Merge pull request #3479 from satijalab/develop

Seurat v3.2.1

.github/workflows/R_CMD_check.yaml

@@ -0,0 +1,30 @@
+on:
+    push:
+        branches:
+            - master
+            - develop
+    pull_request:
+
+jobs:
+    r-cmd-check:
+
+        if: "!contains(github.event.head_commit.message, 'ci-skip')"
+
+        name: R CMD check
+        container:
+            image: satijalab/seurat:develop
+        runs-on: self-hosted 
+
+        steps:
+            - uses: actions/checkout@v2
+
+            - name: Check
+              run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
+              shell: Rscript {0}
+
+            - name: Upload check results
+              if: failure()
+              uses: actions/upload-artifact@master
+              with:
+                  name: results
+                  path: check

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 3.2.0
-Date: 2020-07-15
+Version: 3.2.1
+Date: 2020-09-04
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
 Authors@R: c(
@@ -14,20 +14,19 @@ Authors@R: c(
   person(given = 'Patrick', family = 'Roelli', email = '[email protected]', role = 'ctb'),
   person(given = "Yuhan", family = "Hao", email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0002-1810-0822'))
   )
-URL: http://www.satijalab.org/seurat, https://github.com/satijalab/seurat
+URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat
 BugReports: https://github.com/satijalab/seurat/issues
 Additional_repositories: https://mojaveazure.github.io/loomR
 Depends:
-    R (>= 3.4.0),
+    R (>= 3.6.0),
     methods,
 Imports:
-    ape,
     cluster,
     cowplot,
     fitdistrplus,
     future,
     future.apply,
-    ggplot2 (>= 3.0.0),
+    ggplot2 (>= 3.3.0),
     ggrepel,
     ggridges,
     graphics,
@@ -43,6 +42,7 @@ Imports:
     lmtest,
     MASS,
     Matrix (>= 1.2-14),
+    matrixStats,
     miniUI,
     patchwork,
     pbapply,
@@ -88,6 +88,7 @@ RoxygenNote: 7.1.1
 Encoding: UTF-8
 Suggests:
     loomR,
+    ape,
     testthat,
     hdf5r,
     S4Vectors,

