Merge pull request #5399 from satijalab/develop

Seurat v4.0.6

.Rbuildignore

@@ -13,3 +13,4 @@ CODE_OF_CONDUCT.md
 ^pkgdown$
 ^index\.md$
 ^vignettes$
+^LICENSE\.md$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.5
-Date: 2021-10-04
+Version: 4.0.6
+Date: 2021-12-16
 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>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(
@@ -66,7 +66,7 @@ Imports:
     scales,
     scattermore (>= 0.7),
     sctransform (>= 0.3.2),
-    SeuratObject (>= 4.0.2),
+    SeuratObject (>= 4.0.4),
     shiny,
     spatstat.core,
     spatstat.geom,
@@ -76,7 +76,7 @@ Imports:
     utils,
     uwot (>= 0.1.9)
 LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
-License: GPL-3 | file LICENSE
+License: MIT + file LICENSE
 LazyData: true
 Collate:
     'RcppExports.R'
@@ -119,4 +119,5 @@ Suggests:
     limma,
     metap,
     enrichR,
-    mixtools
+    mixtools,
+    ggrastr

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2021 Seurat authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NAMESPACE

@@ -69,6 +69,9 @@ S3method(RunLDA,default)
 S3method(RunPCA,Assay)
 S3method(RunPCA,Seurat)
 S3method(RunPCA,default)
+S3method(RunSLSI,Assay)
+S3method(RunSLSI,Seurat)
+S3method(RunSLSI,default)
 S3method(RunSPCA,Assay)
 S3method(RunSPCA,Seurat)
 S3method(RunSPCA,default)
@@ -124,6 +127,7 @@ export(AggregateExpression)
 export(AnnotateAnchors)
 export(Assays)
 export(AugmentPlot)
+export(AutoPointSize)
 export(AverageExpression)
 export(BGTextColor)
 export(BarcodeInflectionsPlot)
@@ -247,6 +251,7 @@ export(NormalizeData)
 export(PCAPlot)
 export(PCASigGenes)
 export(PCHeatmap)
+export(PercentAbove)
 export(PercentageFeatureSet)
 export(PlotClusterTree)
 export(PlotPerturbScore)
@@ -284,6 +289,7 @@ export(RunMarkVario)
 export(RunMixscape)
 export(RunMoransI)
 export(RunPCA)
+export(RunSLSI)
 export(RunSPCA)
 export(RunTSNE)
 export(RunUMAP)
@@ -299,8 +305,15 @@ export(SelectIntegrationFeatures)
 export(SetAssayData)
 export(SetIdent)
 export(SetIntegrationData)
+export(SetQuantile)
 export(SeuratAxes)
 export(SeuratTheme)
+export(SingleCorPlot)
+export(SingleDimPlot)
+export(SingleExIPlot)
+export(SingleImageMap)
+export(SingleRasterMap)
+export(SingleSpatialPlot)
 export(SpatialDimPlot)
 export(SpatialFeaturePlot)
 export(SpatialPlot)
@@ -347,7 +360,6 @@ exportClasses(SeuratCommand)
 exportClasses(SpatialImage)
 exportClasses(TransferAnchorSet)
 exportClasses(VisiumV1)
-import(Matrix)
 importClassesFrom(Matrix,dgCMatrix)
 importClassesFrom(SeuratObject,Assay)
 importClassesFrom(SeuratObject,DimReduc)
@@ -360,6 +372,7 @@ importClassesFrom(SeuratObject,SpatialImage)
 importFrom(KernSmooth,bkde)
 importFrom(MASS,glm.nb)
 importFrom(MASS,lda)
+importFrom(Matrix,Matrix)
 importFrom(Matrix,as.matrix)
 importFrom(Matrix,colMeans)
 importFrom(Matrix,colSums)
@@ -369,6 +382,7 @@ importFrom(Matrix,rowMeans)
 importFrom(Matrix,rowSums)
 importFrom(Matrix,sparse.model.matrix)
 importFrom(Matrix,sparseMatrix)
+importFrom(Matrix,t)
 importFrom(RANN,nn2)
 importFrom(RColorBrewer,brewer.pal)
 importFrom(RColorBrewer,brewer.pal.info)
@@ -399,6 +413,7 @@ importFrom(SeuratObject,CreateAssayObject)
 importFrom(SeuratObject,CreateDimReducObject)
