diff --git a/404.html b/404.html
index 793a9dd2..eea55572 100644
--- a/404.html
+++ b/404.html
@@ -28,7 +28,7 @@
     <a href="https://drieslab.github.io/GiottoClass/#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="https://drieslab.github.io/GiottoClass/index.html">GiottoClass</a>
 
@@ -79,7 +79,7 @@
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+<p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/LICENSE.html b/LICENSE.html
index 36868cd1..3f80a186 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="index.html">GiottoClass</a>
 
@@ -246,7 +246,7 @@ <h2 id="how-to-apply-these-terms-to-your-new-programs">How to Apply These Terms
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/authors.html b/authors.html
index 7be8082c..164eca9c 100644
--- a/authors.html
+++ b/authors.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="index.html">GiottoClass</a>
 
@@ -47,7 +47,7 @@
       <h2>Authors</h2>
       
       <ul class="list-unstyled"><li>
-          <p><strong>Ruben Dries</strong>. Author, maintainer. 
+          <p><strong><a href="https://www.drieslab.com" class="external-link">Ruben Dries</a></strong>. Author, maintainer. 
           </p>
         </li>
         <li>
@@ -55,7 +55,7 @@ <h2>Authors</h2>
           </p>
         </li>
         <li>
-          <p><strong>Guo-Cheng Yuan</strong>. Author. 
+          <p><strong><a href="https://labs.icahn.mssm.edu/yuanlab/" class="external-link">Guo-Cheng Yuan</a></strong>. Author. 
           </p>
         </li>
         <li>
@@ -66,19 +66,23 @@ <h2>Authors</h2>
           <p><strong><a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a></strong>. Author. <a href="https://orcid.org/0000-0002-4974-4591" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
         </li>
+        <li>
+          <p><strong>Edward Ruiz</strong>. Author. 
+          </p>
+        </li>
       </ul></div>
 
     <div class="section level2 citation">
       <h2 id="citation">Citation</h2>
       <p></p>
 
-      <p>Dries R, George Chen J, Yuan G, O'Brien M, Chávez J (2023).
+      <p>Dries R, George Chen J, Yuan G, O'Brien M, Chávez J, Ruiz E (2023).
 <em>GiottoClass: Giotto Suite object definitions and framework</em>.
 R package version 0.0.0.9010, <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 Chávez},
+  author = {Ruben Dries and Jiaji {George Chen} and Guo-Cheng Yuan and Matthew O'Brien and Joselyn Chávez and Edward Ruiz},
   year = {2023},
   note = {R package version 0.0.0.9010},
   url = {https://drieslab.github.io/GiottoClass/},
@@ -89,7 +93,7 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/index.html b/index.html
index 022c001b..9bd889fe 100644
--- a/index.html
+++ b/index.html
@@ -40,7 +40,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="index.html">GiottoClass</a>
 
@@ -115,12 +115,15 @@ <h2 data-toc-skip>Citation</h2>
 <div class="developers">
 <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
-<li>Ruben Dries <br><small class="roles"> Author, maintainer </small>  </li>
+<li>
+<a href="https://www.drieslab.com" class="external-link">Ruben Dries</a> <br><small class="roles"> Author, maintainer </small>  </li>
 <li>Jiaji George Chen <br><small class="roles"> Author </small>  </li>
-<li>Guo-Cheng Yuan <br><small class="roles"> Author </small>  </li>
+<li>
+<a href="https://labs.icahn.mssm.edu/yuanlab/" class="external-link">Guo-Cheng Yuan</a> <br><small class="roles"> Author </small>  </li>
 <li>Matthew O'Brien <br><small class="roles"> Author </small>  </li>
 <li>
 <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a> <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0002-4974-4591" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Edward Ruiz <br><small class="roles"> Author </small>  </li>
 </ul>
 </div>
 
@@ -141,7 +144,7 @@ <h2 data-toc-skip>Dev status</h2>
 
     <footer><div class="pkgdown-footer-left">
   <p></p>
-<p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+<p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/news/index.html b/news/index.html
index e6ee7c29..46b90043 100644
--- a/news/index.html
+++ b/news/index.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -48,7 +48,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/pkgdown.yml b/pkgdown.yml
index 5c0ef2b1..d50f32e4 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 2.19.2
 pkgdown: 2.0.7
 pkgdown_sha: ~
 articles: {}
-last_built: 2023-11-29T17:08Z
+last_built: 2023-11-29T18:08Z
 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 aa4df0ef..0e24f0ec 100644
--- a/reference/S3toS4dimObj.html
+++ b/reference/S3toS4dimObj.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/S3toS4spatGridObj.html b/reference/S3toS4spatGridObj.html
index d0baa96b..75425680 100644
--- a/reference/S3toS4spatGridObj.html
+++ b/reference/S3toS4spatGridObj.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/S3toS4spatNetObj.html b/reference/S3toS4spatNetObj.html
index 86f3cc75..218a9ed5 100644
--- a/reference/S3toS4spatNetObj.html
+++ b/reference/S3toS4spatNetObj.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -70,7 +70,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/abb_mat.html b/reference/abb_mat.html
index d362a600..9179d90a 100644
--- a/reference/abb_mat.html
+++ b/reference/abb_mat.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -62,7 +62,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/abb_spatlocs.html b/reference/abb_spatlocs.html
index 34e833ed..1d23ff12 100644
--- a/reference/abb_spatlocs.html
+++ b/reference/abb_spatlocs.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/activeFeatType-generic.html b/reference/activeFeatType-generic.html
index 23524422..2d2609bc 100644
--- a/reference/activeFeatType-generic.html
+++ b/reference/activeFeatType-generic.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -77,7 +77,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/activeSpatUnit-generic.html b/reference/activeSpatUnit-generic.html
index d3afb061..d029cf14 100644
--- a/reference/activeSpatUnit-generic.html
+++ b/reference/activeSpatUnit-generic.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -77,7 +77,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addCellMetadata.html b/reference/addCellMetadata.html
index 5dbaed14..c0d03a29 100644
--- a/reference/addCellMetadata.html
+++ b/reference/addCellMetadata.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -109,7 +109,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addFeatMetadata.html b/reference/addFeatMetadata.html
index 64673c13..56452642 100644
--- a/reference/addFeatMetadata.html
+++ b/reference/addFeatMetadata.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -110,7 +110,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addGiottoImage.html b/reference/addGiottoImage.html
index 859010b9..3202099b 100644
--- a/reference/addGiottoImage.html
+++ b/reference/addGiottoImage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -106,7 +106,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addGiottoImageMG.html b/reference/addGiottoImageMG.html
index 52440ddb..78115b91 100644
--- a/reference/addGiottoImageMG.html
+++ b/reference/addGiottoImageMG.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -99,7 +99,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addGiottoLargeImage.html b/reference/addGiottoLargeImage.html
index 8b9db91a..9ad35b3d 100644
--- a/reference/addGiottoLargeImage.html
+++ b/reference/addGiottoLargeImage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -99,7 +99,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addGiottoPoints.html b/reference/addGiottoPoints.html
index 1c3f312e..d0f894c2 100644
--- a/reference/addGiottoPoints.html
+++ b/reference/addGiottoPoints.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -86,7 +86,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addGiottoPolygons.html b/reference/addGiottoPolygons.html
index 891df8d5..f0645646 100644
--- a/reference/addGiottoPolygons.html
+++ b/reference/addGiottoPolygons.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -77,7 +77,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addNetworkLayout.html b/reference/addNetworkLayout.html
index 9e2cde67..89cceec3 100644
--- a/reference/addNetworkLayout.html
+++ b/reference/addNetworkLayout.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -120,7 +120,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addSpatialCentroidLocations.html b/reference/addSpatialCentroidLocations.html
index 3965c2c8..277b7327 100644
--- a/reference/addSpatialCentroidLocations.html
+++ b/reference/addSpatialCentroidLocations.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -107,7 +107,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/addSpatialCentroidLocationsLayer.html b/reference/addSpatialCentroidLocationsLayer.html
index 3f50837c..2d7f4ffc 100644
--- a/reference/addSpatialCentroidLocationsLayer.html
+++ b/reference/addSpatialCentroidLocationsLayer.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -102,7 +102,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/add_img_array_alpha.html b/reference/add_img_array_alpha.html
index 5cc2c53d..a691b595 100644
--- a/reference/add_img_array_alpha.html
+++ b/reference/add_img_array_alpha.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -81,7 +81,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/aggregateStacks.html b/reference/aggregateStacks.html
index acdae5a2..afea03d0 100644
--- a/reference/aggregateStacks.html
+++ b/reference/aggregateStacks.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -132,7 +132,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/aggregateStacksExpression.html b/reference/aggregateStacksExpression.html
index de047473..c17b9a06 100644
--- a/reference/aggregateStacksExpression.html
+++ b/reference/aggregateStacksExpression.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -113,7 +113,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/aggregateStacksLocations.html b/reference/aggregateStacksLocations.html
index 9c55a85f..ad250de5 100644
--- a/reference/aggregateStacksLocations.html
+++ b/reference/aggregateStacksLocations.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -103,7 +103,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/aggregateStacksPolygonOverlaps.html b/reference/aggregateStacksPolygonOverlaps.html
index f4e58a75..9eacf750 100644
--- a/reference/aggregateStacksPolygonOverlaps.html
+++ b/reference/aggregateStacksPolygonOverlaps.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -98,7 +98,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/aggregateStacksPolygons.html b/reference/aggregateStacksPolygons.html
index f58853f2..d758e7fe 100644
--- a/reference/aggregateStacksPolygons.html
+++ b/reference/aggregateStacksPolygons.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -103,7 +103,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/aggregateStacksPolygonsOLD.html b/reference/aggregateStacksPolygonsOLD.html
index 9594d8aa..8e0ddc82 100644
--- a/reference/aggregateStacksPolygonsOLD.html
+++ b/reference/aggregateStacksPolygonsOLD.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -89,7 +89,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/anndataToGiotto.html b/reference/anndataToGiotto.html
index 98f2b691..f9ffd3cd 100644
--- a/reference/anndataToGiotto.html
+++ b/reference/anndataToGiotto.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -133,7 +133,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/annotateGiotto.html b/reference/annotateGiotto.html
index 79c775eb..971c364b 100644
--- a/reference/annotateGiotto.html
+++ b/reference/annotateGiotto.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -106,7 +106,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/annotateSpatialGrid.html b/reference/annotateSpatialGrid.html
index 585816a9..529a05e8 100644
--- a/reference/annotateSpatialGrid.html
+++ b/reference/annotateSpatialGrid.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -99,7 +99,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/annotateSpatialNetwork.html b/reference/annotateSpatialNetwork.html
index d2a77a48..6e2636c8 100644
--- a/reference/annotateSpatialNetwork.html
+++ b/reference/annotateSpatialNetwork.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -99,7 +99,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/annotate_spatlocs_with_spatgrid_2D.html b/reference/annotate_spatlocs_with_spatgrid_2D.html
index 438443e7..d1cc9fe8 100644
--- a/reference/annotate_spatlocs_with_spatgrid_2D.html
+++ b/reference/annotate_spatlocs_with_spatgrid_2D.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/annotate_spatlocs_with_spatgrid_3D.html b/reference/annotate_spatlocs_with_spatgrid_3D.html
index f8d747b2..0fc115c6 100644
--- a/reference/annotate_spatlocs_with_spatgrid_3D.html
+++ b/reference/annotate_spatlocs_with_spatgrid_3D.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/as.data.table.html b/reference/as.data.table.html
index bf7bd09d..bd58ad8a 100644
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+++ b/reference/as.data.table.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -102,7 +102,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/calculateMetaTable.html b/reference/calculateMetaTable.html
index 1c29926c..a844f82c 100644
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+++ b/reference/calculateMetaTable.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -104,7 +104,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/calculateMetaTableCells.html b/reference/calculateMetaTableCells.html
index d24014c4..29dd04f9 100644
--- a/reference/calculateMetaTableCells.html
+++ b/reference/calculateMetaTableCells.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -99,7 +99,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/calculateOverlap.html b/reference/calculateOverlap.html
index fb1df5a2..82f58237 100644
--- a/reference/calculateOverlap.html
+++ b/reference/calculateOverlap.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -189,7 +189,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/calculateOverlapParallel.html b/reference/calculateOverlapParallel.html
index 8fe279a3..d102916a 100644
--- a/reference/calculateOverlapParallel.html
+++ b/reference/calculateOverlapParallel.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -115,7 +115,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/calculateOverlapPolygonImages.html b/reference/calculateOverlapPolygonImages.html
index 3e628d5e..02782b63 100644
--- a/reference/calculateOverlapPolygonImages.html
+++ b/reference/calculateOverlapPolygonImages.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -114,7 +114,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/calculateOverlapRaster.html b/reference/calculateOverlapRaster.html
index a6f710c0..f4701131 100644
--- a/reference/calculateOverlapRaster.html
+++ b/reference/calculateOverlapRaster.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -130,7 +130,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/calculateOverlapSerial.html b/reference/calculateOverlapSerial.html
index 183abe6d..09e7bdc5 100644
--- a/reference/calculateOverlapSerial.html
+++ b/reference/calculateOverlapSerial.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -114,7 +114,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/calculateSpatCellMetadataProportions.html b/reference/calculateSpatCellMetadataProportions.html
index 90779be5..a8a5ff60 100644
--- a/reference/calculateSpatCellMetadataProportions.html
+++ b/reference/calculateSpatCellMetadataProportions.html
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -110,7 +110,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/calculate_centroids_polygons.html b/reference/calculate_centroids_polygons.html
index dc8df763..09fa36af 100644
--- a/reference/calculate_centroids_polygons.html
+++ b/reference/calculate_centroids_polygons.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -63,7 +63,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/calculate_distance_and_weight.html b/reference/calculate_distance_and_weight.html
index d40f7c4a..d8d9067b 100644
--- a/reference/calculate_distance_and_weight.html
+++ b/reference/calculate_distance_and_weight.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -88,7 +88,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/calculate_overlap_raster.html b/reference/calculate_overlap_raster.html
index 8dd96a05..1d2ef235 100644
--- a/reference/calculate_overlap_raster.html
+++ b/reference/calculate_overlap_raster.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -96,7 +96,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/cellMetaObj-class.html b/reference/cellMetaObj-class.html
index fcba6868..c8a2e21b 100644
--- a/reference/cellMetaObj-class.html
+++ b/reference/cellMetaObj-class.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -80,7 +80,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/centroids-generic.html b/reference/centroids-generic.html
index b7187068..9094d72f 100644
--- a/reference/centroids-generic.html
+++ b/reference/centroids-generic.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -78,7 +78,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/changeGiottoInstructions.html b/reference/changeGiottoInstructions.html
index 4d044cf4..b366cf13 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -100,7 +100,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index ca170d37..3396f9c6 100644
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@@ -94,7 +94,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/checkGiottoEnvironment.html b/reference/checkGiottoEnvironment.html
index 445b76a3..54f54fc8 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -85,7 +85,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index fc794c61..7f9f325a 100644
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@@ -92,7 +92,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index 4645ffa0..ec55c761 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index c47efe7e..051691b3 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/check_expr_obj.html b/reference/check_expr_obj.html
index 968cbc97..5faaef21 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index 2f689f0c..169f7a36 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/check_giotto_python_modules.html b/reference/check_giotto_python_modules.html
index fa13214b..eacc47c3 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/check_py_for_scanpy.html b/reference/check_py_for_scanpy.html
index 07ee747b..c9b763b3 100644
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+++ b/reference/check_py_for_scanpy.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/check_spat_grid_obj.html b/reference/check_spat_grid_obj.html
index 4033fc7f..f81a80ea 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/check_spat_locs_obj.html b/reference/check_spat_locs_obj.html
index 5418af24..7fe25120 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/check_spat_net_obj.html b/reference/check_spat_net_obj.html
index a4f2ecaa..f9ba787f 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/check_spatial_location_data.html b/reference/check_spatial_location_data.html
index 126ff6b3..abbd282a 100644
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@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -62,7 +62,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/circleVertices.html b/reference/circleVertices.html
index a053d705..7e3bded8 100644
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@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -87,7 +87,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/colMeans_flex.html b/reference/colMeans_flex.html
index dace7f79..c095f45c 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/combineCellData.html b/reference/combineCellData.html
index 6c2be8d1..cf09bf14 100644
--- a/reference/combineCellData.html
+++ b/reference/combineCellData.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -109,7 +109,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/combineFeatureData.html b/reference/combineFeatureData.html
index c1f1d8b3..dcb7102e 100644
--- a/reference/combineFeatureData.html
+++ b/reference/combineFeatureData.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -89,7 +89,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/combineFeatureOverlapData.html b/reference/combineFeatureOverlapData.html
index 9c86be42..4718c6c6 100644
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+++ b/reference/combineFeatureOverlapData.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -89,7 +89,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/combineMetadata.html b/reference/combineMetadata.html
index b380a865..8460875c 100644
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@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -102,7 +102,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/combineSpatialCellFeatureInfo.html b/reference/combineSpatialCellFeatureInfo.html
index 481b3704..3b18a5b9 100644
--- a/reference/combineSpatialCellFeatureInfo.html
+++ b/reference/combineSpatialCellFeatureInfo.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -101,7 +101,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/combineSpatialCellMetadataInfo.html b/reference/combineSpatialCellMetadataInfo.html
index 1e435ddc..1eef7517 100644
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+++ b/reference/combineSpatialCellMetadataInfo.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -88,7 +88,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/combineToMultiPolygon.html b/reference/combineToMultiPolygon.html
index ae148145..9d1b58c9 100644
--- a/reference/combineToMultiPolygon.html
+++ b/reference/combineToMultiPolygon.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -93,7 +93,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/combine_matrices.html b/reference/combine_matrices.html
index d252569a..e8bdceec 100644
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+++ b/reference/combine_matrices.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/combine_polygons.html b/reference/combine_polygons.html
index 1fba95b3..6d0d1c1d 100644
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+++ b/reference/combine_polygons.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/combine_spatlocs.html b/reference/combine_spatlocs.html
index bea74933..34d49ff7 100644
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+++ b/reference/combine_spatlocs.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/combine_stack_spatVectors.html b/reference/combine_stack_spatVectors.html
index 552392bc..5b4a98da 100644
--- a/reference/combine_stack_spatVectors.html
+++ b/reference/combine_stack_spatVectors.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -64,7 +64,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/compatible_spatial_network.html b/reference/compatible_spatial_network.html
index e0b3b417..eb1f9d31 100644
--- a/reference/compatible_spatial_network.html
+++ b/reference/compatible_spatial_network.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -73,7 +73,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/convertGiottoLargeImageToMG.html b/reference/convertGiottoLargeImageToMG.html
index b7cc3702..ae6378aa 100644
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+++ b/reference/convertGiottoLargeImageToMG.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -148,7 +148,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/convert_mgImage_to_array_DT.html b/reference/convert_mgImage_to_array_DT.html
index de4e81a1..43bc48e3 100644
--- a/reference/convert_mgImage_to_array_DT.html
+++ b/reference/convert_mgImage_to_array_DT.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -72,7 +72,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/convert_to_full_spatial_network.html b/reference/convert_to_full_spatial_network.html
index 0a4ebbc9..9f187bbf 100644
--- a/reference/convert_to_full_spatial_network.html
+++ b/reference/convert_to_full_spatial_network.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/convert_to_reduced_spatial_network.html b/reference/convert_to_reduced_spatial_network.html
index 16b69cfa..1a45099f 100644
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+++ b/reference/convert_to_reduced_spatial_network.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/copy-generic.html b/reference/copy-generic.html
index 9670d290..6f6dce69 100644
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@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -79,7 +79,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/cor_flex.html b/reference/cor_flex.html
index b6803cc4..cf75c8b2 100644
--- a/reference/cor_flex.html
+++ b/reference/cor_flex.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -70,7 +70,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createBentoAdata.html b/reference/createBentoAdata.html
index 8e7b4970..752c18d9 100644
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+++ b/reference/createBentoAdata.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -79,7 +79,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createCellMetaObj.html b/reference/createCellMetaObj.html
index c6b21644..578ec1d0 100644
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+++ b/reference/createCellMetaObj.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -93,7 +93,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createDimObj.html b/reference/createDimObj.html
index b4b0d1d0..27325026 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -108,7 +108,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createExprObj.html b/reference/createExprObj.html
index 1466021e..87537ea3 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -98,7 +98,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createFeatMetaObj.html b/reference/createFeatMetaObj.html
index e0d98ded..fb547a1a 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -93,7 +93,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createGiottoImage.html b/reference/createGiottoImage.html
index d7b6809d..cb64573d 100644
--- a/reference/createGiottoImage.html
+++ b/reference/createGiottoImage.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -166,7 +166,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createGiottoInstructions.html b/reference/createGiottoInstructions.html
index 523de777..993b861b 100644
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+++ b/reference/createGiottoInstructions.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -143,7 +143,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createGiottoLargeImage.html b/reference/createGiottoLargeImage.html
index 3736dbb4..13503c6e 100644
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+++ b/reference/createGiottoLargeImage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -128,7 +128,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createGiottoLargeImageList.html b/reference/createGiottoLargeImageList.html
index 3ea69833..06474fc2 100644
--- a/reference/createGiottoLargeImageList.html
+++ b/reference/createGiottoLargeImageList.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -132,7 +132,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createGiottoObject.html b/reference/createGiottoObject.html
index 24ce0e91..584fd6fb 100644
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+++ b/reference/createGiottoObject.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -218,7 +218,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createGiottoObjectSubcellular.html b/reference/createGiottoObjectSubcellular.html
index fb208e1b..4121f243 100644
--- a/reference/createGiottoObjectSubcellular.html
+++ b/reference/createGiottoObjectSubcellular.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -174,7 +174,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createGiottoPoints.html b/reference/createGiottoPoints.html
index 7f3594c0..f8f6b3f1 100644
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+++ b/reference/createGiottoPoints.html
@@ -16,7 +16,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -239,7 +239,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createGiottoPolygon.html b/reference/createGiottoPolygon.html
index 77ef20eb..5536cbd9 100644
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+++ b/reference/createGiottoPolygon.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -246,7 +246,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createMetafeats.html b/reference/createMetafeats.html
index cf7ced9e..01ad2b17 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -150,7 +150,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createNearestNetObj.html b/reference/createNearestNetObj.html
index e21bcfa5..e2160eee 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -106,7 +106,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createNearestNetwork.html b/reference/createNearestNetwork.html
index d6f2cb8d..11b94800 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -175,7 +175,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createSpatEnrObj.html b/reference/createSpatEnrObj.html
index 3eec4817..54c72609 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -104,7 +104,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createSpatLocsObj.html b/reference/createSpatLocsObj.html
index 5d293cfc..68211b55 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -93,7 +93,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createSpatNetObj.html b/reference/createSpatNetObj.html
index a29de5aa..ef323a3c 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -118,7 +118,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index 5b90c991..39ea6bd8 100644
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -124,7 +124,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index a1b3c20a..77c7b767 100644
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@@ -158,7 +158,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createSpatialFeaturesKNNnetwork.html b/reference/createSpatialFeaturesKNNnetwork.html
index bf547887..edbf6cb5 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -131,7 +131,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createSpatialFeaturesKNNnetwork_dbscan.html b/reference/createSpatialFeaturesKNNnetwork_dbscan.html
index 919afe59..c548f1d1 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -108,7 +108,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createSpatialGrid.html b/reference/createSpatialGrid.html
index d11801ab..4985f6e8 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -124,7 +124,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createSpatialKNNnetwork.html b/reference/createSpatialKNNnetwork.html
index 994556f6..eae419e1 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -147,7 +147,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createSpatialNetwork.html b/reference/createSpatialNetwork.html
index 0c3188ac..c76d88ce 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -183,7 +183,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/createSpatialWeightMatrix.html b/reference/createSpatialWeightMatrix.html
index 024dff8a..cfcc7b2c 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -110,7 +110,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/create_KNNnetwork_dbscan.html b/reference/create_KNNnetwork_dbscan.html
index 8a2b570a..430e0298 100644
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+++ b/reference/create_KNNnetwork_dbscan.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/create_average_DT.html b/reference/create_average_DT.html
index 4bb888e4..d4211774 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -94,7 +94,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -99,7 +99,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -65,7 +65,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/create_cluster_matrix.html b/reference/create_cluster_matrix.html
index ed01745c..04da8902 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -98,7 +98,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/create_delaunayNetwork2D.html b/reference/create_delaunayNetwork2D.html
index 438d0980..f772dcc6 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -74,7 +74,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index 8f812c82..e61d82fe 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -67,7 +67,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -64,7 +64,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -65,7 +65,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -66,7 +66,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -69,7 +69,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index 515d1987..99abccd5 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -73,7 +73,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index 971b55ae..16d0b259 100644
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@@ -65,7 +65,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index f155f713..a03e6ea8 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -83,7 +83,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/create_giotto_points_object.html b/reference/create_giotto_points_object.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -83,7 +83,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -88,7 +88,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/create_nn_net_obj.html b/reference/create_nn_net_obj.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -67,7 +67,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -75,7 +75,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -67,7 +67,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -103,7 +103,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -65,7 +65,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -71,7 +71,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/create_spatialGrid_default_2D.html b/reference/create_spatialGrid_default_2D.html
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@@ -66,7 +66,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -67,7 +67,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -76,7 +76,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -124,7 +124,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -103,7 +103,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -91,7 +91,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -84,7 +84,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index e79b414a..e577ea37 100644
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -92,7 +92,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index fd41e721..97b44c01 100644
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@@ -121,7 +121,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -112,7 +112,7 @@ <h2 id="plotting-method-hist-">Plotting method <code>'hist'</code><a class="anch
 
 
     <footer><div class="pkgdown-footer-left">
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index f974f287..084b8c58 100644
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@@ -74,7 +74,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -76,7 +76,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -86,7 +86,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -84,7 +84,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -110,7 +110,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/extract-methods.html b/reference/extract-methods.html
index 8b9303d0..5a7e97f0 100644
--- a/reference/extract-methods.html
+++ b/reference/extract-methods.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -322,7 +322,7 @@ <h2 id="-lt-methods-1"><code>`[&lt;-`</code> methods<a class="anchor" aria-label
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/fDataDT.html b/reference/fDataDT.html
index 0f802338..22668b36 100644
--- a/reference/fDataDT.html
+++ b/reference/fDataDT.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -84,7 +84,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/featMetaObj-class.html b/reference/featMetaObj-class.html
index d4b48436..cc20ea6f 100644
--- a/reference/featMetaObj-class.html
+++ b/reference/featMetaObj-class.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -80,7 +80,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/featType-generic.html b/reference/featType-generic.html
index a884eaa5..05be02a5 100644
--- a/reference/featType-generic.html
+++ b/reference/featType-generic.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -80,7 +80,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/featureNetwork-class.html b/reference/featureNetwork-class.html
index 35016b1b..014de26e 100644
--- a/reference/featureNetwork-class.html
+++ b/reference/featureNetwork-class.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -81,7 +81,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/filter_network.html b/reference/filter_network.html
index c5d3d6e0..58164096 100644
--- a/reference/filter_network.html
+++ b/reference/filter_network.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -74,7 +74,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/find_grid_2D.html b/reference/find_grid_2D.html
index 0928a249..98bf87bf 100644
--- a/reference/find_grid_2D.html
+++ b/reference/find_grid_2D.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/find_grid_3D.html b/reference/find_grid_3D.html
index 33a8943d..44173d8a 100644
--- a/reference/find_grid_3D.html
+++ b/reference/find_grid_3D.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/find_grid_x.html b/reference/find_grid_x.html
index 384d76df..32f0dfe6 100644
--- a/reference/find_grid_x.html
+++ b/reference/find_grid_x.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/find_grid_y.html b/reference/find_grid_y.html
index aa8dc283..40c9bcbd 100644
--- a/reference/find_grid_y.html
+++ b/reference/find_grid_y.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/find_grid_z.html b/reference/find_grid_z.html
index 52832620..0e7d09db 100644
--- a/reference/find_grid_z.html
+++ b/reference/find_grid_z.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/find_terra_writeRaster_dataType.html b/reference/find_terra_writeRaster_dataType.html
index e12e1b91..f4d2a762 100644
--- a/reference/find_terra_writeRaster_dataType.html
+++ b/reference/find_terra_writeRaster_dataType.html
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -113,7 +113,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/fix_multipart_geoms.html b/reference/fix_multipart_geoms.html
index 4933206b..588abb44 100644
--- a/reference/fix_multipart_geoms.html
+++ b/reference/fix_multipart_geoms.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/flip-generic.html b/reference/flip-generic.html
index 2fa1ddb6..d5b69570 100644
--- a/reference/flip-generic.html
+++ b/reference/flip-generic.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -113,7 +113,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/gefToGiotto.html b/reference/gefToGiotto.html
index f47408f7..f6992323 100644
--- a/reference/gefToGiotto.html
+++ b/reference/gefToGiotto.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -87,7 +87,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/generate_grid.html b/reference/generate_grid.html
index 219fd5fe..fba104d5 100644
--- a/reference/generate_grid.html
+++ b/reference/generate_grid.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -89,7 +89,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/getCellMetadata.html b/reference/getCellMetadata.html
index f97a5a58..b31c613c 100644
--- a/reference/getCellMetadata.html
+++ b/reference/getCellMetadata.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -98,7 +98,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getDimReduction.html b/reference/getDimReduction.html
index f53434d0..cff6f20a 100644
--- a/reference/getDimReduction.html
+++ b/reference/getDimReduction.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -139,7 +139,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getExpression.html b/reference/getExpression.html
index bcdddde4..b1f21f36 100644
--- a/reference/getExpression.html
+++ b/reference/getExpression.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -129,7 +129,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getFeatureInfo.html b/reference/getFeatureInfo.html
index 2761c93a..ebc87a29 100644
--- a/reference/getFeatureInfo.html
+++ b/reference/getFeatureInfo.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -112,7 +112,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getFeatureMetadata.html b/reference/getFeatureMetadata.html
index 08966594..fb098e3d 100644
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+++ b/reference/getFeatureMetadata.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -98,7 +98,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getGiottoImage.html b/reference/getGiottoImage.html
index 7eb2ae95..f71b4a23 100644
--- a/reference/getGiottoImage.html
+++ b/reference/getGiottoImage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -112,7 +112,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getMultiomics.html b/reference/getMultiomics.html
index 8cac34d6..b7bfa483 100644
--- a/reference/getMultiomics.html
+++ b/reference/getMultiomics.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -122,7 +122,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getNearestNetwork.html b/reference/getNearestNetwork.html
index dd2e7c53..26030dbb 100644
--- a/reference/getNearestNetwork.html
+++ b/reference/getNearestNetwork.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -133,7 +133,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getPolygonInfo.html b/reference/getPolygonInfo.html
index 678ee176..95981fa6 100644
--- a/reference/getPolygonInfo.html
+++ b/reference/getPolygonInfo.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -116,7 +116,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/getRainbowColors.html b/reference/getRainbowColors.html
index e3129c79..96911bda 100644
--- a/reference/getRainbowColors.html
+++ b/reference/getRainbowColors.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -75,7 +75,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getSpatialEnrichment.html b/reference/getSpatialEnrichment.html
index 55c81b18..b59f33ea 100644
--- a/reference/getSpatialEnrichment.html
+++ b/reference/getSpatialEnrichment.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -133,7 +133,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/getSpatialGrid.html b/reference/getSpatialGrid.html
index 9cfc4f49..9458b7b4 100644
--- a/reference/getSpatialGrid.html
+++ b/reference/getSpatialGrid.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -122,7 +122,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/getSpatialLocations.html b/reference/getSpatialLocations.html
index b9f0b39c..0b5a29e0 100644
--- a/reference/getSpatialLocations.html
+++ b/reference/getSpatialLocations.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -136,7 +136,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/getSpatialNetwork.html b/reference/getSpatialNetwork.html
index aeb9b24a..2ff8d084 100644
--- a/reference/getSpatialNetwork.html
+++ b/reference/getSpatialNetwork.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -128,7 +128,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_NearestNetwork.html b/reference/get_NearestNetwork.html
index 516ab1e1..75eb3294 100644
--- a/reference/get_NearestNetwork.html
+++ b/reference/get_NearestNetwork.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -133,7 +133,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_adj_rescale_img.html b/reference/get_adj_rescale_img.html
index 447df85d..c9a09578 100644
--- a/reference/get_adj_rescale_img.html
+++ b/reference/get_adj_rescale_img.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_args.html b/reference/get_args.html
index 451ed09b..4204e098 100644
--- a/reference/get_args.html
+++ b/reference/get_args.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -70,7 +70,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_cell_id.html b/reference/get_cell_id.html
index fbb798f4..d280aa33 100644
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+++ b/reference/get_cell_id.html
