1ql2\"         #> [381] \"Unc93b1\"       \"Tspan15\"       \"Ppp1r14a\"      \"Clic4\"         #> [385] \"Galnt6\"        \"Ccn3\"          \"Rims2\"         \"Zmat4\"         #> [389] \"Cldn11\"        \"Ccdc33\"        \"Slc32a1\"       \"Tgm2\"          #> [393] \"Vstm2l\"        \"Neurod6\"       \"Crygn\"         \"Enpp6\"         #> [397] \"Neurod2\"       \"Satb2\"         \"Pcp4l1\"        \"Txnip\"         #> [401] \"Egr1\"          \"Otud7b\"        \"Car14\"         \"Rgs4\"          #> [405] \"Dock10\"        \"Lpar1\"         \"Trps1\"         \"Ptpn3\"         #> [409] \"Lefty1\"        \"Zfhx3\"         \"St6galnac5\"    \"Ak5\"           #> [413] \"Hrh3\"          \"Nexn\"          \"Adgrl4\"        \"Rlbp1\"         #> [417] \"Igfbp2\"        \"Wfs1\"          \"Cplx3\"         \"Orai2\"         #> [421] \"Olig2\"         \"Gpr37\"         \"Plcb4\"         \"Nxph4\"         #> [425] \"Ndufa4l2\"      \"Cacng5\"        \"Plekhg1\"       \"Cmtm5\"         #> [429] \"Gpr161\"        \"Rfx3\"          \"Igsf21\"        \"Ramp3\"         #> [433] \"Arhgap12\"      \"Nkx6-2\"        \"Ninj2\"         \"Cldn5\"         #> [437] \"Htr2c\"         \"Hspb8\"         \"Fmod\"          \"Prelp\"         #> [441] \"Mpped1\"        \"Rapgef5\"       \"Vwa1\"          \"Stab1\"         #> [445] \"Arl15\"         \"Reln\"          \"Mustn1\"        \"Pbxip1\"        #> [449] \"Dnali1\"        \"Id1\"           \"Lrrtm3\"        \"Tmem212\"       #> [453] \"Epop\"          \"Gjc2\"          \"1190005I06Rik\" \"Ctla2a\"        #> [457] \"Cnr1\"          \"Gpr4\"          \"Sowaha\"        \"Tent5c\"        #> [461] \"Serpinb1a\"     \"S1pr5\"         \"Penk\"          \"Cdc42ep2\"      #> [465] \"Slitrk6\"       \"Hpcal4\"        \"Olig1\"         \"Rprml\"         #> [469] \"Stxbp6\"        \"Hs3st2\"        \"Rbp1\"          \"Ppm1e\"         #> [473] \"Sox18\"         \"Kctd4\"         \"Nxph3\"         \"Vat1l\"         #> [477] \"Cd24a\"         \"Odf3b\"         \"Gjb1\"          \"Selplg\"        #> [481] \"Bcl11b\"        \"Lhfp\"          \"Ranbp3l\"       \"Msx1\"          #> [485] \"Zdhhc22\"       \"Phldb1\"        \"Ctxn1\"         \"Tprn\"          #> [489] \"Vstm2a\"        \"Ndnf\"          \"Pdp1\"          \"Scn3b\"         #> [493] \"Cdc42ep1\"      \"Gal3st1\"       \"Rasd1\"         \"Spink8\"        #> [497] \"Opalin\"        \"Gja4\"          \"Synpo2\"        \"Pcdh20\"        #> [501] \"Adra1b\"        \"Fam131a\"       \"Tmem125\"       \"Mb21d2\"        #> [505] \"Lingo3\"        \"Ncald\"         \"Siglech\"       \"Rgs14\"         #> [509] \"Gm14964\"       \"Gpr17\"         \"Cx3cr1\"        \"Ezr\"           #> [513] \"Adarb2\"        \"Cpne8\"         \"Plekhg3\"       \"Lamb2\"         #> [517] \"Creb5\"         \"Cntn2\"         \"Aldh1a1\"       \"Phgdh\"         #> [521] \"Tnfaip6\"       \"Camk2d\"        \"Shisa6\"        \"Cthrc1\"        #> [525] \"Tmem119\"       \"Hmgb2\"         \"Tmem158\"       \"Dsp\"           #> [529] \"Lrtm2\"         \"Gabra5\"        \"Tns1\"          \"Nell1\"         #> [533] \"Slain1\"        \"Prr18\"         \"S100a8\"        \"S100a9\"        #> [537] \"Col8a2\"        \"Synpr\"         \"Sertm1\"        \"Adgrf5\"        #> [541] \"Capg\"          \"Gjc3\"          \"Fcer1g\"        \"Pde1a\"         #> [545] \"Tafa1\"         \"Ddn\"           \"Hopx\"          \"Ptk2b\"         #> [549] \"Rgs3\"          \"Kcng2\"         \"Ntng1\"         \"H2-Q7\"         #> [553] \"Ifitm2\"        \"Plaat3\"        \"Plekhh1\"       \"Myl4\"          #> [557] \"H2-K1\"         \"Dpp6\"          \"Tmem91\"        \"Cyp2d22\"       #> [561] \"Ttr\"           \"Suclg2\"        \"Patj\"          \"Btbd3\"         #> [565] \"Unc13c\"        \"Syt9\"          \"Shisal1\"       \"Grm4\"          #> [569] \"Sox11\"         \"Slc22a8\"       \"Slc24a3\"       \"Klk8\"          #> [573] \"Ipcef1\"        \"Tnnt1\"         \"Hhip\"          \"Spag8\"         #> [577] \"Fxyd6\"         \"Ppp1r3c\"       \"Cbln4\"         \"Nnat\"          #> [581] \"Myl9\"          \"Vxn\"           \"Lgals1\"        \"Gpr88\"         #> [585] \"Ctxn3\"         \"Lyz2\"          \"Tmem100\"       \"Wfdc17\"        #> [589] \"Ahnak\"         \"Hba-a2\"        \"Hba-a1\"        \"Ccdc153\"       #> [593] \"Ccnd1\"         \"Serpinh1\"      \"Gad1\"          \"Arhgef10\"      #> [597] \"2410004P03Rik\" \"Nt5dc2\"        \"Cebpd\"         \"Sod3\"          #> [601] \"H2-D1\"         \"C4b\"           \"Tmem88b\"       \"Hbb-bt\"        #> [605] \"Rhog\"          \"Rprm\"          \"Ly6a\"          \"Mog\"           #> [609] \"Trbc2\"         \"Igkc\"          \"Smim1\"         \"Hs3st4\"        #> [613] \"Evi2a\"         \"Prkcg\"         \"Ly6c1\"         \"Gbp4\"          #> [617] \"Wipf3\"         \"BC039966\"      \"Gm13889\"       \"Plcxd2\"        #> [621] \"Mia\"           \"Pou3f1\"        \"Lrrc10b\"       \"Apol11b\"       #> [625] \"Gpr62\"         \"Shisa8\"        \"Gm2115\"        \"Kctd12\"        #> [629] \"1700047M11Rik\" \"Lhfpl3\"        \"C030029H02Rik\" \"Gm19935\"       #> [633] \"9630013A20Rik\" \"2900040C04Rik\" featIDs(g, subset = nr_cells < 100) #>  [1] \"Col1a1\"        \"Inmt\"          \"Cp\"            \"Nid1\"          #>  [5] \"Vipr2\"         \"Aldh1a2\"       \"Lbp\"           \"Myh11\"         #>  [9] \"Dcn\"           \"Slc17a8\"       \"Ascl1\"         \"Aebp1\"         #> [13] \"Fbln5\"         \"Akr1c18\"       \"Efcab6\"        \"Clic6\"         #> [17] \"Sncg\"          \"Gzma\"          \"Prph\"          \"Rsph1\"         #> [21] \"Cd74\"          \"Col3a1\"        \"Ncf2\"          \"Cfap126\"       #> [25] \"Meig1\"         \"Enkur\"         \"Myoc\"          \"Lcn2\"          #> [29] \"Edn3\"          \"1110017D15Rik\" \"Tpm2\"          \"Emilin1\"       #> [33] \"1700001C02Rik\" \"Col1a2\"        \"Eln\"           \"Pcolce\"        #> [37] \"Slc13a4\"       \"Gkn3\"          \"Slc6a13\"       \"Nupr1\"         #> [41] \"Slc38a5\"       \"Tagln\"         \"Calml4\"        \"Htr3a\"         #> [45] \"Paqr5\"         \"Cdhr4\"         \"Tie1\"          \"Foxj1\"         #> [49] \"Dynlrb2\"       \"Gjc1\"          \"Tgfbi\"         \"H2-Q4\"         #> [53] \"Ccdc33\"        \"Tgm2\"          \"Crygn\"         \"Nexn\"          #> [57] \"Nxph4\"         \"Fmod\"          \"Stab1\"         \"Mustn1\"        #> [61] \"Dnali1\"        \"Tmem212\"       \"Gpr4\"          \"Tent5c\"        #> [65] \"Slitrk6\"       \"Odf3b\"         \"Ranbp3l\"       \"Msx1\"          #> [69] \"Ndnf\"          \"Gja4\"          \"Gm14964\"       \"Dsp\"           #> [73] \"S100a8\"        \"S100a9\"        \"Col8a2\"        \"Capg\"          #> [77] \"H2-Q7\"         \"Hhip\"          \"Spag8\"         \"Ctxn3\"         #> [81] \"Wfdc17\"        \"Ccdc153\"       \"2410004P03Rik\" \"Igkc\"          #> [85] \"Gbp4\"          \"BC039966\"      \"Mia\"           \"Apol11b\"       #> [89] \"Shisa8\"        \"C030029H02Rik\" \"Gm19935\"       \"9630013A20Rik\" #> [93] \"2900040C04Rik\"  gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\") featIDs(gpoints) #>   [1] \"Mlc1\"      \"Gprc5b\"    \"Gfap\"      \"Ednrb\"     \"Sox9\"      \"Aqp4\"      #>   [7] \"Gjc3\"      \"Sox8\"      \"Ntsr2\"     \"Adcyap1r1\" \"Smo\"       \"Gpr161\"    #>  [13] \"C1qb\"      \"Olig1\"     \"C1qa\"      \"Lmtk2\"     \"Pth1r\"     \"Ephb6\"     #>  [19] \"Gpr26\"     \"Gabbr1\"    \"Adra2a\"    \"Gabbr2\"    \"Timp4\"     \"Abcc9\"     #>  [25] \"Csf1r\"     \"Ntrk2\"     \"Adgrg1\"    \"Ntrk3\"     \"Ddr1\"      \"Erbb4\"     #>  [31] \"Selplg\"    \"Cspg5\"     \"Dlk1\"      \"Gpr37l1\"   \"Fzd1\"      \"Fgfr3\"     #>  [37] \"Slc25a18\"  \"Igf1r\"     \"Adgrl1\"    \"S1pr1\"     \"Ryk\"       \"Grm5\"      #>  [43] \"Eomes\"     \"Axl\"       \"Efemp1\"    \"Adgrb3\"    \"Sstr4\"     \"Fn1\"       #>  [49] \"Adora1\"    \"Erbb2\"     \"Gper1\"     \"Gramd3\"    \"Mertk\"     \"Slc32a1\"   #>  [55] \"Adgra1\"    \"Adgrl2\"    \"Ptgfr\"     \"Fzd2\"      \"Aldh1l1\"   \"Adgrg6\"    #>  [61] \"Egfr\"      \"Gpr162\"    \"Lpar4\"     \"Kit\"       \"Ptgdr\"     \"Gad1\"      #>  [67] \"Lgr4\"      \"Tyro3\"     \"Atp13a5\"   \"Ddr2\"      \"Rspo3\"     \"Arhgap29\"  #>  [73] \"Ackr3\"     \"Gpr146\"    \"Fzd7\"      \"Slc47a1\"   \"Insr\"      \"Ptger3\"    #>  [79] \"Bdkrb1\"    \"Traf4\"     \"Celsr2\"    \"Fzd4\"      \"Fgfr2\"     \"Cx3cr1\"    #>  [85] \"Anxa11\"    \"Adgrb1\"    \"Lpar1\"     \"Gpr17\"     \"Gpr173\"    \"Ror1\"      #>  [91] \"Cxcl12\"    \"Kiss1r\"    \"Epha4\"     \"Gpr182\"    \"Man1a\"     \"Gpr4\"      #>  [97] \"P2ry14\"    \"Hcar1\"     \"Ephb1\"     \"Adrb1\"     \"Grm3\"      \"P2ry1\"     #> [103] \"Nrp2\"      \"Ptk7\"      \"Slco1a4\"   \"Tmem108\"   \"Hrh3\"      \"Insrr\"     #> [109] \"Cmklr1\"    \"Opn3\"      \"Adra1b\"    \"Gpr62\"     \"Npy1r\"     \"Nrp1\"      #> [115] \"Fzd6\"      \"S1pr5\"     \"Pdgfrb\"    \"Flt1\"      \"Chrm3\"     \"Agtr1a\"    #> [121] \"Adgrl4\"    \"Ephb3\"     \"Lpar6\"     \"Epha6\"     \"Fzd5\"      \"Emcn\"      #> [127] \"Cldn5\"     \"Sstr1\"     \"Fzd3\"      \"P2ry12\"    \"Adgrl3\"    \"Sema4d\"    #> [133] \"Adgrf5\"    \"Gpr160\"    \"Mrgpre\"    \"Amigo2\"    \"Adgra3\"    \"P2yr13\"    #> [139] \"Epha3\"     \"Adgre1\"    \"P2ry6\"     \"Cx3cl1\"    \"Epha10\"    \"Tacr1\"     #> [145] \"Peg10\"     \"Ednra\"     \"Plxnb3\"    \"Flt4\"      \"Slc17a7\"   \"Drd2\"      #> [151] \"Tjap1\"     \"Fzd8\"      \"Cd300c2\"   \"Htr4\"      \"Gpr52\"     \"Tek\"       #> [157] \"S1pr2\"     \"Kdr\"       \"Ror2\"      \"Kcnj8\"     \"Hrh1\"      \"Celsr1\"    #> [163] \"Gpr153\"    \"S1pr3\"     \"Adgra2\"    \"Fgfrl1\"    \"Tie1\"      \"Slc15a3\"   #> [169] \"Ccr10\"     \"Pdgfra\"    \"Lhcgr\"     \"Mrgprf\"    \"Ascl1\"     \"Baiap2\"    #> [175] \"Gpr85\"     \"Gpr22\"     \"Gcgr\"      \"Grm1\"      \"Ptafr\"     \"Calcrl\"    #> [181] \"Gpr34\"     \"Cenpe\"     \"Adora2b\"   \"Adrb2\"     \"Ccr2\"      \"Alk\"       #> [187] \"Tacr3\"     \"Chrm5\"     \"Erbb3\"     \"Ccr9\"      \"Gpr21\"     \"Epha7\"     #> [193] \"Adra2b\"    \"Pcdh15\"    \"Blank-104\" \"Adora2a\"   \"Drd1\"      \"Blank-57\"  #> [199] \"Grm7\"      \"Htr1b\"     \"Fzd9\"      \"Grm4\"      \"Blank-152\" \"Aplnr\"     #> [205] \"Gpr176\"    \"F2r\"       \"Vmn1r43\"   \"Gpr156\"    \"Gpr55\"     \"Blank-155\" #> [211] \"Bdkrb2\"    \"C5ar2\"     \"Gpbar1\"    \"Adgrv1\"    \"Gprc5c\"    \"Lmod1\"     #> [217] \"Gpr135\"    \"Rxfp3\"     \"Tbxa2r\"    \"Fzd10\"     \"Ret\"       \"Blank-80\"  #> [223] \"Epha8\"     \"Gpr75\"     \"Ackr1\"     \"Adgrg4\"    \"Chrm1\"     \"Epha1\"     #> [229] \"Vmn2r1\"    \"Syt4\"      \"Tas2r135\"  \"Ccr1\"      \"Lpar2\"     \"Myh11\"     #> [235] \"Gipr\"      \"Musk\"      \"Gpr183\"    \"Cnr1\"      \"C3ar1\"     \"S1pr4\"     #> [241] \"Grm2\"      \"C5ar1\"     \"Ephb2\"     \"Fpr1\"      \"Rho\"       \"Gpr27\"     #> [247] \"Adra1d\"    \"Gpr157\"    \"Adgrg2\"    \"Blank-45\"  \"Gpr20\"     \"Casr\"      #> [253] \"Avpr2\"     \"Mc5r\"      \"Sctr\"      \"Epha5\"     \"Gpr158\"    \"Cxcr4\"     #> [259] \"Vipr1\"     \"Gpr6\"      \"Blank-148\" \"Celsr3\"    \"Uts2r\"     \"Hrh2\"      #> [265] \"Htr6\"      \"Slc17a6\"   \"Gpr1\"      \"Glp2r\"     \"Ppp1r3g\"   \"V1ra8\"     #> [271] \"Trhr\"      \"Sstr3\"     \"Gpr63\"     \"Htr1a\"     \"F2rl3\"     \"Pln\"       #> [277] \"Grin2b\"    \"Gpr37\"     \"Chrm4\"     \"Lgr6\"      \"Gpr61\"     \"Taar7e\"    #> [283] \"Mas1\"      \"Npy2r\"     \"Ptger2\"    \"P2ry2\"     \"Oprm1\"     \"Prokr2\"    #> [289] \"Adra1a\"    \"Gpr45\"     \"Mc4r\"      \"Blank-128\" \"Sstr2\"     \"Flt3\"      #> [295] \"Htr5a\"     \"Ghsr\"      \"Galr1\"     \"Blank-95\"  \"Gpr83\"     \"Crhr1\"     #> [301] \"Brs3\"      \"Drd5\"      \"Gpr139\"    \"Taar6\"     \"Htr5b\"     \"Vmn1r40\"   #> [307] \"Rrh\"       \"Blank-83\"  \"Crhr2\"     \"Blank-161\" \"Vmn1r50\"   \"Tas1r3\"    #> [313] \"Taar2\"     \"P2ry4\"     \"Mchr1\"     \"Tas1r1\"    \"Blank-69\"  \"Htr7\"      #> [319] \"Hcrtr2\"    \"Htr2a\"     \"Cysltr2\"   \"Vmn1r46\"   \"Grpr\"      \"Adgrf2\"    #> [325] \"Blank-127\" \"Opn5\"      \"Taar3\"     \"Oxtr\"      \"Cckbr\"     \"Nmbr\"      #> [331] \"Ptger4\"    \"Blank-145\" \"Gpr101\"    \"Slc17a8\"   \"Adgrf4\"    \"Epha2\"     #> [337] \"Blank-139\""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatLocsObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 spatLocsObj Class — spatLocsObj-class","title":"S4 spatLocsObj Class — spatLocsObj-class","text":"Framework store spatial location information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatLocsObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 spatLocsObj Class — spatLocsObj-class","text":"spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatLocsObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 spatLocsObj Class — spatLocsObj-class","text":"name name spatLocsObj coordinates data.table spatial coordinates/locations spat_unit spatial unit tag provenance origin aggregated information (applicable)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatLocsObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 spatLocsObj Class — spatLocsObj-class","text":"","code":"GiottoData::loadSubObjectMini(\"spatLocsObj\") #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatQueryGiottoPolygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","title":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","text":"Recursively select polygons based list spatial filters. Results returned new polygon-based spatial unit selection information recorded associated cell metadata. final item provided param filters layer information queried.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatQueryGiottoPolygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","text":"","code":"spatQueryGiottoPolygons(   gobject,   filters,   name = \"query_polys\",   feat_type = NULL,   clip = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatQueryGiottoPolygons.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","text":"gobject Giotto object filters list characters. Named list IDs query spatial filters names designate spatial unit use character values either '' vector cell_IDs use. name (optional) character. NULL, new spatial unit name generated results feat_type (optional) May changed future. Determines feature type metadata hierarchical selection information stored. clip boolean. Default = FALSE. Whether final round querying return polygons clipped polygons used select . TRUE, value must provided name param generate new spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatQueryGiottoPolygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatially query polygons within Giotto object — spatQueryGiottoPolygons","text":"giottoPolygon","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatially shift an object — spatShift","title":"Spatially shift an object — spatShift","text":"Shift spatial locations object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatially shift an object — spatShift","text":"","code":"# S4 method for class 'giotto' spatShift(   x,   dx = 0,   dy = 0,   spat_unit = \":all:\",   feat_type = \":all:\",   images = \":all:\" )  # S4 method for class 'SpatExtent' spatShift(x, dx = 0, dy = 0)  # S4 method for class 'spatLocsObj' spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)  # S4 method for class 'data.frame' spatShift(   x,   dx = 0,   dy = 0,   dz = 0,   copy_obj = TRUE,   geom = c(\"sdimx\", \"sdimy\", \"sdimz\"),   ... )  # S4 method for class 'spatialNetworkObj' spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)  # S4 method for class 'giottoPolygon' spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for class 'giottoPoints' spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for class 'giottoLargeImage' spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for class 'giottoImage' spatShift(x, dx = 0, dy = 0, ...)  # S4 method for class 'giottoAffineImage' spatShift(x, dx = 0, dy = 0, ...)  # S4 method for class 'affine2d' spatShift(x, dx = 0, dy = 0, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatially shift an object — spatShift","text":"x object dx numeric. shift x axis dy numeric. shift y axis spat_unit character vector. spatial units affect feat_type character vector. feature types affect images character vector. Images affect. dz numeric. shift z axis copy_obj Default = TRUE ... additional params pass methods geom character. Named vector colnames x, y, (z) coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\")","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatially shift an object — spatShift","text":"object shifted spatial locations","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Spatially shift an object — spatShift","text":"giotto object, \"::\" token can passed spat_unit, feat_type, images arguments affect available items.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Spatially shift an object — spatShift","text":"spatShift(spatialNetworkObj): Shift locations spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatShift.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatially shift an object — spatShift","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  spatShift(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial unit information — spatUnit-generic","title":"Spatial unit information — spatUnit-generic","text":"access set spat_unit slot S4 subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial unit information — spatUnit-generic","text":"","code":"# S4 method for class 'ANY' spatUnit(x)  # S4 method for class 'list' spatUnit(x)  # S4 method for class 'spatData' spatUnit(x)  # S4 method for class 'giottoPolygon' spatUnit(x)  # S4 method for class 'spatData' spatUnit(x) <- value  # S4 method for class 'giottoPolygon' spatUnit(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial unit information — spatUnit-generic","text":"x Giotto S4 class subobject spatial unit value value set spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial unit information — spatUnit-generic","text":"spat_unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Spatial unit information — spatUnit-generic","text":"spatUnit(): Get spatial unit information spatUnit(spatData): Get spatial unit information spatUnit(giottoPolygon): Get spatial unit information spatUnit(spatData) <- value: Set spatial unit information spatUnit(giottoPolygon) <- value: Set giottoPolygon spat_unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatUnit-generic.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial unit information — spatUnit-generic","text":"","code":"g <- GiottoData::loadSubObjectMini(\"featMetaObj\")  spatUnit(g) #> [1] \"aggregate\""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":null,"dir":"Reference","previous_headings":"","what":"Giotto object spatial values — spatValues","title":"Giotto object spatial values — spatValues","text":"Retrieve specific values giotto object specific spat_unit feat_type. Values returned data.table features requested cell_ID column. function may updated future search additional sets information. see currently available slot checks, see details.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Giotto object spatial values — spatValues","text":"","code":"spatValues(   gobject,   spat_unit = NULL,   feat_type = NULL,   feats,   expression_values = NULL,   spat_loc_name = NULL,   spat_enr_name = NULL,   poly_info = NULL,   dim_reduction_to_use = NULL,   dim_reduction_name = NULL,   verbose = NULL,   debug = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Giotto object spatial values — spatValues","text":"gobject giotto object spat_unit character. spatial unit check feat_type character. feature type check feats character vector. One features values find within giotto object expression_values character. (optional) Name expression information use spat_loc_name character. (optional) Name spatial locations information use spat_enr_name character. (optional) Name spatial enrichments use poly_info character. (optional) Name polygons use dim_reduction_to_use character. (optional) type dimension reduction use dim_reduction_name character. (optional) Name dimension reduction use verbose verbosity debug logical. (default = FALSE) See details.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Giotto object spatial values — spatValues","text":"data.table cell_ID column whichever feats requested","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Giotto object spatial values — spatValues","text":"[search] spatValues searches set available information within giotto object matches feats. current search order cell expression cell metadata spatial locations spatial enrichment dimension reduction polygon info specific name one types information provided via param expression_values, spat_enr_name, etc, search performed type data.[debug] function uses Giotto's accessor functions can usually throw errors whenever specific set data features within set exist. function muffles errors, sends error data found getters fail. setting debug = TRUE, can see errors returned failed getter printed messages easier debugging.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatValues.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Giotto object spatial values — spatValues","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  # expression spatValues(g, spat_unit = \"aggregate\", feats = c(\"Mlc1\", \"Gfap\")) #> Getting values from [aggregate][rna][raw] expression #>                                      cell_ID  Mlc1  Gfap #>                                       <char> <num> <num> #>   1: 240649020551054330404932383065726870513     0     2 #>   2: 274176126496863898679934791272921588227     0     0 #>   3: 323754550002953984063006506310071917306     0     2 #>   4:  87260224659312905497866017323180367450     0     1 #>   5:  17817477728742691260808256980746537959     0     0 #>  ---                                                     #> 458:   6380671372744430258754116433861320161     2     2 #> 459:  75286702783716447443887872812098770697     1     2 #> 460:   9677424102111816817518421117250891895     3     1 #> 461:  17685062374745280598492217386845129350     0     3 #> 462:  32422253415776258079819139802733069941     0     4 spatValues(g,     spat_unit = \"aggregate\", feats = c(\"Mlc1\", \"Gfap\"),     expression_values = \"normalized\" ) #> Getting values from [aggregate][rna][normalized] expression #>                                      cell_ID     Mlc1      Gfap #>                                       <char>    <num>     <num> #>   1: 240649020551054330404932383065726870513 0.000000 10.481367 #>   2: 274176126496863898679934791272921588227 0.000000  0.000000 #>   3: 323754550002953984063006506310071917306 0.000000  7.901442 #>   4:  87260224659312905497866017323180367450 0.000000  5.886051 #>   5:  17817477728742691260808256980746537959 0.000000  0.000000 #>  ---                                                            #> 458:   6380671372744430258754116433861320161 6.701726  6.701726 #> 459:  75286702783716447443887872812098770697 5.644422  6.629928 #> 460:   9677424102111816817518421117250891895 7.878817  6.306062 #> 461:  17685062374745280598492217386845129350 0.000000 11.065993 #> 462:  32422253415776258079819139802733069941 0.000000 10.041155  # spatial enrichment spatValues(g, spat_unit = \"aggregate\", feats = c(\"1\", \"3\")) #> Getting values from [aggregate][rna][cluster_metagene] spatial enrichment #>                                      cell_ID         1         3 #>                                       <char>     <num>     <num> #>   1: 240649020551054330404932383065726870513 1.0148370 0.3160792 #>   2: 274176126496863898679934791272921588227 3.2074150 0.6728505 #>   3: 323754550002953984063006506310071917306 3.9536614 0.0000000 #>   4:  87260224659312905497866017323180367450 4.0936217 0.1962017 #>   5:  17817477728742691260808256980746537959 0.9789911 1.9563931 #>  ---                                                             #> 458:   6380671372744430258754116433861320161 2.2465293 0.1905173 #> 459:  75286702783716447443887872812098770697 1.3827322 0.0000000 #> 460:   9677424102111816817518421117250891895 3.6843575 0.0000000 #> 461:  17685062374745280598492217386845129350 1.0010248 0.0000000 #> 462:  32422253415776258079819139802733069941 2.3449006 0.0000000  # polygon info spatValues(g, spat_unit = \"aggregate\", feats = c(\"agg_n\", \"valid\")) #> Getting values from [aggregate] polygon info #>                                      cell_ID agg_n valid #>                                       <char> <int> <int> #>   1: 100210519278873141813371229408401071444     2     1 #>   2: 101161259912191124732236989250178928032     2     1 #>   3: 101488859781016188084173008420811094152     2     1 #>   4: 101523780333017320796881555775415156847     2     1 #>   5: 102184699197574201819246996094734116255     2     1 #>  ---                                                     #> 458:   9677424102111816817518421117250891895     2     1 #> 459:  97068595823890802071024838798130036179     2     1 #> 460:  97411078642927912684859796714759494710     2     1 #> 461:   9816437869021910185567097363182418837     2     1 #> 462:  98561957902191275233320065611022298397     2     1  # cell meta spatValues(g, spat_unit = \"aggregate\", feats = c(\"nr_feats\")) #> Getting values from [aggregate][rna] cell metadata #>                                      cell_ID nr_feats #>                                       <char>    <int> #>   1: 240649020551054330404932383065726870513        5 #>   2: 274176126496863898679934791272921588227       27 #>   3: 323754550002953984063006506310071917306       23 #>   4:  87260224659312905497866017323180367450       37 #>   5:  17817477728742691260808256980746537959       18 #>  ---                                                  #> 458:   6380671372744430258754116433861320161       54 #> 459:  75286702783716447443887872812098770697       45 #> 460:   9677424102111816817518421117250891895       30 #> 461:  17685062374745280598492217386845129350        5 #> 462:  32422253415776258079819139802733069941       12"},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"Convert spatialNetworkObj non-directed igraph representation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"","code":"spat_net_to_igraph(spatialNetworkObj, attr = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"spatialNetworkObj spatialNetworkObj attr columns include edge attributes.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"igraph","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spat_net_to_igraph.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert spatialNetworkObj to igraph — spat_net_to_igraph","text":"","code":"sn <- GiottoData::loadSubObjectMini(\"spatialNetworkObj\") # only name attribute g <- spat_net_to_igraph(sn)  # view other column info besides to and from cols head(sn[], 1) #>                                       from #>                                     <char> #> 1: 100210519278873141813371229408401071444 #>                                         to sdimx_begin sdimy_begin sdimx_end #>                                     <char>       <num>       <num>     <num> #> 1: 216701996099683814512199402223708471323    6637.881   -5140.465   6612.68 #>    sdimy_end distance     weight #>        <num>    <num>      <num> #> 1: -5145.746 25.74799 0.03883798  # include distance and weight col info g <- spat_net_to_igraph(sn, attr = c(\"distance\", \"weight\"))"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"Utility function convert SpatialExperiment object Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"","code":"spatialExperimentToGiotto(   spe,   python_path,   nn_network = NULL,   sp_network = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"spe Input SpatialExperiment object convert Giotto object. python_path Specify path python. nn_network Specify name nearest neighbour network(s) input SpatialExperiment object. Default NULL use existing networks. sp_network Specify name spatial network(s) input SpatialExperiment object. Default NULL use existing networks. can vector multiple network names. verbose boolean value specifying progress messages displayed . Default TRUE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialExperimentToGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Utility function to convert a SpatialExperiment object to a Giotto object — spatialExperimentToGiotto","text":"","code":"if (FALSE) { # \\dontrun{ library(SpatialExperiment) example(read10xVisium, echo = FALSE) spatialExperimentToGiotto(spe) } # }"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 spatialGridObj Class — spatialGridObj-class","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"Framework store spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"spatialGridObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"S4 object defines spatial grid. structure grid stored data.table within gridDT slot defined start stop spatial locations along spatial axes. data.table also includes names cell grid names spatial axis locations make cell. Grids can annotated spatial feature information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"name name spatialGridObj method method used generate spatial grid parameters additional method-specific parameters used spatial grid generation gridDT data.table holding spatial grid information spat_unit spatial unit feat_type feature type provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialGridObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 spatialGridObj Class — spatialGridObj-class","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatialGridObj\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 spatialNetworkObj Class — spatialNetworkObj-class","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"Framework store spatial network information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"generic access operators work data within networkDT slot (filtered).","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":"slots","dir":"Reference","previous_headings":"","what":"Slots","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"name name spatialNetworkObj method method used generate spatial network parameters additional method-specific parameters used spatial network generation outputObj network geometry object networkDT data.table network connections, distances, weightings networkDT_before_filter unfiltered data.table  network connections, distances, weightings cellShapeObj network cell shape information crossSectionObjects crossSectionObjects spat_unit spatial unit tag provenance origin aggregated information (applicable) misc misc","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialNetworkObj-class.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"S4 spatialNetworkObj Class — spatialNetworkObj-class","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatialNetworkObj\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial binary operations — spatial_binary_ops","title":"Spatial binary operations — spatial_binary_ops","text":"Perform geometric binary operations Giotto spatial classes (giottoPolygon, giottoPoints spatLocsObj) underlying representations (terra SpatVector right now.)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial binary operations — spatial_binary_ops","text":"","code":"# S4 methods for giottoPolygon, giottoPoints, spatLocsObj, SpatVector #  # S4 method for class 'spatialClasses,spatialClasses' erase(x, y, ...)  # S4 method for class 'giottoSpatial' snap(x, y = NULL, tolerance, ...)  # S4 method for class 'spatialClasses,spatialClasses' symdif(x, y, ...)  # S4 method for class 'spatialClasses,spatialClasses' union(x, y)  # S4 method for class 'spatialClasses,spatialClasses' intersect(x, y)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial binary operations — spatial_binary_ops","text":"x spatial object 1 y spatial object 2 (can missing NULL) ... additional args pass tolerance numeric. Snapping tolerance (distance geometries)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spatial binary operations — spatial_binary_ops","text":"class x","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatial_binary_ops.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spatial binary operations — spatial_binary_ops","text":"","code":"gpoly1 <- GiottoData::loadSubObjectMini(\"giottoPolygon\") epoly <- as.polygons(ext(c(6600, 6800, -5000, -4800))) gpoly2 <- spatShift(gpoly1, dx = 20)  plot(gpoly1)  plot(union(gpoly1, gpoly2))  plot(erase(gpoly1, epoly))   plot(union(gpoly1, epoly))   plot(symdif(gpoly1, epoly))   plot(intersect(gpoly1, epoly))   if (FALSE) {     # takes a long time so don't run in checks     plot(snap(gpoly1, tolerance = 0.2)) }"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert SpatialData to Giotto — spatialdataToGiotto","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"Converts saved SpatialData object Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"","code":"spatialdataToGiotto(   spatialdata_path = NULL,   n_key_added = NULL,   spatial_n_key_added = NULL,   delaunay_spat_net = TRUE,   spat_unit = NULL,   feat_type = NULL,   python_path = NULL,   env_name = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"spatialdata_path path SpatialData object n_key_added equivalent \"key_added\" argument scanpy.pp.neighbors(). multiple spatial networks anndata object, list key_added terms may provided. converting anndata object giottoToAnnData, .txt file may provided, generated function, .e. {spat_unit}_{feat_type}_nn_network_keys_added.txt \"spatial\". becomes name nearest network gobject. spatial_n_key_added equivalent \"key_added\" argument squidpy.gr.spatial_neighbors. multiple spatial networks anndata object, list key_added terms may provided. converting anndata object giottoToAnnData, .txt file may provided, generated function, .e. {spat_unit}_{feat_type}_spatial_network_keys_added.txt n_key_added. delaunay_spat_net binary parameter spatial network. TRUE, spatial network delaunay network. spat_unit desired spatial unit conversion, default NULL feat_type desired feature type conversion, default NULL python_path path python executable within conda/miniconda environment env_name name environment containing python_path executable","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatialdataToGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Convert SpatialData to Giotto — spatialdataToGiotto","text":"Function beta. Converts structured SpatialData file Giotto object. returned Giotto Object take default insructions exception python path, may customized. See changeGiottoInstructions modify instructions creation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":null,"dir":"Reference","previous_headings":"","what":"Spin an object — spin","title":"Spin an object — spin","text":"Spin (rotate) object spatially (usually limited xy rotations)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spin an object — spin","text":"","code":"# S4 method for class 'giotto' spin(x, angle, x0 = NULL, y0 = NULL, spat_unit = \":all:\", feat_type = \":all:\")  # S4 method for class 'giottoPolygon' spin(x, angle, x0 = NULL, y0 = NULL)  # S4 method for class 'giottoPoints' spin(x, angle, x0 = NULL, y0 = NULL)  # S4 method for class 'spatLocsObj' spin(   x,   angle = NULL,   x0 = NULL,   y0 = NULL,   z0 = NULL,   xy_angle = NULL,   zy_angle = NULL,   xz_angle = NULL )  # S4 method for class 'data.frame' spin(   x,   angle = NULL,   x0 = NULL,   y0 = NULL,   z0 = NULL,   xy_angle = NULL,   zy_angle = NULL,   xz_angle = NULL,   geom = c(\"sdimx\", \"sdimy\", \"sdimz\") )  # S4 method for class 'giottoLargeImage' spin(x, angle = NULL, x0 = NULL, y0 = NULL, ...)  # S4 method for class 'giottoAffineImage' spin(x, angle = NULL, x0 = NULL, y0 = NULL, ...)  # S4 method for class 'affine2d' spin(x, angle = NULL, x0 = NULL, y0 = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spin an object — spin","text":"x object angle numeric. Angle rotation degrees x0 numeric. x-coordinate center rotation. Defaults center x val given. y0 numeric. y-coordinate center rotation. Defaults center y val given. spat_unit character vector. spatial units affect feat_type character vector. feature types affect (giottoPoints ). z0 spatLocsObj specific. Numeric. z-coordinate center rotation. Depending z data present, defaults either 0 center z val given. xy_angle spatLocsObj specific. xy plane rotation degrees. Overrides angle param zy_angle spatLocsObj specific. zy plane rotation xz_angle spatLocsObj specific. xz plane rotation geom character. Named vector colnames x, y, (z) coordinate columns. Default c(\"sdimx\", \"sdimy\", \"sdimz\") ... additional params pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Spin an object — spin","text":"spun object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Spin an object — spin","text":"","code":"g <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  spin(g) #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Split a Giotto Object — splitGiotto","title":"Split a Giotto Object — splitGiotto","text":"Split Giotto object based cell metadata column list multiple Giotto objects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Split a Giotto Object — splitGiotto","text":"","code":"splitGiotto(gobject, by, spat_unit = NULL, feat_type = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Split a Giotto Object — splitGiotto","text":"gobject giotto object split cell metadata column split object spat_unit character. Controls spatial unit pull splitting information . However, spatial units always affected split. feat_type character. Split affects feature type(s). Default \"rna\"","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Split a Giotto Object — splitGiotto","text":"list giotto objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/splitGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Split a Giotto Object — splitGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" splitGiotto(g, \"leiden_clus\") #> $leiden_clus_2 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 122 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_5 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 84 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_1 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 162 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_3 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 108 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_6 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 45 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_7 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 10 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>  #> $leiden_clus_4 #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 93 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"standardise_flex — standardise_flex","title":"standardise_flex — standardise_flex","text":"standardizes matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"standardise_flex — standardise_flex","text":"","code":"standardise_flex(x, center = TRUE, scale = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"standardise_flex — standardise_flex","text":"x matrix center center data scale scale data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"standardise_flex — standardise_flex","text":"standardized matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/standardise_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"standardise_flex — standardise_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  standardise_flex(m)"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":null,"dir":"Reference","previous_headings":"","what":"stitchFieldCoordinates — stitchFieldCoordinates","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"Helper function stitch field coordinates together form one complete picture","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"","code":"stitchFieldCoordinates(   location_file,   offset_file,   cumulate_offset_x = FALSE,   cumulate_offset_y = FALSE,   field_col = \"Field of View\",   X_coord_col = \"X\",   Y_coord_col = \"Y\",   reverse_final_x = FALSE,   reverse_final_y = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"location_file location dataframe X Y coordinates offset_file dataframe describes offset field (see details) cumulate_offset_x (boolean) x-axis offset values need cumulated? cumulate_offset_y (boolean) y-axis offset values need cumulated? field_col column indicates field within location_file X_coord_col column indicates x coordinates Y_coord_col column indicates x coordinates reverse_final_x (boolean) final x coordinates need reversed? reverse_final_y (boolean) final y coordinates need reversed?","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"Updated location dataframe new X ['X_final'] Y ['Y_final'] coordinates","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchFieldCoordinates.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"stitchFieldCoordinates — stitchFieldCoordinates","text":"Stitching fields: cell locations: least 3 columns: field, X, Y create offset file: offset file 3 columns: field, x_offset, y_offset create new cell location file stitching original cell locations stitchFieldCoordinates provide new cell location file createGiottoObject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"Function stitch together multiple field view (FOV) images single final image. Images loaded Giotto giottoLargeImage stitched based set FOV positions single final giottoLargeImage.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"","code":"stitchGiottoLargeImage(   largeImage_list = NULL,   gobject_list = NULL,   largeImage_nameList = NULL,   FOV_positions = NULL,   FOV_xcol = NULL,   FOV_ycol = NULL,   FOV_inverty = FALSE,   method = c(\"mosaic\", \"merge\"),   round_positions = FALSE,   filename = NULL,   dataType = NULL,   fileType = NULL,   dryRun = TRUE,   overwrite = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"largeImage_list list giottoLargeImage objects gobject_list list gobjects containing giottoLargeImages largeImage_nameList list names giottoLargeImages within gobjects FOV_positions dataframe FOV positions. Values () directly added current image mapping FOV_xcol column name FOV position x values FOV_ycol column name FOV position y values FOV_inverty make FOV y position values negative method method stitching images (mosaic: average overlapping area values, merge:values get priority order images given) round_positions boolean. Round image positions. May necessary run. filename file name write stitched image . Defaults \"save_dir/stitch.tif\" save_dir param found first gobject's Giotto instructions dataType (optional) values dataType \"INT1U\", \"INT2U\", \"INT2S\", \"INT4U\", \"INT4S\", \"FLT4S\", \"FLT8S\". first three letters indicate whether dataType integer (whole numbers) real number (decimal numbers), fourth character indicates number bytes used (allowing large numbers /precision), \"S\" \"U\" indicate whether values signed (negative positive) unsigned (positive values ). fileType (optional) image format (e.g. .tif) given, defaults format given filename dryRun boolean. Plot placeholder bounding rectangles FOV images stitched without actually proceeding full image stitching saving process. overwrite boolean. Overwrite filename save image already exists. Defaults TRUE verbose boolean. verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"largeGiottoImage object pointer stitched image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"function time consuming. Setting save location filename parameter also highly recommended file size likely large. function creates single stitched image multiple FOV tiles saves image disk works. finished, pointer new image loaded giottoLargeImage object. Note: Dry runs default dryRun param must set FALSE proceed final stitching operation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"dry-runs-are-default","dir":"Reference","previous_headings":"","what":"Dry runs are default","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"ensure disk space time wasted, function defaults previewing stitching operation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"fov-positions","dir":"Reference","previous_headings":"","what":"FOV positions","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"final image stitched together multiple FOV tiles. FOV_positions parameter accepts table x y values FOV tile placed performing stitch. columns x y values determined FOV_xcol FOV_ycol params respectively. FOV tiles full resolution starting position either lower left upper left image touch origin depending value FOV_inverty param. FOV image translated according x y shift values.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"fov-invert-y","dir":"Reference","previous_headings":"","what":"FOV invert y","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"Many imaging systems may treat origin according image convention (0,0) upper left image. odds coordinate convention Giotto uses internally coordinate (0,0) lower left. FOV_inverty defaults FALSE, set TRUE, FOV tile images start upper left touching (0,0) y values given FOV_positions FOV_ycol treated negative y shift values.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"datatype","dir":"Reference","previous_headings":"","what":"dataType","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"multiple datatypes defining range intensity values images can saved . Setting value dataType para optional Giotto attempts determine compatible data type save image automatically.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Stitch multiple giottoLargeImage objects into a single giottoLargeImage object — stitchGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- getGiottoImage(g, image_type = \"largeImage\")  stitchGiottoLargeImage(largeImage_list = list(g_image))  #> NULL"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":null,"dir":"Reference","previous_headings":"","what":"stitchTileCoordinates — stitchTileCoordinates","title":"stitchTileCoordinates — stitchTileCoordinates","text":"Helper function stitch tile coordinates together form one complete picture","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"stitchTileCoordinates — stitchTileCoordinates","text":"","code":"stitchTileCoordinates(location_file, Xtilespan, Ytilespan)"},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"stitchTileCoordinates — stitchTileCoordinates","text":"location_file location dataframe X Y coordinates Xtilespan numerical value specifying width tile Ytilespan numerical value specifying height tile","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"stitchTileCoordinates — stitchTileCoordinates","text":"data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/stitchTileCoordinates.