Add Seurat v5 checks

AlexsLemonade · Dec 9, 2024 · 80f0703 · 80f0703
1 parent 36296d9
commit 80f0703
Showing 1 changed file with 80 additions and 12 deletions.
diff --git a/tests/testthat/test-make-seurat.R b/tests/testthat/test-make-seurat.R
@@ -1,6 +1,7 @@
 test_that("SCE to Seurat with no id conversion works", {
   sce <- readRDS(test_path("data", "scpca_sce.rds"))
   seurat_obj <- sce_to_seurat(sce, use_symbols = FALSE)
+  expect_s4_class(seurat_obj, "Seurat")
 
   expect_equal(dim(seurat_obj), dim(sce))
   expect_setequal(rownames(seurat_obj), rownames(sce))
@@ -9,7 +10,11 @@ test_that("SCE to Seurat with no id conversion works", {
   expect_equal(names(seurat_obj@assays), c("RNA", "spliced"))
   expect_equal(Seurat::DefaultAssay(seurat_obj), "RNA")
 
-  # array contents
+  # assay types
+  expect_s4_class(seurat_obj[["RNA"]], "Assay")
+  expect_s4_class(seurat_obj[["spliced"]], "Assay")
+
+  # assay contents
   expect_contains(
     slotNames(seurat_obj[["RNA"]]),
     c("counts", "data", "scale.data", "var.features", "meta.features")
@@ -18,9 +23,10 @@ test_that("SCE to Seurat with no id conversion works", {
   expect_equal(seurat_obj[["RNA"]]$counts, counts(sce))
   expect_equal(seurat_obj[["RNA"]]$data, logcounts(sce))
 
-  expect_setequal(
-    seurat_obj[["RNA"]]@var.features,
-    metadata(sce)$highly_variable_genes
+  expect_equal(
+    Seurat::VariableFeatures(seurat_obj[["RNA"]]),
+    metadata(sce)$highly_variable_genes,
+    ignore_attr = TRUE
   )
 
   expect_equal(names(seurat_obj@reductions), c("pca", "umap"))
@@ -40,6 +46,7 @@ test_that("SCE to Seurat with id conversion works as expected", {
   expect_warning(
     seurat_obj <- sce_to_seurat(sce, use_symbols = TRUE, reference = "sce")
   )
+  expect_s4_class(seurat_obj, "Seurat")
 
   new_genes <- suppressMessages(
     ensembl_to_symbol(rownames(sce), unique = TRUE, sce = sce)
@@ -58,15 +65,20 @@ test_that("SCE to Seurat with id conversion works as expected", {
   expect_equal(names(seurat_obj@assays), c("RNA", "spliced"))
   expect_equal(Seurat::DefaultAssay(seurat_obj), "RNA")
 
-  # array contents
+  # assay types
+  expect_s4_class(seurat_obj[["RNA"]], "Assay")
+  expect_s4_class(seurat_obj[["spliced"]], "Assay")
+
+  # assay contents
   expect_contains(
     slotNames(seurat_obj[["RNA"]]),
     c("counts", "data", "scale.data", "var.features", "meta.features")
   )
 
-  expect_setequal(
-    seurat_obj[["RNA"]]@var.features,
-    hv_genes
+  expect_equal(
+    Seurat::VariableFeatures(seurat_obj[["RNA"]]),
+    hv_genes,
+    ignore_attr = TRUE
   )
   expect_equal(names(seurat_obj@reductions), c("pca", "umap"))
   expect_equal(names(seurat_obj@reductions), c("pca", "umap"))
@@ -83,6 +95,7 @@ test_that("SCE to Seurat with id conversion works as expected", {
 test_that("SCE to Seurat with id conversion and 10x reference works as expected", {
   sce <- readRDS(test_path("data", "scpca_sce.rds"))
   seurat_obj <- sce_to_seurat(sce, use_symbols = TRUE, reference = "10x2020")
+  expect_s4_class(seurat_obj, "Seurat")
 
   new_genes <- suppressMessages(
     ensembl_to_symbol(rownames(sce), unique = TRUE, reference = "10x2020")
@@ -101,15 +114,21 @@ test_that("SCE to Seurat with id conversion and 10x reference works as expected"
   expect_equal(names(seurat_obj@assays), c("RNA", "spliced"))
   expect_equal(Seurat::DefaultAssay(seurat_obj), "RNA")
 