@@ -12,7 +12,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -124,7 +124,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_cell_metadata.html b/reference/get_cell_metadata.html
index 9646978c..7e4dcb95 100644
--- a/reference/get_cell_metadata.html
+++ b/reference/get_cell_metadata.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -98,7 +98,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_dimReduction.html b/reference/get_dimReduction.html
index a9590cfe..28a32ab7 100644
--- a/reference/get_dimReduction.html
+++ b/reference/get_dimReduction.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -139,7 +139,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/get_distance.html b/reference/get_distance.html
index b1105860..d042b024 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -73,7 +73,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_expression_values.html b/reference/get_expression_values.html
index ef939c27..2a50b5fc 100644
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+++ b/reference/get_expression_values.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -96,7 +96,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_feat_id.html b/reference/get_feat_id.html
index e6a88864..2209b492 100644
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+++ b/reference/get_feat_id.html
@@ -12,7 +12,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -118,7 +118,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_feature_info.html b/reference/get_feature_info.html
index bc0a1dda..f04920cb 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -119,7 +119,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_feature_metadata.html b/reference/get_feature_metadata.html
index d7c81a2d..99804db9 100644
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+++ b/reference/get_feature_metadata.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -98,7 +98,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/get_giottoImage.html b/reference/get_giottoImage.html
index c9352783..5d7fbbfb 100644
--- a/reference/get_giottoImage.html
+++ b/reference/get_giottoImage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -112,7 +112,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/get_giottoImage_MG.html b/reference/get_giottoImage_MG.html
index fcf6ff22..6b085dc1 100644
--- a/reference/get_giottoImage_MG.html
+++ b/reference/get_giottoImage_MG.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_giottoLargeImage.html b/reference/get_giottoLargeImage.html
index 73ce6182..874cca4c 100644
--- a/reference/get_giottoLargeImage.html
+++ b/reference/get_giottoLargeImage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/get_img_minmax.html b/reference/get_img_minmax.html
index c912a131..ed68e897 100644
--- a/reference/get_img_minmax.html
+++ b/reference/get_img_minmax.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -70,7 +70,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/get_multiomics.html b/reference/get_multiomics.html
index 864839c8..af7cd9bc 100644
--- a/reference/get_multiomics.html
+++ b/reference/get_multiomics.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -122,7 +122,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_polygon_info.html b/reference/get_polygon_info.html
index c5fac528..99e815c6 100644
--- a/reference/get_polygon_info.html
+++ b/reference/get_polygon_info.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -116,7 +116,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_prev_fname.html b/reference/get_prev_fname.html
index c4858760..8c6d1a15 100644
--- a/reference/get_prev_fname.html
+++ b/reference/get_prev_fname.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -70,7 +70,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_spatialGrid.html b/reference/get_spatialGrid.html
index c0b18b93..ff2ce7c3 100644
--- a/reference/get_spatialGrid.html
+++ b/reference/get_spatialGrid.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -122,7 +122,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_spatialNetwork.html b/reference/get_spatialNetwork.html
index 149482a4..0c3ec4da 100644
--- a/reference/get_spatialNetwork.html
+++ b/reference/get_spatialNetwork.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -128,7 +128,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/get_spatial_enrichment.html b/reference/get_spatial_enrichment.html
index a521906e..342e6a84 100644
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+++ b/reference/get_spatial_enrichment.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -133,7 +133,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_spatial_locations.html b/reference/get_spatial_locations.html
index d5320c1f..4adae152 100644
--- a/reference/get_spatial_locations.html
+++ b/reference/get_spatial_locations.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -136,7 +136,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/giotto-class.html b/reference/giotto-class.html
index 90c17ee5..de70a33c 100644
--- a/reference/giotto-class.html
+++ b/reference/giotto-class.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -159,7 +159,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/giottoImage-class.html b/reference/giottoImage-class.html
index 70b3fa4c..2cc6a01e 100644
--- a/reference/giottoImage-class.html
+++ b/reference/giottoImage-class.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -99,7 +99,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/giottoLargeImage-class.html b/reference/giottoLargeImage-class.html
index 4d6ff0b8..73470b72 100644
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+++ b/reference/giottoLargeImage-class.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -104,7 +104,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/giottoMasterToSuite.html b/reference/giottoMasterToSuite.html
index 52f90047..87318f4b 100644
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+++ b/reference/giottoMasterToSuite.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/giottoPoints-class.html b/reference/giottoPoints-class.html
index 4e81a941..dac7829b 100644
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+++ b/reference/giottoPoints-class.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -81,7 +81,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/giottoPolygon-class.html b/reference/giottoPolygon-class.html
index 3da198f4..8f15c10c 100644
--- a/reference/giottoPolygon-class.html
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@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -85,7 +85,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/giottoToAnnData.html b/reference/giottoToAnnData.html
index 4656f941..7950e5b5 100644
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@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -114,7 +114,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/giottoToSeurat.html b/reference/giottoToSeurat.html
index 7d4b5a76..544de6f7 100644
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+++ b/reference/giottoToSeurat.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -87,7 +87,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/giottoToSeuratV4.html b/reference/giottoToSeuratV4.html
index a34819b5..8c132b8d 100644
--- a/reference/giottoToSeuratV4.html
+++ b/reference/giottoToSeuratV4.html
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -86,7 +86,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/giottoToSeuratV5.html b/reference/giottoToSeuratV5.html
index e7089193..ef3121c6 100644
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+++ b/reference/giottoToSeuratV5.html
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -86,7 +86,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/giottoToSpatialExperiment.html b/reference/giottoToSpatialExperiment.html
index 2d7f502c..d505007a 100644
--- a/reference/giottoToSpatialExperiment.html
+++ b/reference/giottoToSpatialExperiment.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -85,7 +85,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/giotto_alloc_dt_slots.html b/reference/giotto_alloc_dt_slots.html
index a16dea12..3c75cd0c 100644
--- a/reference/giotto_alloc_dt_slots.html
+++ b/reference/giotto_alloc_dt_slots.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -69,7 +69,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/hexVertices.html b/reference/hexVertices.html
index b913dd7d..2eed3577 100644
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+++ b/reference/hexVertices.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -85,7 +85,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/identify_background_range_polygons.html b/reference/identify_background_range_polygons.html
index 30440583..50604018 100644
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+++ b/reference/identify_background_range_polygons.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/index.html b/reference/index.html
index 2626846c..328ec01b 100644
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@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -1878,7 +1878,7 @@ <h2 id="deprecated">Deprecated<a class="anchor" aria-label="anchor" href="#depre
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/init_cell_metadata.html b/reference/init_cell_metadata.html
index 27af0722..0bee4a35 100644
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+++ b/reference/init_cell_metadata.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -71,7 +71,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -73,7 +73,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -71,7 +71,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -77,7 +77,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -94,7 +94,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -98,7 +98,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -89,7 +89,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -72,7 +72,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_feature_info_names.html b/reference/list_feature_info_names.html
index feaa3f92..df902622 100644
--- a/reference/list_feature_info_names.html
+++ b/reference/list_feature_info_names.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -72,7 +72,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_giotto_data.html b/reference/list_giotto_data.html
index d982ec93..79387b90 100644
--- a/reference/list_giotto_data.html
+++ b/reference/list_giotto_data.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -80,7 +80,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_images.html b/reference/list_images.html
index 09cda96b..99244ed8 100644
--- a/reference/list_images.html
+++ b/reference/list_images.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_images_names.html b/reference/list_images_names.html
index 16b520a9..6194581d 100644
--- a/reference/list_images_names.html
+++ b/reference/list_images_names.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_nearest_networks.html b/reference/list_nearest_networks.html
index 68c3a077..16306fb4 100644
--- a/reference/list_nearest_networks.html
+++ b/reference/list_nearest_networks.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -94,7 +94,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_nearest_networks_names.html b/reference/list_nearest_networks_names.html
index f10cbb3b..e2d0ac4e 100644
--- a/reference/list_nearest_networks_names.html
+++ b/reference/list_nearest_networks_names.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -93,7 +93,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_enrichments.html b/reference/list_spatial_enrichments.html
index b6e2c07e..ea5c73c7 100644
--- a/reference/list_spatial_enrichments.html
+++ b/reference/list_spatial_enrichments.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -80,7 +80,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_enrichments_names.html b/reference/list_spatial_enrichments_names.html
index 43c9c6d2..9c9e6488 100644
--- a/reference/list_spatial_enrichments_names.html
+++ b/reference/list_spatial_enrichments_names.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -80,7 +80,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_grids.html b/reference/list_spatial_grids.html
index a00ca141..e97a176f 100644
--- a/reference/list_spatial_grids.html
+++ b/reference/list_spatial_grids.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -89,7 +89,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_grids_names.html b/reference/list_spatial_grids_names.html
index bbc871a0..9d832d44 100644
--- a/reference/list_spatial_grids_names.html
+++ b/reference/list_spatial_grids_names.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -89,7 +89,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_info.html b/reference/list_spatial_info.html
index 00b547e0..fbe09f68 100644
--- a/reference/list_spatial_info.html
+++ b/reference/list_spatial_info.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -72,7 +72,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_info_names.html b/reference/list_spatial_info_names.html
index c67c2d79..9e07af95 100644
--- a/reference/list_spatial_info_names.html
+++ b/reference/list_spatial_info_names.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -72,7 +72,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_locations.html b/reference/list_spatial_locations.html
index 59dbb75d..920bb770 100644
--- a/reference/list_spatial_locations.html
+++ b/reference/list_spatial_locations.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -80,7 +80,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_locations_names.html b/reference/list_spatial_locations_names.html
index acb26c65..a70cdb42 100644
--- a/reference/list_spatial_locations_names.html
+++ b/reference/list_spatial_locations_names.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_networks.html b/reference/list_spatial_networks.html
index e76d8aff..e5d083a0 100644
--- a/reference/list_spatial_networks.html
+++ b/reference/list_spatial_networks.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -80,7 +80,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/list_spatial_networks_names.html b/reference/list_spatial_networks_names.html
index 0443f43d..66453508 100644
--- a/reference/list_spatial_networks_names.html
+++ b/reference/list_spatial_networks_names.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/loadGiotto.html b/reference/loadGiotto.html
index 38a8131e..7e7aeab4 100644
--- a/reference/loadGiotto.html
+++ b/reference/loadGiotto.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -103,7 +103,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/makePseudoVisium.html b/reference/makePseudoVisium.html
index 441053a5..5f4ed3ea 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -94,7 +94,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/mean_flex.html b/reference/mean_flex.html
index 5668827f..54c55416 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -70,7 +70,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index cf0666ff..6da3846c 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -68,7 +68,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/merge_spatial_locs_feat_info.html b/reference/merge_spatial_locs_feat_info.html
index 3fb7c1df..231fa13b 100644
--- a/reference/merge_spatial_locs_feat_info.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index 76fc1928..866884d0 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -61,7 +61,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/my_arowMeans.html b/reference/my_arowMeans.html
index ea8232da..6e0c6074 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/my_growMeans.html b/reference/my_growMeans.html
index 72b2d386..d3757671 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -70,7 +70,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/my_rowMeans.html b/reference/my_rowMeans.html
index 413b3a45..e3a5173f 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -74,7 +74,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/nnDT_to_kNN.html b/reference/nnDT_to_kNN.html
index 31cb3b23..ef0ac9d5 100644
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+++ b/reference/nnDT_to_kNN.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -72,7 +72,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/nnNetObj-class.html b/reference/nnNetObj-class.html
index 89fd3351..1230b84e 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -88,7 +88,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/objHistory.html b/reference/objHistory.html
index 20644b7a..861ec677 100644
--- a/reference/objHistory.html
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/objName-generic.html b/reference/objName-generic.html
index 8b3f93a3..242de553 100644
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+++ b/reference/objName-generic.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -99,7 +99,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/overlapImagesToMatrix.html b/reference/overlapImagesToMatrix.html
index 1c3b8889..511b1928 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -114,7 +114,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/overlapToMatrix.html b/reference/overlapToMatrix.html
index 60e12661..f5b9dd35 100644
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@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -159,7 +159,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/overlapToMatrixMultiPoly.html b/reference/overlapToMatrixMultiPoly.html
index aab4a456..1fd3f811 100644
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@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -102,7 +102,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/overlap_points_per_polygon.html b/reference/overlap_points_per_polygon.html
index aad18925..b531f458 100644
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+++ b/reference/overlap_points_per_polygon.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -64,7 +64,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/overlap_points_per_polygon_wrapped.html b/reference/overlap_points_per_polygon_wrapped.html
index bb69dae2..d6d5826c 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -63,7 +63,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/overlap_points_single_polygon.html b/reference/overlap_points_single_polygon.html
index e2d47d2e..c89a050f 100644
--- a/reference/overlap_points_single_polygon.html
+++ b/reference/overlap_points_single_polygon.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/overlaps-generic.html b/reference/overlaps-generic.html
index c777a8d4..0b515179 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/pDataDT.html b/reference/pDataDT.html
index 185c1eff..a9e1a19c 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -84,7 +84,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/plot-generic.html b/reference/plot-generic.html
index d7bf9170..a3b7d829 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -121,7 +121,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/plotGiottoImage.html b/reference/plotGiottoImage.html
index fc6cc2ff..9a4dca62 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -140,7 +140,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/plot_auto_largeImage_resample.html b/reference/plot_auto_largeImage_resample.html
index 09ab73d8..70164fd8 100644
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+++ b/reference/plot_auto_largeImage_resample.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -191,7 +191,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/plot_giottoImage_MG.html b/reference/plot_giottoImage_MG.html
index e378fbfd..db974b44 100644
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+++ b/reference/plot_giottoImage_MG.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -80,7 +80,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/plot_giottoLargeImage.html b/reference/plot_giottoLargeImage.html
index 8caa9747..dff2bb18 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -158,7 +158,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index a1629d85..4f1d2b90 100644
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@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -146,7 +146,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/polygon_to_raster.html b/reference/polygon_to_raster.html
index a6d326a8..6c6feebe 100644
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+++ b/reference/polygon_to_raster.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -71,7 +71,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/polygon_to_raster_OLD.html b/reference/polygon_to_raster_OLD.html
index e4af0bc3..88bc47aa 100644
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@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -62,7 +62,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/print_leaf.html b/reference/print_leaf.html
index 3287128e..f315e310 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -83,7 +83,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/prov-generic.html b/reference/prov-generic.html
index 467823e3..5504f8ce 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -80,7 +80,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/prov_match.html b/reference/prov_match.html
index 0c958c8e..24085e62 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -70,7 +70,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/py_install_prompt.html b/reference/py_install_prompt.html
index a060d3a8..95511d5f 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -70,7 +70,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/r_spatial_conversions.html b/reference/r_spatial_conversions.html
index 0ec4c47e..450fd7f1 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -150,7 +150,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/rbind-generic.html b/reference/rbind-generic.html
index abfd08a9..2b0dcf6d 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -85,7 +85,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -12,7 +12,7 @@
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@@ -89,7 +89,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/rbind2_giotto_polygon_homo.html b/reference/rbind2_giotto_polygon_homo.html
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@@ -73,7 +73,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -93,7 +93,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -114,7 +114,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -98,7 +98,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -73,7 +73,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -81,7 +81,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index 949abbc2..7744b00b 100644
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@@ -88,7 +88,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -112,7 +112,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index fcc808ba..d83ef724 100644
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@@ -88,7 +88,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -97,7 +97,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -83,7 +83,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/read_cell_metadata.html b/reference/read_cell_metadata.html
index f4beb2e6..3618098c 100644
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@@ -8,7 +8,7 @@
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -103,7 +103,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -77,7 +77,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -88,7 +88,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -132,7 +132,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
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+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/reconnect_giottoLargeImage.html b/reference/reconnect_giottoLargeImage.html
index 7152d089..fa3f868f 100644
--- a/reference/reconnect_giottoLargeImage.html
+++ b/reference/reconnect_giottoLargeImage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/reconnect_image_object.html b/reference/reconnect_image_object.html
index 9fb67c51..fb6a7477 100644
--- a/reference/reconnect_image_object.html
+++ b/reference/reconnect_image_object.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -89,7 +89,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/rectVertices.html b/reference/rectVertices.html
index 0cba3ca4..5ce3a57b 100644
--- a/reference/rectVertices.html
+++ b/reference/rectVertices.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -84,7 +84,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/removeCellAnnotation.html b/reference/removeCellAnnotation.html
index 27b16411..27195475 100644
--- a/reference/removeCellAnnotation.html
+++ b/reference/removeCellAnnotation.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -98,7 +98,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/removeFeatAnnotation.html b/reference/removeFeatAnnotation.html
index 24106da6..975cda86 100644
--- a/reference/removeFeatAnnotation.html
+++ b/reference/removeFeatAnnotation.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -98,7 +98,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/removeGiottoEnvironment.html b/reference/removeGiottoEnvironment.html
index f9672ea4..1212a769 100644
--- a/reference/removeGiottoEnvironment.html
+++ b/reference/removeGiottoEnvironment.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -77,7 +77,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/replaceGiottoInstructions.html b/reference/replaceGiottoInstructions.html
index a3b696d5..15471f80 100644
--- a/reference/replaceGiottoInstructions.html
+++ b/reference/replaceGiottoInstructions.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -83,7 +83,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/rescale-generic.html b/reference/rescale-generic.html
index 3d261332..514d52c4 100644
--- a/reference/rescale-generic.html
+++ b/reference/rescale-generic.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -100,7 +100,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/rescalePolygons.html b/reference/rescalePolygons.html
index ff053f65..ce8246da 100644
--- a/reference/rescalePolygons.html
+++ b/reference/rescalePolygons.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -104,7 +104,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/rescale_polygons.html b/reference/rescale_polygons.html
index ce4a31c2..7938419e 100644
--- a/reference/rescale_polygons.html
+++ b/reference/rescale_polygons.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/return_giotto_environment_path.html b/reference/return_giotto_environment_path.html
index 439d18ff..85654c22 100644
--- a/reference/return_giotto_environment_path.html
+++ b/reference/return_giotto_environment_path.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/return_giotto_environment_path_executable.html b/reference/return_giotto_environment_path_executable.html
index ee622a6a..546c89b3 100644
--- a/reference/return_giotto_environment_path_executable.html
+++ b/reference/return_giotto_environment_path_executable.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/rotate_spatial_locations.html b/reference/rotate_spatial_locations.html
index 4cad7e4f..babfa7b3 100644
--- a/reference/rotate_spatial_locations.html
+++ b/reference/rotate_spatial_locations.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -84,7 +84,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/row-plus-colnames-generic.html b/reference/row-plus-colnames-generic.html
index cf8ea86a..360b29be 100644
--- a/reference/row-plus-colnames-generic.html
+++ b/reference/row-plus-colnames-generic.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/rowMeans_flex.html b/reference/rowMeans_flex.html
index c9493a87..75661fc7 100644
--- a/reference/rowMeans_flex.html
+++ b/reference/rowMeans_flex.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/rowSums_flex.html b/reference/rowSums_flex.html
index 9d4a326b..ab8559ed 100644
--- a/reference/rowSums_flex.html
+++ b/reference/rowSums_flex.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/saveGiotto.html b/reference/saveGiotto.html
index 3752e410..3a1ee17e 100644
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+++ b/reference/saveGiotto.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -120,7 +120,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/scale_spatial_locations.html b/reference/scale_spatial_locations.html
index edd11617..167f96df 100644
--- a/reference/scale_spatial_locations.html
+++ b/reference/scale_spatial_locations.html
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -91,7 +91,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/select_gimage.html b/reference/select_gimage.html
index 653d9bce..5bf7f811 100644
--- a/reference/select_gimage.html
+++ b/reference/select_gimage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -68,7 +68,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setCellMetadata.html b/reference/setCellMetadata.html
index 4d3d2de2..c1029a7f 100644
--- a/reference/setCellMetadata.html
+++ b/reference/setCellMetadata.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -139,7 +139,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setDimReduction.html b/reference/setDimReduction.html
index 068589a3..37536475 100644
--- a/reference/setDimReduction.html
+++ b/reference/setDimReduction.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -161,7 +161,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setExpression.html b/reference/setExpression.html
index 6e58a0b7..3cca91db 100644
--- a/reference/setExpression.html
+++ b/reference/setExpression.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -148,7 +148,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setFeatureInfo.html b/reference/setFeatureInfo.html
index d621b98c..b0510b83 100644
--- a/reference/setFeatureInfo.html
+++ b/reference/setFeatureInfo.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -127,7 +127,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setFeatureMetadata.html b/reference/setFeatureMetadata.html
index ae7d0e0b..62a8905c 100644
--- a/reference/setFeatureMetadata.html
+++ b/reference/setFeatureMetadata.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -139,7 +139,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setGiotto.html b/reference/setGiotto.html
index 1e2805da..f345144d 100644
--- a/reference/setGiotto.html
+++ b/reference/setGiotto.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -108,7 +108,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setGiottoImage.html b/reference/setGiottoImage.html
index 5da82892..9a42abc9 100644
--- a/reference/setGiottoImage.html
+++ b/reference/setGiottoImage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -141,7 +141,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setMultiomics.html b/reference/setMultiomics.html
index 63d89125..8fc6078a 100644
--- a/reference/setMultiomics.html
+++ b/reference/setMultiomics.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -141,7 +141,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setNearestNetwork.html b/reference/setNearestNetwork.html
index 0331e2ec..08db8f80 100644
--- a/reference/setNearestNetwork.html
+++ b/reference/setNearestNetwork.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -154,7 +154,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setPolygonInfo.html b/reference/setPolygonInfo.html
index de19749b..3c7c6323 100644
--- a/reference/setPolygonInfo.html
+++ b/reference/setPolygonInfo.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -151,7 +151,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/setSpatialEnrichment.html b/reference/setSpatialEnrichment.html
index 64098057..7af5ce49 100644
--- a/reference/setSpatialEnrichment.html
+++ b/reference/setSpatialEnrichment.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -148,7 +148,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/setSpatialGrid.html b/reference/setSpatialGrid.html
index 6e9194b8..8073dc66 100644
--- a/reference/setSpatialGrid.html
+++ b/reference/setSpatialGrid.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -142,7 +142,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/setSpatialLocations.html b/reference/setSpatialLocations.html
index 4eedb05d..13d2a99b 100644
--- a/reference/setSpatialLocations.html
+++ b/reference/setSpatialLocations.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -149,7 +149,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/setSpatialNetwork.html b/reference/setSpatialNetwork.html
index 251ba23a..65f34e45 100644
--- a/reference/setSpatialNetwork.html
+++ b/reference/setSpatialNetwork.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -143,7 +143,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/reference/set_NearestNetwork.html b/reference/set_NearestNetwork.html
index 07a1585e..aef3dad4 100644
--- a/reference/set_NearestNetwork.html
+++ b/reference/set_NearestNetwork.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -159,7 +159,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_cell_id.html b/reference/set_cell_id.html
index bbe87382..642d0fc5 100644
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+++ b/reference/set_cell_id.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -144,7 +144,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/set_cell_metadata.html b/reference/set_cell_metadata.html
index b93039b4..d3824e23 100644
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+++ b/reference/set_cell_metadata.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -145,7 +145,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_default_feat_type.html b/reference/set_default_feat_type.html
index 6d136b07..a957297e 100644
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+++ b/reference/set_default_feat_type.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -77,7 +77,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_default_spat_unit.html b/reference/set_default_spat_unit.html
index 369d911f..50e66c14 100644
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+++ b/reference/set_default_spat_unit.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -73,7 +73,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_dimReduction.html b/reference/set_dimReduction.html
index 406e4ccf..91f74a09 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -163,7 +163,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_expression_values.html b/reference/set_expression_values.html
index 92e31647..de31fdcf 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -152,7 +152,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/set_feat_id.html b/reference/set_feat_id.html
index a6cfb26c..32c6da5a 100644
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+++ b/reference/set_feat_id.html
@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -145,7 +145,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_feature_info.html b/reference/set_feature_info.html
index 6f51a5aa..fa54d3fe 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -143,7 +143,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_feature_metadata.html b/reference/set_feature_metadata.html
index edd4b33c..dd2d5044 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -145,7 +145,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_giottoImage.html b/reference/set_giottoImage.html
index 439be3f4..258e6f4a 100644
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+++ b/reference/set_giottoImage.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -141,7 +141,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_giottoImage_MG.html b/reference/set_giottoImage_MG.html
index 59b05fea..9dd5ca6e 100644
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+++ b/reference/set_giottoImage_MG.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -84,7 +84,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/set_giottoLargeImage.html b/reference/set_giottoLargeImage.html
index c8d33f30..7a551125 100644
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+++ b/reference/set_giottoLargeImage.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -84,7 +84,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_giotto_python_path.html b/reference/set_giotto_python_path.html
index ba580483..69098197 100644
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+++ b/reference/set_giotto_python_path.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -79,7 +79,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_multiomics.html b/reference/set_multiomics.html
index b00a930b..aa28f48e 100644
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+++ b/reference/set_multiomics.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -141,7 +141,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_polygon_info.html b/reference/set_polygon_info.html
index 3b8f0642..2909e97a 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -133,7 +133,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_spatialGrid.html b/reference/set_spatialGrid.html
index 03558818..2385df4d 100644
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+++ b/reference/set_spatialGrid.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -142,7 +142,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_spatialNetwork.html b/reference/set_spatialNetwork.html
index 60dc8cba..1457a8a8 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -148,7 +148,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_spatial_enrichment.html b/reference/set_spatial_enrichment.html
index dc1e9ac1..aaeaa177 100644
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+++ b/reference/set_spatial_enrichment.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -153,7 +153,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/set_spatial_locations.html b/reference/set_spatial_locations.html
index b63bf456..1168ffad 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -161,7 +161,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/seuratToGiotto.html b/reference/seuratToGiotto.html
index 7c8337f8..729f048f 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -87,7 +87,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/seuratToGiottoV4.html b/reference/seuratToGiottoV4.html
index 270daf8e..3ef2f76f 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -91,7 +91,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/seuratToGiottoV5.html b/reference/seuratToGiottoV5.html
index e8bf621d..70dc3f48 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -91,7 +91,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/shift_spatial_locations.html b/reference/shift_spatial_locations.html
index a68b817a..0c042eec 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -103,7 +103,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/shift_spatial_network.html b/reference/shift_spatial_network.html
index 6fd43a5a..91213c0d 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -82,7 +82,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/show-methods.html b/reference/show-methods.html
index c15a39ba..79eda4b3 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -121,7 +121,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoCellMetadata.html b/reference/showGiottoCellMetadata.html
index 199fcadc..fedd264c 100644
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@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -91,7 +91,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoDimRed.html b/reference/showGiottoDimRed.html
index 4ebea399..6223a71f 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -95,7 +95,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoExpression.html b/reference/showGiottoExpression.html
index 2e137b62..8b2685cf 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -95,7 +95,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoFeatInfo.html b/reference/showGiottoFeatInfo.html
index 3eab37d0..673edb74 100644
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+++ b/reference/showGiottoFeatInfo.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -81,7 +81,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoFeatMetadata.html b/reference/showGiottoFeatMetadata.html
index 2387b914..ba7751e5 100644
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+++ b/reference/showGiottoFeatMetadata.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -91,7 +91,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoImageNames.html b/reference/showGiottoImageNames.html
index 05243249..4f2da570 100644
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+++ b/reference/showGiottoImageNames.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -87,7 +87,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoInstructions.html b/reference/showGiottoInstructions.html
index 2ddac6b6..dcc09ec2 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -72,7 +72,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoNearestNetworks.html b/reference/showGiottoNearestNetworks.html
index ceac8a4f..b6ea9d0c 100644
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+++ b/reference/showGiottoNearestNetworks.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -91,7 +91,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoSpatEnrichments.html b/reference/showGiottoSpatEnrichments.html
index 92c83f38..59963dd6 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -91,7 +91,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoSpatGrids.html b/reference/showGiottoSpatGrids.html
index 588c7b57..0d293e12 100644
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+++ b/reference/showGiottoSpatGrids.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -91,7 +91,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/showGiottoSpatLocs.html b/reference/showGiottoSpatLocs.html
index 3c485d96..0e7be59f 100644
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+++ b/reference/showGiottoSpatLocs.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -91,7 +91,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoSpatNetworks.html b/reference/showGiottoSpatNetworks.html
index 9d252cba..468d67db 100644
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -91,7 +91,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGiottoSpatialInfo.html b/reference/showGiottoSpatialInfo.html
index 539d968e..ab337ebe 100644
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     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -81,7 +81,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showGrids.html b/reference/showGrids.html
index 87ab1cd0..c56ebf77 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -77,7 +77,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/showNetworks.html b/reference/showNetworks.html
index bc438b23..61515925 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -77,7 +77,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/showProcessingSteps.html b/reference/showProcessingSteps.html
index 93dc4eac..d90f85aa 100644
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+++ b/reference/showProcessingSteps.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -75,7 +75,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/smoothGiottoPolygons.html b/reference/smoothGiottoPolygons.html
index 2a37127e..44513320 100644
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+++ b/reference/smoothGiottoPolygons.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -98,7 +98,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatEnrObj-class.html b/reference/spatEnrObj-class.html
index 99e902a0..198a4ecd 100644
--- a/reference/spatEnrObj-class.html
+++ b/reference/spatEnrObj-class.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -88,7 +88,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatIDs-generic.html b/reference/spatIDs-generic.html
index 9dc1979f..94c9d0e6 100644
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+++ b/reference/spatIDs-generic.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -129,7 +129,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatLocsObj-class.html b/reference/spatLocsObj-class.html
index e98d227f..524e5d75 100644
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+++ b/reference/spatLocsObj-class.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -76,7 +76,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatQueryGiottoPolygons.html b/reference/spatQueryGiottoPolygons.html