 importFrom(SeuratObject,CreateSeuratObject)
 importFrom(SeuratObject,DefaultAssay)
+importFrom(SeuratObject,DefaultDimReduc)
 importFrom(SeuratObject,Distances)
 importFrom(SeuratObject,Embeddings)
 importFrom(SeuratObject,FetchData)
@@ -417,6 +432,7 @@ importFrom(SeuratObject,Loadings)
 importFrom(SeuratObject,LogSeuratCommand)
 importFrom(SeuratObject,Misc)
 importFrom(SeuratObject,Neighbors)
+importFrom(SeuratObject,PackageCheck)
 importFrom(SeuratObject,Project)
 importFrom(SeuratObject,Radius)
 importFrom(SeuratObject,Reductions)
@@ -545,11 +561,13 @@ importFrom(grDevices,col2rgb)
 importFrom(grDevices,colorRampPalette)
 importFrom(grDevices,rgb)
 importFrom(graphics,axis)
+importFrom(graphics,image)
 importFrom(graphics,locator)
 importFrom(graphics,par)
 importFrom(graphics,plot)
 importFrom(graphics,plot.new)
 importFrom(graphics,smoothScatter)
+importFrom(graphics,title)
 importFrom(grid,addGrob)
 importFrom(grid,editGrob)
 importFrom(grid,gTree)
@@ -617,6 +635,7 @@ importFrom(reticulate,py_module_available)
 importFrom(reticulate,py_set_seed)
 importFrom(rlang,"!!")
 importFrom(rlang,as_label)
+importFrom(rlang,invoke)
 importFrom(scales,brewer_pal)
 importFrom(scales,hue_pal)
 importFrom(scales,rescale)
@@ -690,6 +709,7 @@ importFrom(utils,argsAnywhere)
 importFrom(utils,capture.output)
 importFrom(utils,file_test)
 importFrom(utils,globalVariables)
+importFrom(utils,head)
 importFrom(utils,isS3method)
 importFrom(utils,isS3stdGeneric)
 importFrom(utils,methods)
@@ -698,8 +718,10 @@ importFrom(utils,read.csv)
 importFrom(utils,read.delim)
 importFrom(utils,read.table)
 importFrom(utils,setTxtProgressBar)
+importFrom(utils,tail)
 importFrom(utils,txtProgressBar)
 importFrom(utils,write.table)
 importFrom(uwot,umap)
 importFrom(uwot,umap_transform)
+importMethodsFrom(Matrix,t)
 useDynLib(Seurat)

NEWS.md

@@ -1,10 +1,24 @@
-# Seurat 4.0.5 (2020-10-04)
+# Seurat 4.0.6 (2021-12-16)
+## Added
+
+- Implement supervised LSI
+
+## Changes
+- Add `raster` parameter to `VlnPlot` to optionally rasterize individual points ([#5076](https://github.com/satijalab/seurat/pull/5076))
+- Add `min.cells.group` parameter to `FindConservedMarkers` ([#5079](https://github.com/satijalab/seurat/pull/5079))
+- Set `do.center` to FALSE for `lsiproject` in `FindTransferAnchors`
+- Fix error message in `ReadMtx()` ([#5158](https://github.com/satijalab/seurat/issues/5158))
+- Add `label.color` parameter to `FeaturePlot` ([#5314](https://github.com/satijalab/seurat/pull/5314))
+- Fix issues in `ProjectUMAP` ([#5257](https://github.com/satijalab/seurat/issues/5257), [#5104](https://github.com/satijalab/seurat/issues/5104), [#5373](https://github.com/satijalab/seurat/issues/5373))
+
+# Seurat 4.0.5 (2021-10-04)
 ## Changes
 - Update documentation for `to.upper` parameter in `Load10X_Spatial()` ([#4576](https://github.com/satijalab/seurat/issues/4576))
 - Update concept tags for `RunSPCA()` ([#4978](https://github.com/satijalab/seurat/discussions/4987))
 - Conditionally run tests/packages that use suggested packages ([#5160](https://github.com/satijalab/seurat/pull/5160))
+- Set random state in `RunUMAP()` when using the `umap-learn` method ([#5194](https://github.com/satijalab/seurat/issues/5194))
 
