fix v5 import

R/seurat_to_sce.R

@@ -5,8 +5,13 @@ seurat_to_sce <- function(sdata, dataset_name) {
   Seurat::DefaultAssay(sdata) <- 'RNA'
 
   # join layers if v5
-  if (methods::is(sdata[['RNA']], 'Assay5')) {
+  # use meta.features (v3) or meta.data (v5)
+  meta_name <- 'meta.features'
+  is.v5 <- methods::is(sdata[['RNA']], 'Assay5')
+
+  if (is.v5) {
     sdata[['RNA']] <- SeuratObject::JoinLayers(sdata[['RNA']])
+    meta_name <- 'meta.data'
   }
 
   # normalize if need to
@@ -20,7 +25,7 @@ seurat_to_sce <- function(sdata, dataset_name) {
   # meta.features need to have same row.names as assay
   for (assay_name in Seurat::Assays(sdata)) {
     assay <- sdata[[assay_name]]
-    assay@meta.features <- assay@meta.features[row.names(assay), ]
+    slot(assay, meta_name) <- slot(assay, meta_name)[row.names(assay), ]
     sdata[[assay_name]] <- assay
   }
 
@@ -51,14 +56,14 @@ seurat_to_sce <- function(sdata, dataset_name) {
   sce$cluster <- unname(Seurat::Idents(sdata))
 
   # default HVGs unless integrated assay
-  hvgs <- sdata[['RNA']]@var.features
+  hvgs <- SeuratObject::VariableFeatures(sdata, assay = 'RNA')
 
   is.integrated <- have.samples | have.integrated
   if (is.integrated) {
 
     # get HVGs and transfer reductions from integrated assay if present
     if (have.integrated) {
-      hvgs <- sdata[['integrated']]@var.features
+      hvgs <- SeuratObject::VariableFeatures(sdata, assay = 'integrated')
       SingleCellExperiment::reducedDims(sce) <-
         SingleCellExperiment::reducedDims(SingleCellExperiment::altExp(sce, 'integrated'))
     }

tests/testthat/test_import_scseq.R

@@ -89,13 +89,6 @@ test_that("cellranger .h5 files with multiple assays can be imported", {
     tx2gene_dir <- file.path(tempdir(), 'tx2gene')
     dir.create(tx2gene_dir)
 