index 25bdde1b..0cb9b1e7 100644
--- a/reference/spatQueryGiottoPolygons.html
+++ b/reference/spatQueryGiottoPolygons.html
@@ -12,7 +12,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -109,7 +109,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatShift.html b/reference/spatShift.html
index 4a9d134f..6b532251 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -105,7 +105,7 @@ <h2 id="methods-by-class-">Methods (by class)<a class="anchor" aria-label="ancho
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatUnit-generic.html b/reference/spatUnit-generic.html
index 393c3814..5f1ee631 100644
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+++ b/reference/spatUnit-generic.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -88,7 +88,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatVector_to_dt.html b/reference/spatVector_to_dt.html
index 562351fa..72e3f37a 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -59,7 +59,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index afc4f6b3..2e570e9f 100644
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@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -62,7 +62,7 @@ <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage">
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spat_net_to_igraph.html b/reference/spat_net_to_igraph.html
index b93be48f..e29143c7 100644
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+++ b/reference/spat_net_to_igraph.html
@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -91,7 +91,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatialExperimentToGiotto.html b/reference/spatialExperimentToGiotto.html
index 3afd16b5..328f3416 100644
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+++ b/reference/spatialExperimentToGiotto.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -108,7 +108,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatialGridObj-class.html b/reference/spatialGridObj-class.html
index 8a75419c..9317227b 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -101,7 +101,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spatialNetworkObj-class.html b/reference/spatialNetworkObj-class.html
index 86105c55..78560796 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -110,7 +110,7 @@ <h2 id="slots">Slots<a class="anchor" aria-label="anchor" href="#slots"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index a49ad7f9..0eb7f502 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
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@@ -74,7 +74,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index 3bc449d1..738b64a7 100644
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@@ -119,7 +119,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/spline_poly.html b/reference/spline_poly.html
index a80a9bc7..975f97dd 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -78,7 +78,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index df6c7352..dd565676 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -80,7 +80,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/stitchFieldCoordinates.html b/reference/stitchFieldCoordinates.html
index 405a6868..8fc72436 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -121,7 +121,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/stitchGiottoLargeImage.html b/reference/stitchGiottoLargeImage.html
index c67ea2fe..ff5054ab 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -203,7 +203,7 @@ <h2 id="datatype">dataType<a class="anchor" aria-label="anchor" href="#datatype"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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index e5576bbb..adbe23a0 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -74,7 +74,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/subsetGiotto.html b/reference/subsetGiotto.html
index 687c450a..7ff478f0 100644
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -140,7 +140,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/subsetGiottoLocs.html b/reference/subsetGiottoLocs.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -146,7 +146,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/subsetGiottoLocsMulti.html b/reference/subsetGiottoLocsMulti.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -117,7 +117,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/subsetGiottoLocsSubcellular.html b/reference/subsetGiottoLocsSubcellular.html
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -114,7 +114,7 @@ <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
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@@ -79,7 +79,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -79,7 +79,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
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-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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@@ -166,7 +166,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/t_flex.html b/reference/t_flex.html
index a1db338c..893df7af 100644
--- a/reference/t_flex.html
+++ b/reference/t_flex.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/terraVectData-class.html b/reference/terraVectData-class.html
index e0d3a289..a6525db7 100644
--- a/reference/terraVectData-class.html
+++ b/reference/terraVectData-class.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -58,7 +58,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/tessellate.html b/reference/tessellate.html
index db8d0ca4..e9665bd6 100644
--- a/reference/tessellate.html
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -135,7 +135,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/transpose-generic.html b/reference/transpose-generic.html
index a97c9ca4..a0d913af 100644
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@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -82,7 +82,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/updateGiottoImage.html b/reference/updateGiottoImage.html
index b56a4282..ab0a1e56 100644
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+++ b/reference/updateGiottoImage.html
@@ -8,7 +8,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -150,7 +150,7 @@ <h2 id="see-also">See also<a class="anchor" aria-label="anchor" href="#see-also"
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/updateGiottoImageMG.html b/reference/updateGiottoImageMG.html
index b24048c7..d584873a 100644
--- a/reference/updateGiottoImageMG.html
+++ b/reference/updateGiottoImageMG.html
@@ -10,7 +10,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -156,7 +156,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/updateGiottoLargeImage.html b/reference/updateGiottoLargeImage.html
index ada3abd3..90125c52 100644
--- a/reference/updateGiottoLargeImage.html
+++ b/reference/updateGiottoLargeImage.html
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -145,7 +145,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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 <div class="pkgdown-footer-right">
diff --git a/reference/updateGiottoObject.html b/reference/updateGiottoObject.html
index 1b45992d..7db1af1f 100644
--- a/reference/updateGiottoObject.html
+++ b/reference/updateGiottoObject.html
@@ -8,7 +8,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -81,7 +81,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/updateGiottoPointsObject.html b/reference/updateGiottoPointsObject.html
index 54d5d582..cfd5b8d5 100644
--- a/reference/updateGiottoPointsObject.html
+++ b/reference/updateGiottoPointsObject.html
@@ -6,7 +6,7 @@
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-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/updateGiottoPolygonObject.html b/reference/updateGiottoPolygonObject.html
index 742cb6e9..07aba6cd 100644
--- a/reference/updateGiottoPolygonObject.html
+++ b/reference/updateGiottoPolygonObject.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -66,7 +66,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/update_giotto_params.html b/reference/update_giotto_params.html
index 8fb7db6d..70dc140c 100644
--- a/reference/update_giotto_params.html
+++ b/reference/update_giotto_params.html
@@ -6,7 +6,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -84,7 +84,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/wrap-generic.html b/reference/wrap-generic.html
index 7893cb8e..e7f8d02d 100644
--- a/reference/wrap-generic.html
+++ b/reference/wrap-generic.html
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -98,7 +98,7 @@ <h2 id="functions">Functions<a class="anchor" aria-label="anchor" href="#functio
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
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diff --git a/reference/writeGiottoLargeImage.html b/reference/writeGiottoLargeImage.html
index fe3f0e03..39e63761 100644
--- a/reference/writeGiottoLargeImage.html
+++ b/reference/writeGiottoLargeImage.html
@@ -10,7 +10,7 @@
     <a href="#main" class="visually-hidden-focusable">Skip to contents</a>
     
 
-    <nav class="navbar fixed-top navbar-light navbar-expand-lg bg-light"><div class="container">
+    <nav class="navbar fixed-top navbar-dark navbar-expand-lg bg-dark"><div class="container">
     
     <a class="navbar-brand me-2" href="../index.html">GiottoClass</a>
 
@@ -115,7 +115,7 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
     <footer><div class="pkgdown-footer-left">
-  <p></p><p>Developed by Ruben Dries, Jiaji George Chen, Guo-Cheng Yuan, Matthew O’Brien, <a href="https://josschavezf.github.io" class="external-link">Joselyn Chávez</a>.</p>
+  <p></p><p>Developed by <a href="https://www.drieslab.com" class="external-link">Ruben Dries</a>, Jiaji George Chen, <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 Chávez</a>, Edward Ruiz.</p>
 </div>
 
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diff --git a/search.json b/search.json
index 9e21d911..54d7b866 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
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Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. Conveying Verbatim Copies","title":"GNU General Public License","text":"may convey verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice; keep intact notices stating License non-permissive terms added accord section 7 apply code; keep intact notices absence warranty; give recipients copy License along Program. may charge price price copy convey, may offer support warranty protection fee.","code":""},{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":"id_5-conveying-modified-source-versions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"5. Conveying Modified Source Versions","title":"GNU General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: ) work must carry prominent notices stating modified , giving relevant date. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see <http://www.gnu.org/licenses/>. GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"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 Chávez. 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 J (2023). GiottoClass: Giotto Suite object definitions framework. R package version 0.0.0.9010, 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 Chávez},   year = {2023},   note = {R package version 0.0.0.9010},   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/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/S3toS4spatNetObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial Networks — S3toS4spatNetObj","title":"Spatial Networks — S3toS4spatNetObj","text":"convert S3 spatialNetworkObj S4","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatNetObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial Networks — S3toS4spatNetObj","text":"","code":"S3toS4spatNetObj(object, spat_unit = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatNetObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial Networks — S3toS4spatNetObj","text":"object S3 spatNetworkObj spat_unit spatial unit metadata append","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/abb_mat.html","id":null,"dir":"Reference","previous_headings":"","what":"Print abbreviated matrix — abb_mat","title":"Print abbreviated matrix — abb_mat","text":"print abbreviated matrix exprObj. Works Matrix pkg denseMatrix, matrix, data.frame classes inherit .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/abb_mat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print abbreviated matrix — abb_mat","text":"","code":"abb_mat(exprObj, nrows, ncols, header = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/abb_spatlocs.html","id":null,"dir":"Reference","previous_headings":"","what":"Print abbreviated spatlocs — abb_spatlocs","title":"Print abbreviated spatlocs — abb_spatlocs","text":"print abbreviated spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/abb_spatlocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print abbreviated spatlocs — abb_spatlocs","text":"","code":"abb_spatlocs(spatLocsObj, nrows)"},{"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 giotto activeFeatType(gobject)  # S4 method for 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/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 giotto activeSpatUnit(gobject)  # S4 method for 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/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_name (optional) custom name provide single vector 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 two manners: 1. Provide data.table data.frame cell annotations order cell_ID column pDataDT(gobject) 2. Provide data.table data.frame cell annotations specify column contains cell IDs, cell IDs need match cell_ID column pDataDT(gobject)","code":""},{"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,   by_column = F,   column_feat_ID = NULL,   vector_name = 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) by_column merge metadata based feat_ID column fDataDT column_feat_ID column name new metadata use by_column = TRUE vector_name (optional) custom name provide single vector","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 two manners: Provide data.table data.frame feature annotations order feat_ID column fDataDT(gobject) Provide data.table data.frame feature annotations specify column contains feature IDs, feature IDs need match feat_ID column fDataDT(gobject)","code":""},{"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 giottoImages add largeImages list giottoLargeImages add 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/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/addGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"addGiottoLargeImage — addGiottoLargeImage","title":"addGiottoLargeImage — addGiottoLargeImage","text":"Adds 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/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/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/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/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/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/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/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/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/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/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/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/aggregateStacksPolygonsOLD.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","title":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","text":"aggregate polygons different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonsOLD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","text":"","code":"aggregateStacksPolygonsOLD(gobject, spat_units, new_spat_unit = \"aggregate\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonsOLD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","text":"gobject giotto object spat_units spatial units aggregate new_spat_unit new name aggregated spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonsOLD.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","text":"giotto object","code":""},{"path":[]},{"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,   deluanay_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. deluanay_spat_net binary parameter spatial network. TRUE, spatial network deluanay network. spat_unit desired spatial unit conversion, default NULL feat_type desired feature type 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 insructions 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 clustering — annotateGiotto","title":"Annotate giotto clustering — annotateGiotto","text":"Converts cluster results user provided annotation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate giotto clustering — 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 clustering — annotateGiotto","text":"gobject giotto object spat_unit spatial unit feat_type feature type annotation_vector named annotation vector (names = cluster ids) cluster_column cluster column convert annotation names 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 clustering — 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 clustering — annotateGiotto","text":"need specifify (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/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/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/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_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/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 SpatVector as.data.table(   x,   keep.rownames = FALSE,   geom = NULL,   include_values = TRUE,   ... )  # S3 method for giottoPolygon as.data.table(x, ...)  # S3 method for 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":[]},{"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/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/calculateOverlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate features overlapped by polygons — calculateOverlap","title":"Calculate features overlapped by polygons — calculateOverlap","text":"Calculate features overlapped polygons","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 giotto,missing calculateOverlap(   x,   name_overlap = NULL,   spatial_info = NULL,   feat_info = NULL,   image_names = NULL,   poly_subset_ids = NULL,   feat_subset_column = NULL,   feat_subset_ids = NULL,   count_info_column = NULL,   return_gobject = TRUE,   verbose = TRUE,   ... )  # S4 method for 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 giottoPolygon,SpatRaster calculateOverlap(   x,   y,   name_overlap = NULL,   poly_subset_ids = NULL,   return_gpolygon = TRUE,   verbose = TRUE,   ... )  # S4 method for SpatVector,SpatRaster calculateOverlap(x, y, poly_subset_ids = NULL, verbose = TRUE, ...)  # S4 method for 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 (optional) character vector poly_IDs use 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 ... additional params pass methods y Object features overlap: giottoPoints, giottoLargeImage, SpatVector points SpatRaster 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":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate features overlapped by polygons — calculateOverlap","text":"","code":"if (FALSE) { x <- GiottoData::loadSubObjectMini(\"giottoPolygon\") y <- GiottoData::loadSubObjectMini(\"giottoPoints\") x@overlaps <- NULL overlaps(x) # Should now be NULL  a <- calculateOverlap(x, y) overlaps(a) }"},{"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/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/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/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/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/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/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/calculate_distance_and_weight.html","id":null,"dir":"Reference","previous_headings":"","what":"calculate_distance_and_weight — calculate_distance_and_weight","title":"calculate_distance_and_weight — calculate_distance_and_weight","text":"calculate_distance_and_weight","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculate_distance_and_weight.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculate_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/calculate_distance_and_weight.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculate_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/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/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/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/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/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":"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/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 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":"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/changeGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Change giotto instruction(s) associated with giotto object — changeGiottoInstructions","title":"Change giotto instruction(s) associated with giotto object — 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":"Change giotto instruction(s) associated with giotto object — 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":"Change giotto instruction(s) associated with giotto object — 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":"Change giotto instruction(s) associated with giotto object — changeGiottoInstructions","text":"giotto object one changed instructions","code":""},{"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/checkGiottoEnvironment.html","id":null,"dir":"Reference","previous_headings":"","what":"checkGiottoEnvironment — checkGiottoEnvironment","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"checkGiottoEnvironment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkGiottoEnvironment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"","code":"checkGiottoEnvironment(mini_install_path = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/checkGiottoEnvironment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"mini_install_path (optional) path miniconda conda directory within giotto environment lives provided, automatically determined reticulate::miniconda_path() Note required input format: Correct format --> mini_install_path = \"C://conda/lives/\" \"C:\\\\conda\\lives\\\" INCORRECT formats --> mini_install_path = \"C://conda/lives//\" \"C:\\\\conda\\lives\\\\\" verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkGiottoEnvironment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"logical","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkGiottoEnvironment.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"Checks miniconda giotto environment can found. Can installed installGiottoEnvironment.","code":""},{"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":"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_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/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/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/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/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/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/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/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/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/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/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/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/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 Giotto python modules python environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 = c(\"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/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/combineSpatialCellFeatureInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"Combine spatial cell information (e.g. polygon) spatial feature information (e.g. transcript locations)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellFeatureInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"","code":"combineSpatialCellFeatureInfo(   gobject,   spat_unit = NULL,   feat_type = NULL,   selected_features = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellFeatureInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"gobject Giotto object spat_unit spatial unit feat_type feature type(s) selected_features select set features","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellFeatureInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"list data.table(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellFeatureInfo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"returned data.table following columns: sdimx: spatial feature location x-axis sdimy: spatial feature location y-axis feat_ID: unique feature ID cell_ID: unique cell ID used: often feature used/assigned cell feat: selected feature(s)","code":""},{"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/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":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"","code":"if (FALSE) { gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") groups <- data.table::data.table(   poly_ID = gpoly$poly_ID,   group_ID = sort(rep(LETTERS[1:5], length.out = nrow(gpoly))) # make 5 groups ) multi_gp <- combineToMultiPolygon(gpoly, groups)  plot(multi_gp[\"A\"]) }"},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_matrices.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_matrices — combine_matrices","title":"combine_matrices — combine_matrices","text":"combine_matrices","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_matrices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_matrices — combine_matrices","text":"","code":"combine_matrices(mat_list, summarize = \"sum\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_polygons — combine_polygons","title":"combine_polygons — combine_polygons","text":"combine_polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_polygons — combine_polygons","text":"","code":"combine_polygons(polygon_list)"},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_spatlocs.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_spatlocs — combine_spatlocs","title":"combine_spatlocs — combine_spatlocs","text":"combine_spatlocs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_spatlocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_spatlocs — combine_spatlocs","text":"","code":"combine_spatlocs(spatlocs_list, summarize = \"mean\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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_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","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_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","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/copy-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy an entire object — copy-generic","title":"Copy an entire object — copy-generic","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-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy an entire object — copy-generic","text":"","code":"# S4 method for coordDataDT copy(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/copy-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy an entire object — copy-generic","text":"x Giotto S4 class subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/copy-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Copy an entire object — copy-generic","text":"copy(coordDataDT): Copy data.table-based spatial locations object.","code":""},{"path":[]},{"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/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/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/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/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/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/createGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Create instructions for giotto functions — createGiottoInstructions","title":"Create instructions for giotto functions — createGiottoInstructions","text":"Function set global instructions giotto functions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create instructions for giotto functions — createGiottoInstructions","text":"","code":"createGiottoInstructions(   python_path = NULL,   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 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create instructions for giotto functions — createGiottoInstructions","text":"python_path path python binary use 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","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create instructions for giotto functions — createGiottoInstructions","text":"named vector giotto instructions","code":""},{"path":[]},{"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 terra SpatRaster image object 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/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/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 list large images 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/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 list large images 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/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 SpatVector createGiottoPoints(   x,   feat_type = \"rna\",   verbose = TRUE,   split_keyword = NULL,   unique_IDs = NULL )  # S4 method for data.frame createGiottoPoints(   x,   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","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":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create giotto points object — createGiottoPoints","text":"","code":"# data.frame input x <- data.frame(   ID = letters[1:6],   x = 1:6,   y = 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 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)","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 SpatVector createGiottoPolygon(x, name = \"cell\", calc_centroids = FALSE, verbose = TRUE)  # S4 method for 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,   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   fix_multipart = TRUE,   remove_unvalid_polygons = TRUE,   calc_centroids = FALSE,   verbose = TRUE )  # S4 method for data.frame createGiottoPolygon(   x,   name = \"cell\",   calc_centroids = FALSE,   skip_eval_dfr = FALSE,   copy_dt = TRUE,   verbose = TRUE )  # S4 method for character createGiottoPolygon(x, ...)  createGiottoPolygonsFromMask(   maskfile,   mask_method = c(\"guess\", \"single\", \"multiple\"),   name = \"cell\",   remove_background_polygon = FALSE,   background_algo = c(\"range\"),   fill_holes = TRUE,   poly_IDs = NULL,   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   calc_centroids = FALSE,   fix_multipart = TRUE,   remove_unvalid_polygons = TRUE )  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. name name giottoPolygon object created calc_centroids (default FALSE) calculate centroids polygons verbose verbose mask_method mask file defines individual segmentation annotations remove_background_polygon try remove background polygon (default: FALSE) background_algo algorithm remove background polygon fill_holes fill holes within created polygons poly_IDs unique names polygon mask file 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) fix_multipart try split polygons multiple parts (default: TRUE) 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 ... additional params pass. character method, params pass SpatRaster SpatVector methods, depending whether x filepath maskfile spatial file (ex: wkt, shp, GeoJSON) respectively. maskfile path mask file 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":"giotto polygon object","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/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,   name = \"metafeat\",   return_gobject = TRUE )"},{"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 name name metagene results return_gobject return giotto object","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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createMetafeats — createMetafeats","text":"","code":"if (FALSE) { # load a dataset g <- GiottoData::loadGiottoMini(\"viz\") # set a spat unit to use activeSpatUnit(g) <- \"aggregate\"  # create the metafeats # We do this by making an annotation vector which is a numerical vector # of cluster assignments where each number is named by the feature it describes. # # Here we create an example annotation vector by arbitrarily using the first 6 # features and putting 3 in cluster 1 and the other 3 in cluster 2. feats_to_use <- featIDs(g)[1:6] clust_to_use <- c(1, 1, 1, 2, 2, 2) names(clust_to_use) <- feats_to_use  # show clust_to_use  g <- createMetafeats(   gobject = g,   feat_clusters = clust_to_use,   name = \"new_metagene\" )  GiottoVisuals::spatCellPlot(   gobject = g,   spat_enr_names = \"new_metagene\",   cell_annotation_values = c(\"1\", \"2\"),   point_size = 3.5,   cow_n_col = 2 ) }"},{"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":"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/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 = 1:10,   feats_to_use = NULL,   genes_to_use = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   name = NULL,   return_gobject = TRUE,   k = 30,   minimum_shared = 5,   top_shared = 3,   verbose = T,   ... )"},{"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 genes_to_use deprecated, use feats_to_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: 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/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/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/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/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/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 = T,   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 wisker\" value distance vector neighbors used; see boxplotgraphics documentation details.(default = \"auto\") minimum_k minimum number neigbhours maximum_distance != NULL options (geometry) String containing extra control options underlying Qhull command; see Qhull documentation (../doc/qhull/html/qdelaun.html) 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 boolean: return giotto object (default = TRUE) output 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/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 = c(\"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_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/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/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 = F,   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 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/createSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"createSpatialNetwork — createSpatialNetwork","title":"createSpatialNetwork — createSpatialNetwork","text":"Create spatial network based cell centroid physical distances.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createSpatialNetwork — 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 = F,   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":"createSpatialNetwork — 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 Delaunay method use maximum_distance_delaunay distance cuttof nearest neighbors consider Delaunay network options (geometry) String containing extra control options underlying Qhull command; see Qhull documentation (../doc/qhull/html/qdelaun.html) 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 neigbhours maximum_distance != NULL knn_method method create kNN network k number nearest neighbors based physical distance maximum_distance_knn distance cuttof nearest neighbors consider kNN network verbose verbose return_gobject boolean: return giotto object (default = TRUE) output 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":"createSpatialNetwork — 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":"createSpatialNetwork — 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 specififies spatial dimensions use, e.g. c(\"sdimx', \"sdimy\") numerical vector, e.g. 2:3","code":""},{"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":"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/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_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 epression values factor","code":""},{"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_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_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_delaunayNetwork2D.html","id":null,"dir":"Reference","previous_headings":"","what":"create_delaunayNetwork2D — create_delaunayNetwork2D","title":"create_delaunayNetwork2D — create_delaunayNetwork2D","text":"Create spatial 2D Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_delaunayNetwork2D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_delaunayNetwork2D — create_delaunayNetwork2D","text":"","code":"create_delaunayNetwork2D(   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 = T,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_delaunayNetwork3D.html","id":null,"dir":"Reference","previous_headings":"","what":"create_delaunayNetwork3D — create_delaunayNetwork3D","title":"create_delaunayNetwork3D — create_delaunayNetwork3D","text":"Create spatial 3D Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_delaunayNetwork3D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_delaunayNetwork3D — create_delaunayNetwork3D","text":"","code":"create_delaunayNetwork3D(   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/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/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/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/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/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/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/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/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/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_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_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_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_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_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_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_segm_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Create segmentation polygons — create_segm_polygons","title":"Create segmentation polygons — create_segm_polygons","text":"creates giotto polygons segmentation mask data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_segm_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create segmentation polygons — create_segm_polygons","text":"","code":"create_segm_polygons(   maskfile,   name = \"cell\",   poly_IDs = NULL,   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   remove_background_polygon = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_segm_polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create segmentation polygons — create_segm_polygons","text":"giotto polygon","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_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_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_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_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/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/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/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/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/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, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/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 verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/crop-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Crop to a spatial subset — crop-generic","title":"Crop to a spatial subset — crop-generic","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-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Crop to a spatial subset — crop-generic","text":"","code":"# S4 method for giottoLargeImage crop(x, y, ...)  # S4 method for giottoPoints crop(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)  # S4 method for giottoPolygon crop(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/crop-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Crop to a spatial subset — crop-generic","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-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Crop to a spatial subset — crop-generic","text":"crop(giottoLargeImage): Crop giottoLargeImage crop(giottoPoints): Crop giottoPoints crop(giottoPolygon): Crop giottoPoints","code":""},{"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/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","code":""},{"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 image_type image object type (supports largeImage set default)","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":"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/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 giottoPoints nrow(x)  # S4 method for giottoPolygon nrow(x)  # S4 method for spatLocsObj nrow(x)  # S4 method for exprData nrow(x)  # S4 method for metaData nrow(x)  # S4 method for spatialNetworkObj nrow(x)  # S4 method for enrData nrow(x)  # S4 method for exprData ncol(x)  # S4 method for metaData ncol(x)  # S4 method for enrData ncol(x)  # S4 method for exprData dim(x)  # S4 method for metaData dim(x)  # S4 method for enrData dim(x)  # S4 method for giottoLargeImage 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":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Dimensions of giotto objects — dims-generic","text":"nrow(giottoPoints): Find rows giottoPoints object nrow(giottoPolygon): Find rows giottoPolygon object nrow(spatLocsObj): Find rows giotto S4s data.table based coordinates slots nrow(exprData): Find rows giotto S4s data.table based coordinates slots nrow(metaData): Find rows giotto S4s data.table based coordinates slots nrow(spatialNetworkObj): Find rows spatialNetworkObj ncol(exprData): Find cols giotto S4s Matrix based exprMat slots ncol(metaData): Find cols giotto S4s data.table based metaDT slots ncol(enrData): Find cols giotto S4s enrData dim(exprData): Find dimensions giotto S4s Matrix based exprMat slots dim(metaData): Find dimensions giotto S4s data.table based metaDT slots","code":""},{"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\") )"},{"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","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/do_gpoly.html","id":null,"dir":"Reference","previous_headings":"","what":"do_gpoly — do_gpoly","title":"do_gpoly — do_gpoly","text":"Perform function spatVector-based slots giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/do_gpoly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"do_gpoly — do_gpoly","text":"","code":"do_gpoly(x, what, args = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/do_gpoly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"do_gpoly — do_gpoly","text":"x giottoPolygon call args list additional args","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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/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/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 = 1:50)"},{"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/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":"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/ext-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a SpatExtent — ext-generic","title":"Get a SpatExtent — ext-generic","text":"Get SpatExtent object. spatial minmax x y object mapped .