tests/testthat/test-cellTypeLabeling.R

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

# SingleR
library(singleCellTK)
context("Testing Cell Type Labeling functions")
data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = 'type != "EmptyDroplet"')
sce <- scaterlogNormCounts(sce, "logcounts")
rownames(sce) <- rowData(sce)$feature_name

test_that(desc = "Testing SingleR", {
  tryCatch({
    ref <- celldex::HumanPrimaryCellAtlasData()
  }, error = function(e) {
    message("Error importing reference with `celldex` library. ",
            "Skipping runSingleR test.")
  }, finally = {
    sce <- runSingleR(sce, level = "main")
    testthat::expect_true("SingleR_hpca_main_scores" %in% names(colData(sce)))
    testthat::expect_true("SingleR_hpca_main_labels" %in% names(colData(sce)))
    testthat::expect_true("SingleR_hpca_main_first.labels" %in% names(colData(sce)) | "SingleR_hpca_main_delta.next" %in% names(colData(sce)))
    testthat::expect_true("SingleR_hpca_main_pruned.labels" %in% names(colData(sce)))
  })
})