Update sce_to_seurat function

DESCRIPTION

@@ -10,15 +10,19 @@ Authors@R: c(
     person(c("Joshua", "A."), "Shapiro", 
            email = "josh.shapiro@ccdatalab.org",
            comment = list(ORCID = "0000-0002-6224-0347"),
-           role = c("aut"))
+           role = c("aut")),
+    person(c("Stephanie", "J."), "Spielman", 
+           email = "stephanie.spielman@ccdatalab.org",
+           comment = list(ORCID = "0000-0002-9090-4788"),
+           role = c("aut"))           
     )
 Maintainer: Ally Hawkins <ally.hawkins@ccdatalab.org>
 Description: Tools for processing single cell data associated with the 
     Alex's Lemonade Stand Foundation Single Cell Pediatric Cancer Atlas.
 License: BSD_3_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.1
 Depends: 
     R (>= 4.1.0)
 Imports: 

R/sce_to_seurat.R

@@ -2,6 +2,10 @@
 #' Convert SingleCellExperiment object to Seurat object
 #'
 #' @param sce SingleCellExperiment object
+#' @param assay_name The assay name (default "counts") to include in
+#'   the Seurat object. This name will be applied as the assay name in
+#'   the Seurat object. If the default "count" assay is used, then the
+#'   assay name will instead be "RNA".
 #'
 #' @return Seurat object
 #'
@@ -13,7 +17,8 @@
 #' \dontrun{
 #' sce_to_seurat(sce = sce_object)
 #' }
-sce_to_seurat <- function(sce){
+sce_to_seurat <- function(sce,
+                          assay_name = "counts") {
 
   if (!requireNamespace("Seurat", quietly = TRUE)) {
     stop("The Seurat package must be installed to create a Seurat object. No output returned.")
@@ -23,6 +28,10 @@ sce_to_seurat <- function(sce){
     stop("Input must be a SingleCellExperiment object.")
   }
 
+  if (!assay_name %in% assayNames(sce)) {
+    stop("Provided assay name is not present in the SingleCellExperiment object.")
+  }
+
   # remove miQC model from metadata
   if(!is.null(metadata(sce)$miQC_model)){
     metadata(sce)$miQC_model <- NULL
@@ -31,7 +40,8 @@ sce_to_seurat <- function(sce){
 
 
   # Seurat counts need to be integers
-  sce_counts <- round(counts(sce))
+  # extract the given `assay_name`
+  sce_counts <- round(assay(sce, assay_name))
 
   # Seurat will not like zero count calls
   sce_sum <- Matrix::colSums(sce_counts)
@@ -43,12 +53,17 @@ sce_to_seurat <- function(sce){
   rowdata <- as.data.frame(rowData(sce))
 
 
-  # create seurat object
+  # create seurat object, with new assay name
+  # use "RNA" as assay name if `counts` is being used from SCE
+  if (assay_name == "counts") {
+    assay_name <- "RNA"
+  }
   seurat_obj <- Seurat::CreateSeuratObject(counts = sce_counts,
-                                           meta.data = coldata)
+                                           meta.data = coldata,
+                                           assay = assay_name)
 
   # add rowdata and metadata separately adding it while creating leaves the slots empty without warning
-  seurat_obj[["RNA"]]@var.features <- rowdata
+  seurat_obj[[assay_name]]@var.features <- rowdata
   seurat_obj@misc <- metadata(sce)
 
   # grab names of altExp, if any

tests/testthat/.gitignore

@@ -0,0 +1,3 @@
+_snaps/
+test_anndata.h5
+

tests/testthat/test-sce_to_seurat.R

@@ -20,6 +20,8 @@ rowData(altExp(sce, alt_name)) <- data.frame("alt_test_row" = sample(0:5, 10, re
   tibble::column_to_rownames("alt_id") %>%
   DataFrame()
 
+logcounts(sce) <- counts(sce) # dummy logcounts to test the assay_name argument
+
 test_that("Converting SCE to Seurat objects works as expected", {
 
   seurat_object <- sce_to_seurat(sce)
@@ -34,7 +36,32 @@ test_that("Converting SCE to Seurat objects works as expected", {
 
   # can't directly check that coldata is equal because of added columns in seurat object
   expect_true(all(colnames(coldata_sce) %in% colnames(seurat_object@meta.data)))
-  expect_equal(rowdata_sce, seurat_object[["RNA"]]@var.features)
+  expect_equal(rowdata_sce, seurat_object[["RNA"]]@var.features) # since default "counts" is used, RNA name is expected here
+  expect_equal(metadata(sce), seurat_object@misc)
+
+  # check that altExp data was converted and rowData
+  expect_s4_class(seurat_object[[alt_name]], 'Assay')
+  alt_rowdata_sce <- as.data.frame(rowData(altExp(sce, alt_name)))
+  expect_equal(alt_rowdata_sce, seurat_object[[alt_name]]@var.features)
+
+})
+
+
+test_that("Converting SCE to Seurat objects works as expected for custom assay name", {
+
+  seurat_object <- sce_to_seurat(sce, assay_name = "logcounts")
+
+  # check that column names of Seurat object are derived from SCE object
+  # they won't necessarily be equal if some cells with 0 counts were removed
+  expect_true(all(colnames(seurat_object) %in% colnames(sce)))
+
+  # check that attached metadata/coldata/rowdata in SCE are present in seurat object
+  coldata_sce <- as.data.frame(colData(sce))
+  rowdata_sce <- as.data.frame(rowData(sce))
+
+  # can't directly check that coldata is equal because of added columns in seurat object
+  expect_true(all(colnames(coldata_sce) %in% colnames(seurat_object@meta.data)))
+  expect_equal(rowdata_sce, seurat_object[["logcounts"]]@var.features) # since default "counts" is used, RNA name is expected here
   expect_equal(metadata(sce), seurat_object@misc)
 
   # check that altExp data was converted and rowData