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a SpatExtent — ext-generic","text":"","code":"# S4 method for spatLocsObj ext(x, ...)  # S4 method for giottoPolygon ext(x, ...)  # S4 method for giottoPoints ext(x, ...)  # S4 method for spatialNetworkObj ext(x, ...)  # S4 method for giottoLargeImage ext(x, ...)  # S4 method for giottoPoints,SpatExtent ext(x) <- value  # S4 method for giottoPolygon,SpatExtent ext(x) <- value  # S4 method for giottoLargeImage,SpatExtent ext(x) <- value  # S4 method for ANY,ANY ext(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/ext-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a SpatExtent — ext-generic","text":"x spatial object ... additional params pass value value set. Accepts object ext() work ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Get a SpatExtent — ext-generic","text":"ext(spatLocsObj): Get extent spatLocsObj ext(giottoPolygon): Get extent giottoPolygon ext(giottoPoints): Get extent giottoPoints ext(spatialNetworkObj): Get extent spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract or replace parts of an object — extract-methods","title":"Extract or replace parts of an object — extract-methods","text":"Operators Giotto S4 internal data.tables extract replace parts.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract or replace parts of an object — extract-methods","text":"","code":"# S4 method for coordDataDT $(x, name)  # S4 method for coordDataDT $(x, name) <- value  # S4 method for metaData $(x, name)  # S4 method for metaData $(x, name) <- value  # S4 method for terraVectData $(x, name)  # S4 method for terraVectData $(x, name) <- value  # S4 method for gdtData,gIndex,gIndex,missing [(x, i, j)  # S4 method for gdtData,logical,missing,missing [(x, i, j)  # S4 method for gdtData,character,missing,missing [(x, i, j)  # S4 method for gdtData,missing,numeric,missing [(x, i, j)  # S4 method for gdtData,missing,logical,missing [(x, i, j)  # S4 method for coordDataDT,ANY,ANY,missing [(x, i, j)  # S4 method for coordDataDT,missing,ANY,missing [(x, i, j)  # S4 method for coordDataDT,missing,character,missing [(x, i, j)  # S4 method for coordDataDT,ANY,missing,missing [(x, i, j)  # S4 method for coordDataDT,missing,missing,missing [(x, i, j)  # S4 method for coordDataDT,missing,missing,ANY [(x, i, j) <- value  # S4 method for giottoPoints,gIndex,missing,missing [(x, i, j)  # S4 method for metaData,missing,ANY,missing [(x, i, j)  # S4 method for metaData,missing,character,missing [(x, i, j)  # S4 method for metaData,ANY,missing,missing [(x, i, j)  # S4 method for metaData,missing,missing,missing [(x, i, j)  # S4 method for metaData,missing,missing,ANY [(x, i, j) <- value  # S4 method for dimObj,ANY,ANY,missing [(x, i, j)  # S4 method for dimObj,missing,missing,missing [(x, i, j)  # S4 method for dimObj,missing,missing,ANY [(x, i, j) <- value  # S4 method for exprData,missing,ANY,missing [(x, i, j)  # S4 method for exprData,ANY,missing,missing [(x, i, j)  # S4 method for exprData,ANY,ANY,missing [(x, i, j)  # S4 method for exprData,missing,missing,missing [(x, i, j)  # S4 method for exprData,missing,missing,ANY [(x, i, j) <- value  # S4 method for spatNetData,missing,missing,missing [(x, i, j)  # S4 method for spatNetData,missing,missing,ANY [(x, i, j) <- value  # S4 method for nnData,missing,missing,missing [(x, i, j)  # S4 method for nnData,missing,missing,ANY [(x, i, j) <- value  # S4 method for enrData,missing,missing,missing [(x, i, j)  # S4 method for enrData,ANY,missing,missing [(x, i, j)  # S4 method for enrData,missing,ANY,missing [(x, i, j)  # S4 method for enrData,missing,character,missing [(x, i, j)  # S4 method for enrData,missing,missing,ANY [(x, i, j) <- value  # S4 method for spatGridData,missing,missing,missing [(x, i, j)  # S4 method for spatGridData,missing,missing,ANY [(x, i, j) <- value  # S4 method for giottoPoints,missing,missing,missing [(x, i, j)  # S4 method for giottoPoints,gIndex,missing,missing [(x, i, j)  # S4 method for giottoPoints,character,missing,missing [(x, i, j)  # S4 method for giottoPoints,missing,gIndex,missing [(x, i, j)  # S4 method for giottoPoints,missing,missing,ANY [(x, i, j) <- value  # S4 method for giottoPolygon,missing,missing,missing [(x, i, j)  # S4 method for giottoPolygon,gIndex,missing,missing [(x, i, j)  # S4 method for giottoPolygon,character,missing,missing [(x, i, j)  # S4 method for giottoPolygon,missing,gIndex,missing [(x, i, j)  # S4 method for terraVectData,gIndex,gIndex,missing [(x, i, j)  # S4 method for giottoPolygon,missing,missing,ANY [(x, i, j) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract or replace parts of an object — extract-methods","text":"x Giotto S4 object extract columns name literal character string (possibly backtick quoted). value value(s) set normally matched colnames data.table object within S4. , j indices specifying elements extract replace. Indices numeric character vectors empty","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"-methods","dir":"Reference","previous_headings":"","what":"`$` methods","title":"Extract or replace parts of an object — extract-methods","text":"Select colname giotto S4 data.table coordinates slot. Select colname giotto S4 data.table metaDT slot. Select colname giotto S4 spatVector slot.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"-lt-methods","dir":"Reference","previous_headings":"","what":"`$<-` methods","title":"Extract or replace parts of an object — extract-methods","text":"Set values colname giotto S4 data.table coordinates slot. Works via data.table methods Set values colname giotto S4 data.table metaDT slot. Works via data.table methods Set values colname giotto S4 spatVector slot.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"-methods-1","dir":"Reference","previous_headings":"","what":"`[` methods","title":"Extract or replace parts of an object — extract-methods","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":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"-lt-methods-1","dir":"Reference","previous_headings":"","what":"`[<-` methods","title":"Extract or replace parts of an object — extract-methods","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","code":""},{"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/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":"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/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 featData featType(x)  # S4 method for 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":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Feature type information — featType-generic","text":"featType(featData): Get feature type information featType(featData) <- value: Set feature type information","code":""},{"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":"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/filter_network.html","id":null,"dir":"Reference","previous_headings":"","what":"filter_network — filter_network","title":"filter_network — filter_network","text":"function filter spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/filter_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"filter_network — filter_network","text":"","code":"filter_network(networkDT = NULL, maximum_distance = NULL, minimum_k = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/filter_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"filter_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/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/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/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/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/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/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/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/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/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/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/find_terra_writeRaster_dataType.html","id":null,"dir":"Reference","previous_headings":"","what":"find_terra_writeRaster_dataType — find_terra_writeRaster_dataType","title":"find_terra_writeRaster_dataType — find_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/find_terra_writeRaster_dataType.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"find_terra_writeRaster_dataType — find_terra_writeRaster_dataType","text":"","code":"find_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/find_terra_writeRaster_dataType.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"find_terra_writeRaster_dataType — find_terra_writeRaster_dataType","text":"giottoLargeImage giottoLargeImage object determine max_intensity, min_intensity, is_int 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 quick_INTU_maxval Treat maximum intensity find compatible unsigned integer settings","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/find_terra_writeRaster_dataType.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"find_terra_writeRaster_dataType — find_terra_writeRaster_dataType","text":"datatype terra writeRaster function","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/flip-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Flip an object — flip-generic","title":"Flip an object — flip-generic","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-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flip an object — flip-generic","text":"","code":"# S4 method for giottoPolygon flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for giottoPoints flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for spatLocsObj flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for spatialNetworkObj flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for giottoLargeImage flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for SpatExtent flip(x, direction = \"vertical\", x0 = 0, y0 = 0)"},{"path":"https://drieslab.github.io/GiottoClass/reference/flip-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flip an object — flip-generic","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 ... additional args pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/flip-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Flip an object — flip-generic","text":"flip(giottoPolygon): Flip giottoPolygon object flip(giottoPoints): Flip giottoPoints object flip(spatLocsObj): Flip spatLocsObj flip(spatialNetworkObj): Flip spatialNetworkObj flip(giottoLargeImage): Flip giottoLargeImage flip(SpatExtent): Flip SpatExtent","code":""},{"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":"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":"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":[]},{"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 = c(\"pca\", \"umap\", \"tsne\"),   name = \"pca\",   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/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/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 )"},{"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.","code":""},{"path":[]},{"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":[]},{"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 image object 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 = NULL,   image_type = c(\"image\", \"largeImage\"),   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 type giotto image object. Either \"image\" \"largeImage\" name name giotto image object showGiottoImageNames","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/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/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 igraph data.table object. Default 'igraph' 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":"igraph data.table object","code":""},{"path":[]},{"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 )"},{"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","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getRainbowColors.html","id":null,"dir":"Reference","previous_headings":"","what":"getRainbowColors — getRainbowColors","title":"getRainbowColors — getRainbowColors","text":"Returns number rainbow colors spaced around spectrum. 100 unique colors supplied recycled.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getRainbowColors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getRainbowColors — getRainbowColors","text":"","code":"getRainbowColors(n)"},{"path":"https://drieslab.github.io/GiottoClass/reference/getRainbowColors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getRainbowColors — getRainbowColors","text":"n number colors wanted","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getRainbowColors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getRainbowColors — getRainbowColors","text":"character vector hexadecimal rainbow colors","code":""},{"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":"data.table fractions","code":""},{"path":[]},{"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":[]},{"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 )"},{"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.","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/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 )"},{"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","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_NearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Get nearest network — get_NearestNetwork","title":"Get nearest network — get_NearestNetwork","text":"Get NN-network Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_NearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get nearest network — get_NearestNetwork","text":"","code":"get_NearestNetwork(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_network_to_use = NULL,   network_name = NULL,   output = c(\"nnNetObj\", \"igraph\", \"data.table\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_NearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get nearest network — get_NearestNetwork","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_network_to_use \"kNN\" \"sNN\" network_name name NN network used output return igraph data.table object. Default 'igraph' set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_NearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get nearest network — get_NearestNetwork","text":"igraph data.table object","code":""},{"path":[]},{"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_args.html","id":null,"dir":"Reference","previous_headings":"","what":"Log args used — get_args","title":"Log args used — get_args","text":"Get arguments passed function call.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_args.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Log args used — get_args","text":"","code":"get_args(toplevel = 2L, verbose = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_args.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Log args used — get_args","text":"toplevel integer. Relative stack function call made. verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Get cell IDs for a given spatial unit — get_cell_id","title":"Get cell IDs for a given spatial unit — get_cell_id","text":"Data spatial unit expected agree single set cell_IDs shared across feature types. cell_IDs stored within giotto object's cell_ID slot. Getters setters slot directly retrieve (get) replace (set) slot.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get cell IDs for a given spatial unit — get_cell_id","text":"","code":"get_cell_id(gobject, spat_unit = NULL, set_defaults = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get cell IDs for a given spatial unit — get_cell_id","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get cell IDs for a given spatial unit — get_cell_id","text":"character vector cell_IDs","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get cell metadata — get_cell_metadata","title":"Get cell metadata — get_cell_metadata","text":"Get cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get cell metadata — get_cell_metadata","text":"","code":"get_cell_metadata(   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/get_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get cell metadata — get_cell_metadata","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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_dimReduction.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dimension reduction — get_dimReduction","title":"Get dimension reduction — get_dimReduction","text":"Function get dimension reduction object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_dimReduction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dimension reduction — get_dimReduction","text":"","code":"get_dimReduction(   gobject,   spat_unit = NULL,   feat_type = NULL,   reduction = c(\"cells\", \"feats\"),   reduction_method = c(\"pca\", \"umap\", \"tsne\"),   name = \"pca\",   output = c(\"dimObj\", \"matrix\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_dimReduction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dimension reduction — get_dimReduction","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/get_dimReduction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dimension reduction — get_dimReduction","text":"dim reduction object (default) dim reduction coordinates","code":""},{"path":[]},{"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_expression_values.html","id":null,"dir":"Reference","previous_headings":"","what":"get_expression_values — get_expression_values","title":"get_expression_values — get_expression_values","text":"get_expression_values","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_expression_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_expression_values — get_expression_values","text":"","code":"get_expression_values(   gobject,   spat_unit = NULL,   feat_type = NULL,   values = NULL,   output = c(\"exprObj\", \"matrix\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_expression_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_expression_values — get_expression_values","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") values expression values extract (e.g. \"raw\", \"normalized\", \"scaled\") 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/get_feat_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Get feat IDs for a given feature type — get_feat_id","title":"Get feat IDs for a given feature type — get_feat_id","text":"Across single modality/feature type, feature information expected share single set feat_IDs. feat_IDs stored within giotto object's feat_ID slot. Getters setters slot directly (get) replace (set) slot.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feat_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get feat IDs for a given feature type — get_feat_id","text":"","code":"get_feat_id(gobject, feat_type = NULL, set_defaults = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feat_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get feat IDs for a given feature type — get_feat_id","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get feature info — get_feature_info","title":"Get feature info — get_feature_info","text":"Get giotto points spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get feature info — get_feature_info","text":"","code":"get_feature_info(   gobject,   feat_type = NULL,   set_defaults = TRUE,   return_giottoPoints = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get feature info — get_feature_info","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. return_giottoPoints return giottoPoints object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get feature info — get_feature_info","text":"SpatVector (default) giottoPoints object depending value return_giottoPoints","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get feature metadata — get_feature_metadata","title":"Get feature metadata — get_feature_metadata","text":"Get feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get feature metadata — get_feature_metadata","text":"","code":"get_feature_metadata(   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/get_feature_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get feature metadata — get_feature_metadata","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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get giotto image object — get_giottoImage","title":"Get giotto image object — get_giottoImage","text":"Get giotto image object gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get giotto image object — get_giottoImage","text":"","code":"get_giottoImage(   gobject = NULL,   image_type = c(\"image\", \"largeImage\"),   name = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get giotto image object — get_giottoImage","text":"gobject giotto object image_type type giotto image object. Either \"image\" \"largeImage\" name name giotto image object showGiottoImageNames","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get giotto image object — get_giottoImage","text":"giotto image object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage_MG.html","id":null,"dir":"Reference","previous_headings":"","what":"Get magick-based giotto image — get_giottoImage_MG","title":"Get magick-based giotto image — get_giottoImage_MG","text":"Get giottoImage giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage_MG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get magick-based giotto image — get_giottoImage_MG","text":"","code":"get_giottoImage_MG(gobject = NULL, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage_MG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get magick-based giotto image — get_giottoImage_MG","text":"gobject giotto object name name giottoImage showGiottoImageNames","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage_MG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get magick-based giotto image — get_giottoImage_MG","text":"giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get terra-based giotto largeImage — get_giottoLargeImage","title":"Get terra-based giotto largeImage — get_giottoLargeImage","text":"Set giottoLargeImage giottoObject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get terra-based giotto largeImage — get_giottoLargeImage","text":"","code":"get_giottoLargeImage(gobject = NULL, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get terra-based giotto largeImage — get_giottoLargeImage","text":"gobject giotto object name name giottoLargeImage showGiottoImageNames","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get terra-based giotto largeImage — get_giottoLargeImage","text":"giottoLargeImage","code":""},{"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_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_polygon_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get polygon info — get_polygon_info","title":"Get polygon info — get_polygon_info","text":"Get giotto polygon spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_polygon_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get polygon info — get_polygon_info","text":"","code":"get_polygon_info(   gobject,   polygon_name = NULL,   polygon_overlap = NULL,   return_giottoPolygon = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_polygon_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get polygon info — get_polygon_info","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","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_prev_fname.html","id":null,"dir":"Reference","previous_headings":"","what":"Get previous function name — get_prev_fname","title":"Get previous function name — get_prev_fname","text":"Get previous function name","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_prev_fname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get previous function name — get_prev_fname","text":"","code":"get_prev_fname(toplevel = 3L, verbose = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_prev_fname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get previous function name — get_prev_fname","text":"toplevel integer. Relative stack previous function call made verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial grid — get_spatialGrid","title":"Get spatial grid — get_spatialGrid","text":"Function get spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial grid — get_spatialGrid","text":"","code":"get_spatialGrid(   gobject,   spat_unit = NULL,   feat_type = NULL,   name = NULL,   return_grid_Obj = FALSE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial grid — get_spatialGrid","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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial network — get_spatialNetwork","title":"Get spatial network — get_spatialNetwork","text":"Function get spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial network — get_spatialNetwork","text":"","code":"get_spatialNetwork(   gobject,   spat_unit = NULL,   name = NULL,   output = c(\"spatialNetworkObj\", \"networkDT\", \"networkDT_before_filter\", \"outputObj\"),   set_defaults = TRUE,   copy_obj = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial network — get_spatialNetwork","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","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_enrichment.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial enrichment — get_spatial_enrichment","title":"Get spatial enrichment — get_spatial_enrichment","text":"Function get spatial enrichment data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_enrichment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial enrichment — get_spatial_enrichment","text":"","code":"get_spatial_enrichment(   gobject,   spat_unit = NULL,   feat_type = NULL,   enrichm_name = \"DWLS\",   output = c(\"spatEnrObj\", \"data.table\"),   copy_obj = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_enrichment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial enrichment — get_spatial_enrichment","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") enrichm_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/get_spatial_enrichment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial enrichment — get_spatial_enrichment","text":"data.table fractions","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial locations — get_spatial_locations","title":"Get spatial locations — get_spatial_locations","text":"Function get spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial locations — get_spatial_locations","text":"","code":"get_spatial_locations(   gobject,   spat_unit = NULL,   spat_loc_name = NULL,   output = c(\"spatLocsObj\", \"data.table\"),   copy_obj = TRUE,   verbose = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial locations — get_spatial_locations","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") spat_loc_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.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial locations — get_spatial_locations","text":"data.table coordinates spatLocsObj depending output","code":""},{"path":[]},{"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":"Framework giotto object store work spatial expression data","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":"[expression] several ways provide expression information: [expression_feat] different features modalities rna, protein, metabolites, ... provided expression slot.","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 available features (e.g. rna, protein, ...) 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 images largeImages slot store giottoLargeImage objects parameters slot save parameters used instructions slot global function instructions offset_file offset file used stitch together image fields OS_platform Operating System run Giotto analysis join_info information joined Giotto objects multiomics multiomics integration results h5_file path h5 file","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":"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/giottoLargeImage-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giottoLargeImage Class — giottoLargeImage-class","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"class handle images large load normally magick","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 raster 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 value set maximum intensity color scaling min_intensity minimum value found 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/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":"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/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":"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/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, ...)"},{"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') ... 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/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) { mini_gobject <- GiottoData::loadGiottoMini(\"vizgen\") giottoToSpatialExperiment(mini_gobject) }"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_alloc_dt_slots.html","id":null,"dir":"Reference","previous_headings":"","what":"Over-allocation for giotto DT-based info — giotto_alloc_dt_slots","title":"Over-allocation for giotto DT-based info — giotto_alloc_dt_slots","text":"Finds DT based objects, overallocates data.tables, sets objects back giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_alloc_dt_slots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Over-allocation for giotto DT-based info — giotto_alloc_dt_slots","text":"","code":"giotto_alloc_dt_slots(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_alloc_dt_slots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Over-allocation for giotto DT-based info — giotto_alloc_dt_slots","text":"gobject giotto object","code":""},{"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/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 based largest range","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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)"},{"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_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/installGiottoEnvironment.html","id":null,"dir":"Reference","previous_headings":"","what":"installGiottoEnvironment — installGiottoEnvironment","title":"installGiottoEnvironment — installGiottoEnvironment","text":"Installs giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/installGiottoEnvironment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"installGiottoEnvironment — installGiottoEnvironment","text":"","code":"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\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   force_miniconda = FALSE,   force_environment = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/installGiottoEnvironment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"installGiottoEnvironment — installGiottoEnvironment","text":"packages_to_install python modules (packages) installed Giotto work python_version python version use within giotto conda environment mini_install_path (optional) desired location miniconda installation. provided, chosen reticulate::install_miniconda() Note required input format: Correct format --> mini_install_path = \"C://conda/lives/\" \"C:\\\\conda\\lives\\\" INCORRECT formats --> mini_install_path = \"C://conda/lives//\" \"C:\\\\conda\\lives\\\\\" force_miniconda force reinstallation miniconda force_environment force reinstallation giotto environment verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/installGiottoEnvironment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"installGiottoEnvironment — installGiottoEnvironment","text":"installs giotto environment using reticulate miniconda system","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/installGiottoEnvironment.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"installGiottoEnvironment — installGiottoEnvironment","text":"function install local giotto environment using miniconda system implemented reticulate. giotto environment installed automatically detected run Giotto toolbox. want use python path can set python_path createGiottoInstructions provide instructions createGiottoObject function. default, Python v3.10.2 used following python modules Giotto Suite implementations: 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/installGiottoEnvironment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"installGiottoEnvironment — installGiottoEnvironment","text":"","code":"if (FALSE) {  # this command will install r-miniconda # and a giotto environment with all necessary python modules installGiottoEnvironment() }"},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/install_giotto_environment_specific.html","id":null,"dir":"Reference","previous_headings":"","what":"install_giotto_environment_specific — install_giotto_environment_specific","title":"install_giotto_environment_specific — install_giotto_environment_specific","text":"installation giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/install_giotto_environment_specific.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"install_giotto_environment_specific — install_giotto_environment_specific","text":"","code":"install_giotto_environment_specific(   packages_to_install = c(\"pandas\", \"networkx\", \"python-igraph\", \"leidenalg\",     \"python-louvain\", \"python.app\", \"scikit-learn\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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/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/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/instructions-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Access giotto instructions — instructions-generic","title":"Access giotto instructions — instructions-generic","text":"Retrieve set giotto instructions. Specific instructions can replaced using field param. Additionally, using instructions<-, initialize() called giotto object initialize param TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/instructions-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Access giotto instructions — instructions-generic","text":"","code":"# S4 method for giotto,missing instructions(gobject)  # S4 method for giotto,missing,missing instructions(gobject, initialize) <- value  # S4 method for giotto,missing,logical instructions(gobject, initialize) <- value  # S4 method for giotto,character instructions(gobject, param)  # S4 method for giotto,character,missing instructions(gobject, param, initialize) <- value  # S4 method for giotto,character,logical instructions(gobject, param, initialize) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/instructions-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Access giotto instructions — instructions-generic","text":"gobject giotto object initialize (boolean, default = TRUE) whether initialize giotto object value value set param Specific param instructions access modify","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,   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 list values shift along x-axis method shift y_shift list values shift along y-axis method shift x_padding padding datasets/images method shift y_padding padding datasets/images method shift 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. \"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. \"no_change\"  changes applied spatial locations datasets joining.","code":"\\strong{If shift values are given then a value is needed for each giotto object to be joined in \\code{gobject_list}. Order matters.}If a regular step value is desired instead of a specific list of values, use \\code{x_padding} and \\code{y_padding}. Both shift and padding values can be used at the same time.Leaving \\code{x_shift} and \\code{y_shift} values as \\code{NULL} will have Giotto estimate an appropriate \\code{x_shift} value based on the x dimension of available image objects. If no image objects are available, a default behavior of \\code{x_padding = 1000} will be applied. Alternatively, a single numeric value can be supplied to \\code{z_vals} in which case this input will be treated as a z step value."},{"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_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_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_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_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_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_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_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_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_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_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_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_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)"},{"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 \"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_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_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_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_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_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_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_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_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_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_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_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_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/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,   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 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/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/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/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/merge_spatial_locs_feat_info.html","id":null,"dir":"Reference","previous_headings":"","what":"merge_spatial_locs_feat_info — merge_spatial_locs_feat_info","title":"merge_spatial_locs_feat_info — merge_spatial_locs_feat_info","text":"merge spatial cell feature location information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/merge_spatial_locs_feat_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"merge_spatial_locs_feat_info — merge_spatial_locs_feat_info","text":"","code":"merge_spatial_locs_feat_info(spatial_info, feature_info)"},{"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/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_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_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/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/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":"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/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)"},{"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","code":""},{"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 nameData objName(x)  # S4 method for giottoPoints objName(x)  # S4 method for giottoLargeImage objName(x)  # S4 method for giottoImage objName(x)  # S4 method for nameData objName(x) <- value  # S4 method for giottoImage objName(x) <- value  # S4 method for giottoLargeImage objName(x) <- value  # S4 method for 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":"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/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 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 giottoPolygon overlapToMatrix(   x,   feat_info = \"rna\",   type = c(\"point\", \"intensity\"),   count_info_column = NULL,   output = c(\"Matrix\", \"data.table\"),   ... )  # S4 method for SpatVector overlapToMatrix(   x,   col_names = NULL,   row_names = NULL,   count_info_column = NULL,   output = c(\"Matrix\", \"data.table\"),   verbose = TRUE,   ... )  # S4 method for 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/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/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/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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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 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":"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/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/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 giottoImage,missing plot(x, y, ...)  # S4 method for giottoLargeImage,missing plot(x, y, ...)  # S4 method for giottoPolygon,missing plot(x, point_size = 0.1, type = c(\"poly\", \"centroid\"), ...)  # S4 method for giottoPoints,missing plot(x, point_size = 0, feats = NULL, raster = TRUE, raster_size = 600, ...)  # S4 method for spatLocsObj,missing plot(x, y, ...)  # S4 method for spatialNetworkObj,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 point_size size points plotting giottoPoints type plot: either 'poly' (default) polygon 'centroid' feats specific features plot within giottoPoints object (defaults NULL, meaning available features) raster default = TRUE, whether plot points rasterized plot size based size param raster_size Default 600. used raster TRUE","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 = spatialNetworkObj, y = missing): Plot spatialNetworkObj","code":""},{"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":"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/plot_auto_largeImage_resample.html","id":null,"dir":"Reference","previous_headings":"","what":"Optimized largeImage resampling — plot_auto_largeImage_resample","title":"Optimized largeImage resampling — plot_auto_largeImage_resample","text":"Downsample largeImage plotting. Uses spatSample load portion original image, speeding plotting lowering memory footprint. Default behavior spatSample crop smaller ROI needed plotting followed sampling process order reduce wasted sampling focusing sample space. large ROIs, crop can time intensive require writing disk. function examines ROI dimensions defined limits spatial locations plotted, decides following two methods order avoid issue: Method . First crop original image sample n values n = 500,000 generate final image Method B. First oversample n values crop, n = 500,000 scaled value >1. Scaling factor increases smaller ROI defined : original dimensions/crop dimensions larger ratio x y dims chosen. Scale factor capped max_resample_scale Control points function set max_crop decides max ROI area switchover method B happens order avoid laborious crops max_resample_scale determines maximum scale factor number values sample. values can adjusted depending system resources. Additionally, flex_resample determines switching behavior happens. set FALSE, method used.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot_auto_largeImage_resample.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Optimized largeImage resampling — plot_auto_largeImage_resample","text":"","code":"plot_auto_largeImage_resample(   gobject,   giottoLargeImage = NULL,   largeImage_name = NULL,   spat_unit = NULL,   spat_loc_name = NULL,   polygon_feat_type = NULL,   include_image_in_border = TRUE,   flex_resample = TRUE,   max_crop = 1e+08,   max_resample_scale = 100 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/plot_auto_largeImage_resample.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Optimized largeImage resampling — plot_auto_largeImage_resample","text":"gobject gobject containing largeImage object giottoLargeImage largeImage object resample provided gobject largeImage_name largeImage_name name largeImage gobject spat_unit spatial unit spat_loc_name name spatial locations plot polygon_feat_type name polygon/spatial_info plot include_image_in_border logical. expand extent sampled also show image border regions included spatlocs. prevents images plots sharply cut around furthest spatial locations. (default TRUE) flex_resample logical. Whether allow automatic selection sampling workflow defined details sections. (default TRUE) max_crop maximum crop size allowed method switching method B (see description) max_resample_scale maximum cells allowed resample compensate decreased resolution cropping sampling","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot_auto_largeImage_resample.