-# Seurat 4.0.4 (2020-08-19)
+# Seurat 4.0.4 (2021-08-19)
 ## Added
 - Add `reduction` parameter to `BuildClusterTree()` ([#4598](https://github.com/satijalab/seurat/issues/4598))
 - Add DensMAP option to `RunUMAP()` ([#4630](https://github.com/satijalab/seurat/pull/4630))
@@ -15,6 +29,7 @@
 - Add the `image.alpha` parameter to `SpatialDimPlot()` and `SpatialFeaturePlot()`
 - Add support for the correlation metric in `RunUMAP` ([#4972](https://github.com/satijalab/seurat/issues/4972))
 
+
 ## Changes
 - Warn and continue rather than erroring if not all features are available in `FindSpatiallyVariableFeatures()` ([#4611](https://github.com/satijalab/seurat/issues/4611))
 - Bug fix for SCT-based integration in selecting proper reference model ([#4355](https://github.com/satijalab/seurat/issues/4355))
@@ -26,7 +41,7 @@
 - Fix issue in SingleCellExperiment conversion where the mainExp would not be set properly
 - Fix for default dispersion info displayed in `VariableFeaturePlot()`
 
-# Seurat 4.0.3 (2020-06-10)
+# Seurat 4.0.3 (2021-06-10)
 ## Added
 - Add `jitter` parameter to `FeatureScatter()`
 

R/RcppExports.R

@@ -109,3 +109,15 @@ SNN_SmallestNonzero_Dist <- function(snn, mat, n, nearest_dist) {
     .Call('_Seurat_SNN_SmallestNonzero_Dist', PACKAGE = 'Seurat', snn, mat, n, nearest_dist)
 }
 
+row_sum_dgcmatrix <- function(x, i, rows, cols) {
+    .Call('_Seurat_row_sum_dgcmatrix', PACKAGE = 'Seurat', x, i, rows, cols)
+}
+
+row_mean_dgcmatrix <- function(x, i, rows, cols) {
+    .Call('_Seurat_row_mean_dgcmatrix', PACKAGE = 'Seurat', x, i, rows, cols)
+}
+
+row_var_dgcmatrix <- function(x, i, rows, cols) {
+    .Call('_Seurat_row_var_dgcmatrix', PACKAGE = 'Seurat', x, i, rows, cols)
+}
+

R/differential_expression.R

@@ -241,6 +241,7 @@ FindConservedMarkers <- function(
   grouping.var,
   assay = 'RNA',
   slot = 'data',
+  min.cells.group = 3,
   meta.method = metap::minimump,
   verbose = TRUE,
   ...
@@ -298,6 +299,20 @@ FindConservedMarkers <- function(
     }
     ident.2 <- ident.2.save
     cells.1 <- WhichCells(object = object, idents = ident.use.1)
+    if (length(cells.1) < min.cells.group) {
+      warning(
+        level.use,
+        " has fewer than ",
+        min.cells.group,
+        " cells in Identity: ",
+        paste(ident.1, collapse = ", "),
+        ". Skipping ",
+        level.use,
+        call. = FALSE,
+        immediate. = TRUE
+      )
+      next
+    }
     if (is.null(x = ident.2)) {
       cells.2 <- setdiff(x = cells[[i]], y = cells.1)
       ident.use.2 <- names(x = which(x = table(Idents(object = object)[cells.2]) > 0))