NAMESPACE

@@ -10,6 +10,7 @@ S3method("DefaultAssay<-",Graph)
 S3method("DefaultAssay<-",Seurat)
 S3method("DefaultAssay<-",SpatialImage)
 S3method("Idents<-",Seurat)
+S3method("Index<-",Neighbor)
 S3method("JS<-",DimReduc)
 S3method("JS<-",JackStrawData)
 S3method("Key<-",Assay)
@@ -41,6 +42,7 @@ S3method(.DollarNames,SeuratCommand)
 S3method(AddMetaData,Assay)
 S3method(AddMetaData,Seurat)
 S3method(Cells,DimReduc)
+S3method(Cells,Neighbor)
 S3method(Cells,STARmap)
 S3method(Cells,SlideSeq)
 S3method(Cells,SpatialImage)
@@ -55,6 +57,7 @@ S3method(DefaultAssay,Graph)
 S3method(DefaultAssay,Seurat)
 S3method(DefaultAssay,SeuratCommand)
 S3method(DefaultAssay,SpatialImage)
+S3method(Distances,Neighbor)
 S3method(Embeddings,DimReduc)
 S3method(Embeddings,Seurat)
 S3method(FindClusters,Seurat)
@@ -87,6 +90,8 @@ S3method(GetTissueCoordinates,VisiumV1)
 S3method(HVFInfo,Assay)
 S3method(HVFInfo,Seurat)
 S3method(Idents,Seurat)
+S3method(Index,Neighbor)
+S3method(Indices,Neighbor)
 S3method(IsGlobal,DimReduc)
 S3method(IsGlobal,SpatialImage)
 S3method(IsGlobal,default)
@@ -115,6 +120,7 @@ S3method(ReadH5AD,H5File)
 S3method(ReadH5AD,character)
 S3method(RenameCells,Assay)
 S3method(RenameCells,DimReduc)
+S3method(RenameCells,Neighbor)
 S3method(RenameCells,STARmap)
 S3method(RenameCells,Seurat)
 S3method(RenameCells,SlideSeq)
@@ -169,7 +175,9 @@ S3method(WhichCells,Seurat)
 S3method(WriteH5AD,Seurat)
 S3method(as.CellDataSet,Seurat)
 S3method(as.Graph,Matrix)
+S3method(as.Graph,Neighbor)
 S3method(as.Graph,matrix)
+S3method(as.Neighbor,Graph)
 S3method(as.Seurat,CellDataSet)
 S3method(as.Seurat,SingleCellExperiment)
 S3method(as.Seurat,loom)
@@ -184,6 +192,7 @@ S3method(as.sparse,data.frame)
 S3method(as.sparse,matrix)
 S3method(dim,Assay)
 S3method(dim,DimReduc)
+S3method(dim,Neighbor)
 S3method(dim,STARmap)
 S3method(dim,Seurat)
 S3method(dim,SlideSeq)
@@ -209,6 +218,7 @@ S3method(subset,SpatialImage)
 S3method(subset,VisiumV1)
 export("DefaultAssay<-")
 export("Idents<-")
+export("Index<-")
 export("JS<-")
 export("Key<-")
 export("Loadings<-")
@@ -252,6 +262,7 @@ export(DietSeurat)
 export(DimHeatmap)
 export(DimPlot)
 export(DiscretePalette)
+export(Distances)
 export(DoHeatmap)
 export(DotPlot)
 export(ElbowPlot)
@@ -260,6 +271,7 @@ export(ExpMean)
 export(ExpSD)
 export(ExpVar)
 export(ExportToCellbrowser)
+export(FastRowScale)
 export(FeatureLocator)
 export(FeaturePlot)
 export(FeatureScatter)
@@ -294,6 +306,8 @@ export(ISpatialDimPlot)
 export(ISpatialFeaturePlot)
 export(Idents)
 export(Images)
+export(Index)
+export(Indices)
 export(IntegrateData)
 export(Intensity)
 export(IsGlobal)
@@ -308,6 +322,7 @@ export(LabelPoints)
 export(LinkedDimPlot)
 export(LinkedFeaturePlot)
 export(Load10X_Spatial)
+export(LoadAnnoyIndex)
 export(LoadSTARmap)
 export(Loadings)
 export(LocalStruct)
@@ -320,6 +335,7 @@ export(MetaFeature)
 export(MinMax)
 export(Misc)
 export(MixingMetric)
+export(Neighbors)
 export(NoAxes)
 export(NoGrid)
 export(NoLegend)
@@ -367,6 +383,7 @@ export(RunUMAP)
 export(SCTransform)
 export(SVFInfo)
 export(SampleUMI)
+export(SaveAnnoyIndex)
 export(ScaleData)
 export(ScaleFactors)
 export(ScoreJackStraw)
@@ -392,6 +409,7 @@ export(TSNEPlot)
 export(Tool)
 export(TopCells)
 export(TopFeatures)
+export(TopNeighbors)
 export(TransferData)
 export(UMAPPlot)
 export(UpdateSeuratObject)
@@ -404,6 +422,7 @@ export(WhichCells)
 export(WhiteBackground)
 export(as.CellDataSet)
 export(as.Graph)
+export(as.Neighbor)
 export(as.Seurat)
 export(as.SingleCellExperiment)
 export(as.loom)
@@ -415,6 +434,7 @@ exportClasses(DimReduc)
 exportClasses(Graph)
 exportClasses(IntegrationData)
 exportClasses(JackStrawData)
+exportClasses(Neighbor)
 exportClasses(Seurat)
 exportClasses(SeuratCommand)
 exportClasses(SpatialImage)
@@ -442,11 +462,6 @@ importFrom(RcppAnnoy,AnnoyEuclidean)
 importFrom(RcppAnnoy,AnnoyHamming)
 importFrom(RcppAnnoy,AnnoyManhattan)
 importFrom(Rtsne,Rtsne)
-importFrom(ape,Moran.I)
-importFrom(ape,as.phylo)
-importFrom(ape,drop.tip)
-importFrom(ape,nodelabels)
-importFrom(ape,plot.phylo)
 importFrom(cluster,clara)
 importFrom(cowplot,get_legend)
 importFrom(cowplot,plot_grid)
@@ -485,6 +500,7 @@ importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_polygon)
 importFrom(ggplot2,geom_raster)
+importFrom(ggplot2,geom_rect)
 importFrom(ggplot2,geom_smooth)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,geom_tile)
@@ -579,6 +595,9 @@ importFrom(irlba,irlba)
 importFrom(jsonlite,fromJSON)
 importFrom(leiden,leiden)
 importFrom(lmtest,lrtest)
+importFrom(matrixStats,rowMeans2)
+importFrom(matrixStats,rowSds)
+importFrom(matrixStats,rowSums2)
 importFrom(methods,"slot<-")
 importFrom(methods,.hasSlot)
 importFrom(methods,as)