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Optimized largeImage resampling — plot_auto_largeImage_resample","text":"giottoLargeImage cropped resampled properly plotting","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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/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/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) boolean. 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/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/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":"returns 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_\", 1:10) ) 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_OLD.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert polygon to raster — polygon_to_raster_OLD","title":"Convert polygon to raster — polygon_to_raster_OLD","text":"function convert terra SpatVector Polygon shape terra SpatRaster TODO: can removed","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster_OLD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert polygon to raster — polygon_to_raster_OLD","text":"","code":"polygon_to_raster_OLD(polygon, field = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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 ident characters print level (top level '')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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 provData prov(x)  # S4 method for 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":"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_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/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/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/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/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/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/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 sf as.sp(x)  # S4 method for SpatVector as.sp(x)  # S4 method for stars as.sp(x)  # S4 method for Spatial as.sp(x)  # S4 method for giottoPolygon as.sp(x, drop = TRUE)  # S4 method for giottoPoints as.sp(x, drop = TRUE)  # S4 method for SpatVector as.sf(x)  # S4 method for Spatial as.sf(x)  # S4 method for stars as.sf(x)  # S4 method for sf as.sf(x)  # S4 method for giottoPolygon as.sf(x, drop = TRUE)  # S4 method for giottoPoints as.sf(x, drop = TRUE)  # S4 method for SpatVector as.stars(x)  # S4 method for sf as.stars(x)  # S4 method for Spatial as.stars(x)  # S4 method for stars as.stars(x)  # S4 method for giottoPolygon as.stars(x, drop = TRUE)  # S4 method for giottoPoints as.stars(x, drop = TRUE)  # S4 method for SpatVector as.terra(x)  # S4 method for sf as.terra(x)  # S4 method for stars as.terra(x, type = c(\"vector\", \"raster\"))  # S4 method for Spatial as.terra(x)  # S4 method for giottoPolygon as.terra(x, drop = TRUE)  # S4 method for 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":[]},{"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 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 add_list_ID whether generate list_ID column giottoPolygons append different names ... additional params pass methods","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/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 poly_names sorted polygon names used combined giottoPolygon object","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/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/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":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read expression data — readExprData","text":"mylistA = list('' = matrix(1:5), 'b' = matrix(1:5)) depth(mylistA) mylistB = list(= list('' = matrix(1:5), 'b' = matrix(1:5)), B = list('c' = matrix(1:5),'d' = matrix(1:5))) depth(mylistB) mylistC = list('RNA' = list('RAW' = list('cell' = matrix(1:5), 'nucleus' = matrix(6:10)), 'NORM' = list('cell' = matrix(11:15),'nucleus' = matrix(20:25))), 'PROT' = list('RAW' = list('cell' = matrix(16:20)))) depth(mylistC) mymatD = matrix(data = 1:4)","code":""},{"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/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/readGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Read giotto instructions associated with giotto object — readGiottoInstructions","title":"Read giotto instructions associated with giotto object — 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":"Read giotto instructions associated with giotto object — 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":"Read giotto instructions associated with giotto object — 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":"Read giotto instructions associated with giotto object — readGiottoInstructions","text":"specific parameter","code":""},{"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/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/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/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/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/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 read cell metadata list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/read_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read cell metadata — read_cell_metadata","text":"","code":"readCellMetadata(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )  read_cell_metadata(   metadata,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/read_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read cell metadata — read_cell_metadata","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 provenance information (optional) verbose verbose metadata nested list cell metadata information","code":""},{"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_feature_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read feature metadata — read_feature_metadata","title":"Read feature metadata — read_feature_metadata","text":"read feature metadata listt","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/read_feature_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read feature metadata — read_feature_metadata","text":"","code":"readFeatMetadata(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/read_feature_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read feature metadata — read_feature_metadata","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/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/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/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/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/removeGiottoEnvironment.html","id":null,"dir":"Reference","previous_headings":"","what":"removeGiottoEnvironment — removeGiottoEnvironment","title":"removeGiottoEnvironment — removeGiottoEnvironment","text":"removeGiottoEnvironment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeGiottoEnvironment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"removeGiottoEnvironment — removeGiottoEnvironment","text":"","code":"removeGiottoEnvironment(mini_path = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeGiottoEnvironment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"removeGiottoEnvironment — removeGiottoEnvironment","text":"mini_path path anaconda/miniconda. Default: reticulate::miniconda_path() .e. \"C://conda/lives/\" \"C:\\\\conda\\lives\\\" verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeGiottoEnvironment.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"removeGiottoEnvironment — removeGiottoEnvironment","text":"Removes previously installed giotto environment. See installGiottoEnvironment.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace all giotto instructions in giotto object — replaceGiottoInstructions","title":"Replace all giotto instructions in giotto object — 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":"Replace all giotto instructions in giotto object — 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":"Replace all giotto instructions in giotto object — 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":"Replace all giotto instructions in giotto object — replaceGiottoInstructions","text":"giotto object replaces instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Rescale an object — rescale-generic","title":"Rescale an object — rescale-generic","text":"Rescale object spatially. Z dimension scaling supported types subobjects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rescale an object — rescale-generic","text":"","code":"# S4 method for spatLocsObj rescale(x, fx = 1, fy = fx, fz = fx, x0, y0, z0)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rescale an object — rescale-generic","text":"x object fx numeric > 0. horizontal scaling factor fy numeric > 0. vertical scaling factor fz numeric > 0. z scaling factor (supported objects) x0 numeric. x-coordinate center rescaling. missing, center extent x used y0 numeric. y-coordinate center rescaling. missing, center extent x used z0 numeric. z-coordinate center rescaling. missing, center extent x used (supported objects)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Rescale an object — rescale-generic","text":"rescale(spatLocsObj): Rescale spatLocsObj","code":""},{"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/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/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/return_giotto_environment_path.html","id":null,"dir":"Reference","previous_headings":"","what":"return_giotto_environment_path — return_giotto_environment_path","title":"return_giotto_environment_path — return_giotto_environment_path","text":"returns path detected giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"return_giotto_environment_path — return_giotto_environment_path","text":"","code":"return_giotto_environment_path()"},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"return_giotto_environment_path — return_giotto_environment_path","text":"string path","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path_executable.html","id":null,"dir":"Reference","previous_headings":"","what":"return_giotto_environment_path_executable — return_giotto_environment_path_executable","title":"return_giotto_environment_path_executable — return_giotto_environment_path_executable","text":"returns path detected giotto environment executable","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path_executable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"return_giotto_environment_path_executable — return_giotto_environment_path_executable","text":"","code":"return_giotto_environment_path_executable()"},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path_executable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"return_giotto_environment_path_executable — return_giotto_environment_path_executable","text":"string path","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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(x = 0, y = 0, z = 0) )"},{"path":"https://drieslab.github.io/GiottoClass/reference/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)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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 exprObj colnames(x)  # S4 method for exprObj 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/rowMeans_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"rowMeans_flex — rowMeans_flex","title":"rowMeans_flex — 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/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/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 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/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.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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(x = 1, y = 1, z = 1),   scenter = c(x = 0, y = 0, z = 0) )"},{"path":"https://drieslab.github.io/GiottoClass/reference/scale_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scale spatial locations — scale_spatial_locations","text":"spatlocs spatial locations information scale scale_factor scaling factor apply coordinates. scenter center scale spatial coordinates. Given vector xy(z) coordinates.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/select_gimage.html","id":null,"dir":"Reference","previous_headings":"","what":"select_gimage — select_gimage","title":"select_gimage — select_gimage","text":"selects (possibly resamples) giotto images plotting","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/select_gimage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"select_gimage — select_gimage","text":"","code":"select_gimage(   gobject,   gimage = NULL,   image_name = NULL,   largeImage_name = NULL,   spat_unit = NULL,   spat_loc_name = NULL,   feat_type = NULL,   polygon_feat_type = NULL )"},{"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","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/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","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/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","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/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","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/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","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/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 giotto,cellMetaObj setGiotto(gobject, x, ...)  # S4 method for giotto,featMetaObj setGiotto(gobject, x, ...)  # S4 method for giotto,exprObj setGiotto(gobject, x, ...)  # S4 method for giotto,giottoPoints setGiotto(gobject, x, ...)  # S4 method for giotto,giottoPolygon setGiotto(gobject, x, ...)  # S4 method for giotto,dimObj setGiotto(gobject, x, ...)  # S4 method for giotto,spatLocsObj setGiotto(gobject, x, ...)  # S4 method for giotto,spatEnrObj setGiotto(gobject, x, ...)  # S4 method for giotto,nnNetObj setGiotto(gobject, x, ...)  # S4 method for giotto,spatialNetworkObj setGiotto(gobject, x, ...)  # S4 method for giotto,giottoLargeImage setGiotto(gobject, x, ...)  # S4 method for 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 ... additional params pass specific Giotto setter functions","code":""},{"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 = NULL,   image = NULL,   image_type = NULL,   name = NULL,   verbose = TRUE )"},{"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 type giotto image object. Either \"image\" \"largeImage\" 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/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","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/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","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/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","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/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","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/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.","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/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","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/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","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/set_NearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Set nearest network — set_NearestNetwork","title":"Set nearest network — set_NearestNetwork","text":"Set NN-network Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_NearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set nearest network — set_NearestNetwork","text":"","code":"set_NearestNetwork(   gobject,   nn_network,   spat_unit = NULL,   feat_type = NULL,   nn_network_to_use = \"sNN\",   network_name = \"sNN.pca\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_NearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set nearest network — set_NearestNetwork","text":"gobject giotto object nn_network nnNetObj igraph nearest network object. Data.table yet supported. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_network_to_use \"kNN\" \"sNN\" network_name name NN network used provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_NearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set nearest network — set_NearestNetwork","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cell IDs for a given spatial unit — set_cell_id","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"Setter function cell_ID slot. Directly replaces (sets) slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"","code":"set_cell_id(   gobject,   spat_unit = NULL,   cell_IDs,   set_defaults = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") cell_IDs character vector cell IDs set. (See details) set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"giotto object set cell_ID slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"Data spatial unit expected agree single set cell_IDs shared across feature types. cell_IDs stored within giotto object's cell_ID slot. Pass NULL cell_IDs param order delete entry.  Pass 'initialize' cell_IDs param order initialize specified entry. NOTE: main purpose setter initialize, cell_ID values AUTOMATICALLY updated every time initialize() called giotto object.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cell metadata — set_cell_metadata","title":"Set cell metadata — set_cell_metadata","text":"Function set cell metadata information giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cell metadata — set_cell_metadata","text":"","code":"set_cell_metadata(   gobject,   metadata,   spat_unit = NULL,   feat_type = NULL,   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cell metadata — set_cell_metadata","text":"gobject giotto object metadata cellMetaObj data.table containing cell metadata. Setting NULL remove object. Passing 'initialize' reset object. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance provenance information set verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cell metadata — set_cell_metadata","text":"giotto object","code":""},{"path":[]},{"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_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_dimReduction.html","id":null,"dir":"Reference","previous_headings":"","what":"Set dimension reduction — set_dimReduction","title":"Set dimension reduction — set_dimReduction","text":"Function set dimension reduction slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_dimReduction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set dimension reduction — set_dimReduction","text":"","code":"set_dimReduction(   gobject,   dimObject,   spat_unit = NULL,   feat_type = NULL,   reduction = c(\"cells\", \"feats\"),   reduction_method = c(\"pca\", \"umap\", \"tsne\"),   name = \"pca\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_dimReduction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set dimension reduction — set_dimReduction","text":"gobject giotto object dimObject dimension object result set spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") reduction reduction cells features reduction_method reduction method (e.g. \"pca\") name name reduction results provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_dimReduction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set dimension reduction — set_dimReduction","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_expression_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Set expression values — set_expression_values","title":"Set expression values — set_expression_values","text":"Function set expression values giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_expression_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set expression values — set_expression_values","text":"","code":"set_expression_values(   gobject,   values,   spat_unit = NULL,   feat_type = NULL,   name = \"test\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_expression_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set expression values — set_expression_values","text":"gobject giotto object values exprObj NULL, object removed. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name expression slot provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning. set TRUE called external","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_expression_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set expression values — set_expression_values","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feat IDs for a given feature type — set_feat_id","title":"Set feat IDs for a given feature type — set_feat_id","text":"Setter function feat_ID slot. Directly replaces (sets) slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feat IDs for a given feature type — set_feat_id","text":"","code":"set_feat_id(   gobject,   feat_type = NULL,   feat_IDs,   set_defaults = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feat IDs for a given feature type — set_feat_id","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") feat_IDs character vector feature IDs set. set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feat IDs for a given feature type — set_feat_id","text":"giotto object set cell_ID slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set feat IDs for a given feature type — set_feat_id","text":"Across single modality/feature type, within spatial unit, feature information expected share single set feat_IDs. feat_IDs stored within giotto object's feat_ID slot separated feat_type. Pass NULL feat_IDs param order delete entry.  Pass 'initialize' feat_IDs param order initialize specified entry. NOTE: main purpose setter initialize, feat_ID values AUTOMATICALLY updated every time initialize() called giotto object.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feature info — set_feature_info","title":"Set feature info — set_feature_info","text":"Set giotto polygon spatVector features","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feature info — set_feature_info","text":"","code":"set_feature_info(   gobject,   gpoints,   feat_type = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE,   gpolygon = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feature info — set_feature_info","text":"gobject giotto object gpoints giotto points object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning gpolygon typo use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feature info — set_feature_info","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feature metadata — set_feature_metadata","title":"Set feature metadata — set_feature_metadata","text":"Function set feature metadata information giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feature metadata — set_feature_metadata","text":"","code":"set_feature_metadata(   gobject,   metadata,   spat_unit = NULL,   feat_type = NULL,   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feature metadata — set_feature_metadata","text":"gobject giotto object metadata featMetaObj data.table containing feature metadata. Setting NULL remove object. Passing 'initialize' reset object. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance provenance information set verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feature metadata — set_feature_metadata","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Set giotto image object — set_giottoImage","title":"Set giotto image object — set_giottoImage","text":"Directly attach giotto image giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set giotto image object — set_giottoImage","text":"","code":"set_giottoImage(   gobject = NULL,   image = NULL,   image_type = NULL,   name = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set giotto image object — set_giottoImage","text":"gobject giotto object image giotto image object attached without modification giotto object image_type type giotto image object. Either \"image\" \"largeImage\" name name giotto image object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set giotto image object — set_giottoImage","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set giotto image object — set_giottoImage","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/set_giottoImage_MG.html","id":null,"dir":"Reference","previous_headings":"","what":"Set magick-based giotto image — set_giottoImage_MG","title":"Set magick-based giotto image — set_giottoImage_MG","text":"Set giottoImage giotto object additional modifications","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage_MG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set magick-based giotto image — set_giottoImage_MG","text":"","code":"set_giottoImage_MG(gobject, image_object, name = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage_MG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set magick-based giotto image — set_giottoImage_MG","text":"gobject giotto object image_object giottoImage object name name assign giottoImage verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage_MG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set magick-based giotto image — set_giottoImage_MG","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Set terra-based giotto largeImage — set_giottoLargeImage","title":"Set terra-based giotto largeImage — set_giottoLargeImage","text":"Set giottoLargeImage giotto object additional modifications","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set terra-based giotto largeImage — set_giottoLargeImage","text":"","code":"set_giottoLargeImage(gobject, largeImage_object, name = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set terra-based giotto largeImage — set_giottoLargeImage","text":"gobject giotto object largeImage_object giottoLargeImage object name name assign giottoLargeImage verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set terra-based giotto largeImage — set_giottoLargeImage","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giotto_python_path.html","id":null,"dir":"Reference","previous_headings":"","what":"set_giotto_python_path — set_giotto_python_path","title":"set_giotto_python_path — set_giotto_python_path","text":"detects sets python path. Exits without anything getOption('giotto.use_conda') FALSE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giotto_python_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"set_giotto_python_path — set_giotto_python_path","text":"","code":"set_giotto_python_path(python_path = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giotto_python_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"set_giotto_python_path — set_giotto_python_path","text":"python_path character. Full path python executable verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giotto_python_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"set_giotto_python_path — set_giotto_python_path","text":"path python executable","code":""},{"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_polygon_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Set polygon info — set_polygon_info","title":"Set polygon info — set_polygon_info","text":"Set giotto polygon spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_polygon_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set polygon info — set_polygon_info","text":"","code":"set_polygon_info(   gobject,   gpolygon,   polygon_name = \"cell\",   verbose = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_polygon_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set polygon info — set_polygon_info","text":"gobject giotto object gpolygon giottoPolygon object polygon_name name polygons. Default \"cell\" (used gpolygon length 1) verbose verbose initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_polygon_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set polygon info — set_polygon_info","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial grid — set_spatialGrid","title":"Set spatial grid — set_spatialGrid","text":"Function set spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial grid — set_spatialGrid","text":"","code":"set_spatialGrid(   gobject,   spatial_grid,   spat_unit = NULL,   feat_type = NULL,   name = NULL,   verbose = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial grid — set_spatialGrid","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.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial grid — set_spatialGrid","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial network — set_spatialNetwork","title":"Set spatial network — set_spatialNetwork","text":"Function set spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial network — set_spatialNetwork","text":"","code":"set_spatialNetwork(   gobject,   spatial_network,   spat_unit = NULL,   name = NULL,   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial network — set_spatialNetwork","text":"gobject giotto object spatial_network spatial network spat_unit spatial unit (e.g. \"cell\") name name spatial network provenance provenance name verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial network — set_spatialNetwork","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_enrichment.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial enrichment — set_spatial_enrichment","title":"Set spatial enrichment — set_spatial_enrichment","text":"Function set spatial enrichment slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_enrichment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial enrichment — set_spatial_enrichment","text":"","code":"set_spatial_enrichment(   gobject,   spatenrichment,   spat_unit = NULL,   feat_type = NULL,   enrichm_name = \"enrichment\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_enrichment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial enrichment — set_spatial_enrichment","text":"gobject giotto object spatenrichment spatial enrichment results spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") enrichm_name name spatial enrichment results. Default \"DWLS\" provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_enrichment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial enrichment — set_spatial_enrichment","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial locations — set_spatial_locations","title":"Set spatial locations — set_spatial_locations","text":"Function set spatial location slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial locations — set_spatial_locations","text":"","code":"set_spatial_locations(   gobject,   spatlocs,   spat_unit = NULL,   spat_loc_name = \"raw\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial locations — set_spatial_locations","text":"gobject giotto object spatlocs spatial locations (accepts either data.table spatLocsObj) spat_unit spatial unit (e.g. \"cell\") spat_loc_name name spatial locations, default \"raw\" provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial locations — set_spatial_locations","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set spatial locations — set_spatial_locations","text":"spatLocsObj provided spatlocs param attached name spat_unit info used input function's spat_loc_name spat_unitparams, overridden alternative specific inputs params.  ie: spatLocsObj spat_unit slot == 'cell' automatically nested spat_unit 'cell' using set_spatial_locations long param spat_unit = NULL. param spat_unit = 'nucleus' spatLocsObj nested spat_unit 'nucleus' instead spat_unit slot changed 'nucleus'","code":""},{"path":[]},{"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/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\" )"},{"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 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/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 = \"Vizgen\" )"},{"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 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/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/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,   xtranslate = NULL,   ytranslate = NULL,   ztranslate = NULL,   copy_obj = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/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 xtranslate deprecated. use dx ytranslate deprecated. use dy ztranslate deprecated. use dz copy_obj copy/duplicate object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/show-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"show method for giotto class — show,giotto-method","title":"show method for giotto class — show,giotto-method","text":"show method giotto class show method exprObj class Show method dimObj class Show method nnNetObj class show method spatLocsObj class show method spatialNetworkObj class show method spatialGridObj class show method spatEnrObj class show method giottoImage class show method giottoLargeImage class","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/show-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"show method for giotto class — show,giotto-method","text":"","code":"# S4 method for giotto show(object)  # S4 method for exprObj show(object)  # S4 method for dimObj show(object)  # S4 method for nnNetObj show(object)  # S4 method for spatLocsObj show(object)  # S4 method for spatialNetworkObj show(object)  # S4 method for spatialGridObj show(object)  # S4 method for spatEnrObj show(object)  # S4 method for giottoImage show(object)  # S4 method for giottoLargeImage show(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/show-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"show method for giotto class — show,giotto-method","text":"object giottoLargeImage object","code":""},{"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/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/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/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":[]},{"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/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/showGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Show giotto instructions associated with giotto object — showGiottoInstructions","title":"Show giotto instructions associated with giotto object — 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":"Show giotto instructions associated with giotto object — showGiottoInstructions","text":"","code":"showGiottoInstructions(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show giotto instructions associated with giotto object — showGiottoInstructions","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show giotto instructions associated with giotto object — showGiottoInstructions","text":"named vector giotto instructions","code":""},{"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/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/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/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/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/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":[]},{"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":[]},{"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":[]},{"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/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/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":"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/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","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 giotto spatIDs(x, spat_unit = NULL, ...)  # S4 method for exprObj spatIDs(x, ...)  # S4 method for spatLocsObj spatIDs(x, ...)  # S4 method for cellMetaObj spatIDs(x, ...)  # S4 method for spatialNetworkObj spatIDs(x, ...)  # S4 method for dimObj spatIDs(x, ...)  # S4 method for giottoPolygon spatIDs(x, use_cache = TRUE, uniques = TRUE, ...)  # S4 method for spatEnrObj spatIDs(x, ...)  # S4 method for nnNetObj spatIDs(x, ...)  # S4 method for giotto featIDs(x, feat_type = NULL, ...)  # S4 method for exprObj featIDs(x, ...)  # S4 method for featMetaObj featIDs(x, ...)  # S4 method for giottoPoints featIDs(x, use_cache = TRUE, uniques = TRUE, ...)  # S4 method for 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 ... additional parameters pass 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/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":"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/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":"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 spatLocsObj spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)  # S4 method for spatialNetworkObj spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)  # S4 method for giottoPolygon spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for giottoPoints spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for giottoLargeImage spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)"},{"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 dz numeric. shift z axis copy_obj Default = TRUE ... additional params pass methods","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(spatLocsObj): Shift locations spatLocsObj spatShift(spatialNetworkObj): Shift locations spatialNetworkObj","code":""},{"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 spatData spatUnit(x)  # S4 method for giottoPolygon spatUnit(x)  # S4 method for spatData spatUnit(x) <- value  # S4 method for 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":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Spatial unit information — spatUnit-generic","text":"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/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/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/spatVector_to_dt2.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert spatVector to data.table — spatVector_to_dt2","title":"Convert spatVector to data.table — spatVector_to_dt2","text":"convert spatVector data.table. Faster barebones suitable points data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatVector_to_dt2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert spatVector to data.table — spatVector_to_dt2","text":"","code":"spatVector_to_dt2(spatvector, include_values = TRUE)"},{"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":"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 #> 1: 100210519278873141813371229408401071444 #>                                         to sdimx_begin sdimy_begin sdimx_end #> 1: 216701996099683814512199402223708471323    6637.881   -5140.465   6612.68 #>    sdimy_end distance     weight #> 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) { 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":"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/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":"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/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 values SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/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 verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Spin an object — spin-generic","title":"Spin an object — spin-generic","text":"Spin (rotate) object spatially (limited xy rotations)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spin an object — spin-generic","text":"","code":"# S4 method for giottoPolygon spin(x, angle, x0 = NULL, y0 = NULL)  # S4 method for giottoPoints spin(x, angle, x0 = NULL, y0 = NULL)  # S4 method for spatLocsObj spin(   x,   angle = NULL,   x0 = NULL,   y0 = NULL,   z0 = NULL,   xy_angle = NULL,   zy_angle = NULL,   xz_angle = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spin-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spin an object — spin-generic","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. 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","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Spin an object — spin-generic","text":"spin(giottoPolygon): Spin giottoPolygon object spin(giottoPoints): Spin giottoPoints object spin(spatLocsObj): Spin spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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 = F,   cumulate_offset_y = F,   field_col = \"Field of View\",   X_coord_col = \"X\",   Y_coord_col = \"Y\",   reverse_final_x = F,   reverse_final_y = T )"},{"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: 1. cell locations: least 3 columns: field, X, Y 2. create offset file: offset file 3 columns: field, x_offset, y_offset 3. create new cell location file stitching original cell locations stitchFieldCoordinates 4. 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/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/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 = NULL,   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/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 )"},{"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","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/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/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_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset cell metadata — subset_cell_metadata","title":"Subset cell metadata — subset_cell_metadata","text":"Subset cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset cell metadata — subset_cell_metadata","text":"","code":"subset_cell_metadata(   gobject,   spat_unit = \":all:\",   feat_type_ssub = \":all:\",   cell_ids = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset cell metadata — subset_cell_metadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") cell_ids cell ids keep","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_feature_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset feature metadata — subset_feature_metadata","title":"Subset feature metadata — subset_feature_metadata","text":"Subset feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_feature_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset feature metadata — subset_feature_metadata","text":"","code":"subset_feature_metadata(   gobject,   feat_type = \":all:\",   spat_unit_fsub = \":all:\",   feat_ids = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_feature_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset feature metadata — subset_feature_metadata","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") feat_ids feature ids keep","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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/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/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-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Transpose — transpose-generic","title":"Transpose — transpose-generic","text":"Transpose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transpose — transpose-generic","text":"","code":"# S4 method for spatLocsObj t(x)  # S4 method for spatialNetworkObj t(x)  # S4 method for giottoPoints t(x)  # S4 method for giottoPolygon t(x)  # S3 method for spatLocsObj t(x)  # S3 method for spatialNetworkObj t(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transpose — transpose-generic","text":"x object transposed","code":""},{"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 = F","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/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/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":"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":"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":"if (FALSE) { gobject <- updateGiottoObject(gobject) }"},{"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/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/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","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap giotto terra pointer information — wrap-generic","title":"Wrap giotto terra pointer information — wrap-generic","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-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap giotto terra pointer information — wrap-generic","text":"","code":"# S4 method for giottoPolygon wrap(x)  # S4 method for giotto wrap(x)  # S4 method for giottoPoints wrap(x)  # S4 method for packedGiottoPolygon vect(x)  # S4 method for packedGiottoPoints vect(x)  # S4 method for packedGiotto vect(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap giotto terra pointer information — wrap-generic","text":"x giottoPolygon giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Wrap giotto terra pointer information — wrap-generic","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/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/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc. <http://fsf.org/> Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. 