-    mock_uploaded_data(dataset_name,
-                       sc_dir,
-                       uploaded_data_dir,
-                       type = 'h5',
-                       version = '3',
-                       gene.type = c(rep('Gene Expression', 199), 'Antibody Capture'))
-
     expect_error(
         suppressWarnings(import_scseq(dataset_name, uploaded_data_dir, sc_dir, tx2gene_dir)),
         NA
@@ -104,3 +97,133 @@ test_that("cellranger .h5 files with multiple assays can be imported", {
     # cleanup
     unlink(c(sc_dir, uploaded_data_dir, tx2gene_dir), recursive = TRUE)
 })
+
+
+test_that("Seurat files with RNA Assay5 can be imported", {
+  # setup
+  dataset_name <- 'test'
+  sc_dir <- file.path(tempdir(), 'single-cell')
+  dir.create(sc_dir)
+  uploaded_data_dir <- file.path(tempdir(), 'uploads')
+  dir.create(uploaded_data_dir)
+
+  tx2gene_dir <- file.path(tempdir(), 'tx2gene')
+  dir.create(tx2gene_dir)
+
+  # create Seurat object
+  pbmc_raw <- read.table(
+    file = system.file("extdata", "pbmc_raw.txt", package = "Seurat"),
+    as.is = TRUE
+  )
+
+  # can upload non-split Assay5
+  pbmc_raw <- as(as.matrix(pbmc_raw), 'dgCMatrix')
+  scdata <- Seurat::CreateSeuratObject(counts = pbmc_raw)
+  expect_true(methods::is(scdata[['RNA']], 'Assay5'))
+
+
+  qs::qsave(scdata, file.path(uploaded_data_dir, 'scdata.qs'))
+
+  expect_error(
+    suppressWarnings(import_scseq(
+      dataset_name,
+      species = 'Homo sapiens',
+      uploaded_data_dir,
+      sc_dir,
+      tx2gene_dir,
+      metrics = NULL)),
+    NA
+  )
+
+  # cleanup
+  unlink(c(sc_dir, uploaded_data_dir, tx2gene_dir), recursive = TRUE)
+})
+
+test_that("Seurat files with split RNA Assay5 can be imported", {
+  # setup
+  dataset_name <- 'test'
+  sc_dir <- file.path(tempdir(), 'single-cell')
+  dir.create(sc_dir)
+  uploaded_data_dir <- file.path(tempdir(), 'uploads')
+  dir.create(uploaded_data_dir)
+
+  tx2gene_dir <- file.path(tempdir(), 'tx2gene')
+  dir.create(tx2gene_dir)
+
+  # create Seurat object
+  pbmc_raw <- read.table(
+    file = system.file("extdata", "pbmc_raw.txt", package = "Seurat"),
+    as.is = TRUE
+  )
+
+  # can upload non-split Assay5
+  pbmc_raw <- as(as.matrix(pbmc_raw), 'dgCMatrix')
+  scdata <- Seurat::CreateSeuratObject(counts = pbmc_raw)
+  expect_true(methods::is(scdata[['RNA']], 'Assay5'))
+
+  scdata$batch <- c('a', 'b', 'c')
+  scdata[["RNA"]] <- split(scdata[["RNA"]], f = scdata$batch)
+
+  expect_equal(SeuratObject::Layers(scdata), c("counts.a", "counts.b", "counts.c"))
+
+
+  qs::qsave(scdata, file.path(uploaded_data_dir, 'scdata.qs'))
+
+  expect_error(
+    suppressWarnings(import_scseq(
+      dataset_name,
+      species = 'Homo sapiens',
+      uploaded_data_dir,
+      sc_dir,
+      tx2gene_dir,
+      metrics = NULL)),
+    NA
+  )
+
+  # cleanup
+  unlink(c(sc_dir, uploaded_data_dir, tx2gene_dir), recursive = TRUE)
+})
+
+
+test_that("Seurat object with RNA Assay v3 can be imported", {
+
+  options(Seurat.object.assay.version = "v3")
+  # setup
+  dataset_name <- 'test'
+  sc_dir <- file.path(tempdir(), 'single-cell')
+  dir.create(sc_dir)
+  uploaded_data_dir <- file.path(tempdir(), 'uploads')
+  dir.create(uploaded_data_dir)
+
+  tx2gene_dir <- file.path(tempdir(), 'tx2gene')
+  dir.create(tx2gene_dir)
+
+  # create Seurat object
+  pbmc_raw <- read.table(
+    file = system.file("extdata", "pbmc_raw.txt", package = "Seurat"),
+    as.is = TRUE
+  )
+
+  # can upload Assay
+  pbmc_raw <- as(as.matrix(pbmc_raw), 'dgCMatrix')
+  scdata <- Seurat::CreateSeuratObject(counts = pbmc_raw)
+  expect_true(methods::is(scdata[['RNA']], 'Assay'))
+
+
+  qs::qsave(scdata, file.path(uploaded_data_dir, 'scdata.qs'))
+
+  expect_error(
+    suppressWarnings(import_scseq(
+      dataset_name,
+      species = 'Homo sapiens',
+      uploaded_data_dir,
+      sc_dir,
+      tx2gene_dir,
+      metrics = NULL)),
+    NA
+  )
+
+  # cleanup
+  options(Seurat.object.assay.version = "v5")
+  unlink(c(sc_dir, uploaded_data_dir, tx2gene_dir), recursive = TRUE)
+})