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"stitchTileCoordinates — stitchTileCoordinates","text":"","code":"location_file <- data.table::data.table(     field = rep(c(1, 2), 5),     X.X = rnorm(10), Y.Y = rnorm(10), XtileIndex = seq_len(10),     YtileIndex = seq_len(10) )  stitchTileCoordinates(location_file, Xtilespan = 0.5, Ytilespan = 0.5) #>     field         X.X        Y.Y XtileIndex YtileIndex      Xcoord      Ycoord #>     <num>       <num>      <num>      <int>      <int>       <num>       <num> #>  1:     1  0.01308331  0.7811606          1          1  0.01308331  0.78116058 #>  2:     2  0.64365001  0.3784188          2          2  1.14365001  0.87841880 #>  3:     1 -2.48768926 -1.0124020          3          3 -1.48768926 -0.01240202 #>  4:     2  0.93101913 -2.0656557          4          4  2.43101913 -0.56565571 #>  5:     1 -1.89955741  1.0928168          5          5  0.10044259  3.09281676 #>  6:     2  1.21015863 -1.7202851          6          6  3.71015863  0.77971492 #>  7:     1 -1.46457418 -0.3058085          7          7  1.53542582  2.69419149 #>  8:     2  0.75557357 -0.3731366          8          8  4.25557357  3.12686344 #>  9:     1  0.42274803  0.4004511          9          9  4.42274803  4.40045106 #> 10:     2 -0.43002963  1.1347597         10         10  4.06997037  5.63475968"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":null,"dir":"Reference","previous_headings":"","what":"subsetGiotto — subsetGiotto","title":"subsetGiotto — subsetGiotto","text":"Subsets Giotto object including previous analyses. subsetting subcellular information without editing aggregate information, use subsetGiottoLocsSubcellular","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"subsetGiotto — subsetGiotto","text":"","code":"subsetGiotto(   gobject,   spat_unit = \":all:\",   feat_type = \"rna\",   cell_ids = NULL,   feat_ids = NULL,   poly_info = spat_unit,   all_spat_units = NULL,   all_feat_types = NULL,   spat_unit_fsub = \":all:\",   feat_type_ssub = \":all:\",   verbose = FALSE,   toplevel_params = 2 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"subsetGiotto — subsetGiotto","text":"gobject giotto object spat_unit, feat_type character vector. (default = '::') One spatial units feature types subset. Accepts '::' token subset across available. cell_ids character. cell IDs keep feat_ids character. feature IDs keep poly_info character. polygon info(s) subset present. (defaults spat_unit) all_spat_units deprecated. use spat_unit_fsub = '::' all_feat_types deprecated. use feat_type_ssub = '::' spat_unit_fsub character vector. (default = '::') limit feat_id subsets spat_units feat_type_ssub character vector. (default = '::') limit cell_id subsets feat_types verbose verbose toplevel_params parameters extract","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"subsetGiotto — subsetGiotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"subsetGiotto — subsetGiotto","text":"Subsets Giotto object specific spatial unit feature type","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"subsetGiotto — subsetGiotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  subsetGiotto(g, cell_ids = c(\"AACTCGATGGCGCAGT-1\", \"GGCTGGCTAGCTTAAA-1\")) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 2 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset by spatial locations — subsetGiottoLocs","title":"Subset by spatial locations — subsetGiottoLocs","text":"Subsets Giotto object spatially defining set cropping bounds. information subset preferred spatial locations. spat_loc_name given, first available set spatial locations spat_unit picked. spatial locations available, polygon information subset. Spatial IDs surviving crop applied rest Giotto object using subsetGiotto.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset by spatial locations — subsetGiottoLocs","text":"","code":"subsetGiottoLocs(   gobject,   spat_unit = NULL,   feat_type = NULL,   feat_type_ssub = \":all:\",   spat_loc_name = NULL,   x_max = NULL,   x_min = NULL,   y_max = NULL,   y_min = NULL,   z_max = NULL,   z_min = NULL,   poly_info = NULL,   return_gobject = TRUE,   verbose = FALSE,   toplevel_params = 5 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset by spatial locations — subsetGiottoLocs","text":"gobject giotto object spat_unit spatial unit subset feat_type (optional) feat type use return_gobject = TRUE combined data.table output desired. feat_type_ssub feat types across apply spatial subset spat_loc_name name spatial locations use within spat_unit x_max, x_min, y_max, y_min, z_max, z_min minimum maximum x, y, z coordinates subset poly_info character. polygon information subset (considered separately spat_units subset) return_gobject return Giotto object verbose verbose toplevel_params parameters extract","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset by spatial locations — subsetGiottoLocs","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Subset by spatial locations — subsetGiottoLocs","text":"return_gobject = FALSE, filtered combined metadata data.table returned","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocs.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset by spatial locations — subsetGiottoLocs","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  subsetGiottoLocs(g, x_max = 4000, y_max = -1000) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 175 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsMulti.html","id":null,"dir":"Reference","previous_headings":"","what":"deprecated — subsetGiottoLocsMulti","title":"deprecated — subsetGiottoLocsMulti","text":"deprecated","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsMulti.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"deprecated — subsetGiottoLocsMulti","text":"","code":"subsetGiottoLocsMulti(   gobject,   spat_unit = \":all:\",   feat_type = NULL,   feat_type_ssub = \":all:\",   spat_loc_name = NULL,   x_max = NULL,   x_min = NULL,   y_max = NULL,   y_min = NULL,   z_max = NULL,   z_min = NULL,   poly_info = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsMulti.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"deprecated — subsetGiottoLocsMulti","text":"gobject giotto object spat_unit spatial unit subset feat_type (optional) feat type use return_gobject = TRUE combined data.table output desired. feat_type_ssub feat types across apply spatial subset spat_loc_name name spatial locations use within spat_unit x_max, x_min, y_max, y_min, z_max, z_min minimum maximum x, y, z coordinates subset poly_info named list character vectors. names correspond spat_unit character vectors polygons associated spat units return_gobject return Giotto object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsMulti.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"deprecated — subsetGiottoLocsMulti","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"Subsets Giotto object based spatial coordinates. subset function intended poly_info feat_types matching aggregated information.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"","code":"subsetGiottoLocsSubcellular(   gobject,   poly_info = NULL,   feat_type = NULL,   x_min = NULL,   x_max = NULL,   y_min = NULL,   y_max = NULL,   z_max = NULL,   z_min = NULL,   verbose = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"gobject giotto object poly_info character. polygons spatially subset feat_type character. feature info spatially subset x_max, x_min, y_max, y_min, z_max, z_min minimum maximum x, y, z coordinates subset verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subsetGiottoLocsSubcellular.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Subset raw subcellular information by location — subsetGiottoLocsSubcellular","text":"separate subsetGiottoLocs spat_units attached aggregated information removed using cell_ids-based approach order ensure paired information removed together. Polygons points information without associated aggregated values issue can directly spatially subset.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset part of an object with [ — subset_bracket","title":"Subset part of an object with [ — subset_bracket","text":"Extract values Giotto classes. Providing empty brackets : x[] usually extract main contained data representation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset part of an object with [ — subset_bracket","text":"","code":"# S4 method for class 'gdtData,gIndex,gIndex,missing' x[i, j]  # S4 method for class 'gdtData,logical,missing,missing' x[i, j]  # S4 method for class 'gdtData,character,missing,missing' x[i, j]  # S4 method for class 'gdtData,missing,numeric,missing' x[i, j]  # S4 method for class 'gdtData,missing,logical,missing' x[i, j]  # S4 method for class 'coordDataDT,ANY,ANY,missing' x[i, j]  # S4 method for class 'coordDataDT,missing,ANY,missing' x[i, j]  # S4 method for class 'coordDataDT,missing,character,missing' x[i, j]  # S4 method for class 'coordDataDT,ANY,missing,missing' x[i, j]  # S4 method for class 'coordDataDT,missing,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,gIndex,missing,missing' x[i, j]  # S4 method for class 'metaData,missing,ANY,missing' x[i, j]  # S4 method for class 'metaData,missing,character,missing' x[i, j]  # S4 method for class 'metaData,ANY,missing,missing' x[i, j]  # S4 method for class 'metaData,missing,missing,missing' x[i, j]  # S4 method for class 'dimObj,ANY,ANY,missing' x[i, j]  # S4 method for class 'dimObj,missing,missing,missing' x[i, j]  # S4 method for class 'exprData,missing,ANY,missing' x[i, j]  # S4 method for class 'exprData,ANY,missing,missing' x[i, j]  # S4 method for class 'exprData,ANY,ANY,missing' x[i, j]  # S4 method for class 'exprData,missing,missing,missing' x[i, j]  # S4 method for class 'spatNetData,missing,missing,missing' x[i, j]  # S4 method for class 'nnData,missing,missing,missing' x[i, j]  # S4 method for class 'enrData,missing,missing,missing' x[i, j]  # S4 method for class 'enrData,ANY,missing,missing' x[i, j]  # S4 method for class 'enrData,missing,ANY,missing' x[i, j]  # S4 method for class 'enrData,missing,character,missing' x[i, j]  # S4 method for class 'spatGridData,missing,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,missing,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,gIndex,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,character,missing,missing' x[i, j]  # S4 method for class 'giottoPoints,missing,gIndex,missing' x[i, j]  # S4 method for class 'giottoPolygon,missing,missing,missing' x[i, j]  # S4 method for class 'giottoPolygon,gIndex,missing,missing' x[i, j]  # S4 method for class 'giottoPolygon,character,missing,missing' x[i, j]  # S4 method for class 'giottoPolygon,missing,gIndex,missing' x[i, j]  # S4 method for class 'terraVectData,gIndex,gIndex,missing' x[i, j]  # S4 method for class 'giottoLargeImage,missing,missing,missing' x[i, j]  # S4 method for class 'giottoImage,missing,missing,missing' x[i, j]  # S4 method for class 'affine2d,missing,missing,missing' x[i, j]"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset part of an object with [ — subset_bracket","text":"x Giotto S4 object subset information , j indices specifying elements extract. Indices numeric character vectors, empty","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset part of an object with [ — subset_bracket","text":"x unless brackets empty case, main internal representation returned.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"-methods","dir":"Reference","previous_headings":"","what":"`[` methods","title":"Subset part of an object with [ — subset_bracket","text":"Return coordinates slot data.table giotto S4 Select rows () cols (j) giotto S4 metaDT slot Return metaDT slot data.table giotto S4 Return coordinates slot matrix giotto S4 dimObj Select rows () cols (j) giotto S4 exprMat slot Return exprMat slot Matrix object giotto S4 Return spatNetData slot network data.table object giotto S4 Return nnData slot igraph object giotto S4 Return enrData slot enrichment data.table object giotto S4 Return spatGridData slot data.table object giotto S4 Return giottoPoints spatVector slot Return giottoPolygon spatVector slot","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_bracket.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset part of an object with [ — subset_bracket","text":"","code":"gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\")  # extract contained `SpatVector` gpoints[] #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3  # subset by feature gpoints[c(\"Mlc1\", \"Gfap\")] #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 5464, 3  (geometries, attributes) #>  extent      : 6400.037, 6899.441, -5149.827, -4700.029  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                   Gfap        0            3 #>                   Gfap        0            4 #>   # subset by feature and colname gpoints[\"Mlc1\", c(\"feat_ID\", \"feat_ID_uniq\")] #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 488, 2  (geometries, attributes) #>  extent      : 6400.037, 6899.308, -5149.827, -4703.377  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID feat_ID_uniq #>  type        :   <chr>        <int> #>  values      :    Mlc1            1 #>                   Mlc1           55 #>                   Mlc1          127 #>   # subset by index gpoints[seq(20)] #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 20, 3  (geometries, attributes) #>  extent      : 6400.037, 6400.745, -5096.167, -4770.126  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset part of an object with $ — subset_dollar","title":"Subset part of an object with $ — subset_dollar","text":"Subset values Giotto Class using $ operator.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset part of an object with $ — subset_dollar","text":"","code":"# S4 method for class 'giotto' x$name  # S4 method for class 'coordDataDT' x$name  # S4 method for class 'spatEnrObj' x$name  # S4 method for class 'dimObj' x$name  # S4 method for class 'metaData' x$name  # S4 method for class 'terraVectData' x$name  # S4 method for class 'affine2d' x$name"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset part of an object with $ — subset_dollar","text":"x Giotto S4 object extract columns name literal character string (possibly backtick quoted). normally matched colnames.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset part of an object with $ — subset_dollar","text":"vector values requested column","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Subset part of an object with $ — subset_dollar","text":"$: Subset giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"-methods","dir":"Reference","previous_headings":"","what":"`$` methods","title":"Subset part of an object with $ — subset_dollar","text":"Select colname giotto S4 data.table coordinates slot. Select colname giotto S4 spatEnrObj Select entries misc slot giotto S4 dimObj. Select colname giotto S4 data.table metaDT slot. Select colname giotto S4 spatVector slot. Select piecewise transform values affine2d","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_dollar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset part of an object with $ — subset_dollar","text":"","code":"enr <- GiottoData::loadSubObjectMini(\"spatEnrObj\")  enr$cell_ID #>   [1] \"240649020551054330404932383065726870513\" #>   [2] \"274176126496863898679934791272921588227\" #>   [3] \"323754550002953984063006506310071917306\" #>   [4] \"87260224659312905497866017323180367450\"  #>   [5] \"17817477728742691260808256980746537959\"  #>   [6] \"182132384503107798660396708280285136358\" #>   [7] \"316289522368890354495930310222776908199\" #>   [8] \"318995879282318989627235045690211636294\" #>   [9] \"104570855383158731814075192607294301741\" #>  [10] \"115370283894795045523368609208878185314\" #>  [11] \"123860671559578247432410194986927758864\" #>  [12] \"126981423897188762239468136959275655616\" #>  [13] \"134398773695365619188678200952912609063\" #>  [14] \"15242486364109501724975900940581726845\"  #>  [15] \"152684748256642370929802439227360458069\" #>  [16] \"153751792203577791006158581642177087065\" #>  [17] \"16326589507615554063401897357427439030\"  #>  [18] \"165786478473465185470745991122188406667\" #>  [19] \"167710327060928309829388429279250508392\" #>  [20] \"172181421897607556322673704318102678295\" #>  [21] \"176844289786228093052039491926955764947\" #>  [22] \"182235958169292445695483205478317795477\" #>  [23] \"183227745956657225549068107012033843521\" #>  [24] \"186988931894710833920932112634285943415\" #>  [25] \"190687643154627893064711601675234362640\" #>  [26] \"20548793658722995878220914240286086757\"  #>  [27] \"206702762285684421190019779213421380201\" #>  [28] \"216701996099683814512199402223708471323\" #>  [29] \"21934936165997373583174173761929761438\"  #>  [30] \"230344318208995342827768566280706457626\" #>  [31] \"251905496166492083168644493421091558216\" #>  [32] \"262996653580953175020435707363716649390\" #>  [33] \"27666206735695437393204421885258583706\"  #>  [34] \"286906689872367261752702769926754066848\" #>  [35] \"288822108801800165318171357739905375883\" #>  [36] \"301054712356664458042996323827909441002\" #>  [37] \"304842190541754537761816256358565562302\" #>  [38] \"318439340668767417720582355350205310941\" #>  [39] \"335295524680090725199231409883288198017\" #>  [40] \"35118346554513854436644695033199584696\"  #>  [41] \"41054036480225512911591384807281320971\"  #>  [42] \"43731708947199618294982749003938483862\"  #>  [43] \"48024672048124996997588408479044670509\"  #>  [44] \"51348907619842676963078202479438175138\"  #>  [45] \"67532821514617092397935003422482443295\"  #>  [46] \"77151711298730578178892667721058396928\"  #>  [47] \"77782228870577724567477221255169934206\"  #>  [48] \"8777587181320516093160667806451882030\"   #>  [49] \"95838678880751873613229512065975406368\"  #>  [50] \"95947958963963707263153541936375959179\"  #>  [51] \"9668748337336721830701975018211142813\"   #>  [52] \"97411078642927912684859796714759494710\"  #>  [53] \"101161259912191124732236989250178928032\" #>  [54] \"110615983935499449765434338770904504245\" #>  [55] \"110858042010405247711695373195937122852\" #>  [56] \"110900719814678261966908552089216814729\" #>  [57] \"12925323527075390484710711277617599454\"  #>  [58] \"137348923180371322628727011975895485209\" #>  [59] \"138859376429590720661963324654447571708\" #>  [60] \"140543565961583233746802451796981444137\" #>  [61] \"143386081176260440019925196855300710659\" #>  [62] \"143408196806895889016075556052288734233\" #>  [63] \"145421744145915784890159499930205641713\" #>  [64] \"148336156782096202859532636956126767457\" #>  [65] \"150082699777048696177232440639953146354\" #>  [66] \"15247055772869406897093633424720409278\"  #>  [67] \"15834776842182822801451197571763335013\"  #>  [68] \"170833460535439412738579124041592991444\" #>  [69] \"173780780834031059819946658163431921979\" #>  [70] \"174306823762889142173283452439684229948\" #>  [71] \"175540604452034099044348476236813150837\" #>  [72] \"177757177666889772027017950398587309639\" #>  [73] \"17868848607867654301368031294266874310\"  #>  [74] \"180947508370750255585892730777436680945\" #>  [75] \"187952627468949069447188707715308813657\" #>  [76] \"1900302715660571356090444774019116326\"   #>  [77] \"203192161403397797138670022274582721699\" #>  [78] \"206016050634629330546630679047044021073\" #>  [79] \"214394514156259228118188949454902817376\" #>  [80] \"221669638772738575000116137509912039310\" #>  [81] \"224458376429228506642398057779371677646\" #>  [82] \"226912346807310637711937183879196326571\" #>  [83] \"227232155811404089141823608874580791245\" #>  [84] \"236677629222667262221261861475728542818\" #>  [85] \"244015124549889909957742476033146111487\" #>  [86] \"244247765904337326625465691380839405459\" #>  [87] \"244448312826260498647079278647004353269\" #>  [88] \"244840145612854293464477850603474951260\" #>  [89] \"262797098003740683881650619022037793005\" #>  [90] \"265185306239991354232232246957204545228\" #>  [91] \"266413162898429280572455841453688616870\" #>  [92] \"275784684664527332374777211328350223506\" #>  [93] \"277057315125198906319398446608128392905\" #>  [94] \"291975341311453330406711526698967834209\" #>  [95] \"295193149306421749943849825086053455411\" #>  [96] \"30222355550742125173065032035537805062\"  #>  [97] \"304560432600831995659079356647103974886\" #>  [98] \"30571638947438619177947320407779261750\"  #>  [99] \"306415949245581212081161219410047325001\" #> [100] \"311565496674213535805029947713320284697\" #> [101] \"314397389362641167108869069386457433770\" #> [102] \"3188909098022617910378369321966273882\"   #> [103] \"322879686187630160969459793861944841206\" #> [104] \"330850389163886577071114668277958486114\" #> [105] \"334199301045926627171760429217123408914\" #> [106] \"339814056401091912617621500767389941735\" #> [107] \"36648998424868029072860674954666559763\"  #> [108] \"39033692777509843205319060807429911979\"  #> [109] \"3942785923272820952395109293003259310\"   #> [110] \"47275912178029130797780898068213599096\"  #> [111] \"56815638009315000170441964570512336625\"  #> [112] \"57203625626451579261315887898923502046\"  #> [113] \"62669443199671326763841071380380779477\"  #> [114] \"64228015236811922665804882776457047292\"  #> [115] \"68418314542386876178693610244900595267\"  #> [116] \"70219882915166469874938407731799217344\"  #> [117] \"75660428514717127988983246148828583482\"  #> [118] \"75682347267697870039469591993208007445\"  #> [119] \"87903363874776475366779322866396664731\"  #> [120] \"88743795534206169429467675642537392511\"  #> [121] \"9538866320245722231901445225545432644\"   #> [122] \"96091484747656303270745913028146994621\"  #> [123] \"116860147088450350976374609398998546737\" #> [124] \"133061403473432310288273623600023558748\" #> [125] \"137154375879163008723188861204335796821\" #> [126] \"185903314401459366597627436588666236388\" #> [127] \"217996462208701069168232210617040322639\" #> [128] \"226667648171626631993624597360362535576\" #> [129] \"254829253202043893331055483138743800247\" #> [130] \"271967915636064836314881508293335292245\" #> [131] \"273673567134859598195435250950149370161\" #> [132] \"305306955532868686456926844192964831687\" #> [133] \"307030440204593378842812081935039092344\" #> [134] \"311587331826654155209560142756469108973\" #> [135] \"44197902970141946871502798467323259089\"  #> [136] \"44721220002773982161418195292536576043\"  #> [137] \"65855854848879329159292019718060662708\"  #> [138] \"76322781861215450124167009829890606622\"  #> [139] \"11065258297873257226330942251431244138\"  #> [140] \"118071411587380747913796380721014165557\" #> [141] \"123540785709544435621019288242840920053\" #> [142] \"130428604684362047522418850101908720496\" #> [143] \"134509424346276649608483685115101376571\" #> [144] \"136341171141277731884608634279863298546\" #> [145] \"137356600627014280700323828086313714576\" #> [146] \"151798130004305208790801168757831384604\" #> [147] \"162684318525520950869468479178769741207\" #> [148] \"164424478098970510930576318421517316799\" #> [149] \"166456955228473064319115194076209471689\" #> [150] \"168376325588102040437463621554621047372\" #> [151] \"179297712006471333306826676970515917851\" #> [152] \"19311588976622944909682910864587104989\"  #> [153] \"204611834270911643022584999768859598082\" #> [154] \"212501669348639182111017279862555064555\" #> [155] \"222047855782557501653245982274520432658\" #> [156] \"231212643322278795528005770495251497705\" #> [157] \"233229703476821612486041386363745481186\" #> [158] \"23470744401352443589618734383441183930\"  #> [159] \"234988593327199604253479621078255555503\" #> [160] 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\"264234489423886906860498828392801290668\" #> [457] \"328891726607418454659643302361160567789\" #> [458] \"6380671372744430258754116433861320161\"   #> [459] \"75286702783716447443887872812098770697\"  #> [460] \"9677424102111816817518421117250891895\"   #> [461] \"17685062374745280598492217386845129350\"  #> [462] \"32422253415776258079819139802733069941\""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset a giotto object — subset_giotto","title":"Subset a giotto object — subset_giotto","text":"Subset giotto object [ subset() generic. implementation different subsetGiotto() spatial units always affected. feature type subset can specified.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset a giotto object — subset_giotto","text":"","code":"# S4 method for class 'giotto,gIndex,missing,missing' x[i, j, ..., drop = TRUE]  # S4 method for class 'giotto,missing,gIndex,missing' x[i, j, ..., drop = TRUE]  # S4 method for class 'giotto,gIndex,gIndex,missing' x[i, j, ..., drop = TRUE]  # S4 method for class 'giotto,missing,missing,missing' x[i, j, ..., drop = TRUE]  # S4 method for class 'giotto' subset(   x,   subset,   feat_ids = NULL,   cell_ids = NULL,   spat_unit = NULL,   feat_type = NULL,   negate = FALSE,   quote = TRUE,   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset a giotto object — subset_giotto","text":"x giotto object ... additional params pass spatValues used subset param drop used subset Logical expression evaluated expression values feat_ids, character vector. Feature IDs subset object . cell_ids, j character vector. Cell/spatial IDs subset object . spat_unit character. Controls spatial unit pull subsetting information using cell_ids/j subset params. However, spatial units always affected subset. feat_type character. Subset affects feature type(s). Default \"rna\" negate logical. TRUE IDs subset selected quote logical. TRUE, subset param quoted substitute(). Set FALSE calling function, although may recommended since NSE output can unexpected used interactively.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset a giotto object — subset_giotto","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Subset a giotto object — subset_giotto","text":"x[: Subset giotto objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset a giotto object — subset_giotto","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  # `[` examples g[1:5] #> Warning: [cell] subset poly: no overlap between poly_IDs and cell_ids to keep #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 5, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used g[, 2:10] #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 9 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used g[1:5, 2:10] #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 5, 9 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used g[c(TRUE, FALSE), ] #> Warning: [cell] subset poly: no overlap between poly_IDs and cell_ids to keep #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 317, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used  # subset() examples subset(g, nr_feats > 300) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 218 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used subset(g, nr_feats > 300,     cell_ids = c(\"GAATCGCCGGACACGG-1\", \"GAGGGCATCGCGTATC-1\") ) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 1 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used subset(g, Gfap + Gna12 > 10) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 97 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset giotto subobjects — subset_giotto_subobjects","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"Subset giotto object [[ disassemble list Giotto S4 subobjects. drop FALSE, selected subobjects reassembled new giotto object. Note indexing within [[ filters subobjects attributes. may remove unexpected information. specifically splitting giotto object spatial unit /feature type keeping expected information, use sliceGiotto()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"","code":"# S4 method for class 'giotto,missing,missing' x[[spat_unit = NULL, feat_type = NULL, drop = TRUE, ...]]  # S4 method for class 'giotto,character,missing' x[[i, spat_unit = NULL, feat_type = NULL, drop = TRUE, ...]]  # S4 method for class 'giotto,missing,character' x[[j, spat_unit = NULL, feat_type = NULL, drop = TRUE, ...]]  # S4 method for class 'giotto,character,character' x[[i, j, spat_unit = NULL, feat_type = NULL, drop = TRUE, ...]]"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"x giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type use (e.g. \"rna\", \"protein\") drop logical. Default = TRUE ... additional arguments character. Indicates slot name j character. Indicates subobject name","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"giotto subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_giotto_subobjects.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Subset giotto subobjects — subset_giotto_subobjects","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" force(g) #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : z0 z1 aggregate  #> features      : rna  #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #> attached images ------------------ #> images      : 4 items... #>  #>  #> Use objHistory() to see steps and params used  # return as lists of subobjects with drop = TRUE (default) g[[, \"raw\"]] #> [[1]] #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"z0\" #> provenance: z0  #> dimensions: 498 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6405.067 -4780.499  40951783403982682273285375368232495429 #> 2: 6426.020 -4972.519 240649020551054330404932383065726870513 #> 3: 6428.456 -4799.158 274176126496863898679934791272921588227 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6402.438 -5146.726 #> [2,] 6899.203 -4700.157 #>  #>  #> [[2]] #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"z1\" #> provenance: z1  #> dimensions: 504 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6404.014 -4779.625  40951783403982682273285375368232495429 #> 2: 6408.296 -4970.794  17685062374745280598492217386845129350 #> 3: 6401.148 -4991.061 223553142498364321238189328942498473503 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.148 -5147.193 #> [2,] 6899.323 -4700.410 #>  #>  #> [[3]] #> An object of class spatLocsObj : \"raw\" #> spat_unit : \"aggregate\" #> provenance: z0 z1  #> dimensions: 462 3  #> preview   : #>       sdimx     sdimy                                 cell_ID #>       <num>     <num>                                  <char> #> 1: 6637.881 -5140.465 100210519278873141813371229408401071444 #> 2: 6471.978 -4883.541 101161259912191124732236989250178928032 #> 3: 6801.610 -4968.685 101488859781016188084173008420811094152 #>  #> ranges: #>         sdimx     sdimy #> [1,] 6401.412 -5146.747 #> [2,] 6899.108 -4700.326 #>  #>  #> [[4]] #> An object of class exprObj : \"raw\" #> spat_unit : \"z0\" #> feat_type : \"rna\" #> provenance: z0  #>  #> contains: #> 337 x 498 sparse Matrix of class \"dgCMatrix\" #>                                          #> Mlc1   . . . . . . . .  . . . . . ...... #> Gprc5b . . 1 . 1 . . .  1 . 2 . . ...... #> Gfap   . . . 1 1 . . . 27 . . . . ...... #>  #>  ........suppressing 485 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  40951783403982682273285375368232495429 #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306  #>  #> [[5]] #> An object of class exprObj : \"raw\" #> spat_unit : \"z1\" #> feat_type : \"rna\" #> provenance: z1  #>  #> contains: #> 337 x 504 sparse Matrix of class \"dgCMatrix\" #>                                          #> Mlc1   . . . . . . . . . . .  1 . ...... #> Gprc5b . . . . . . . 2 . . .  1 . ...... #> Gfap   . 3 . 2 . 1 4 . . . . 18 . ...... #>  #>  ........suppressing 491 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  40951783403982682273285375368232495429 #>  17685062374745280598492217386845129350 #>  223553142498364321238189328942498473503 #>  240649020551054330404932383065726870513  #>  #> [[6]] #> An object of class exprObj : \"raw\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                          #> Mlc1   . . . . . .  1 . . 1 . . . ...... #> Gprc5b . 1 . 3 . .  2 . 4 2 . 1 . ...... #> Gfap   2 . 2 1 . . 45 . 1 1 . . . ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>  g[[\"expression\", spat_unit = \"aggregate\"]] #> [[1]] #> An object of class exprObj : \"raw\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                          #> Mlc1   . . . . . .  1 . . 1 . . . ...... #> Gprc5b . 1 . 3 . .  2 . 4 2 . 1 . ...... #> Gfap   2 . 2 1 . . 45 . 1 1 . . . ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>  #> [[2]] #> An object of class exprObj : \"normalized\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #> 337 x 462 sparse Matrix of class \"dgCMatrix\" #>                                                                                           #> Mlc1    .       .        .        .        . .  5.291601 . .        5.821597 . .        . #> Gprc5b  .       6.398031 .        7.454658 . .  6.273066 . 7.680054 6.808785 . 5.082989 . #> Gfap   10.48137 .        7.901442 5.886051 . . 10.746982 . 5.701006 5.821597 . .        . #>               #> Mlc1   ...... #> Gprc5b ...... #> Gfap   ...... #>  #>  ........suppressing 449 columns and 331 rows in show(); maybe adjust options(max.print=, width=) #>                                            #> Adgrf4    . . . . . . . . . . . . . ...... #> Epha2     . . . . . . . . . . . . . ...... #> Blank-139 . . . . . . . . . . . . . ...... #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>  #> [[3]] #> An object of class exprObj : \"scaled\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #>   Provenance: z0 z1 #> 337 x 462 dense matrix of class \"dgeMatrix\" #>  #>                  [,1]       [,2]       [,3]       [,4]       [,5]       [,6] #> Mlc1      -0.51096453 -0.4718074 -0.3859440 -0.4383384 -0.3827836 -0.3152653 #> Gprc5b    -0.97549417  1.6804631 -0.5746594  1.2850731 -0.5794505 -0.4583322 #> Gfap       5.46807822 -0.7367558  1.3902670  0.5804327 -0.6152080 -0.4843442 #> Ednrb      9.34063752  3.7384966  2.5412669  1.5736461  2.8570134 -0.2823656 #> Sox9      -0.59906517 -0.5143258  2.4318798 -0.4671338 -0.4200826 -0.3423988 #> Aqp4      -0.64987710 -0.5388482  2.0705344  1.0223253  1.9919249 -0.3580479 #> Gjc3       0.02982685  5.0161718 -0.1662473 -0.2615829 -0.1538300 -0.1487112 #> Sox8      -0.47826316  3.5325216  2.5366322 -0.4276501 -0.3689389 -0.3051939 #> Ntsr2      6.06580557  2.6068464  1.7367543  1.1330202 -0.6019376 -0.4746906 #> Adcyap1r1 -2.17060870  0.8282834  0.8492637 -0.9807865 -1.0854235 -0.8264062 #>                [,7]       [,8]       [,9]      [,10] #> Mlc1       1.546533 -0.3614888 -0.5076115  2.5761153 #> Gprc5b     1.235844 -0.5485629  1.6600474  2.0842933 #> Gfap       1.944454 -0.5825762  0.6870865  1.1388811 #> Ednrb      1.705886 -0.3184691 -0.4650954  3.3799076 #> Sox9       1.888188 -0.3969684 -0.5426758  2.2576086 #> Aqp4       2.116905 -0.4174313  1.7014365  2.5684989 #> Gjc3       4.531175 -0.1437027 -0.2923745 -0.2723587 #> Sox8       1.695510 -0.3483194 -0.4945962  2.8035269 #> Ntsr2      1.406620 -0.5699532  1.7102932  2.7162251 #> Adcyap1r1 -1.160557 -1.0298563  0.3757894  0.7075043 #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>  #> [[4]] #> An object of class exprObj : \"pearson\" #> spat_unit : \"aggregate\" #> feat_type : \"rna\" #> provenance: z0 z1  #>  #> contains: #>   Provenance: z0 z1 #> 337 x 462 dense matrix of class \"dgeMatrix\" #>  #>                 [,1]       [,2]       [,3]       [,4]       [,5]       [,6] #> Mlc1      -0.1671233 -0.4887705 -0.4090814 -0.5848627 -0.3515289 -0.3681237 #> Gprc5b    -0.2390668  0.7264405 -0.5847568  2.7313611 -0.5026041 -0.5262978 #> Gfap       4.1820021 -1.2576333  0.8204327 -0.8491028 -0.9074561 -0.9499730 #> Ednrb      6.2681837  8.3133382  2.2399348  1.2854419  2.7238921 -0.3428383 #> Sox9      -0.1862585 -0.5445941  3.9225159 -0.6515799 -0.3917326 -0.4102193 #> Aqp4      -0.2836816 -0.8280158  2.1766489  0.0105117  1.0752709 -0.6242357 #> Gjc3      -0.1409193  4.4308083 -0.3450090 -0.4933833 -0.2964520 -0.3104520 #> Sox8      -0.1577216  6.0278079  2.2000617 -0.5520553 -0.3317706 -0.3474348 #> Ntsr2      5.2211595 12.2321831  2.5314771  1.9147811 -0.7517658 -0.7870865 #> Adcyap1r1 -0.3682081 -0.1508472  0.2046257 -1.2808439 -0.7730688 -0.8093776 #>                 [,7]       [,8]       [,9]      [,10] #> Mlc1       0.6581840 -0.4139145 -0.6241861  1.0672640 #> Gprc5b     0.8940330 -0.5916531  3.5614736  1.4696046 #> Gfap      21.4941853 -1.0670577 -0.9900047 -0.8977729 #> Ednrb      0.8099276 -0.3854930 -0.5814107  3.0206482 #> Sox9       2.9072540 -0.4612263 -0.6953491  0.8272268 #> Aqp4       6.8660546 -0.7016483  1.7534888  1.9205849 #> Gjc3      12.4888269 -0.3490872 -0.5265923 -0.5046983 #> Sox8       0.7812349 -0.3906598 -0.5891883  1.2004721 #> Ntsr2      2.2943725 -0.8844258  6.0655865  8.7636477 #> Adcyap1r1 -1.5740789 -0.9094310 -0.6471715 -0.5594111 #>  #>  First four colnames: #>  240649020551054330404932383065726870513 #>  274176126496863898679934791272921588227 #>  323754550002953984063006506310071917306 #>  87260224659312905497866017323180367450  #>   # return as a subset giotto object with drop = FALSE g[[, \"raw\", drop = FALSE]] #> An object of class giotto  #> >Active spat_unit:  z0  #> >Active feat_type:  rna  #> dimensions    : 337, 498 (features, cells) #> [SUBCELLULAR INFO] #> [AGGREGATE INFO] #> expression ----------------------- #>   [z0][rna] raw #>   [z1][rna] raw #>   [aggregate][rna] raw #> spatial locations ---------------- #>   [z0] raw #>   [z1] raw #>   [aggregate] raw #>  #>  #> Use objHistory() to see steps and params used g[[spat_unit = \"aggregate\", drop = FALSE]] #> An object of class giotto  #> >Active spat_unit:  aggregate  #> >Active feat_type:  rna  #> dimensions    : 337, 462 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : aggregate  #> [AGGREGATE INFO] #> expression ----------------------- #>   [aggregate][rna] raw normalized scaled pearson #> spatial locations ---------------- #>   [aggregate] raw #> spatial networks ----------------- #>   [aggregate] Delaunay_network kNN_network #> spatial enrichments -------------- #>   [aggregate][rna] cluster_metagene #> dim reduction -------------------- #>   [aggregate][rna] pca umap tsne #> nearest neighbor networks -------- #>   [aggregate][rna] sNN.pca #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"t_flex — t_flex","title":"t_flex — t_flex","text":"t_flex","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"t_flex — t_flex","text":"","code":"t_flex(mymatrix)"},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"t_flex — t_flex","text":"mymatrix matrix use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"t_flex — t_flex","text":"matrix","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/t_flex.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"t_flex — t_flex","text":"","code":"m <- matrix(rnorm(100), nrow = 10)  t_flex(m) #>             [,1]       [,2]        [,3]       [,4]        [,5]       [,6] #>  [1,] -0.1236010  0.8402388  0.09488557 -0.3051016  2.61356953  0.4033562 #>  [2,] -0.7598318  1.2102308 -0.79255887 -1.0285583  0.53468162 -0.2549574 #>  [3,]  0.5285784  0.6529490  1.65551988  0.8628259  1.48753032 -0.7928009 #>  [4,]  0.6828611  1.2112902  0.95150212 -2.6957950 -0.90818349 -3.0512252 #>  [5,] -0.3990772 -0.2482703 -0.07380394 -1.9934812 -1.42041042  1.2947209 #>  [6,] -0.5727822 -1.8640852  0.09639107 -0.5443541  1.48551609 -0.3448927 #>  [7,]  0.1086828  0.7365619  0.09315147  0.0132255 -1.04726906 -0.7027522 #>  [8,] -0.7109888  0.2669893  0.53664180  0.2404480  0.01366106 -0.5580017 #>  [9,]  0.6553744  0.1503795 -0.59067813  0.6122497  0.37854906 -0.7803218 #> [10,] -0.2506748 -0.6089946 -0.88808468 -0.6624071  0.73643913  0.6153136 #>             [,7]        [,8]        [,9]       [,10] #>  [1,]  2.4011713  1.49373183 -0.07131230  1.23346046 #>  [2,] -1.3450848  0.25582422 -1.24728794 -0.07576892 #>  [3,] -0.4488620 -1.00887476 -1.68556568 -2.09101499 #>  [4,]  0.7783738  2.81270232 -0.73703947  0.47029282 #>  [5,] -1.1102363  0.08404357 -0.09540202  0.50937786 #>  [6,] -0.2134763  1.15903245 -0.45740931 -2.18684352 #>  [7,] -0.2350337  0.82302884  1.67890702 -1.31266853 #>  [8,] -0.4879339  0.87933344  0.87836272  1.59534811 #>  [9,] -0.9206261  0.67446169 -1.17164534  2.50702432 #> [10,] -1.5068803 -1.14078881 -0.48878187 -2.01225221"},{"path":"https://drieslab.github.io/GiottoClass/reference/terraVectData-class.html","id":null,"dir":"Reference","previous_headings":"","what":"Basic class for terra SpatVector-based objects — terraVectData-class","title":"Basic class for terra SpatVector-based objects — terraVectData-class","text":"Classes inherit class contain spatVector slot meant hold work terra SpatVector objects","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/terraVectData-class.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Basic class for terra SpatVector-based objects — terraVectData-class","text":"object spatVector slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":null,"dir":"Reference","previous_headings":"","what":"Tessellated grid of polygons — tessellate","title":"Tessellated grid of polygons — tessellate","text":"Generates tessellated grid polygons within provided spatial extent","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Tessellated grid of polygons — tessellate","text":"","code":"tessellate(   extent,   shape = c(\"hexagon\", \"square\"),   shape_size = NULL,   gap = 0,   radius = NULL,   id_prefix = \"ID_\",   name = \"grid\" )"},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Tessellated grid of polygons — tessellate","text":"extent SpatExtent anything else SpatExtent can extracted created shape Shape tessellation grid. Available options \"hexagon\" \"square\". shape_size numeric. Size shape tessellate. (x-axis width hexagons, side length squares) gap numeric. Shrink polygons add gap tessellated polygons radius deprecated. numeric. Radius size tessellation grid. id_prefix character. prefix add poly_ID names generated name name giottoPolygons grid make","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Tessellated grid of polygons — tessellate","text":"giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Tessellated grid of polygons — tessellate","text":"function generates tessellated grid spatial locations based input spatial locations. shape tessellation grid can either hexagonal square. shape_size parameter determines size grid cells bin size.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/tessellate.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Tessellated grid of polygons — tessellate","text":"","code":"# Create an extent across which to generate tessellated polygons e <- ext(0, 100, 0, 100) # produce hexagons with a diameter of 10 x <- tessellate(extent = e, shape = \"hexagon\", shape_size = 10) #> 104 polygons generated plot(x)   # same size grid, but now with a gap x <- tessellate(extent = e, shape = \"hexagon\", shape_size = 10, gap = 1) #> 104 polygons generated plot(x)   # square grid with a gap x <- tessellate(extent = e, shape = \"square\", shape_size = 10, gap = 1) #> 100 polygons generated plot(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":null,"dir":"Reference","previous_headings":"","what":"Transpose — transpose","title":"Transpose — transpose","text":"Spatially transpose object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transpose — transpose","text":"","code":"# S4 method for class 'giotto' t(x)  # S4 method for class 'spatLocsObj' t(x)  # S4 method for class 'spatialNetworkObj' t(x)  # S4 method for class 'giottoPoints' t(x)  # S4 method for class 'giottoPolygon' t(x)  # S4 method for class 'giottoLargeImage' t(x)  # S4 method for class 'giottoAffineImage' t(x)  # S4 method for class 'affine2d' t(x)  # S3 method for class 'spatLocsObj' t(x)  # S3 method for class 'spatialNetworkObj' t(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transpose — transpose","text":"x object transposed","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Transpose — transpose","text":"transposed object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Transpose — transpose","text":"","code":"sl <- GiottoData::loadSubObjectMini(\"spatLocsObj\")  plot(t(sl))"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"updateGiottoImage — updateGiottoImage","title":"updateGiottoImage — updateGiottoImage","text":"Updates spatial positioning sizing giotto image largeImage attached giotto object.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"updateGiottoImage — updateGiottoImage","text":"","code":"updateGiottoImage(   gobject = NULL,   image_name = NULL,   largeImage_name = NULL,   xmax_adj = 0,   xmin_adj = 0,   ymax_adj = 0,   ymin_adj = 0,   x_shift = 0,   y_shift = 0,   scale_factor = NULL,   scale_x = 1,   scale_y = 1,   order = c(\"first_adj\", \"first_scale\"),   xmax_set = NULL,   xmin_set = NULL,   ymax_set = NULL,   ymin_set = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"updateGiottoImage — updateGiottoImage","text":"gobject gobject containing desired image object image_name name giotto image object largeImage_name name giotto largeImage object xmax_adj, xmin_adj, ymax_adj, ymin_adj adjust image boundaries increasing maximum decreasing minimum bounds respectively xy bounds x_shift, y_shift shift entire image along xy axes scale_factor set scale_x scale_y params time scale_x, scale_y independently scale x y axis image mapping coordinate origin order order operations fine adjustments (adjustment shift parameters) scaling xmin_set, xmax_set, ymin_set, ymax_set directly set xy image boundaries. Overrides minmax values spatial anchor. return_gobject return giotto object TRUE, giotto image object FALSE verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"updateGiottoImage — updateGiottoImage","text":"giotto object updated giotto image object return_gobject = FALSE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"updateGiottoImage — updateGiottoImage","text":"function works image objects associated Giotto.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"updateGiottoImage — updateGiottoImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  updateGiottoImage(g, largeImage_name = \"image\") #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":null,"dir":"Reference","previous_headings":"","what":"updateGiottoImageMG — updateGiottoImageMG","title":"updateGiottoImageMG — updateGiottoImageMG","text":"Updates boundaries giotto image object attached giotto object gobject image_name params given. Alternatively can directly accept return image","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"updateGiottoImageMG — updateGiottoImageMG","text":"","code":"updateGiottoImageMG(   gobject = NULL,   image_name = NULL,   giottoImage = NULL,   xmax_adj = 0,   xmin_adj = 0,   ymax_adj = 0,   ymin_adj = 0,   x_shift = 0,   y_shift = 0,   scale_factor = NULL,   scale_x = 1,   scale_y = 1,   order = c(\"first_adj\", \"first_scale\"),   xmin_set = NULL,   xmax_set = NULL,   ymin_set = NULL,   ymax_set = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"updateGiottoImageMG — updateGiottoImageMG","text":"gobject giotto object containing giotto image object image_name name giotto image object giottoImage image object directly update xmax_adj, xmin_adj, ymax_adj, ymin_adj adjust image boundaries increasing maximum decreasing minimum bounds respectively xy bounds x_shift, y_shift shift entire image along xy axes scale_factor set scale_x scale_y params time scale_x, scale_y independently scale x y axis image mapping coordinate origin order order operations fine adjustments (adjustment shift parameters) scaling xmin_set set image xmin boundary. Applied adjustments xmax_set set image xmax boundary. Applied adjustments ymin_set set image ymin boundary. Applied adjustments ymax_set set image ymax boundary. Applied adjustments return_gobject return giotto object TRUE, giotto image object FALSE verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"updateGiottoImageMG — updateGiottoImageMG","text":"giotto object updated giotto image object return_gobject = FALSe","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoImageMG.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"updateGiottoImageMG — updateGiottoImageMG","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" g_image <- convertGiottoLargeImageToMG(g,     largeImage_name = \"image\",     return_gobject = FALSE )  updateGiottoImageMG(g, giottoImage = g_image) #> giottoImage argument is given and will take priority #>  #>  return_gobject set to FALSE #> Error in updateGiottoImageMG(g, giottoImage = g_image): object 'g_image' not found"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"updateGiottoLargeImage — updateGiottoLargeImage","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"Updates boundaries giotto largeImage object attached giotto object gobject largeImage_name params given. Alternatively can directly accept return largeImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"","code":"updateGiottoLargeImage(   gobject = NULL,   largeImage_name = NULL,   giottoLargeImage = NULL,   xmax_adj = 0,   xmin_adj = 0,   ymax_adj = 0,   ymin_adj = 0,   x_shift = 0,   y_shift = 0,   scale_factor = NULL,   scale_x = 1,   scale_y = 1,   order = c(\"first_adj\", \"first_scale\"),   xmin_set = NULL,   xmax_set = NULL,   ymin_set = NULL,   ymax_set = NULL,   return_gobject = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"gobject giotto object containing giotto largeImage object largeImage_name name giotto largeImage object giottoLargeImage largeImage object directly update xmax_adj, xmin_adj, ymax_adj, ymin_adj adjust image boundaries increasing maximum decreasing minimum bounds respectively xy bounds x_shift, y_shift shift entire image along xy axes scale_factor set scale_x scale_y params time scale_x, scale_y independently scale x y axis image mapping coordinate origin order order operations fine adjustments (adjustment shift parameters) scaling xmin_set, xmax_set, ymin_set, ymax_set directly set xy image boundaries. Overrides minmax values spatial anchor. return_gobject return giotto object TRUE, giotto largeImage object FALSE verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"giotto object updated giotto largeImage object return_gobject = FALSE","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"updateGiottoLargeImage — updateGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  updateGiottoLargeImage(g, largeImage_name = \"image\") #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":null,"dir":"Reference","previous_headings":"","what":"Update giotto object — updateGiottoObject","title":"Update giotto object — updateGiottoObject","text":"Updates giotto object changes structure backwards compatibility earlier versions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update giotto object — updateGiottoObject","text":"","code":"updateGiottoObject(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update giotto object — updateGiottoObject","text":"gobject giotto object update","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update giotto object — updateGiottoObject","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Update giotto object — updateGiottoObject","text":"Supported updates: 3.2.0 update adding multiomics slot master branch suite - TODO","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoObject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update giotto object — updateGiottoObject","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  g <- updateGiottoObject(g)"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":null,"dir":"Reference","previous_headings":"","what":"Update giotto points object — updateGiottoPointsObject","title":"Update giotto points object — updateGiottoPointsObject","text":"Update giotto points object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update giotto points object — updateGiottoPointsObject","text":"","code":"updateGiottoPointsObject(gpoints)"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update giotto points object — updateGiottoPointsObject","text":"gpoints giotto points object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update giotto points object — updateGiottoPointsObject","text":"GiottoPointsObject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPointsObject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update giotto points object — updateGiottoPointsObject","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  updateGiottoPointsObject(g) #> An object of class giottoPoints #> feat_type : \"rna\" #> Feature Information: #>  class       : SpatVector  #>  geometry    : points  #>  dimensions  : 79761, 3  (geometries, attributes) #>  extent      : 6400.037, 6900.032, -5149.983, -4699.979  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       : feat_ID global_z feat_ID_uniq #>  type        :   <chr>    <int>        <int> #>  values      :    Mlc1        0            1 #>                 Gprc5b        0            2 #>                   Gfap        0            3 #>"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":null,"dir":"Reference","previous_headings":"","what":"Update giotto polygon object — updateGiottoPolygonObject","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"Update giotto polygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"","code":"updateGiottoPolygonObject(gpoly)"},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"gpoly giotto polygon object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"GiottoPolygonObject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/updateGiottoPolygonObject.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update giotto polygon object — updateGiottoPolygonObject","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPolygon\")  updateGiottoPolygonObject(g) #> An object of class giottoPolygon #> spat_unit : \"aggregate\" #> Spatial Information: #>  class       : SpatVector  #>  geometry    : polygons  #>  dimensions  : 462, 4  (geometries, attributes) #>  extent      : 6391.466, 6903.573, -5153.897, -4694.868  (xmin, xmax, ymin, ymax) #>  coord. ref. :   #>  names       :                   poly_ID stack agg_n valid #>  type        :                     <chr> <chr> <int> <int> #>  values      : 100210519278873141813371~    NA     2     1 #>                101161259912191124732236~    NA     2     1 #>                101488859781016188084173~    NA     2     1 #>  centroids   : calculated #>  overlaps    : rna"},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":null,"dir":"Reference","previous_headings":"","what":"Update giotto parameters — update_giotto_params","title":"Update giotto parameters — update_giotto_params","text":"Update giotto parameters","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Update giotto parameters — update_giotto_params","text":"","code":"update_giotto_params(   gobject,   description = \"_test\",   return_gobject = TRUE,   toplevel = 2 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Update giotto parameters — update_giotto_params","text":"gobject giotto object description description function run return_gobject logical. Whether giotto object returned toplevel expected relative stackframe call recorded made. negative, param recording skipped","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Update giotto parameters — update_giotto_params","text":"giotto object list parameters","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/update_giotto_params.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Update giotto parameters — update_giotto_params","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  update_giotto_params(g, toplevel = 1) #> An object of class giotto  #> >Active spat_unit:  cell  #> >Active feat_type:  rna  #> dimensions    : 634, 624 (features, cells) #> [SUBCELLULAR INFO] #> polygons      : cell  #> [AGGREGATE INFO] #> expression ----------------------- #>   [cell][rna] raw normalized scaled #> spatial locations ---------------- #>   [cell] raw #> spatial networks ----------------- #>   [cell] Delaunay_network spatial_network #> spatial enrichments -------------- #>   [cell][rna] cluster_metagene DWLS #> dim reduction -------------------- #>   [cell][rna] pca custom_pca umap custom_umap tsne #> nearest neighbor networks -------- #>   [cell][rna] sNN.pca custom_NN #> attached images ------------------ #> images      : alignment image  #>  #>  #> Use objHistory() to see steps and params used"},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap giotto terra pointer information — wrap","title":"Wrap giotto terra pointer information — wrap","text":"Extension wrap methods terra Giotto's terra-based S4 objects. Allows pointer information packaged memory can passed connection (e.g. nodes computer cluster)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap giotto terra pointer information — wrap","text":"","code":"# S4 method for class 'giottoPolygon' wrap(x)  # S4 method for class 'giotto' wrap(x)  # S4 method for class 'giottoPoints' wrap(x)  # S4 method for class 'packedGiottoPolygon' vect(x)  # S4 method for class 'packedGiottoPoints' vect(x)  # S4 method for class 'packedGiotto' vect(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap giotto terra pointer information — wrap","text":"x giottoPolygon giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Wrap giotto terra pointer information — wrap","text":"wrapped giottoPolygon giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"methods-by-class-","dir":"Reference","previous_headings":"","what":"Methods (by class)","title":"Wrap giotto terra pointer information — wrap","text":"wrap(giottoPolygon): Wrap giottoPolygon wrap(giotto): Wrap giotto wrap(giottoPoints): Wrap giottoPoints vect(packedGiottoPolygon): Unwrap giottoPolygon vect(packedGiottoPoints): Unwrap giottoPolygon vect(packedGiotto): Unwrap giotto","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Wrap giotto terra pointer information — wrap","text":"","code":"g <- GiottoData::loadSubObjectMini(\"giottoPoints\")  wrap(g) #> [1] \"This is a packedGiottoPoints object. Use 'GiottoClass::vect()' to unpack it\""},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"writeGiottoLargeImage — writeGiottoLargeImage","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"Write full resolution image file. Filetype extension included filename argument. careful write time disk space needed image large.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"","code":"writeGiottoLargeImage(   giottoLargeImage = NULL,   gobject = NULL,   largeImage_name = NULL,   filename = NULL,   dataType = NULL,   max_intensity = NULL,   overwrite = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"giottoLargeImage giottoLargeImage object gobject giotto object largeImage_name name giottoLargeImage filename file name path write image dataType (optional) values dataType \"INT1U\", \"INT2U\", \"INT2S\", \"INT4U\", \"INT4S\", \"FLT4S\", \"FLT8S\". first three letters indicate whether dataType integer (whole numbers) real number (decimal numbers), fourth character indicates number bytes used (allowing large numbers /precision), \"S\" \"U\" indicate whether values signed (negative positive) unsigned (positive values ). max_intensity (optional) image max intensity value dataType can automatically determined overwrite Overwrite filename already existing verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"image local file","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/writeGiottoLargeImage.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"writeGiottoLargeImage — writeGiottoLargeImage","text":"","code":"g <- GiottoData::loadGiottoMini(\"visium\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\"  writeGiottoLargeImage(     gobject = g, largeImage_name = \"image\",     filename = paste0(\"tempfile()\", \".png\") ) #> Writing image to disk as INT1U"},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":null,"dir":"Reference","previous_headings":"","what":"Zoom a Giotto spatial object — zoom","title":"Zoom a Giotto spatial object — zoom","text":"Works like terra::zoom(). Zoom plot providing new extent, default done clicking twice existing plot. passing SpatExtent without drawing, pre-existing plot needed.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Zoom a Giotto spatial object — zoom","text":"","code":"# S4 method for class 'giottoLargeImage' zoom(x, e = terra::draw(), ...)  # S4 method for class 'giottoPolygon' zoom(x, e = terra::draw(), ...)  # S4 method for class 'giottoPoints' zoom(x, e = terra::draw(), ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Zoom a Giotto spatial object — zoom","text":"x giotto image, giottoPolygon, giottoPoints object e SpatExtent ... additional parameters pass plot()","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Zoom a Giotto spatial object — zoom","text":"SpatExtent (invisibly)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/zoom.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Zoom a Giotto spatial object — zoom","text":"","code":"g <- GiottoData::loadGiottoMini(\"vizgen\") #> 1. read Giotto object #> 2. read Giotto feature information #> 3. read Giotto spatial information #> 3.1 read Giotto spatial shape information #> 3.2 read Giotto spatial centroid information #> 3.3 read Giotto spatial overlap information #> 4. read Giotto image information #> python already initialized in this session #>  active environment : 'giotto_env' #>  python version : 3.10 #> checking default envname 'giotto_env' #> a system default python environment was found #> Using python path: #>  \"/usr/share/miniconda/envs/giotto_env/bin/python\" gimg <- getGiottoImage(g, image_type = \"largeImage\") gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") gpoints <- GiottoData::loadSubObjectMini(\"giottoPoints\") e <- ext(6400, 6800, -4860, -4750) # arbitrary  # With extent passed zoom(gimg, e)  zoom(gpoly, e)  zoom(gpoints, e)"},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-4-1","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.4.1 (2024/10/28)","text":"buffer() giottoPolygon, giottoPoints, spatLocsObj. Default crop voronoi borders settleGeom() settleGeom() giottoPolygon SpatVector finding non overlapping borders determined voronoi","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-4-0","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.4.0 (2024/10/27)","text":"stop exporting deprecated internal accessors terra requirement raised 1.7.41 minCircle()","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-4-0","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.4.0 (2024/10/27)","text":"fix dimnames() subobjects fix joinGiottoObject() gobjects poly point data #233 fix joinGiottoObject() gobjects image intensity overlaps features fix subsetting error due expression matrix drop numeric one cell left shift_vertical_step shift_horizontal_step args createGiottoPolygonsFromMask() numeric now shift steps based dims image instead just numerical value provided. fix feature metadata mixedsorted join fix non-inclusive subsetting minmax values supplied subsetGiottoLocs() fix giottoAffineImage loading saved","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-4-0","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.4.0 (2024/10/27)","text":"python packages install pip now settable installGiottoEnvironment() #224 giotto initialize() slot checking behavior can toggled now using 'giotto.init' 'giotto.check_valid' options. #946 rbutleriii setGiotto() now initializes performs checks items added list input provided. instructions() args now call createGiottoInstructions(). can also supply named args. instructions(gobject, param) instructions(gobject, param)<- now work giottoInstructions objects convenience. [, [[, $, $<-, subset() giotto see ?GiottoClass::subset_giotto subset spatIDs() featIDs() objName(), spatUnit(), featType() generics now return NA_character_ instead erroring used unsupported classes. ext() ext<-() can now used get set extent affine2d rownames(), colnames(), dimnames() giotto spatValues() can get values multiple spatial units. createGiottoPolygonsFromMask() now works anything terra::rast() can read createGiottoLargeImage() now works anything terra::rast() can read","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-4-0","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.4.0 (2024/10/27)","text":"sliceGiotto() pulling specific spatial units feature types independent giotto objects splitGiotto() splitting Giotto object list Giotto objects based cell metadata column .list() method giotto dump data list subobjects XY() XY<-() accessing setting coordinate values subobjects