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Protecting Users’ Legal Rights From Anti-Circumvention Law","title":"GNU General Public License","text":"covered work shall deemed part effective technological measure applicable law fulfilling obligations article 11 WIPO copyright treaty adopted 20 December 1996, similar laws prohibiting restricting circumvention measures. convey covered work, waive legal power forbid circumvention technological measures extent circumvention effected exercising rights License respect covered work, disclaim intention limit operation modification work means enforcing, work’s users, third parties’ legal rights forbid circumvention technological measures.","code":""},{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":"id_4-conveying-verbatim-copies","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"4. 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Conveying Modified Source Versions","title":"GNU General Public License","text":"may convey work based Program, modifications produce Program, form source code terms section 4, provided also meet conditions: ) work must carry prominent notices stating modified , giving relevant date. b) work must carry prominent notices stating released License conditions added section 7. requirement modifies requirement section 4 “keep intact notices”. c) must license entire work, whole, License anyone comes possession copy. License therefore apply, along applicable section 7 additional terms, whole work, parts, regardless packaged. 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Termination","title":"GNU General Public License","text":"may propagate modify covered work except expressly provided License. attempt otherwise propagate modify void, automatically terminate rights License (including patent licenses granted third paragraph section 11). However, cease violation License, license particular copyright holder reinstated () provisionally, unless copyright holder explicitly finally terminates license, (b) permanently, copyright holder fails notify violation reasonable means prior 60 days cessation. Moreover, license particular copyright holder reinstated permanently copyright holder notifies violation reasonable means, first time received notice violation License (work) copyright holder, cure violation prior 30 days receipt notice. 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Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. 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Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://drieslab.github.io/GiottoClass/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. 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GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read <http://www.gnu.org/philosophy/--lgpl.html>.","code":"<one line to give the program's name and a brief idea of what it does.> Copyright (C) <year>  <name of author>  This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.  This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.  You should have received a copy of the GNU General Public License along with this program.  If not, see <http://www.gnu.org/licenses/>. <program>  Copyright (C) <year>  <name of author> This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"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 Chávez. 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 J, Ruiz E (2023). GiottoClass: Giotto Suite object definitions framework. R package version 0.0.0.9010, 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 Chávez and Edward Ruiz},   year = {2023},   note = {R package version 0.0.0.9010},   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/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/S3toS4spatNetObj.html","id":null,"dir":"Reference","previous_headings":"","what":"Spatial Networks — S3toS4spatNetObj","title":"Spatial Networks — S3toS4spatNetObj","text":"convert S3 spatialNetworkObj S4","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatNetObj.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spatial Networks — S3toS4spatNetObj","text":"","code":"S3toS4spatNetObj(object, spat_unit = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/S3toS4spatNetObj.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spatial Networks — S3toS4spatNetObj","text":"object S3 spatNetworkObj spat_unit spatial unit metadata append","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/abb_mat.html","id":null,"dir":"Reference","previous_headings":"","what":"Print abbreviated matrix — abb_mat","title":"Print abbreviated matrix — abb_mat","text":"print abbreviated matrix exprObj. Works Matrix pkg denseMatrix, matrix, data.frame classes inherit .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/abb_mat.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print abbreviated matrix — abb_mat","text":"","code":"abb_mat(exprObj, nrows, ncols, header = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/abb_spatlocs.html","id":null,"dir":"Reference","previous_headings":"","what":"Print abbreviated spatlocs — abb_spatlocs","title":"Print abbreviated spatlocs — abb_spatlocs","text":"print abbreviated spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/abb_spatlocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Print abbreviated spatlocs — abb_spatlocs","text":"","code":"abb_spatlocs(spatLocsObj, nrows)"},{"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 giotto activeFeatType(gobject)  # S4 method for 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/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 giotto activeSpatUnit(gobject)  # S4 method for 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/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_name (optional) custom name provide single vector 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 two manners: 1. Provide data.table data.frame cell annotations order cell_ID column pDataDT(gobject) 2. Provide data.table data.frame cell annotations specify column contains cell IDs, cell IDs need match cell_ID column pDataDT(gobject)","code":""},{"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,   by_column = F,   column_feat_ID = NULL,   vector_name = 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) by_column merge metadata based feat_ID column fDataDT column_feat_ID column name new metadata use by_column = TRUE vector_name (optional) custom name provide single vector","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 two manners: Provide data.table data.frame feature annotations order feat_ID column fDataDT(gobject) Provide data.table data.frame feature annotations specify column contains feature IDs, feature IDs need match feat_ID column fDataDT(gobject)","code":""},{"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 giottoImages add largeImages list giottoLargeImages add 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/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/addGiottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"addGiottoLargeImage — addGiottoLargeImage","title":"addGiottoLargeImage — addGiottoLargeImage","text":"Adds 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/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/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/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/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/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/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/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/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/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/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/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/aggregateStacksPolygonsOLD.html","id":null,"dir":"Reference","previous_headings":"","what":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","title":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","text":"aggregate polygons different z-stacks","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonsOLD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","text":"","code":"aggregateStacksPolygonsOLD(gobject, spat_units, new_spat_unit = \"aggregate\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonsOLD.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","text":"gobject giotto object spat_units spatial units aggregate new_spat_unit new name aggregated spatial unit","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/aggregateStacksPolygonsOLD.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"aggregateStacksPolygonsOLD — aggregateStacksPolygonsOLD","text":"giotto object","code":""},{"path":[]},{"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,   deluanay_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. deluanay_spat_net binary parameter spatial network. TRUE, spatial network deluanay network. spat_unit desired spatial unit conversion, default NULL feat_type desired feature type 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 insructions 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 clustering — annotateGiotto","title":"Annotate giotto clustering — annotateGiotto","text":"Converts cluster results user provided annotation.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/annotateGiotto.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Annotate giotto clustering — 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 clustering — annotateGiotto","text":"gobject giotto object spat_unit spatial unit feat_type feature type annotation_vector named annotation vector (names = cluster ids) cluster_column cluster column convert annotation names 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 clustering — 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 clustering — annotateGiotto","text":"need specifify (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/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/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/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_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/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 SpatVector as.data.table(   x,   keep.rownames = FALSE,   geom = NULL,   include_values = TRUE,   ... )  # S3 method for giottoPolygon as.data.table(x, ...)  # S3 method for 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":[]},{"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/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/calculateOverlap.html","id":null,"dir":"Reference","previous_headings":"","what":"Calculate features overlapped by polygons — calculateOverlap","title":"Calculate features overlapped by polygons — calculateOverlap","text":"Calculate features overlapped polygons","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 giotto,missing calculateOverlap(   x,   name_overlap = NULL,   spatial_info = NULL,   feat_info = NULL,   image_names = NULL,   poly_subset_ids = NULL,   feat_subset_column = NULL,   feat_subset_ids = NULL,   count_info_column = NULL,   return_gobject = TRUE,   verbose = TRUE,   ... )  # S4 method for 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 giottoPolygon,SpatRaster calculateOverlap(   x,   y,   name_overlap = NULL,   poly_subset_ids = NULL,   return_gpolygon = TRUE,   verbose = TRUE,   ... )  # S4 method for SpatVector,SpatRaster calculateOverlap(x, y, poly_subset_ids = NULL, verbose = TRUE, ...)  # S4 method for 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 (optional) character vector poly_IDs use 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 ... additional params pass methods y Object features overlap: giottoPoints, giottoLargeImage, SpatVector points SpatRaster 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":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Calculate features overlapped by polygons — calculateOverlap","text":"","code":"if (FALSE) { x <- GiottoData::loadSubObjectMini(\"giottoPolygon\") y <- GiottoData::loadSubObjectMini(\"giottoPoints\") x@overlaps <- NULL overlaps(x) # Should now be NULL  a <- calculateOverlap(x, y) overlaps(a) }"},{"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/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/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/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/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/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/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/calculate_distance_and_weight.html","id":null,"dir":"Reference","previous_headings":"","what":"calculate_distance_and_weight — calculate_distance_and_weight","title":"calculate_distance_and_weight — calculate_distance_and_weight","text":"calculate_distance_and_weight","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/calculate_distance_and_weight.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"calculate_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/calculate_distance_and_weight.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"calculate_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/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/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/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/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/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":"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/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 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":"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/changeGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Change giotto instruction(s) associated with giotto object — changeGiottoInstructions","title":"Change giotto instruction(s) associated with giotto object — 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":"Change giotto instruction(s) associated with giotto object — 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":"Change giotto instruction(s) associated with giotto object — 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":"Change giotto instruction(s) associated with giotto object — changeGiottoInstructions","text":"giotto object one changed instructions","code":""},{"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/checkGiottoEnvironment.html","id":null,"dir":"Reference","previous_headings":"","what":"checkGiottoEnvironment — checkGiottoEnvironment","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"checkGiottoEnvironment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkGiottoEnvironment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"","code":"checkGiottoEnvironment(mini_install_path = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/checkGiottoEnvironment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"mini_install_path (optional) path miniconda conda directory within giotto environment lives provided, automatically determined reticulate::miniconda_path() Note required input format: Correct format --> mini_install_path = \"C://conda/lives/\" \"C:\\\\conda\\lives\\\" INCORRECT formats --> mini_install_path = \"C://conda/lives//\" \"C:\\\\conda\\lives\\\\\" verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkGiottoEnvironment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"logical","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/checkGiottoEnvironment.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"checkGiottoEnvironment — checkGiottoEnvironment","text":"Checks miniconda giotto environment can found. Can installed installGiottoEnvironment.","code":""},{"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":"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_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/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/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/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/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/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/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/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/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/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/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/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/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 Giotto python modules python environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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_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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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/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 = c(\"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/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/combineSpatialCellFeatureInfo.html","id":null,"dir":"Reference","previous_headings":"","what":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"Combine spatial cell information (e.g. polygon) spatial feature information (e.g. transcript locations)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellFeatureInfo.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"","code":"combineSpatialCellFeatureInfo(   gobject,   spat_unit = NULL,   feat_type = NULL,   selected_features = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellFeatureInfo.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"gobject Giotto object spat_unit spatial unit feat_type feature type(s) selected_features select set features","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellFeatureInfo.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"list data.table(s)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combineSpatialCellFeatureInfo.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"combineSpatialCellFeatureInfo — combineSpatialCellFeatureInfo","text":"returned data.table following columns: sdimx: spatial feature location x-axis sdimy: spatial feature location y-axis feat_ID: unique feature ID cell_ID: unique cell ID used: often feature used/assigned cell feat: selected feature(s)","code":""},{"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/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":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine giottoPolygon geometries — combineToMultiPolygon","text":"","code":"if (FALSE) { gpoly <- GiottoData::loadSubObjectMini(\"giottoPolygon\") groups <- data.table::data.table(   poly_ID = gpoly$poly_ID,   group_ID = sort(rep(LETTERS[1:5], length.out = nrow(gpoly))) # make 5 groups ) multi_gp <- combineToMultiPolygon(gpoly, groups)  plot(multi_gp[\"A\"]) }"},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_matrices.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_matrices — combine_matrices","title":"combine_matrices — combine_matrices","text":"combine_matrices","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_matrices.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_matrices — combine_matrices","text":"","code":"combine_matrices(mat_list, summarize = \"sum\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_polygons — combine_polygons","title":"combine_polygons — combine_polygons","text":"combine_polygons","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_polygons — combine_polygons","text":"","code":"combine_polygons(polygon_list)"},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_spatlocs.html","id":null,"dir":"Reference","previous_headings":"","what":"combine_spatlocs — combine_spatlocs","title":"combine_spatlocs — combine_spatlocs","text":"combine_spatlocs","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/combine_spatlocs.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"combine_spatlocs — combine_spatlocs","text":"","code":"combine_spatlocs(spatlocs_list, summarize = \"mean\")"},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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_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","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_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","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/copy-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Copy an entire object — copy-generic","title":"Copy an entire object — copy-generic","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-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Copy an entire object — copy-generic","text":"","code":"# S4 method for coordDataDT copy(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/copy-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Copy an entire object — copy-generic","text":"x Giotto S4 class subobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/copy-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Copy an entire object — copy-generic","text":"copy(coordDataDT): Copy data.table-based spatial locations object.","code":""},{"path":[]},{"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/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/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/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/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/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/createGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Create instructions for giotto functions — createGiottoInstructions","title":"Create instructions for giotto functions — createGiottoInstructions","text":"Function set global instructions giotto functions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoInstructions.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create instructions for giotto functions — createGiottoInstructions","text":"","code":"createGiottoInstructions(   python_path = NULL,   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 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create instructions for giotto functions — createGiottoInstructions","text":"python_path path python binary use 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","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create instructions for giotto functions — createGiottoInstructions","text":"named vector giotto instructions","code":""},{"path":[]},{"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 terra SpatRaster image object 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/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/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 list large images 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/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 list large images 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/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 SpatVector createGiottoPoints(   x,   feat_type = \"rna\",   verbose = TRUE,   split_keyword = NULL,   unique_IDs = NULL )  # S4 method for data.frame createGiottoPoints(   x,   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","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":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create giotto points object — createGiottoPoints","text":"","code":"# data.frame input x <- data.frame(   ID = letters[1:6],   x = 1:6,   y = 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 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)","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 SpatVector createGiottoPolygon(x, name = \"cell\", calc_centroids = FALSE, verbose = TRUE)  # S4 method for 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,   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   fix_multipart = TRUE,   remove_unvalid_polygons = TRUE,   calc_centroids = FALSE,   verbose = TRUE )  # S4 method for data.frame createGiottoPolygon(   x,   name = \"cell\",   calc_centroids = FALSE,   skip_eval_dfr = FALSE,   copy_dt = TRUE,   verbose = TRUE )  # S4 method for character createGiottoPolygon(x, ...)  createGiottoPolygonsFromMask(   maskfile,   mask_method = c(\"guess\", \"single\", \"multiple\"),   name = \"cell\",   remove_background_polygon = FALSE,   background_algo = c(\"range\"),   fill_holes = TRUE,   poly_IDs = NULL,   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   calc_centroids = FALSE,   fix_multipart = TRUE,   remove_unvalid_polygons = TRUE )  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. name name giottoPolygon object created calc_centroids (default FALSE) calculate centroids polygons verbose verbose mask_method mask file defines individual segmentation annotations remove_background_polygon try remove background polygon (default: FALSE) background_algo algorithm remove background polygon fill_holes fill holes within created polygons poly_IDs unique names polygon mask file 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) fix_multipart try split polygons multiple parts (default: TRUE) 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 ... additional params pass. character method, params pass SpatRaster SpatVector methods, depending whether x filepath maskfile spatial file (ex: wkt, shp, GeoJSON) respectively. maskfile path mask file 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":"giotto polygon object","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/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,   name = \"metafeat\",   return_gobject = TRUE )"},{"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 name name metagene results return_gobject return giotto object","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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/createMetafeats.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"createMetafeats — createMetafeats","text":"","code":"if (FALSE) { # load a dataset g <- GiottoData::loadGiottoMini(\"viz\") # set a spat unit to use activeSpatUnit(g) <- \"aggregate\"  # create the metafeats # We do this by making an annotation vector which is a numerical vector # of cluster assignments where each number is named by the feature it describes. # # Here we create an example annotation vector by arbitrarily using the first 6 # features and putting 3 in cluster 1 and the other 3 in cluster 2. feats_to_use <- featIDs(g)[1:6] clust_to_use <- c(1, 1, 1, 2, 2, 2) names(clust_to_use) <- feats_to_use  # show clust_to_use  g <- createMetafeats(   gobject = g,   feat_clusters = clust_to_use,   name = \"new_metagene\" )  GiottoVisuals::spatCellPlot(   gobject = g,   spat_enr_names = \"new_metagene\",   cell_annotation_values = c(\"1\", \"2\"),   point_size = 3.5,   cow_n_col = 2 ) }"},{"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":"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/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 = 1:10,   feats_to_use = NULL,   genes_to_use = NULL,   expression_values = c(\"normalized\", \"scaled\", \"custom\"),   name = NULL,   return_gobject = TRUE,   k = 30,   minimum_shared = 5,   top_shared = 3,   verbose = T,   ... )"},{"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 genes_to_use deprecated, use feats_to_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: 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/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/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/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/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/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 = T,   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 wisker\" value distance vector neighbors used; see boxplotgraphics documentation details.(default = \"auto\") minimum_k minimum number neigbhours maximum_distance != NULL options (geometry) String containing extra control options underlying Qhull command; see Qhull documentation (../doc/qhull/html/qdelaun.html) 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 boolean: return giotto object (default = TRUE) output 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/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 = c(\"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_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/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/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 = F,   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 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/createSpatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"createSpatialNetwork — createSpatialNetwork","title":"createSpatialNetwork — createSpatialNetwork","text":"Create spatial network based cell centroid physical distances.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/createSpatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"createSpatialNetwork — 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 = F,   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":"createSpatialNetwork — 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 Delaunay method use maximum_distance_delaunay distance cuttof nearest neighbors consider Delaunay network options (geometry) String containing extra control options underlying Qhull command; see Qhull documentation (../doc/qhull/html/qdelaun.html) 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 neigbhours maximum_distance != NULL knn_method method create kNN network k number nearest neighbors based physical distance maximum_distance_knn distance cuttof nearest neighbors consider kNN network verbose verbose return_gobject boolean: return giotto object (default = TRUE) output 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":"createSpatialNetwork — 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":"createSpatialNetwork — 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 specififies spatial dimensions use, e.g. c(\"sdimx', \"sdimy\") numerical vector, e.g. 2:3","code":""},{"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":"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/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_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 epression values factor","code":""},{"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_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_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_delaunayNetwork2D.html","id":null,"dir":"Reference","previous_headings":"","what":"create_delaunayNetwork2D — create_delaunayNetwork2D","title":"create_delaunayNetwork2D — create_delaunayNetwork2D","text":"Create spatial 2D Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_delaunayNetwork2D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_delaunayNetwork2D — create_delaunayNetwork2D","text":"","code":"create_delaunayNetwork2D(   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 = T,   return_gobject = TRUE,   output = c(\"spatialNetworkObj\", \"data.table\"),   ... )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_delaunayNetwork3D.html","id":null,"dir":"Reference","previous_headings":"","what":"create_delaunayNetwork3D — create_delaunayNetwork3D","title":"create_delaunayNetwork3D — create_delaunayNetwork3D","text":"Create spatial 3D Delaunay network.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_delaunayNetwork3D.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"create_delaunayNetwork3D — create_delaunayNetwork3D","text":"","code":"create_delaunayNetwork3D(   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/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/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/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/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/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/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/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/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/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_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_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_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_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_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_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_segm_polygons.html","id":null,"dir":"Reference","previous_headings":"","what":"Create segmentation polygons — create_segm_polygons","title":"Create segmentation polygons — create_segm_polygons","text":"creates giotto polygons segmentation mask data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/create_segm_polygons.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create segmentation polygons — create_segm_polygons","text":"","code":"create_segm_polygons(   maskfile,   name = \"cell\",   poly_IDs = NULL,   flip_vertical = TRUE,   shift_vertical_step = TRUE,   flip_horizontal = TRUE,   shift_horizontal_step = TRUE,   remove_background_polygon = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/create_segm_polygons.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create segmentation polygons — create_segm_polygons","text":"giotto polygon","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_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_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_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_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/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/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/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/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/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, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/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 verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/crop-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Crop to a spatial subset — crop-generic","title":"Crop to a spatial subset — crop-generic","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-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Crop to a spatial subset — crop-generic","text":"","code":"# S4 method for giottoLargeImage crop(x, y, ...)  # S4 method for giottoPoints crop(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)  # S4 method for giottoPolygon crop(x, y, DT = TRUE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, ...)"},{"path":"https://drieslab.github.io/GiottoClass/reference/crop-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Crop to a spatial subset — crop-generic","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-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Crop to a spatial subset — crop-generic","text":"crop(giottoLargeImage): Crop giottoLargeImage crop(giottoPoints): Crop giottoPoints crop(giottoPolygon): Crop giottoPoints","code":""},{"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/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","code":""},{"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 image_type image object type (supports largeImage set default)","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":"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/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 giottoPoints nrow(x)  # S4 method for giottoPolygon nrow(x)  # S4 method for spatLocsObj nrow(x)  # S4 method for exprData nrow(x)  # S4 method for metaData nrow(x)  # S4 method for spatialNetworkObj nrow(x)  # S4 method for enrData nrow(x)  # S4 method for exprData ncol(x)  # S4 method for metaData ncol(x)  # S4 method for enrData ncol(x)  # S4 method for exprData dim(x)  # S4 method for metaData dim(x)  # S4 method for enrData dim(x)  # S4 method for giottoLargeImage 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":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Dimensions of giotto objects — dims-generic","text":"nrow(giottoPoints): Find rows giottoPoints object nrow(giottoPolygon): Find rows giottoPolygon object nrow(spatLocsObj): Find rows giotto S4s data.table based coordinates slots nrow(exprData): Find rows giotto S4s data.table based coordinates slots nrow(metaData): Find rows giotto S4s data.table based coordinates slots nrow(spatialNetworkObj): Find rows spatialNetworkObj ncol(exprData): Find cols giotto S4s Matrix based exprMat slots ncol(metaData): Find cols giotto S4s data.table based metaDT slots ncol(enrData): Find cols giotto S4s enrData dim(exprData): Find dimensions giotto S4s Matrix based exprMat slots dim(metaData): Find dimensions giotto S4s data.table based metaDT slots","code":""},{"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\") )"},{"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","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/do_gpoly.html","id":null,"dir":"Reference","previous_headings":"","what":"do_gpoly — do_gpoly","title":"do_gpoly — do_gpoly","text":"Perform function spatVector-based slots giottoPolygon","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/do_gpoly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"do_gpoly — do_gpoly","text":"","code":"do_gpoly(x, what, args = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/do_gpoly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"do_gpoly — do_gpoly","text":"x giottoPolygon call args list additional args","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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/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/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 = 1:50)"},{"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/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":"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/ext-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Get a SpatExtent — ext-generic","title":"Get a SpatExtent — ext-generic","text":"Get SpatExtent object. spatial minmax x y object mapped .","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get a SpatExtent — ext-generic","text":"","code":"# S4 method for spatLocsObj ext(x, ...)  # S4 method for giottoPolygon ext(x, ...)  # S4 method for giottoPoints ext(x, ...)  # S4 method for spatialNetworkObj ext(x, ...)  # S4 method for giottoLargeImage ext(x, ...)  # S4 method for giottoPoints,SpatExtent ext(x) <- value  # S4 method for giottoPolygon,SpatExtent ext(x) <- value  # S4 method for giottoLargeImage,SpatExtent ext(x) <- value  # S4 method for ANY,ANY ext(x) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/ext-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get a SpatExtent — ext-generic","text":"x spatial object ... additional params pass value value set. Accepts object ext() work ","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/ext-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Get a SpatExtent — ext-generic","text":"ext(spatLocsObj): Get extent spatLocsObj ext(giottoPolygon): Get extent giottoPolygon ext(giottoPoints): Get extent giottoPoints ext(spatialNetworkObj): Get extent spatialNetworkObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"Extract or replace parts of an object — extract-methods","title":"Extract or replace parts of an object — extract-methods","text":"Operators Giotto S4 internal data.tables extract replace parts.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Extract or replace parts of an object — extract-methods","text":"","code":"# S4 method for coordDataDT $(x, name)  # S4 method for coordDataDT $(x, name) <- value  # S4 method for metaData $(x, name)  # S4 method for metaData $(x, name) <- value  # S4 method for terraVectData $(x, name)  # S4 method for terraVectData $(x, name) <- value  # S4 method for gdtData,gIndex,gIndex,missing [(x, i, j)  # S4 method for gdtData,logical,missing,missing [(x, i, j)  # S4 method for gdtData,character,missing,missing [(x, i, j)  # S4 method for gdtData,missing,numeric,missing [(x, i, j)  # S4 method for gdtData,missing,logical,missing [(x, i, j)  # S4 method for coordDataDT,ANY,ANY,missing [(x, i, j)  # S4 method for coordDataDT,missing,ANY,missing [(x, i, j)  # S4 method for coordDataDT,missing,character,missing [(x, i, j)  # S4 method for coordDataDT,ANY,missing,missing [(x, i, j)  # S4 method for coordDataDT,missing,missing,missing [(x, i, j)  # S4 method for coordDataDT,missing,missing,ANY [(x, i, j) <- value  # S4 method for giottoPoints,gIndex,missing,missing [(x, i, j)  # S4 method for metaData,missing,ANY,missing [(x, i, j)  # S4 method for metaData,missing,character,missing [(x, i, j)  # S4 method for metaData,ANY,missing,missing [(x, i, j)  # S4 method for metaData,missing,missing,missing [(x, i, j)  # S4 method for metaData,missing,missing,ANY [(x, i, j) <- value  # S4 method for dimObj,ANY,ANY,missing [(x, i, j)  # S4 method for dimObj,missing,missing,missing [(x, i, j)  # S4 method for dimObj,missing,missing,ANY [(x, i, j) <- value  # S4 method for exprData,missing,ANY,missing [(x, i, j)  # S4 method for exprData,ANY,missing,missing [(x, i, j)  # S4 method for exprData,ANY,ANY,missing [(x, i, j)  # S4 method for exprData,missing,missing,missing [(x, i, j)  # S4 method for exprData,missing,missing,ANY [(x, i, j) <- value  # S4 method for spatNetData,missing,missing,missing [(x, i, j)  # S4 method for spatNetData,missing,missing,ANY [(x, i, j) <- value  # S4 method for nnData,missing,missing,missing [(x, i, j)  # S4 method for nnData,missing,missing,ANY [(x, i, j) <- value  # S4 method for enrData,missing,missing,missing [(x, i, j)  # S4 method for enrData,ANY,missing,missing [(x, i, j)  # S4 method for enrData,missing,ANY,missing [(x, i, j)  # S4 method for enrData,missing,character,missing [(x, i, j)  # S4 method for enrData,missing,missing,ANY [(x, i, j) <- value  # S4 method for spatGridData,missing,missing,missing [(x, i, j)  # S4 method for spatGridData,missing,missing,ANY [(x, i, j) <- value  # S4 method for giottoPoints,missing,missing,missing [(x, i, j)  # S4 method for giottoPoints,gIndex,missing,missing [(x, i, j)  # S4 method for giottoPoints,character,missing,missing [(x, i, j)  # S4 method for giottoPoints,missing,gIndex,missing [(x, i, j)  # S4 method for giottoPoints,missing,missing,ANY [(x, i, j) <- value  # S4 method for giottoPolygon,missing,missing,missing [(x, i, j)  # S4 method for giottoPolygon,gIndex,missing,missing [(x, i, j)  # S4 method for giottoPolygon,character,missing,missing [(x, i, j)  # S4 method for giottoPolygon,missing,gIndex,missing [(x, i, j)  # S4 method for terraVectData,gIndex,gIndex,missing [(x, i, j)  # S4 method for giottoPolygon,missing,missing,ANY [(x, i, j) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Extract or replace parts of an object — extract-methods","text":"x Giotto S4 object extract columns name literal character string (possibly backtick quoted). value value(s) set normally matched colnames data.table object within S4. , j indices specifying elements extract replace. Indices numeric character vectors empty","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"-methods","dir":"Reference","previous_headings":"","what":"`$` methods","title":"Extract or replace parts of an object — extract-methods","text":"Select colname giotto S4 data.table coordinates slot. Select colname giotto S4 data.table metaDT slot. Select colname giotto S4 spatVector slot.