-  # array contents
+
+  # assay types
+  expect_s4_class(seurat_obj[["RNA"]], "Assay")
+  expect_s4_class(seurat_obj[["spliced"]], "Assay")
+
+  # assay contents
   expect_contains(
     slotNames(seurat_obj[["RNA"]]),
     c("counts", "data", "scale.data", "var.features", "meta.features")
   )
 
-  expect_setequal(
-    seurat_obj[["RNA"]]@var.features,
-    hv_genes
+  expect_equal(
+    Seurat::VariableFeatures(seurat_obj[["RNA"]]),
+    hv_genes,
+    ignore_attr = TRUE
   )
   expect_equal(names(seurat_obj@reductions), c("pca", "umap"))
   expect_equal(names(seurat_obj@reductions), c("pca", "umap"))
@@ -132,11 +151,60 @@ test_that("conversion works with altExps", {
   )
 
   seurat_obj <- sce_to_seurat(sce, use_symbols = FALSE)
+  expect_s4_class(seurat_obj, "Seurat")
 
   expect_equal(dim(seurat_obj), dim(sce))
   expect_setequal(rownames(seurat_obj), rownames(sce))
   expect_setequal(colnames(seurat_obj), colnames(sce))
 
   expect_setequal(names(seurat_obj@assays), c("RNA", "spliced", "alt1", "alt2"))
   expect_equal(Seurat::DefaultAssay(seurat_obj), "RNA")
+
+  # assay types
+  expect_s4_class(seurat_obj[["RNA"]], "Assay")
+  expect_s4_class(seurat_obj[["spliced"]], "Assay")
+  expect_s4_class(seurat_obj[["alt1"]], "Assay")
+  expect_s4_class(seurat_obj[["alt2"]], "Assay")
+})
+
+test_that("Seurat v5 conversion works", {
+  sce <- readRDS(test_path("data", "scpca_sce.rds"))
+  seurat_obj <- sce_to_seurat(sce, use_symbols = FALSE, seurat_assay_version = "v5")
+  expect_s4_class(seurat_obj, "Seurat")
+
+  expect_equal(dim(seurat_obj), dim(sce))
+  expect_setequal(rownames(seurat_obj), rownames(sce))
+  expect_setequal(colnames(seurat_obj), colnames(sce))
+
+  expect_equal(names(seurat_obj@assays), c("RNA", "spliced"))
+  expect_equal(Seurat::DefaultAssay(seurat_obj), "RNA")
+
+  # assay types
+  expect_s4_class(seurat_obj[["RNA"]], "Assay5")
+  expect_s4_class(seurat_obj[["spliced"]], "Assay5")
+
+  # expected layers present
+  expect_contains(
+    names(seurat_obj[["RNA"]]@layers),
+    c("counts", "data", "scale.data")
+  )
+
+  expect_equal(seurat_obj[["RNA"]]$counts, counts(sce))
+  expect_equal(seurat_obj[["RNA"]]$data, logcounts(sce))
+
+  expect_equal(
+    Seurat::VariableFeatures(seurat_obj[["RNA"]]),
+    metadata(sce)$highly_variable_genes,
+    ignore_attr = TRUE
+  )
+
+  expect_equal(names(seurat_obj@reductions), c("pca", "umap"))
+  expect_equal(
+    dim(seurat_obj[["pca"]]),
+    dim(reducedDim(sce, "PCA"))
+  )
+  expect_equal(
+    dim(seurat_obj[["umap"]]),
+    dim(reducedDim(sce, "UMAP"))
+  )
 })