matrix terra convHull(), minRect(), minCircle() Giotto spatial vector classes area() SpatVector giottoPolygon","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-3-5","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.3.5 (2024/08/28)","text":"set_giotto_python_path() now also initialize python env set default print python env active, otherwise nothing python env already initialized. deprecated readGiottoInstructions(), showGiottoInstructions(), changeGiottoInstructions(), replaceGiottoInstructions() favor instructions() generic","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-5","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.5 (2024/08/28)","text":"intensity images now automatically scale estimated highest value giottoPolygon plot() default max_poly raised 1e6 giottoInstructions longer lose class specific params replaced ometif_to_tif() now checks imagecodecs package well anndataToGiotto() giottoToAnndata now check anndata package well. fix joinGiottoObjects() \"z_stack\" join method fix error documentation #214 shaojunyu fix error installGiottoEnvironment() #1006 13954380607","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-5","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.5 (2024/08/28)","text":"print() method giottoInstructions rbind() spatLocsObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-4","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.4 (2024/08/04)","text":"hotfix anndata matrix support #216 wwang-chcn","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-3","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.3 (2024/07/29)","text":"fix flipping issue giottoAffineImage certain affine transforms","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-3","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.3 (2024/07/29)","text":"missing method affine() instantiates affine2d object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-3-2","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.3.2 (2024/07/26)","text":"python environment installation relates default settings .condarc may changed. giottoImage name slot now requires character accept NULL","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-2","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.2 (2024/07/26)","text":"loadGiotto() longer errors similarly named spat_units feat_types (e.g. “cell” “new_cell” previously throw error) fix giottoToSpatialExperiment() fix giottoToSeuratV5 cosmx mini dataset #989 guillermoturiel fix issue prints createGiottoCosMxObject() #960 GBeattie","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-2","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.2 (2024/07/26)","text":"verbose param createNearestNetwork() checkGiottoEnvironment() addition full filepaths, also now supports name environment installation directory installGiottoEnvironment(), removeGiottoEnvironment() now conda param setting path conda executable envname param specifying environment name installGiottoEnvironment() now confirm param skipping path input checks t() giotto now affects images well.","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-3-2","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.3.2 (2024/07/26)","text":"affine() giottoPolygon, giottoPoints, spatLocsObj, giotto shear() giottoPoints, giottoPolygon, spatLocsObj, affine2d affine2d class accumulating linear transforms used affine() initialize(), [, $, show(), plot(), methods affine2d spin(), rescale, spatShift(), affine(), flip(), shear() t() methods affine2d giottoAffineImage class just--time affine transformed images initialize(), method giottoLargeImage initialize(), ext(), crop(), rescale(), spatShift(), plot(), methods giottoAffineImage rescale() method giottoImage spin(), shear(), affine(), flip(), t() methods giottoAffineImage giottoLargeImage (converts giottoAffineImage) () conversion giottoLargeImage giottoAffineImage .get_centroid_xy() internal getting numeric centroid xy values object responds ext() .bound_poly() internal generating dummy polygon extent object responds ext() .aff_shift_2d(), .aff_shift_2d<-(), .aff_linear_2d, .aff_linear_2d()<- internals accessing manipulating affine matrices","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-1","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.1 (2024/05/21)","text":"allow passing additional params setGiotto() ... spatShift() can now perform z shifts start spatLocsObj z information fix bug joinGiottoObjects() v0.3.0 looks now non-existent @largeImages slot fix bug .update_image_slot() v0.3.0 NULL @largeImages slot result error fix bugs spatShift() rescale() methods giotto setting default spat_unit feat_type","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-1","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.1 (2024/05/21)","text":"joinGiottoObjects() extent detection xshift defaults now depend ext() gobject instead images (available) joinGiottoObjects() now dry_run param previewing datasets spatially located join","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-3-1","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.3.1 (2024/05/21)","text":"() conversion giottoLargeImage array .matrix() method spatLocsObj()","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-3-0","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.3.0 (2024/05/13)","text":"deprecation reconnect_image_object(), reconnect_giottoImage_MG() reconnect_giottoLargeImage() internals favor simpler reconnect() generic giotto @largeImage slot removed. images now exist @images slot. backwards compatibility S3 spatialNetworkObj removed finding specific spatialNetworkObj getSpatialNetwork() now upgraded error instead returning NULL line accessors. backwards compatibility bare data.table spatial coordinates information removed","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-3-0","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.3.0 (2024/05/13)","text":"fix plot() params passing giottoPolygon type = \"centroid\" fix ext() output giottoImage spatShift() rescale() now also affect gobject attached images #945 rbutleriii","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-3-0","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.3.0 (2024/05/13)","text":"use faster terra::rasterize() terra::plot() instead scattermore::scattermoreplot() giottoPoints plot() method plot() giottoPoints method now plots density dens = TRUE show_max param density() hist() plot image object’s max_window setting .identify_background_range_polygons() now finds polygons larger threshold percentage overall extent SpatVector input. ext() can now used giotto objects #945 rbutleriii ext()<- can now used giottoImage conversion giottoLargeImage giottoImage (giottoImage sampled) crop() works spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-3-0","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.3.0 (2024/05/13)","text":"new spatValues() get specific values giotto object data.table format new ometif_to_tif convert .ome.tif .tif new terra::density() terra::hist() wrappers giottoLargeImage","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-2-3","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.2.3 (2024/03/12)","text":"fix saveGiotto overwrite = TRUE #870 rbutlerii fix plot() method param passing giottoLargeImage. Ensure access terra params","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-2-3","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.2.3 (2024/03/12)","text":"createGiottoPoints data.frame method can now select columns use x_colname, y_colname, feat_ID_colname params giotto now responds spatial manipulation generics: t(), flip(), rescale(), spatShift(), spin() spatUnit() featType() now vectorized internal get_spatial_locations_list() get_spatial_network_list() accessors now accept “::” token get available, ignoring spat_unit","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-2-2","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.2.2 (2024/03/01)","text":"fix createGiottoPolygonsFromMask() IDs applied sync mask values fix createGiottoPolygon() character method dispatch raster inputs remove unused fix_multipart param createGiottoPolygonsFromMask() fix giottoPolygon ID caching rbind()","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-2-2","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.2.2 (2024/03/01)","text":"createGiottoPolygonsFromMask() now ID_fmt param finer control automatic poly_ID generation .flip_spatvect() internal flipping SpatVector across arbitrary x y vals","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-2-1","dir":"Changelog","previous_headings":"","what":"breaking changes","title":"GiottoClass 0.2.1 (2024/02/28)","text":"giotto slot versions supercedes OS_platform. Used tracking GiottoClass version.","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-2-1","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.2.1 (2024/02/28)","text":"fix subsetGiotto unused argument fix giotto object saving image intensities overlaps data present. fix exprObj show() small matrices fix giotto calculateOverlap() method working image intensities data.","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-2-1","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.2.1 (2024/02/28)","text":"createNetwork() hub function creation Giotto NN spatial networks directly matrices. Mainly developers advanced users. edge_distances() calculating euclidean distances numeric m x n matrix (nodes) data.table cols define node connections.","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-2-1","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.2.1 (2024/02/28)","text":"addCellMetadata() addFeatMetadata() now support merging names provided vector factor data metadata cell_ID/feat_ID.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-1-3","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.1.3 (2024/01/12)","text":"fix unexpected sorting addCellMetadata() addFeatMetadata() #853 rbutleriii","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"new-0-1-3","dir":"Changelog","previous_headings":"","what":"new","title":"GiottoClass 0.1.3 (2024/01/12)","text":"init_gobject param loadGiotto() control whether object initialization also performed load vignette image tools","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"enhancements-0-1-3","dir":"Changelog","previous_headings":"","what":"enhancements","title":"GiottoClass 0.1.3 (2024/01/12)","text":"ID sorts now use gtools::mixedsort() #853 rbutleriii subobjects respond colnames, rownames, dimnames plot() show() now handle 3D spatLocsObj","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"added-0-1-2","dir":"Changelog","previous_headings":"","what":"Added","title":"GiottoClass 0.1.2 (2024/01/02)","text":"Added: max_window colors slots giottoLargeImage. Use GiottoClass:::.update_giotto_image() update outdated objects. Added: .bitdepth() internal function detect image bitdepth sampled values Added: re-export getMonochromeColors() GiottoUtils Added: giottoPolygon, giottoLargeImage method calculateOverlap() Added: vignette working spatial classes Added: output param .spatraster_sample_values(). Can now return sampled data.frame, array, magick, EBImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"bug-fixes-0-1-2","dir":"Changelog","previous_headings":"","what":"bug fixes","title":"GiottoClass 0.1.2 (2024/01/02)","text":"param fixes raster calculateOverlap() workflows","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-1-1","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"GiottoClass 0.1.1 (2023/12/16)","text":"Removed: getRainbowColors() GiottoUtils Removed: get_prev_fname() get_args() GiottoUtils Removed: aggregateStacksPolygonsOLD()","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"added-0-1-1","dir":"Changelog","previous_headings":"","what":"Added","title":"GiottoClass 0.1.1 (2023/12/16)","text":"Added: .gstop() GiottoClass specific errors Added: plot() method dimObj Added: ncol() nrow() methods dimObj Added: dimObj additional info now accessible using $ $<- Added: spatEnrObj cols now accessible using $ $<- Added: evaluate_input() exported wrapper evaluate functions Added: .polygons() data.frame method correctly formatted data.tables (replaces internal dt_to_spatvector_polygon()) Added: .polygons() data.frame method correctly formatted data.tables (replaces internal dt_to_spatvector_points()) Added: autocompletes $ spatLocsObj, spatEnrObj, dimObj, cellMetaObj, featMetaObj, giottoPolygon, giottoPoints Added: toplevel_params param subsetGiottoLocs() Added: spin, spatShift, rescale methods data.frame","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"changes-0-1-1","dir":"Changelog","previous_headings":"","what":"Changes","title":"GiottoClass 0.1.1 (2023/12/16)","text":"Fixed: Provenance now accidentally created list addSpatialCentroidLocations() Changed: giottoPolygon plot() now automatically switches centroid plotting 1e4 polys Changed: Package internal functions now . prefix","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"breaking-changes-0-1-0","dir":"Changelog","previous_headings":"","what":"Breaking Changes","title":"GiottoClass 0.1.0 (2023/11/29)","text":"Giotto subsetting rework","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"added-0-1-0","dir":"Changelog","previous_headings":"","what":"Added","title":"GiottoClass 0.1.0 (2023/11/29)","text":"Added: terraVectData virtual parent class giottoPolygon giottoPoints classes Added: $ $<- methods terraVectData Added: ext<-() method giottoPolygon, giottoPoints Added: crop() method giottoLargeImage, giottoPoints Added: [ subsetting giottoPoints giottoPolygon numerical, logical, character (ID) Added: .sf() .stars() converters giottoPoints giottoPolygon Added: setGiotto() generic Added: gap param tessellate() introduces variable gap polygons tessellated Added: triGrid() Added: orthoGrid() Added: DelayedMatrixStats suggests Added: calculateOverlap() overlapToMatrix() generic functions feature image overlap aggregations","code":""},{"path":"https://drieslab.github.io/GiottoClass/news/index.html","id":"changes-0-1-0","dir":"Changelog","previous_headings":"","what":"Changes","title":"GiottoClass 0.1.0 (2023/11/29)","text":"Improved: performance gefToGiotto() Updated: spatIDs() featIDs() methods giottoPolygon giottoPoints allow returning non-unique IDs Added: check plot() giottoPolygon giottoPoints objects contain geometries Added: warning crop() giottoLargeImage, giottoPolygon, giottoPoints objects cropped extent include information Changed: Conversion createGiottoPoints() generic function Deprecate: radius param favor shape_size tessellate() Fixed: python .install_github_link_pip() param Fixed: python create_AnnData() added globals.R","code":""}]
diff --git a/sitemap.xml b/sitemap.xml
index fe58b7e6..cde996e3 100644
--- a/sitemap.xml
+++ b/sitemap.xml
@@ -44,6 +44,7 @@
 <url><loc>https://drieslab.github.io/GiottoClass/reference/as.matrix.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/as.points.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/as.polygons.html</loc></url>
+<url><loc>https://drieslab.github.io/GiottoClass/reference/buffer.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/calculateMetaTable.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/calculateMetaTableCells.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/calculateOverlap.html</loc></url>
@@ -343,6 +344,7 @@
 <url><loc>https://drieslab.github.io/GiottoClass/reference/set_default_feat_type.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/set_default_spat_unit.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/set_multiomics.html</loc></url>
+<url><loc>https://drieslab.github.io/GiottoClass/reference/settleGeom.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/seuratToGiotto.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV4.html</loc></url>
 <url><loc>https://drieslab.github.io/GiottoClass/reference/seuratToGiottoV5.html</loc></url>