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"-lt-methods","dir":"Reference","previous_headings":"","what":"`$<-` methods","title":"Extract or replace parts of an object — extract-methods","text":"Set values colname giotto S4 data.table coordinates slot. Works via data.table methods Set values colname giotto S4 data.table metaDT slot. Works via data.table methods Set values colname giotto S4 spatVector slot.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"-methods-1","dir":"Reference","previous_headings":"","what":"`[` methods","title":"Extract or replace parts of an object — extract-methods","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":"https://drieslab.github.io/GiottoClass/reference/extract-methods.html","id":"-lt-methods-1","dir":"Reference","previous_headings":"","what":"`[<-` methods","title":"Extract or replace parts of an object — extract-methods","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","code":""},{"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/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":"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/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 featData featType(x)  # S4 method for 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":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Feature type information — featType-generic","text":"featType(featData): Get feature type information featType(featData) <- value: Set feature type information","code":""},{"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":"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/filter_network.html","id":null,"dir":"Reference","previous_headings":"","what":"filter_network — filter_network","title":"filter_network — filter_network","text":"function filter spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/filter_network.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"filter_network — filter_network","text":"","code":"filter_network(networkDT = NULL, maximum_distance = NULL, minimum_k = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/filter_network.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"filter_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/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/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/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/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/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/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/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/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/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/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/find_terra_writeRaster_dataType.html","id":null,"dir":"Reference","previous_headings":"","what":"find_terra_writeRaster_dataType — find_terra_writeRaster_dataType","title":"find_terra_writeRaster_dataType — find_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/find_terra_writeRaster_dataType.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"find_terra_writeRaster_dataType — find_terra_writeRaster_dataType","text":"","code":"find_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/find_terra_writeRaster_dataType.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"find_terra_writeRaster_dataType — find_terra_writeRaster_dataType","text":"giottoLargeImage giottoLargeImage object determine max_intensity, min_intensity, is_int 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 quick_INTU_maxval Treat maximum intensity find compatible unsigned integer settings","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/find_terra_writeRaster_dataType.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"find_terra_writeRaster_dataType — find_terra_writeRaster_dataType","text":"datatype terra writeRaster function","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/flip-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Flip an object — flip-generic","title":"Flip an object — flip-generic","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-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Flip an object — flip-generic","text":"","code":"# S4 method for giottoPolygon flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for giottoPoints flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for spatLocsObj flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for spatialNetworkObj flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for giottoLargeImage flip(x, direction = \"vertical\", x0 = 0, y0 = 0, ...)  # S4 method for SpatExtent flip(x, direction = \"vertical\", x0 = 0, y0 = 0)"},{"path":"https://drieslab.github.io/GiottoClass/reference/flip-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Flip an object — flip-generic","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 ... additional args pass","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/flip-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Flip an object — flip-generic","text":"flip(giottoPolygon): Flip giottoPolygon object flip(giottoPoints): Flip giottoPoints object flip(spatLocsObj): Flip spatLocsObj flip(spatialNetworkObj): Flip spatialNetworkObj flip(giottoLargeImage): Flip giottoLargeImage flip(SpatExtent): Flip SpatExtent","code":""},{"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":"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":"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":[]},{"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 = c(\"pca\", \"umap\", \"tsne\"),   name = \"pca\",   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/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/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 )"},{"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.","code":""},{"path":[]},{"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":[]},{"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 image object 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 = NULL,   image_type = c(\"image\", \"largeImage\"),   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 type giotto image object. Either \"image\" \"largeImage\" name name giotto image object showGiottoImageNames","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/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/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 igraph data.table object. Default 'igraph' 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":"igraph data.table object","code":""},{"path":[]},{"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 )"},{"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","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/getRainbowColors.html","id":null,"dir":"Reference","previous_headings":"","what":"getRainbowColors — getRainbowColors","title":"getRainbowColors — getRainbowColors","text":"Returns number rainbow colors spaced around spectrum. 100 unique colors supplied recycled.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getRainbowColors.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"getRainbowColors — getRainbowColors","text":"","code":"getRainbowColors(n)"},{"path":"https://drieslab.github.io/GiottoClass/reference/getRainbowColors.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"getRainbowColors — getRainbowColors","text":"n number colors wanted","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/getRainbowColors.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"getRainbowColors — getRainbowColors","text":"character vector hexadecimal rainbow colors","code":""},{"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":"data.table fractions","code":""},{"path":[]},{"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":[]},{"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 )"},{"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.","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/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 )"},{"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","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_NearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Get nearest network — get_NearestNetwork","title":"Get nearest network — get_NearestNetwork","text":"Get NN-network Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_NearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get nearest network — get_NearestNetwork","text":"","code":"get_NearestNetwork(   gobject,   spat_unit = NULL,   feat_type = NULL,   nn_network_to_use = NULL,   network_name = NULL,   output = c(\"nnNetObj\", \"igraph\", \"data.table\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_NearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get nearest network — get_NearestNetwork","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_network_to_use \"kNN\" \"sNN\" network_name name NN network used output return igraph data.table object. Default 'igraph' set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_NearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get nearest network — get_NearestNetwork","text":"igraph data.table object","code":""},{"path":[]},{"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_args.html","id":null,"dir":"Reference","previous_headings":"","what":"Log args used — get_args","title":"Log args used — get_args","text":"Get arguments passed function call.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_args.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Log args used — get_args","text":"","code":"get_args(toplevel = 2L, verbose = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_args.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Log args used — get_args","text":"toplevel integer. Relative stack function call made. verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Get cell IDs for a given spatial unit — get_cell_id","title":"Get cell IDs for a given spatial unit — get_cell_id","text":"Data spatial unit expected agree single set cell_IDs shared across feature types. cell_IDs stored within giotto object's cell_ID slot. Getters setters slot directly retrieve (get) replace (set) slot.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get cell IDs for a given spatial unit — get_cell_id","text":"","code":"get_cell_id(gobject, spat_unit = NULL, set_defaults = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get cell IDs for a given spatial unit — get_cell_id","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get cell IDs for a given spatial unit — get_cell_id","text":"character vector cell_IDs","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get cell metadata — get_cell_metadata","title":"Get cell metadata — get_cell_metadata","text":"Get cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get cell metadata — get_cell_metadata","text":"","code":"get_cell_metadata(   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/get_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get cell metadata — get_cell_metadata","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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_dimReduction.html","id":null,"dir":"Reference","previous_headings":"","what":"Get dimension reduction — get_dimReduction","title":"Get dimension reduction — get_dimReduction","text":"Function get dimension reduction object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_dimReduction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get dimension reduction — get_dimReduction","text":"","code":"get_dimReduction(   gobject,   spat_unit = NULL,   feat_type = NULL,   reduction = c(\"cells\", \"feats\"),   reduction_method = c(\"pca\", \"umap\", \"tsne\"),   name = \"pca\",   output = c(\"dimObj\", \"matrix\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_dimReduction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get dimension reduction — get_dimReduction","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/get_dimReduction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get dimension reduction — get_dimReduction","text":"dim reduction object (default) dim reduction coordinates","code":""},{"path":[]},{"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_expression_values.html","id":null,"dir":"Reference","previous_headings":"","what":"get_expression_values — get_expression_values","title":"get_expression_values — get_expression_values","text":"get_expression_values","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_expression_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"get_expression_values — get_expression_values","text":"","code":"get_expression_values(   gobject,   spat_unit = NULL,   feat_type = NULL,   values = NULL,   output = c(\"exprObj\", \"matrix\"),   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_expression_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"get_expression_values — get_expression_values","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") values expression values extract (e.g. \"raw\", \"normalized\", \"scaled\") 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/get_feat_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Get feat IDs for a given feature type — get_feat_id","title":"Get feat IDs for a given feature type — get_feat_id","text":"Across single modality/feature type, feature information expected share single set feat_IDs. feat_IDs stored within giotto object's feat_ID slot. Getters setters slot directly (get) replace (set) slot.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feat_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get feat IDs for a given feature type — get_feat_id","text":"","code":"get_feat_id(gobject, feat_type = NULL, set_defaults = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feat_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get feat IDs for a given feature type — get_feat_id","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get feature info — get_feature_info","title":"Get feature info — get_feature_info","text":"Get giotto points spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get feature info — get_feature_info","text":"","code":"get_feature_info(   gobject,   feat_type = NULL,   set_defaults = TRUE,   return_giottoPoints = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get feature info — get_feature_info","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. return_giottoPoints return giottoPoints object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get feature info — get_feature_info","text":"SpatVector (default) giottoPoints object depending value return_giottoPoints","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Get feature metadata — get_feature_metadata","title":"Get feature metadata — get_feature_metadata","text":"Get feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_feature_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get feature metadata — get_feature_metadata","text":"","code":"get_feature_metadata(   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/get_feature_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get feature metadata — get_feature_metadata","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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get giotto image object — get_giottoImage","title":"Get giotto image object — get_giottoImage","text":"Get giotto image object gobject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get giotto image object — get_giottoImage","text":"","code":"get_giottoImage(   gobject = NULL,   image_type = c(\"image\", \"largeImage\"),   name = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get giotto image object — get_giottoImage","text":"gobject giotto object image_type type giotto image object. Either \"image\" \"largeImage\" name name giotto image object showGiottoImageNames","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get giotto image object — get_giottoImage","text":"giotto image object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage_MG.html","id":null,"dir":"Reference","previous_headings":"","what":"Get magick-based giotto image — get_giottoImage_MG","title":"Get magick-based giotto image — get_giottoImage_MG","text":"Get giottoImage giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage_MG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get magick-based giotto image — get_giottoImage_MG","text":"","code":"get_giottoImage_MG(gobject = NULL, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage_MG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get magick-based giotto image — get_giottoImage_MG","text":"gobject giotto object name name giottoImage showGiottoImageNames","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoImage_MG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get magick-based giotto image — get_giottoImage_MG","text":"giottoImage","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Get terra-based giotto largeImage — get_giottoLargeImage","title":"Get terra-based giotto largeImage — get_giottoLargeImage","text":"Set giottoLargeImage giottoObject","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get terra-based giotto largeImage — get_giottoLargeImage","text":"","code":"get_giottoLargeImage(gobject = NULL, name = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get terra-based giotto largeImage — get_giottoLargeImage","text":"gobject giotto object name name giottoLargeImage showGiottoImageNames","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_giottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get terra-based giotto largeImage — get_giottoLargeImage","text":"giottoLargeImage","code":""},{"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_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_polygon_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Get polygon info — get_polygon_info","title":"Get polygon info — get_polygon_info","text":"Get giotto polygon spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_polygon_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get polygon info — get_polygon_info","text":"","code":"get_polygon_info(   gobject,   polygon_name = NULL,   polygon_overlap = NULL,   return_giottoPolygon = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_polygon_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get polygon info — get_polygon_info","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","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_prev_fname.html","id":null,"dir":"Reference","previous_headings":"","what":"Get previous function name — get_prev_fname","title":"Get previous function name — get_prev_fname","text":"Get previous function name","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_prev_fname.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get previous function name — get_prev_fname","text":"","code":"get_prev_fname(toplevel = 3L, verbose = FALSE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_prev_fname.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get previous function name — get_prev_fname","text":"toplevel integer. Relative stack previous function call made verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial grid — get_spatialGrid","title":"Get spatial grid — get_spatialGrid","text":"Function get spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial grid — get_spatialGrid","text":"","code":"get_spatialGrid(   gobject,   spat_unit = NULL,   feat_type = NULL,   name = NULL,   return_grid_Obj = FALSE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial grid — get_spatialGrid","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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial network — get_spatialNetwork","title":"Get spatial network — get_spatialNetwork","text":"Function get spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial network — get_spatialNetwork","text":"","code":"get_spatialNetwork(   gobject,   spat_unit = NULL,   name = NULL,   output = c(\"spatialNetworkObj\", \"networkDT\", \"networkDT_before_filter\", \"outputObj\"),   set_defaults = TRUE,   copy_obj = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial network — get_spatialNetwork","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","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_enrichment.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial enrichment — get_spatial_enrichment","title":"Get spatial enrichment — get_spatial_enrichment","text":"Function get spatial enrichment data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_enrichment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial enrichment — get_spatial_enrichment","text":"","code":"get_spatial_enrichment(   gobject,   spat_unit = NULL,   feat_type = NULL,   enrichm_name = \"DWLS\",   output = c(\"spatEnrObj\", \"data.table\"),   copy_obj = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_enrichment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial enrichment — get_spatial_enrichment","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") enrichm_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/get_spatial_enrichment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial enrichment — get_spatial_enrichment","text":"data.table fractions","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Get spatial locations — get_spatial_locations","title":"Get spatial locations — get_spatial_locations","text":"Function get spatial location data.table","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get spatial locations — get_spatial_locations","text":"","code":"get_spatial_locations(   gobject,   spat_unit = NULL,   spat_loc_name = NULL,   output = c(\"spatLocsObj\", \"data.table\"),   copy_obj = TRUE,   verbose = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get spatial locations — get_spatial_locations","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") spat_loc_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.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/get_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get spatial locations — get_spatial_locations","text":"data.table coordinates spatLocsObj depending output","code":""},{"path":[]},{"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":"Framework giotto object store work spatial expression data","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":"[expression] several ways provide expression information: [expression_feat] different features modalities rna, protein, metabolites, ... provided expression slot.","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 available features (e.g. rna, protein, ...) 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 images largeImages slot store giottoLargeImage objects parameters slot save parameters used instructions slot global function instructions offset_file offset file used stitch together image fields OS_platform Operating System run Giotto analysis join_info information joined Giotto objects multiomics multiomics integration results h5_file path h5 file","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":"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/giottoLargeImage-class.html","id":null,"dir":"Reference","previous_headings":"","what":"S4 giottoLargeImage Class — giottoLargeImage-class","title":"S4 giottoLargeImage Class — giottoLargeImage-class","text":"class handle images large load normally magick","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 raster 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 value set maximum intensity color scaling min_intensity minimum value found 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/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":"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/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":"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/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, ...)"},{"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') ... 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/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) { mini_gobject <- GiottoData::loadGiottoMini(\"vizgen\") giottoToSpatialExperiment(mini_gobject) }"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_alloc_dt_slots.html","id":null,"dir":"Reference","previous_headings":"","what":"Over-allocation for giotto DT-based info — giotto_alloc_dt_slots","title":"Over-allocation for giotto DT-based info — giotto_alloc_dt_slots","text":"Finds DT based objects, overallocates data.tables, sets objects back giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_alloc_dt_slots.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Over-allocation for giotto DT-based info — giotto_alloc_dt_slots","text":"","code":"giotto_alloc_dt_slots(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/giotto_alloc_dt_slots.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Over-allocation for giotto DT-based info — giotto_alloc_dt_slots","text":"gobject giotto object","code":""},{"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/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 based largest range","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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)"},{"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_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/installGiottoEnvironment.html","id":null,"dir":"Reference","previous_headings":"","what":"installGiottoEnvironment — installGiottoEnvironment","title":"installGiottoEnvironment — installGiottoEnvironment","text":"Installs giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/installGiottoEnvironment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"installGiottoEnvironment — installGiottoEnvironment","text":"","code":"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\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   force_miniconda = FALSE,   force_environment = FALSE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/installGiottoEnvironment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"installGiottoEnvironment — installGiottoEnvironment","text":"packages_to_install python modules (packages) installed Giotto work python_version python version use within giotto conda environment mini_install_path (optional) desired location miniconda installation. provided, chosen reticulate::install_miniconda() Note required input format: Correct format --> mini_install_path = \"C://conda/lives/\" \"C:\\\\conda\\lives\\\" INCORRECT formats --> mini_install_path = \"C://conda/lives//\" \"C:\\\\conda\\lives\\\\\" force_miniconda force reinstallation miniconda force_environment force reinstallation giotto environment verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/installGiottoEnvironment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"installGiottoEnvironment — installGiottoEnvironment","text":"installs giotto environment using reticulate miniconda system","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/installGiottoEnvironment.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"installGiottoEnvironment — installGiottoEnvironment","text":"function install local giotto environment using miniconda system implemented reticulate. giotto environment installed automatically detected run Giotto toolbox. want use python path can set python_path createGiottoInstructions provide instructions createGiottoObject function. default, Python v3.10.2 used following python modules Giotto Suite implementations: 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/installGiottoEnvironment.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"installGiottoEnvironment — installGiottoEnvironment","text":"","code":"if (FALSE) {  # this command will install r-miniconda # and a giotto environment with all necessary python modules installGiottoEnvironment() }"},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/install_giotto_environment_specific.html","id":null,"dir":"Reference","previous_headings":"","what":"install_giotto_environment_specific — install_giotto_environment_specific","title":"install_giotto_environment_specific — install_giotto_environment_specific","text":"installation giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/install_giotto_environment_specific.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"install_giotto_environment_specific — install_giotto_environment_specific","text":"","code":"install_giotto_environment_specific(   packages_to_install = c(\"pandas\", \"networkx\", \"python-igraph\", \"leidenalg\",     \"python-louvain\", \"python.app\", \"scikit-learn\"),   python_version = \"3.10.2\",   mini_install_path = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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/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/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/instructions-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Access giotto instructions — instructions-generic","title":"Access giotto instructions — instructions-generic","text":"Retrieve set giotto instructions. Specific instructions can replaced using field param. Additionally, using instructions<-, initialize() called giotto object initialize param TRUE","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/instructions-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Access giotto instructions — instructions-generic","text":"","code":"# S4 method for giotto,missing instructions(gobject)  # S4 method for giotto,missing,missing instructions(gobject, initialize) <- value  # S4 method for giotto,missing,logical instructions(gobject, initialize) <- value  # S4 method for giotto,character instructions(gobject, param)  # S4 method for giotto,character,missing instructions(gobject, param, initialize) <- value  # S4 method for giotto,character,logical instructions(gobject, param, initialize) <- value"},{"path":"https://drieslab.github.io/GiottoClass/reference/instructions-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Access giotto instructions — instructions-generic","text":"gobject giotto object initialize (boolean, default = TRUE) whether initialize giotto object value value set param Specific param instructions access modify","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,   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 list values shift along x-axis method shift y_shift list values shift along y-axis method shift x_padding padding datasets/images method shift y_padding padding datasets/images method shift 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. \"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. \"no_change\"  changes applied spatial locations datasets joining.","code":"\\strong{If shift values are given then a value is needed for each giotto object to be joined in \\code{gobject_list}. Order matters.}If a regular step value is desired instead of a specific list of values, use \\code{x_padding} and \\code{y_padding}. Both shift and padding values can be used at the same time.Leaving \\code{x_shift} and \\code{y_shift} values as \\code{NULL} will have Giotto estimate an appropriate \\code{x_shift} value based on the x dimension of available image objects. If no image objects are available, a default behavior of \\code{x_padding = 1000} will be applied. Alternatively, a single numeric value can be supplied to \\code{z_vals} in which case this input will be treated as a z step value."},{"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_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_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_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_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_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_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_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_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_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_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_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_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)"},{"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 \"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_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_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_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_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_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_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_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_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_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_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_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_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/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,   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 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/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/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/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/merge_spatial_locs_feat_info.html","id":null,"dir":"Reference","previous_headings":"","what":"merge_spatial_locs_feat_info — merge_spatial_locs_feat_info","title":"merge_spatial_locs_feat_info — merge_spatial_locs_feat_info","text":"merge spatial cell feature location information","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/merge_spatial_locs_feat_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"merge_spatial_locs_feat_info — merge_spatial_locs_feat_info","text":"","code":"merge_spatial_locs_feat_info(spatial_info, feature_info)"},{"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/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_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_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/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/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":"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/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)"},{"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","code":""},{"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 nameData objName(x)  # S4 method for giottoPoints objName(x)  # S4 method for giottoLargeImage objName(x)  # S4 method for giottoImage objName(x)  # S4 method for nameData objName(x) <- value  # S4 method for giottoImage objName(x) <- value  # S4 method for giottoLargeImage objName(x) <- value  # S4 method for 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":"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/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 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 giottoPolygon overlapToMatrix(   x,   feat_info = \"rna\",   type = c(\"point\", \"intensity\"),   count_info_column = NULL,   output = c(\"Matrix\", \"data.table\"),   ... )  # S4 method for SpatVector overlapToMatrix(   x,   col_names = NULL,   row_names = NULL,   count_info_column = NULL,   output = c(\"Matrix\", \"data.table\"),   verbose = TRUE,   ... )  # S4 method for 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/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/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/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":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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 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":"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/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/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 giottoImage,missing plot(x, y, ...)  # S4 method for giottoLargeImage,missing plot(x, y, ...)  # S4 method for giottoPolygon,missing plot(x, point_size = 0.1, type = c(\"poly\", \"centroid\"), ...)  # S4 method for giottoPoints,missing plot(x, point_size = 0, feats = NULL, raster = TRUE, raster_size = 600, ...)  # S4 method for spatLocsObj,missing plot(x, y, ...)  # S4 method for spatialNetworkObj,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 point_size size points plotting giottoPoints type plot: either 'poly' (default) polygon 'centroid' feats specific features plot within giottoPoints object (defaults NULL, meaning available features) raster default = TRUE, whether plot points rasterized plot size based size param raster_size Default 600. used raster TRUE","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 = spatialNetworkObj, y = missing): Plot spatialNetworkObj","code":""},{"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":"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/plot_auto_largeImage_resample.html","id":null,"dir":"Reference","previous_headings":"","what":"Optimized largeImage resampling — plot_auto_largeImage_resample","title":"Optimized largeImage resampling — plot_auto_largeImage_resample","text":"Downsample largeImage plotting. Uses spatSample load portion original image, speeding plotting lowering memory footprint. Default behavior spatSample crop smaller ROI needed plotting followed sampling process order reduce wasted sampling focusing sample space. large ROIs, crop can time intensive require writing disk. function examines ROI dimensions defined limits spatial locations plotted, decides following two methods order avoid issue: Method . First crop original image sample n values n = 500,000 generate final image Method B. First oversample n values crop, n = 500,000 scaled value >1. Scaling factor increases smaller ROI defined : original dimensions/crop dimensions larger ratio x y dims chosen. Scale factor capped max_resample_scale Control points function set max_crop decides max ROI area switchover method B happens order avoid laborious crops max_resample_scale determines maximum scale factor number values sample. values can adjusted depending system resources. Additionally, flex_resample determines switching behavior happens. set FALSE, method used.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot_auto_largeImage_resample.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Optimized largeImage resampling — plot_auto_largeImage_resample","text":"","code":"plot_auto_largeImage_resample(   gobject,   giottoLargeImage = NULL,   largeImage_name = NULL,   spat_unit = NULL,   spat_loc_name = NULL,   polygon_feat_type = NULL,   include_image_in_border = TRUE,   flex_resample = TRUE,   max_crop = 1e+08,   max_resample_scale = 100 )"},{"path":"https://drieslab.github.io/GiottoClass/reference/plot_auto_largeImage_resample.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Optimized largeImage resampling — plot_auto_largeImage_resample","text":"gobject gobject containing largeImage object giottoLargeImage largeImage object resample provided gobject largeImage_name largeImage_name name largeImage gobject spat_unit spatial unit spat_loc_name name spatial locations plot polygon_feat_type name polygon/spatial_info plot include_image_in_border logical. expand extent sampled also show image border regions included spatlocs. prevents images plots sharply cut around furthest spatial locations. (default TRUE) flex_resample logical. Whether allow automatic selection sampling workflow defined details sections. (default TRUE) max_crop maximum crop size allowed method switching method B (see description) max_resample_scale maximum cells allowed resample compensate decreased resolution cropping sampling","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/plot_auto_largeImage_resample.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Optimized largeImage resampling — plot_auto_largeImage_resample","text":"giottoLargeImage cropped resampled properly plotting","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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/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/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) boolean. 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/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/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":"returns 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_\", 1:10) ) 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_OLD.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert polygon to raster — polygon_to_raster_OLD","title":"Convert polygon to raster — polygon_to_raster_OLD","text":"function convert terra SpatVector Polygon shape terra SpatRaster TODO: can removed","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/polygon_to_raster_OLD.