Merge pull request #1057 from drieslab/suite_dev

Giotto 4.1.3

.Rbuildignore

@@ -2,6 +2,7 @@
 ^renv\.lock$
 ^Giotto\.Rproj$
 ^\.Rproj\.user$
+^.lintr
 
 ^LICENSE\.md$
 ^README\.Rmd$

.lintr

@@ -0,0 +1,5 @@
+linters: linters_with_defaults(
+  indentation_linter = NULL,
+  object_name_linter = NULL,
+  object_length_linter = NULL)
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Giotto
 Title: Spatial Single-Cell Transcriptomics Toolbox
-Version: 4.1.0
+Version: 4.1.3
 Authors@R: c(
 	person("Ruben", "Dries", email = "rubendries@gmail.com",
 		 role = c("aut", "cre"), comment = c(ORCID = "0000-0001-7650-7754")),
@@ -22,36 +22,27 @@ Authors@R: c(
 Description: Toolbox to process, analyze and visualize spatial single-cell expression data.
 License: MIT + file LICENSE
 Encoding: UTF-8
-LazyData: true
 URL: https://drieslab.github.io/Giotto/, https://github.com/drieslab/Giotto
 BugReports: https://github.com/drieslab/Giotto/issues
 RoxygenNote: 7.3.2
 Depends:
-    base (>= 4.1.0),
-    utils (>= 4.1.0),
-    R (>= 4.1.0),
+    R (>= 4.4.1),
     methods,
     GiottoClass (>= 0.3.3)
 Imports:
     BiocParallel,
     BiocSingular,
     checkmate,
-    cowplot (>= 0.9.4),
     data.table (>= 1.12.2),
     dbscan (>= 1.1-3),
+    ggraph,
     ggplot2 (>= 3.1.1),
-    GiottoUtils (>= 0.1.9),
-    GiottoVisuals (>= 0.2.4),
+    GiottoUtils (>= 0.1.12),
+    GiottoVisuals (>= 0.2.5),
     igraph (>= 1.2.4.1),
-    jsonlite,
-    limma,
     Matrix (>= 1.6-2),
     MatrixGenerics,
-    plotly,
-    progressr,
-    reshape2,
     reticulate (>= 1.25),
-    Rtsne (>= 0.15),
     scales (>= 1.0.0),
     sparseMatrixStats,
     stats,
@@ -78,19 +69,19 @@ Suggests:
     ggalluvial,
     ggdendro,
     ggforce,
-    ggraph,
     ggspavis,
     graphcoloring,
     HDF5Array (>= 1.18.1),
     hdf5r,
-    jackstraw,
     kableExtra,
     knitr,
+    limma,
     MAST,
     miniUI,
     multinet (>= 3.0.2),
     networkD3,
     pheatmap,
+    plotly,
     quadprog,
     harmony,
     R.utils,
@@ -99,6 +90,7 @@ Suggests:
     rlang,
     rhdf5,
     RTriangle (>= 1.6-0.10),
+    Rtsne (>= 0.15),
     Rvision,
     scater,
     scran (>= 1.10.1),
@@ -134,6 +126,7 @@ Collate:
     'differential_expression.R'
     'dimension_reduction.R'
     'feature_set_enrichment.R'
+    'filter.R'
     'general_help.R'
     'giotto_viewer.R'
     'globals.R'
@@ -142,6 +135,7 @@ Collate:
     'image_registration.R'
     'interactivity.R'
     'kriging.R'
+    'normalize.R'
     'package_imports.R'
     'poly_influence.R'
     'python_hmrf.R'