NEWS.md

@@ -1,21 +1,47 @@
 # News
 All notable changes to Seurat will be documented in this file.
-The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
+
+## [3.2.1] - 2020-09-04
+### Added
+- Added support for nearest neighbor input and `return.model` parameter in `RunUMAP()`
+- Enable named color vectors in `DoHeatmap()`
+- Add `label.color` and `label.box` parameters to `DimPlot`
+- Added `shuffle` and `seed` parameters to `DimPlot()` to help with overplotting
+- Added new stacked violin plot functionality
+
+### Changes
+- Allow setting `slot` parameter in `RunUMAP`
+- Added support for FIt-SNE v1.2+
+- Fix for `Spatial*Plot` when running with interactive=TRUE
+- Set max for number of items returned by `Top` and remove duplicate items when balanced=TRUE
+- Fix logging bug when functions were run via `do.call()`
+- Fix handling of weight.by.var parameter when approx=FALSE in `RunPCA()`
+- Fix issue where feature names with dashes crashed `CellSelector`
+- Fix issue where errors in subsetting were being swallowed
+- Fix issue where labeling uncropped spatial plots was broken
+
+### Deprecated
+- `CreateActivityMatrix` deprecated in favor of `Signac::GeneActivity`
+- `ReadAlevin` and `ReadAlevinCsv` deprecated in favor of `SeuratWrappers::ReadAlevin`
+- `ExportToCellbrowser` and `StopCellbrowser` deprecated in favor of `SeuratWrappers::ExportToCellbrowser` and `SeuratWrappers::StopCellbrowser`
+- `ReadH5AD` and `WriteH5AD` deprecated in favor of h5Seurat/H5AD functionality found in SeuratDisk
+- `as.loom` and `as.Seurat.loom` deprecated in favor of functionality found in SeuratDisk
 
 ## [3.2.0] - 2020-07-15
 ### Added
 - Added ability to create a Seurat object from an existing Assay object, or any
 object inheriting from the Assay class
 - Added ability to cluster idents and group features in `DotPlot`
 - Added ability to use RColorBrewer plaettes for split `DotPlots`
-- Added visualization and analysis functionality for spatially resolved datasets (Visium, Slide-seq). 
+- Added visualization and analysis functionality for spatially resolved datasets (Visium, Slide-seq).
 
 ### Changes
 - Removed `add.iter` parameter from `RunTSNE` function
 - Fixed integer overflow error in the WilcoxDETest function
 - Minor visual fixes in `DoHeatmap` group bar + labels
 - Efficiency improvements in anchor scoring (`ScoreAnchors`)
-- Fix bug in `FindClusters()` when the last node has no edges 
+- Fix bug in `FindClusters()` when the last node has no edges
 - Default to weighted = TRUE when constructing igraph objects in `RunLeiden`. Remove corresponding weights parameter from `FindClusters()`.
 - Fix handling of keys in `FeatureScatter()`
 - Change `CellSelector` to use Shiny gadgets instead of SDMTools
@@ -25,7 +51,7 @@ object inheriting from the Assay class
 