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert polygon to raster — polygon_to_raster_OLD","text":"","code":"polygon_to_raster_OLD(polygon, field = NULL)"},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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 ident characters print level (top level '')","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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 provData prov(x)  # S4 method for 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":"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_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/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/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/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/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/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/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 sf as.sp(x)  # S4 method for SpatVector as.sp(x)  # S4 method for stars as.sp(x)  # S4 method for Spatial as.sp(x)  # S4 method for giottoPolygon as.sp(x, drop = TRUE)  # S4 method for giottoPoints as.sp(x, drop = TRUE)  # S4 method for SpatVector as.sf(x)  # S4 method for Spatial as.sf(x)  # S4 method for stars as.sf(x)  # S4 method for sf as.sf(x)  # S4 method for giottoPolygon as.sf(x, drop = TRUE)  # S4 method for giottoPoints as.sf(x, drop = TRUE)  # S4 method for SpatVector as.stars(x)  # S4 method for sf as.stars(x)  # S4 method for Spatial as.stars(x)  # S4 method for stars as.stars(x)  # S4 method for giottoPolygon as.stars(x, drop = TRUE)  # S4 method for giottoPoints as.stars(x, drop = TRUE)  # S4 method for SpatVector as.terra(x)  # S4 method for sf as.terra(x)  # S4 method for stars as.terra(x, type = c(\"vector\", \"raster\"))  # S4 method for Spatial as.terra(x)  # S4 method for giottoPolygon as.terra(x, drop = TRUE)  # S4 method for 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":[]},{"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 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 add_list_ID whether generate list_ID column giottoPolygons append different names ... additional params pass methods","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/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 poly_names sorted polygon names used combined giottoPolygon object","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/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/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":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Read expression data — readExprData","text":"mylistA = list('' = matrix(1:5), 'b' = matrix(1:5)) depth(mylistA) mylistB = list(= list('' = matrix(1:5), 'b' = matrix(1:5)), B = list('c' = matrix(1:5),'d' = matrix(1:5))) depth(mylistB) mylistC = list('RNA' = list('RAW' = list('cell' = matrix(1:5), 'nucleus' = matrix(6:10)), 'NORM' = list('cell' = matrix(11:15),'nucleus' = matrix(20:25))), 'PROT' = list('RAW' = list('cell' = matrix(16:20)))) depth(mylistC) mymatD = matrix(data = 1:4)","code":""},{"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/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/readGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Read giotto instructions associated with giotto object — readGiottoInstructions","title":"Read giotto instructions associated with giotto object — 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":"Read giotto instructions associated with giotto object — 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":"Read giotto instructions associated with giotto object — 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":"Read giotto instructions associated with giotto object — readGiottoInstructions","text":"specific parameter","code":""},{"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/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/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/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/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/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 read cell metadata list","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/read_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read cell metadata — read_cell_metadata","text":"","code":"readCellMetadata(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )  read_cell_metadata(   metadata,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/read_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read cell metadata — read_cell_metadata","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 provenance information (optional) verbose verbose metadata nested list cell metadata information","code":""},{"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_feature_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Read feature metadata — read_feature_metadata","title":"Read feature metadata — read_feature_metadata","text":"read feature metadata listt","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/read_feature_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read feature metadata — read_feature_metadata","text":"","code":"readFeatMetadata(   data_list,   default_spat_unit = NULL,   default_feat_type = NULL,   provenance = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/read_feature_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read feature metadata — read_feature_metadata","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/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/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/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/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/removeGiottoEnvironment.html","id":null,"dir":"Reference","previous_headings":"","what":"removeGiottoEnvironment — removeGiottoEnvironment","title":"removeGiottoEnvironment — removeGiottoEnvironment","text":"removeGiottoEnvironment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeGiottoEnvironment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"removeGiottoEnvironment — removeGiottoEnvironment","text":"","code":"removeGiottoEnvironment(mini_path = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/removeGiottoEnvironment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"removeGiottoEnvironment — removeGiottoEnvironment","text":"mini_path path anaconda/miniconda. Default: reticulate::miniconda_path() .e. \"C://conda/lives/\" \"C:\\\\conda\\lives\\\" verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/removeGiottoEnvironment.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"removeGiottoEnvironment — removeGiottoEnvironment","text":"Removes previously installed giotto environment. See installGiottoEnvironment.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/replaceGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Replace all giotto instructions in giotto object — replaceGiottoInstructions","title":"Replace all giotto instructions in giotto object — 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":"Replace all giotto instructions in giotto object — 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":"Replace all giotto instructions in giotto object — 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":"Replace all giotto instructions in giotto object — replaceGiottoInstructions","text":"giotto object replaces instructions","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Rescale an object — rescale-generic","title":"Rescale an object — rescale-generic","text":"Rescale object spatially. Z dimension scaling supported types subobjects.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Rescale an object — rescale-generic","text":"","code":"# S4 method for spatLocsObj rescale(x, fx = 1, fy = fx, fz = fx, x0, y0, z0)"},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Rescale an object — rescale-generic","text":"x object fx numeric > 0. horizontal scaling factor fy numeric > 0. vertical scaling factor fz numeric > 0. z scaling factor (supported objects) x0 numeric. x-coordinate center rescaling. missing, center extent x used y0 numeric. y-coordinate center rescaling. missing, center extent x used z0 numeric. z-coordinate center rescaling. missing, center extent x used (supported objects)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/rescale-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Rescale an object — rescale-generic","text":"rescale(spatLocsObj): Rescale spatLocsObj","code":""},{"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/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/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/return_giotto_environment_path.html","id":null,"dir":"Reference","previous_headings":"","what":"return_giotto_environment_path — return_giotto_environment_path","title":"return_giotto_environment_path — return_giotto_environment_path","text":"returns path detected giotto environment","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"return_giotto_environment_path — return_giotto_environment_path","text":"","code":"return_giotto_environment_path()"},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"return_giotto_environment_path — return_giotto_environment_path","text":"string path","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path_executable.html","id":null,"dir":"Reference","previous_headings":"","what":"return_giotto_environment_path_executable — return_giotto_environment_path_executable","title":"return_giotto_environment_path_executable — return_giotto_environment_path_executable","text":"returns path detected giotto environment executable","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path_executable.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"return_giotto_environment_path_executable — return_giotto_environment_path_executable","text":"","code":"return_giotto_environment_path_executable()"},{"path":"https://drieslab.github.io/GiottoClass/reference/return_giotto_environment_path_executable.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"return_giotto_environment_path_executable — return_giotto_environment_path_executable","text":"string path","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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(x = 0, y = 0, z = 0) )"},{"path":"https://drieslab.github.io/GiottoClass/reference/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)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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 exprObj colnames(x)  # S4 method for exprObj 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/rowMeans_flex.html","id":null,"dir":"Reference","previous_headings":"","what":"rowMeans_flex — rowMeans_flex","title":"rowMeans_flex — 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/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/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 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/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.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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(x = 1, y = 1, z = 1),   scenter = c(x = 0, y = 0, z = 0) )"},{"path":"https://drieslab.github.io/GiottoClass/reference/scale_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Scale spatial locations — scale_spatial_locations","text":"spatlocs spatial locations information scale scale_factor scaling factor apply coordinates. scenter center scale spatial coordinates. Given vector xy(z) coordinates.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/select_gimage.html","id":null,"dir":"Reference","previous_headings":"","what":"select_gimage — select_gimage","title":"select_gimage — select_gimage","text":"selects (possibly resamples) giotto images plotting","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/select_gimage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"select_gimage — select_gimage","text":"","code":"select_gimage(   gobject,   gimage = NULL,   image_name = NULL,   largeImage_name = NULL,   spat_unit = NULL,   spat_loc_name = NULL,   feat_type = NULL,   polygon_feat_type = NULL )"},{"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","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/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","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/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","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/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","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/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","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/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 giotto,cellMetaObj setGiotto(gobject, x, ...)  # S4 method for giotto,featMetaObj setGiotto(gobject, x, ...)  # S4 method for giotto,exprObj setGiotto(gobject, x, ...)  # S4 method for giotto,giottoPoints setGiotto(gobject, x, ...)  # S4 method for giotto,giottoPolygon setGiotto(gobject, x, ...)  # S4 method for giotto,dimObj setGiotto(gobject, x, ...)  # S4 method for giotto,spatLocsObj setGiotto(gobject, x, ...)  # S4 method for giotto,spatEnrObj setGiotto(gobject, x, ...)  # S4 method for giotto,nnNetObj setGiotto(gobject, x, ...)  # S4 method for giotto,spatialNetworkObj setGiotto(gobject, x, ...)  # S4 method for giotto,giottoLargeImage setGiotto(gobject, x, ...)  # S4 method for 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 ... additional params pass specific Giotto setter functions","code":""},{"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 = NULL,   image = NULL,   image_type = NULL,   name = NULL,   verbose = TRUE )"},{"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 type giotto image object. Either \"image\" \"largeImage\" 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/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","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/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","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/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","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/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","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/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.","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/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","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/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","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/set_NearestNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Set nearest network — set_NearestNetwork","title":"Set nearest network — set_NearestNetwork","text":"Set NN-network Giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_NearestNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set nearest network — set_NearestNetwork","text":"","code":"set_NearestNetwork(   gobject,   nn_network,   spat_unit = NULL,   feat_type = NULL,   nn_network_to_use = \"sNN\",   network_name = \"sNN.pca\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_NearestNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set nearest network — set_NearestNetwork","text":"gobject giotto object nn_network nnNetObj igraph nearest network object. Data.table yet supported. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") nn_network_to_use \"kNN\" \"sNN\" network_name name NN network used provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_NearestNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set nearest network — set_NearestNetwork","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cell IDs for a given spatial unit — set_cell_id","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"Setter function cell_ID slot. Directly replaces (sets) slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"","code":"set_cell_id(   gobject,   spat_unit = NULL,   cell_IDs,   set_defaults = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") cell_IDs character vector cell IDs set. (See details) set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"giotto object set cell_ID slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set cell IDs for a given spatial unit — set_cell_id","text":"Data spatial unit expected agree single set cell_IDs shared across feature types. cell_IDs stored within giotto object's cell_ID slot. Pass NULL cell_IDs param order delete entry.  Pass 'initialize' cell_IDs param order initialize specified entry. NOTE: main purpose setter initialize, cell_ID values AUTOMATICALLY updated every time initialize() called giotto object.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Set cell metadata — set_cell_metadata","title":"Set cell metadata — set_cell_metadata","text":"Function set cell metadata information giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set cell metadata — set_cell_metadata","text":"","code":"set_cell_metadata(   gobject,   metadata,   spat_unit = NULL,   feat_type = NULL,   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set cell metadata — set_cell_metadata","text":"gobject giotto object metadata cellMetaObj data.table containing cell metadata. Setting NULL remove object. Passing 'initialize' reset object. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance provenance information set verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_cell_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set cell metadata — set_cell_metadata","text":"giotto object","code":""},{"path":[]},{"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_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_dimReduction.html","id":null,"dir":"Reference","previous_headings":"","what":"Set dimension reduction — set_dimReduction","title":"Set dimension reduction — set_dimReduction","text":"Function set dimension reduction slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_dimReduction.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set dimension reduction — set_dimReduction","text":"","code":"set_dimReduction(   gobject,   dimObject,   spat_unit = NULL,   feat_type = NULL,   reduction = c(\"cells\", \"feats\"),   reduction_method = c(\"pca\", \"umap\", \"tsne\"),   name = \"pca\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_dimReduction.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set dimension reduction — set_dimReduction","text":"gobject giotto object dimObject dimension object result set spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") reduction reduction cells features reduction_method reduction method (e.g. \"pca\") name name reduction results provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_dimReduction.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set dimension reduction — set_dimReduction","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_expression_values.html","id":null,"dir":"Reference","previous_headings":"","what":"Set expression values — set_expression_values","title":"Set expression values — set_expression_values","text":"Function set expression values giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_expression_values.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set expression values — set_expression_values","text":"","code":"set_expression_values(   gobject,   values,   spat_unit = NULL,   feat_type = NULL,   name = \"test\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_expression_values.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set expression values — set_expression_values","text":"gobject giotto object values exprObj NULL, object removed. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") name name expression slot provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning. set TRUE called external","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_expression_values.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set expression values — set_expression_values","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feat IDs for a given feature type — set_feat_id","title":"Set feat IDs for a given feature type — set_feat_id","text":"Setter function feat_ID slot. Directly replaces (sets) slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feat IDs for a given feature type — set_feat_id","text":"","code":"set_feat_id(   gobject,   feat_type = NULL,   feat_IDs,   set_defaults = TRUE,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feat IDs for a given feature type — set_feat_id","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") feat_IDs character vector feature IDs set. set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feat IDs for a given feature type — set_feat_id","text":"giotto object set cell_ID slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feat_id.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set feat IDs for a given feature type — set_feat_id","text":"Across single modality/feature type, within spatial unit, feature information expected share single set feat_IDs. feat_IDs stored within giotto object's feat_ID slot separated feat_type. Pass NULL feat_IDs param order delete entry.  Pass 'initialize' feat_IDs param order initialize specified entry. NOTE: main purpose setter initialize, feat_ID values AUTOMATICALLY updated every time initialize() called giotto object.","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feature info — set_feature_info","title":"Set feature info — set_feature_info","text":"Set giotto polygon spatVector features","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feature info — set_feature_info","text":"","code":"set_feature_info(   gobject,   gpoints,   feat_type = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE,   gpolygon = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feature info — set_feature_info","text":"gobject giotto object gpoints giotto points object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning gpolygon typo use","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feature info — set_feature_info","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Set feature metadata — set_feature_metadata","title":"Set feature metadata — set_feature_metadata","text":"Function set feature metadata information giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set feature metadata — set_feature_metadata","text":"","code":"set_feature_metadata(   gobject,   metadata,   spat_unit = NULL,   feat_type = NULL,   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set feature metadata — set_feature_metadata","text":"gobject giotto object metadata featMetaObj data.table containing feature metadata. Setting NULL remove object. Passing 'initialize' reset object. spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") provenance provenance information set verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_feature_metadata.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set feature metadata — set_feature_metadata","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Set giotto image object — set_giottoImage","title":"Set giotto image object — set_giottoImage","text":"Directly attach giotto image giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set giotto image object — set_giottoImage","text":"","code":"set_giottoImage(   gobject = NULL,   image = NULL,   image_type = NULL,   name = NULL,   verbose = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set giotto image object — set_giottoImage","text":"gobject giotto object image giotto image object attached without modification giotto object image_type type giotto image object. Either \"image\" \"largeImage\" name name giotto image object verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set giotto image object — set_giottoImage","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set giotto image object — set_giottoImage","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/set_giottoImage_MG.html","id":null,"dir":"Reference","previous_headings":"","what":"Set magick-based giotto image — set_giottoImage_MG","title":"Set magick-based giotto image — set_giottoImage_MG","text":"Set giottoImage giotto object additional modifications","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage_MG.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set magick-based giotto image — set_giottoImage_MG","text":"","code":"set_giottoImage_MG(gobject, image_object, name = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage_MG.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set magick-based giotto image — set_giottoImage_MG","text":"gobject giotto object image_object giottoImage object name name assign giottoImage verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoImage_MG.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set magick-based giotto image — set_giottoImage_MG","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoLargeImage.html","id":null,"dir":"Reference","previous_headings":"","what":"Set terra-based giotto largeImage — set_giottoLargeImage","title":"Set terra-based giotto largeImage — set_giottoLargeImage","text":"Set giottoLargeImage giotto object additional modifications","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoLargeImage.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set terra-based giotto largeImage — set_giottoLargeImage","text":"","code":"set_giottoLargeImage(gobject, largeImage_object, name = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoLargeImage.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set terra-based giotto largeImage — set_giottoLargeImage","text":"gobject giotto object largeImage_object giottoLargeImage object name name assign giottoLargeImage verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giottoLargeImage.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set terra-based giotto largeImage — set_giottoLargeImage","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giotto_python_path.html","id":null,"dir":"Reference","previous_headings":"","what":"set_giotto_python_path — set_giotto_python_path","title":"set_giotto_python_path — set_giotto_python_path","text":"detects sets python path. Exits without anything getOption('giotto.use_conda') FALSE.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giotto_python_path.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"set_giotto_python_path — set_giotto_python_path","text":"","code":"set_giotto_python_path(python_path = NULL, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giotto_python_path.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"set_giotto_python_path — set_giotto_python_path","text":"python_path character. Full path python executable verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_giotto_python_path.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"set_giotto_python_path — set_giotto_python_path","text":"path python executable","code":""},{"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_polygon_info.html","id":null,"dir":"Reference","previous_headings":"","what":"Set polygon info — set_polygon_info","title":"Set polygon info — set_polygon_info","text":"Set giotto polygon spatVector","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_polygon_info.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set polygon info — set_polygon_info","text":"","code":"set_polygon_info(   gobject,   gpolygon,   polygon_name = \"cell\",   verbose = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_polygon_info.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set polygon info — set_polygon_info","text":"gobject giotto object gpolygon giottoPolygon object polygon_name name polygons. Default \"cell\" (used gpolygon length 1) verbose verbose initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_polygon_info.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set polygon info — set_polygon_info","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialGrid.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial grid — set_spatialGrid","title":"Set spatial grid — set_spatialGrid","text":"Function set spatial grid","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialGrid.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial grid — set_spatialGrid","text":"","code":"set_spatialGrid(   gobject,   spatial_grid,   spat_unit = NULL,   feat_type = NULL,   name = NULL,   verbose = TRUE,   set_defaults = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialGrid.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial grid — set_spatialGrid","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.","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialGrid.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial grid — set_spatialGrid","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialNetwork.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial network — set_spatialNetwork","title":"Set spatial network — set_spatialNetwork","text":"Function set spatial network","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialNetwork.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial network — set_spatialNetwork","text":"","code":"set_spatialNetwork(   gobject,   spatial_network,   spat_unit = NULL,   name = NULL,   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialNetwork.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial network — set_spatialNetwork","text":"gobject giotto object spatial_network spatial network spat_unit spatial unit (e.g. \"cell\") name name spatial network provenance provenance name verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatialNetwork.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial network — set_spatialNetwork","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_enrichment.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial enrichment — set_spatial_enrichment","title":"Set spatial enrichment — set_spatial_enrichment","text":"Function set spatial enrichment slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_enrichment.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial enrichment — set_spatial_enrichment","text":"","code":"set_spatial_enrichment(   gobject,   spatenrichment,   spat_unit = NULL,   feat_type = NULL,   enrichm_name = \"enrichment\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_enrichment.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial enrichment — set_spatial_enrichment","text":"gobject giotto object spatenrichment spatial enrichment results spat_unit spatial unit (e.g. \"cell\") feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") enrichm_name name spatial enrichment results. Default \"DWLS\" provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_enrichment.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial enrichment — set_spatial_enrichment","text":"giotto object","code":""},{"path":[]},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":null,"dir":"Reference","previous_headings":"","what":"Set spatial locations — set_spatial_locations","title":"Set spatial locations — set_spatial_locations","text":"Function set spatial location slot","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Set spatial locations — set_spatial_locations","text":"","code":"set_spatial_locations(   gobject,   spatlocs,   spat_unit = NULL,   spat_loc_name = \"raw\",   provenance = NULL,   verbose = TRUE,   set_defaults = TRUE,   initialize = FALSE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Set spatial locations — set_spatial_locations","text":"gobject giotto object spatlocs spatial locations (accepts either data.table spatLocsObj) spat_unit spatial unit (e.g. \"cell\") spat_loc_name name spatial locations, default \"raw\" provenance provenance information (optional) verbose verbose set_defaults set default spat_unit feat_type. Change FALSE expression spat_info expected exist. initialize (default = FALSE) whether initialize gobject returning","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Set spatial locations — set_spatial_locations","text":"giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/set_spatial_locations.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Set spatial locations — set_spatial_locations","text":"spatLocsObj provided spatlocs param attached name spat_unit info used input function's spat_loc_name spat_unitparams, overridden alternative specific inputs params.  ie: spatLocsObj spat_unit slot == 'cell' automatically nested spat_unit 'cell' using set_spatial_locations long param spat_unit = NULL. param spat_unit = 'nucleus' spatLocsObj nested spat_unit 'nucleus' instead spat_unit slot changed 'nucleus'","code":""},{"path":[]},{"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/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\" )"},{"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 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/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 = \"Vizgen\" )"},{"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 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/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/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,   xtranslate = NULL,   ytranslate = NULL,   ztranslate = NULL,   copy_obj = TRUE )"},{"path":"https://drieslab.github.io/GiottoClass/reference/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 xtranslate deprecated. use dx ytranslate deprecated. use dy ztranslate deprecated. use dz copy_obj copy/duplicate object (default = TRUE)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/show-methods.html","id":null,"dir":"Reference","previous_headings":"","what":"show method for giotto class — show,giotto-method","title":"show method for giotto class — show,giotto-method","text":"show method giotto class show method exprObj class Show method dimObj class Show method nnNetObj class show method spatLocsObj class show method spatialNetworkObj class show method spatialGridObj class show method spatEnrObj class show method giottoImage class show method giottoLargeImage class","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/show-methods.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"show method for giotto class — show,giotto-method","text":"","code":"# S4 method for giotto show(object)  # S4 method for exprObj show(object)  # S4 method for dimObj show(object)  # S4 method for nnNetObj show(object)  # S4 method for spatLocsObj show(object)  # S4 method for spatialNetworkObj show(object)  # S4 method for spatialGridObj show(object)  # S4 method for spatEnrObj show(object)  # S4 method for giottoImage show(object)  # S4 method for giottoLargeImage show(object)"},{"path":"https://drieslab.github.io/GiottoClass/reference/show-methods.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"show method for giotto class — show,giotto-method","text":"object giottoLargeImage object","code":""},{"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/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/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/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":[]},{"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/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/showGiottoInstructions.html","id":null,"dir":"Reference","previous_headings":"","what":"Show giotto instructions associated with giotto object — showGiottoInstructions","title":"Show giotto instructions associated with giotto object — 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":"Show giotto instructions associated with giotto object — showGiottoInstructions","text":"","code":"showGiottoInstructions(gobject)"},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Show giotto instructions associated with giotto object — showGiottoInstructions","text":"gobject giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/showGiottoInstructions.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Show giotto instructions associated with giotto object — showGiottoInstructions","text":"named vector giotto instructions","code":""},{"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/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/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/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/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/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":[]},{"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":[]},{"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":[]},{"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/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/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":"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/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","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 giotto spatIDs(x, spat_unit = NULL, ...)  # S4 method for exprObj spatIDs(x, ...)  # S4 method for spatLocsObj spatIDs(x, ...)  # S4 method for cellMetaObj spatIDs(x, ...)  # S4 method for spatialNetworkObj spatIDs(x, ...)  # S4 method for dimObj spatIDs(x, ...)  # S4 method for giottoPolygon spatIDs(x, use_cache = TRUE, uniques = TRUE, ...)  # S4 method for spatEnrObj spatIDs(x, ...)  # S4 method for nnNetObj spatIDs(x, ...)  # S4 method for giotto featIDs(x, feat_type = NULL, ...)  # S4 method for exprObj featIDs(x, ...)  # S4 method for featMetaObj featIDs(x, ...)  # S4 method for giottoPoints featIDs(x, use_cache = TRUE, uniques = TRUE, ...)  # S4 method for 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 ... additional parameters pass 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/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":"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/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":"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 spatLocsObj spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)  # S4 method for spatialNetworkObj spatShift(x, dx = 0, dy = 0, dz = 0, copy_obj = TRUE, ...)  # S4 method for giottoPolygon spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for giottoPoints spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)  # S4 method for giottoLargeImage spatShift(x, dx = 0, dy = 0, copy_obj = FALSE, ...)"},{"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 dz numeric. shift z axis copy_obj Default = TRUE ... additional params pass methods","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(spatLocsObj): Shift locations spatLocsObj spatShift(spatialNetworkObj): Shift locations spatialNetworkObj","code":""},{"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 spatData spatUnit(x)  # S4 method for giottoPolygon spatUnit(x)  # S4 method for spatData spatUnit(x) <- value  # S4 method for 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":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Spatial unit information — spatUnit-generic","text":"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/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/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/spatVector_to_dt2.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert spatVector to data.table — spatVector_to_dt2","title":"Convert spatVector to data.table — spatVector_to_dt2","text":"convert spatVector data.table. Faster barebones suitable points data","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spatVector_to_dt2.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert spatVector to data.table — spatVector_to_dt2","text":"","code":"spatVector_to_dt2(spatvector, include_values = TRUE)"},{"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":"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 #> 1: 100210519278873141813371229408401071444 #>                                         to sdimx_begin sdimy_begin sdimx_end #> 1: 216701996099683814512199402223708471323    6637.881   -5140.465   6612.68 #>    sdimy_end distance     weight #> 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) { 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":"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/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":"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/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 values SpatRaster","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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, verbose = TRUE)"},{"path":"https://drieslab.github.io/GiottoClass/reference/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 verbose verbose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Spin an object — spin-generic","title":"Spin an object — spin-generic","text":"Spin (rotate) object spatially (limited xy rotations)","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Spin an object — spin-generic","text":"","code":"# S4 method for giottoPolygon spin(x, angle, x0 = NULL, y0 = NULL)  # S4 method for giottoPoints spin(x, angle, x0 = NULL, y0 = NULL)  # S4 method for spatLocsObj spin(   x,   angle = NULL,   x0 = NULL,   y0 = NULL,   z0 = NULL,   xy_angle = NULL,   zy_angle = NULL,   xz_angle = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/spin-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Spin an object — spin-generic","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. 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","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/spin-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Spin an object — spin-generic","text":"spin(giottoPolygon): Spin giottoPolygon object spin(giottoPoints): Spin giottoPoints object spin(spatLocsObj): Spin spatLocsObj","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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 = F,   cumulate_offset_y = F,   field_col = \"Field of View\",   X_coord_col = \"X\",   Y_coord_col = \"Y\",   reverse_final_x = F,   reverse_final_y = T )"},{"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: 1. cell locations: least 3 columns: field, X, Y 2. create offset file: offset file 3 columns: field, x_offset, y_offset 3. create new cell location file stitching original cell locations stitchFieldCoordinates 4. 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/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/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 = NULL,   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/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 )"},{"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","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/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/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_cell_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset cell metadata — subset_cell_metadata","title":"Subset cell metadata — subset_cell_metadata","text":"Subset cell metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_cell_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset cell metadata — subset_cell_metadata","text":"","code":"subset_cell_metadata(   gobject,   spat_unit = \":all:\",   feat_type_ssub = \":all:\",   cell_ids = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_cell_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset cell metadata — subset_cell_metadata","text":"gobject giotto object spat_unit spatial unit (e.g. \"cell\") cell_ids cell ids keep","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_feature_metadata.html","id":null,"dir":"Reference","previous_headings":"","what":"Subset feature metadata — subset_feature_metadata","title":"Subset feature metadata — subset_feature_metadata","text":"Subset feature metadata giotto object","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_feature_metadata.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Subset feature metadata — subset_feature_metadata","text":"","code":"subset_feature_metadata(   gobject,   feat_type = \":all:\",   spat_unit_fsub = \":all:\",   feat_ids = NULL )"},{"path":"https://drieslab.github.io/GiottoClass/reference/subset_feature_metadata.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Subset feature metadata — subset_feature_metadata","text":"gobject giotto object feat_type feature type (e.g. \"rna\", \"dna\", \"protein\") feat_ids feature ids keep","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/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/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/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/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/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/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/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-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Transpose — transpose-generic","title":"Transpose — transpose-generic","text":"Transpose","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Transpose — transpose-generic","text":"","code":"# S4 method for spatLocsObj t(x)  # S4 method for spatialNetworkObj t(x)  # S4 method for giottoPoints t(x)  # S4 method for giottoPolygon t(x)  # S3 method for spatLocsObj t(x)  # S3 method for spatialNetworkObj t(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/transpose-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Transpose — transpose-generic","text":"x object transposed","code":""},{"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 = F","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/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/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":"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":"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":"if (FALSE) { gobject <- updateGiottoObject(gobject) }"},{"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/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/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","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap-generic.html","id":null,"dir":"Reference","previous_headings":"","what":"Wrap giotto terra pointer information — wrap-generic","title":"Wrap giotto terra pointer information — wrap-generic","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-generic.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Wrap giotto terra pointer information — wrap-generic","text":"","code":"# S4 method for giottoPolygon wrap(x)  # S4 method for giotto wrap(x)  # S4 method for giottoPoints wrap(x)  # S4 method for packedGiottoPolygon vect(x)  # S4 method for packedGiottoPoints vect(x)  # S4 method for packedGiotto vect(x)"},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap-generic.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Wrap giotto terra pointer information — wrap-generic","text":"x giottoPolygon giottoPoints","code":""},{"path":"https://drieslab.github.io/GiottoClass/reference/wrap-generic.html","id":"functions","dir":"Reference","previous_headings":"","what":"Functions","title":"Wrap giotto terra pointer information — wrap-generic","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/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":""}]