Bugfix to as.SingleCellExperiment

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: Seurat
-Version: 4.0.2
-Date: 2021-05-20
+Version: 4.0.2.9001
+Date: 2021-05-28
 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(

NEWS.md

@@ -1,3 +1,10 @@
+## Seurat develop
+
+## Added
+
+## Changes
+- Fix issues with `as.SingleCellExperiment.Seurat` for the latest verion of SingleCellExperiment ([#4532](https://github.com/satijalab/seurat/pull/4532))
+
 # Seurat 4.0.2 (2020-03-20)
 ## Added
 - New `AddAzimuthScores()` and `AddAzimuthResults()` functions

R/objects.R

@@ -1173,7 +1173,7 @@ as.SingleCellExperiment.Seurat <- function(x, assay = NULL, ...) {
     stop("One or more of the assays you are trying to convert is not in the Seurat object")
   }
   experiments <- list()
-  for (assayn in assay){
+  for (assayn in assay) {
   assays = list(
     counts = GetAssayData(object = x, assay = assayn, slot = "counts"),
     logcounts = GetAssayData(object = x, assay = assayn, slot = "data"))
@@ -1185,24 +1185,45 @@ as.SingleCellExperiment.Seurat <- function(x, assay = NULL, ...) {
   sce <- as(object = experiments[[1]], Class = "SingleCellExperiment")
   sce <- SingleCellExperiment::SingleCellExperiment(sce, altExps = experiments)
   orig.exp.name <- names(x = experiments[1])
-  sce <- SingleCellExperiment::swapAltExp(x = sce, name = orig.exp.name, saved = NULL)
+  sce <- SingleCellExperiment::swapAltExp(
+    x = sce,
+    name = orig.exp.name,
+    saved = NULL
+  )
   metadata <- x[[]]
   metadata$ident <- Idents(object = x)
   SummarizedExperiment::colData(x = sce) <- S4Vectors::DataFrame(metadata)
-  for (assayn in assay){
-    sce <- SingleCellExperiment::swapAltExp(x = sce, name = assayn, saved = orig.exp.name)
-    SummarizedExperiment::rowData(x = sce) <- S4Vectors::DataFrame(x[[assayn]][[]])
-    sce <- SingleCellExperiment::swapAltExp(x = sce, name = orig.exp.name, saved = assayn)
+  for (assayn in assay) {
+    if (assayn != orig.exp.name) {
+      sce <- SingleCellExperiment::swapAltExp(
+        x = sce,
+        name = assayn,
+        saved = orig.exp.name
+      )
+      SummarizedExperiment::rowData(x = sce) <- S4Vectors::DataFrame(x[[assayn]][[]])
+      sce <- SingleCellExperiment::swapAltExp(
+        x = sce,
+        name = orig.exp.name,
+        saved = assayn
+      )
+    }
   }
   for (dr in FilterObjects(object = x, classes.keep = "DimReduc")) {
     assay.used <- DefaultAssay(object = x[[dr]])
     if (assay.used %in% SingleCellExperiment::altExpNames(x = sce)) {
-      sce <- SingleCellExperiment::swapAltExp(x = sce, name = assay.used, saved = orig.exp.name)
-      SingleCellExperiment::reducedDim(x = sce, toupper(x = dr)) <- Embeddings(object = x[[dr]])
-      sce <- SingleCellExperiment::swapAltExp(x = sce, name = orig.exp.name, saved = assay.used)
+      sce <- SingleCellExperiment::swapAltExp(
+        x = sce,
+        name = assay.used,
+        saved = orig.exp.name
+      )
+      SingleCellExperiment::reducedDim(x = sce, type = toupper(x = dr)) <- Embeddings(object = x[[dr]])
+      sce <- SingleCellExperiment::swapAltExp(
+        x = sce,
+        name = orig.exp.name,
+        saved = assay.used
+      )
     }
   }
-  sce <- SingleCellExperiment::swapAltExp(x = sce, name = orig.exp.name, saved = NULL)
   return(sce)
 }
 

tests/testthat/test_objects.R

@@ -341,3 +341,30 @@ test_that("Top works", {
   expect_equal(length(tpc1.sub[[1]]), 40)
   expect_equal(length(tpc1.sub[[2]]), 39)
 })
+
+
+# Tests for SCE conversion
+# ------------------------------------------------------------------------------
+test_that("as.SingleCellExperiment works", {
+  skip_on_cran()
+  if (requireNamespace('SingleCellExperiment', quietly = TRUE)) {
+    mat <- matrix(1:100, ncol = 10)
+    colnames(mat) <- LETTERS[1:10]
+    rownames(mat) <- LETTERS[1:10]
+    seuratObj <- Seurat::CreateSeuratObject(mat)
+    sce <- as.SingleCellExperiment(seuratObj)
+
+    expect_equal(ncol(sce), 10)
+    expect_equal(nrow(sce), 10)
+    # expect_equal(length(SingleCellExperiment::altExps(sce)), 0)
+    # expect_equal(SingleCellExperiment::mainExpName(sce), 'RNA')
+
+    seuratObj <- Seurat::CreateSeuratObject(mat)
+    seuratObj[['ADT']] <- CreateAssayObject(mat)
+    sce <- as.SingleCellExperiment(seuratObj)
+    expect_equal(ncol(sce), 10)
+    expect_equal(nrow(sce), 10)
+    # expect_equal(names(SingleCellExperiment::altExps(sce)), 'ADT')
+    # expect_equal(SingleCellExperiment::mainExpName(sce), 'RNA')
+  }
+})