 ## [3.1.5] - 2020-04-14
 ### Added
-- New `scale` parameter in `DotPlot` 
+- New `scale` parameter in `DotPlot`
 - New `keep.sparse parameter in `CreateGeneActivityMatrix` for a more memory efficient option
 - Added ability to store model learned by UMAP and project new data
 - New `strip.suffix` option in `Read10X`. **This changes the default behavior of `Read10X`**.
@@ -46,7 +72,7 @@ object inheriting from the Assay class
 - Update `assay.used` slot for `DimReduc`s when Assay is renamed
 
 ## [3.1.4] - 2020-02-20
-### Changes 
+### Changes
 - Fixes to `DoHeatmap` to remain compatible with ggplot2 v3.3
 - Adoption of `patchwork` framework to replace `CombinePlots`
 
@@ -61,7 +87,7 @@ object inheriting from the Assay class
 - Fixes for keys with underscores
 - Fix issue with leiden option for `FindClusters`
 - Fix for data transfer when using sctransform
-- SDMTools moved to Suggests as package is orphaned 
+- SDMTools moved to Suggests as package is orphaned
 
 ## [3.1.2] - 2019-12-11
 ### Added
@@ -110,7 +136,7 @@ object inheriting from the Assay class
 - Updates `ReadH5AD` to distinguish FVF methods
 - Fixes to UpdateSeuratObject for v2 objects
 - Sink all output from stdout to stderr
-- Fix to scale.data cell ordering after subsetting 
+- Fix to scale.data cell ordering after subsetting
 - Enable `Assay` specification in `BuildClusterTree`
 - Fix `FeaturePlot` when using both `blend` and `split.by`
 - Fix to `WhichCells` when passing `cells` and `invert`
@@ -181,7 +207,7 @@ object inheriting from the Assay class
 
 ### Changed
 - DiffusionMap dependency replaced with destiny to avoid archival
-- Java dependency removed and functionality rewritten in Rcpp 
+- Java dependency removed and functionality rewritten in Rcpp
 - Speed and efficiency improvements for Rcpp code
 - More robust duplicate handling in CellCycleScoring
 

R/RcppExports.R

@@ -17,12 +17,12 @@ RowMergeMatrices <- function(mat1, mat2, mat1_rownames, mat2_rownames, all_rowna
     .Call('_Seurat_RowMergeMatrices', PACKAGE = 'Seurat', mat1, mat2, mat1_rownames, mat2_rownames, all_rownames)
 }
 
-LogNorm <- function(data, scale_factor, display_progress = TRUE) {
-    .Call('_Seurat_LogNorm', PACKAGE = 'Seurat', data, scale_factor, display_progress)
+RowMergeMatricesList <- function(mat_list, mat_rownames, all_rownames) {
+    .Call('_Seurat_RowMergeMatricesList', PACKAGE = 'Seurat', mat_list, mat_rownames, all_rownames)
 }
 
-FastRowScale <- function(mat, scale = TRUE, center = TRUE, scale_max = 10, display_progress = TRUE) {
-    .Call('_Seurat_FastRowScale', PACKAGE = 'Seurat', mat, scale, center, scale_max, display_progress)
+LogNorm <- function(data, scale_factor, display_progress = TRUE) {
+    .Call('_Seurat_LogNorm', PACKAGE = 'Seurat', data, scale_factor, display_progress)
 }
 
 Standardize <- function(mat, display_progress = TRUE) {
@@ -77,6 +77,10 @@ ReplaceColsC <- function(mat, col_idx, replacement) {
     .Call('_Seurat_ReplaceColsC', PACKAGE = 'Seurat', mat, col_idx, replacement)
 }
 
+GraphToNeighborHelper <- function(mat) {
+    .Call('_Seurat_GraphToNeighborHelper', PACKAGE = 'Seurat', mat)
+}
+
 FindWeightsC <- function(integration_matrix, cells2, distances, anchor_cells2, integration_matrix_rownames, cell_index, anchor_score, min_dist, sd, display_progress) {
     .Call('_Seurat_FindWeightsC', PACKAGE = 'Seurat', integration_matrix, cells2, distances, anchor_cells2, integration_matrix_rownames, cell_index, anchor_score, min_dist, sd, display_progress)
 }