tests/testthat/test-sce_to_seurat.R

In AlexsLemonade/scpcaTools: Single cell data tools for ScPCA

set.seed(1665)
sce <- sim_sce(n_cells = 100, n_genes = 200, n_empty = 0)
colData(sce) <- data.frame(
  "test_column" = sample(0:10, 100, rep = TRUE),
  "barcodes" = colnames(sce)
) |>
  tibble::column_to_rownames("barcodes") |>
  DataFrame()
rowData(sce) <- data.frame(
  "test_row" = sample(0:10, 200, rep = TRUE),
  "gene_id" = rownames(sce)
) |>
  tibble::column_to_rownames("gene_id") |>
  DataFrame()
metadata(sce)$test <- "test"
alt_sce <- sim_sce(n_cells = 100, n_genes = 10, n_empty = 0)
# rename the alt_exp so it has the same column names as the base sce
colnames(alt_sce) <- colnames(sce)
# merge alt into main
alt_name <- "alt"
sce <- merge_altexp(sce, alt_sce, alt_name)
rowData(altExp(sce, alt_name)) <- data.frame(
  "alt_test_row" = sample(0:5, 10, rep = TRUE),
  "alt_id" = rownames(altExp(sce, alt_name))
) |>
  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)

  # 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)))
  expect_true("RNA" %in% names(seurat_object@assays))

  # 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[["RNA"]][[]]) # 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]][[]])
})


test_that("Converting SCE to Seurat objects works as expected for a non-default assay of 'logcounts'", {
  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)))
  expect_true("logcounts" %in% names(seurat_object@assays))

  # 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"]][[]])
  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]][[]])
})