Merge branch 'develop' into feat/FindWeights

.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: 3.2.0.9901
-Date: 2020-07-17
+Version: 3.2.0.9017
+Date: 2020-08-27
 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(
@@ -43,6 +43,7 @@ Imports:
     lmtest,
     MASS,
     Matrix (>= 1.2-14),
+    matrixStats,
     miniUI,
     patchwork,
     pbapply,

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)
@@ -579,6 +599,9 @@ 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

@@ -4,9 +4,19 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 
 ## [unreleased]
 ### 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.
 
 ### 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()`
+
 
 ## [3.2.0] - 2020-07-15
 ### Added

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) {
@@ -77,7 +77,11 @@ ReplaceColsC <- function(mat, col_idx, replacement) {
     .Call('_Seurat_ReplaceColsC', PACKAGE = 'Seurat', mat, col_idx, replacement)
 }
 
-FindWeightsC <- function(cells2, distances, anchor_cells2, integration_matrix_rownames, cell_index, anchor_score, min_dist, sd, display_progress) {
+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', cells2, distances, anchor_cells2, integration_matrix_rownames, cell_index, anchor_score, min_dist, sd, display_progress)
 }
 

R/clustering.R

@@ -281,7 +281,7 @@ FindNeighbors.default <- function(
       searchtype = "standard",
       eps = nn.eps,
       metric = annoy.metric)
-    nn.ranked <- nn.ranked$nn.idx
+    nn.ranked <- Indices(object = nn.ranked)
   } else {
     if (verbose) {
       message("Building SNN based on a provided distance matrix")
@@ -514,6 +514,8 @@ AnnoyNN <- function(data, query = data, metric = "euclidean", n.trees = 50, k,
     k = k,
     search.k = search.k,
     include.distance = include.distance)
+  nn$idx <- idx
+  nn$alg.info <- list(metric = metric, ndim = ncol(x = data))
   return(nn)
 }
 
@@ -633,12 +635,13 @@ GroupSingletons <- function(ids, SNN, group.singletons = TRUE, verbose = TRUE) {
 # @param query Data to query against data
 # @param k Number of nearest neighbors to compute
 # @param method Nearest neighbor method to use: "rann", "annoy"
+# @param cache.index Store algorithm index with results for reuse
 # @param ... additional parameters to specific neighbor finding method
 #
-NNHelper <- function(data, query = data, k, method, ...) {
+NNHelper <- function(data, query = data, k, method, cache.index = FALSE, ...) {
   args <- as.list(x = sys.frame(which = sys.nframe()))
   args <- c(args, list(...))
-  return(
+  results <- (
     switch(
       EXPR = method,
       "rann" = {
@@ -652,6 +655,16 @@ NNHelper <- function(data, query = data, k, method, ...) {
       stop("Invalid method. Please choose one of 'rann', 'annoy'")
     )
   )
+  n.ob <- Neighbor(
+    nn.idx = results$nn.idx,
+    nn.dist = results$nn.dists,
+    alg.info = results$alg.info %||% list(),
+    cell.names = rownames(x = query)
+  )
+  if (isTRUE(x = cache.index) && !is.null(x = results$idx)) {
+    slot(object = n.ob, name = "alg.idx") <- results$idx
+  }
+  return(n.ob)
 }
 
 # Run Leiden clustering algorithm