NAMESPACE

@@ -14,7 +14,6 @@ export("prov<-")
 export("sankeyLabel<-")
 export("sankeyRelate<-")
 export("spatUnit<-")
-export(PAGEEnrich)
 export(activeFeatType)
 export(activeSpatUnit)
 export(addCellIntMetadata)
@@ -98,7 +97,6 @@ export(combineICG)
 export(combineInteractionChangedFeats)
 export(combineInteractionChangedGenes)
 export(combineMetadata)
-export(combineSpatialCellFeatureInfo)
 export(combineSpatialCellMetadataInfo)
 export(combineToMultiPolygon)
 export(compareCellAbundance)
@@ -127,6 +125,7 @@ export(createGiottoPolygon)
 export(createGiottoPolygonsFromDfr)
 export(createGiottoPolygonsFromGeoJSON)
 export(createGiottoPolygonsFromMask)
+export(createGiottoVisiumHDObject)
 export(createGiottoVisiumObject)
 export(createGiottoXeniumObject)
 export(createMerscopeLargeImage)
@@ -138,14 +137,12 @@ export(createSpatLocsObj)
 export(createSpatNetObj)
 export(createSpatialDefaultGrid)
 export(createSpatialDelaunayNetwork)
-export(createSpatialEnrich)
 export(createSpatialFeaturesKNNnetwork)
 export(createSpatialGenomicsObject)
 export(createSpatialGrid)
 export(createSpatialKNNnetwork)
 export(createSpatialNetwork)
 export(createSpatialWeightMatrix)
-export(create_jackstrawplot)
 export(create_screeplot)
 export(crop)
 export(cropGiottoLargeImage)
@@ -242,7 +239,6 @@ export(getGiottoImage)
 export(getMultiomics)
 export(getNearestNetwork)
 export(getONTraCv1Input)
-export(getONTraCv2Input)
 export(getPolygonInfo)
 export(getRainbowColors)
 export(getSpatialEnrichment)
@@ -257,15 +253,14 @@ export(giottoPoints)
 export(giottoPolygon)
 export(giottoSankeyPlan)
 export(giottoToAnnData)
+export(giottoToAnndataZarr)
 export(giottoToSeurat)
 export(giottoToSeuratV4)
 export(giottoToSeuratV5)
 export(giottoToSpatialExperiment)
 export(heatmSpatialCorFeats)
-export(heatmSpatialCorGenes)
 export(hexVertices)
 export(hist)
-export(hyperGeometricEnrich)
 export(identifyTMAcores)
 export(importCosMx)
 export(importVisiumHD)
@@ -274,6 +269,7 @@ export(initHMRF_V2)
 export(insertCrossSectionFeatPlot3D)
 export(insertCrossSectionSpatPlot3D)
 export(installGiottoEnvironment)
+export(installGiottoONTraCEnvironment)
 export(instructions)
 export(interactiveLandmarkSelection)
 export(jackstrawPlot)
@@ -301,7 +297,6 @@ export(plotCCcomDotplot)
 export(plotCCcomHeatmap)
 export(plotCPF)
 export(plotCTCompositionInNicheCluster)
-export(plotCTCompositionInProbCluster)
 export(plotCellProximityFeatSpot)
 export(plotCellProximityFeats)
 export(plotCellTypeNTScore)
@@ -326,6 +321,8 @@ export(plotPCA_3D)
 export(plotPolygons)
 export(plotRankSpatvsExpr)
 export(plotRecovery)
+export(plotSpatNicheClusterBin)
+export(plotSpatNicheClusterProb)
 export(plotStatDelaunayNetwork)
 export(plotTSNE)
 export(plotTSNE_2D)
@@ -339,7 +336,6 @@ export(print.combIcfObject)
 export(print.icfObject)
 export(processGiotto)
 export(prov)
-export(rankEnrich)
 export(rankSpatialCorGroups)
 export(read10xAffineImage)
 export(readCellMetadata)
@@ -360,6 +356,7 @@ export(readSpatLocsData)
 export(readSpatNetData)
 export(reconnectGiottoImage)
 export(rectVertices)
+export(reduceDims)
 export(registerGiottoObjectList)
 export(registerGiottoObjectListFiji)
 export(registerGiottoObjectListRvision)
@@ -374,8 +371,9 @@ export(runDWLSDeconv)
 export(runGiottoHarmony)
 export(runHyperGeometricEnrich)
 export(runIntegratedUMAP)
+export(runNMF)
+export(runONTraCV1)
 export(runPAGEEnrich)
-export(runPAGEEnrich_OLD)
 export(runPCA)
 export(runPCAprojection)
 export(runPCAprojectionBatch)
@@ -514,6 +512,7 @@ export(writeHMRFresults)
 exportMethods("$")
 exportMethods("$<-")
 exportMethods(interpolateFeature)
+exportMethods(labelTransfer)
 import(GiottoClass)
 import(GiottoUtils)
 import(GiottoVisuals)
@@ -575,7 +574,6 @@ importFrom(GiottoClass,combineCellData)
 importFrom(GiottoClass,combineFeatureData)
 importFrom(GiottoClass,combineFeatureOverlapData)
 importFrom(GiottoClass,combineMetadata)
-importFrom(GiottoClass,combineSpatialCellFeatureInfo)
 importFrom(GiottoClass,combineSpatialCellMetadataInfo)
 importFrom(GiottoClass,combineToMultiPolygon)
 importFrom(GiottoClass,convertGiottoLargeImageToMG)

NEWS.md

@@ -1,3 +1,51 @@
+# Giotto 4.1.3 (2024/10/27)
+
+## New
+* Add `giottoToAnndataZarr()` to create a local anndata zarr folder and interact with the vitessceR package.
+* `reduceDims()` API function for dimension reductions
+* `runNMF()` implementation that works via RcppML
+
+## Changes
+* `runWNN()` and `runIntegratedUMAP()` arguments were updated to make the function flexible to handle any number of modalities.
+* update `jackstrawPlot()` to make more flexible and efficient. Changed default params for `scaling`, `centering`, and `feats_to_use` to match `runPCA()`
+* change warning when reduction "feats" is selected in `runtSNE()` to error to avoid accidentally wiping the `giotto` object.
+
+
+# Giotto 4.1.2
+
+## Breaking changes
+* remove deprecated `PAGEEnrich()`. Use `runPAGEEnrich()` instead
+* remove deprecated `rankEnrich()`. Use `runRankEnrich()` instead
+* remove deprecated `hyperGeometricEnrich()`. Use `runHyperGeometricEnrich()` instead
+* remove deprecated `createSpatialEnrich()`. Use `runSpatialEnrich()` instead
+* remove deprecated `heatmSpatialCorGenes()`. Use `heatmSpatialCorFeats()` instead
+* remove deprecated `runPAGEEnrich_OLD()`. Use `runPAGEEnrich()` instead
+* remove `do_pca`, `expression_values`, `feats_to_use` args from `runGiottoHarmony()`. Running PCA during the `harmony::RunHarmony()` call is deprecated.
+
+## Enhancements
+* add `'quantile'` normalization method to `normalizeGiotto()`
+
+## Changes
+* `limma`, `plotly`, and `Rtsne` moved to Suggests
+* move `progressr` and `jsonlite` dependencies to GiottoUtils v0.1.12
+* remove `reshape2` dependency.
+
+## Bug fixes
+* `processGiotto()` can now skip adjust step by default
+
+## New
+* `identifyTMAcores()` for assigning IDs to tissue microarray spatial data.
+* `labelTransfer()` for transferring labels between giotto objects or subsets thereof. Supercedes `doClusterProjection()`
+
+# Giotto 4.1.1
+
+## Bug fixes
+* Allow `giottoInstructions` passing for Xenium convenience functions
+
+## Changes
+* Deprecate `screePlot()` `name` in favor of `dim_reduction_name` param
+
+
 # Giotto 4.1.0 (2024/07/31)
 
 ## Breaking changes