tests/testthat/test-utils.R

In ncborcherding/escape: Easy single cell analysis platform for enrichment

# test script for utils.R - testcases are NOT comprehensive!

test_that(".orderFunction works", {
  
  enrichment <- as.data.frame(getdata("runEscape", "escape.matrix_ssGSEA"))
  enrichment$grouping <- c(rep("g2", 40), rep("g1", 40))
  enrichment <- enrichment[,c(1,3)]
  
  enrichment.order1 <- .orderFunction(enrichment, order.by = "mean", group.by = "grouping")
  
  enrichment.order2 <- .orderFunction(enrichment, order.by = "group.by", group.by = "grouping")
  
  expect_equal(enrichment.order1, 
               getdata("utils", "orderFunction_mean"))
  
  expect_equal(enrichment.order2, 
               getdata("utils", "orderFunction_group"))
})

test_that(".cntEval works", {
  seuratObj <- getdata("runEscape", "pbmc_small_ssGSEA")
  seurat.rna <- .cntEval(seuratObj)
  
  expect_equal(seurat.rna,
               seuratObj@assays$RNA@counts)
  
  sce <- Seurat::as.SingleCellExperiment(seuratObj)
  sce.rna <- .cntEval(sce)
  
  expect_equal(sce.rna,
               sce@assays@data$counts)
})


test_that(".makeDFfromSCO works", {
  seuratObj <- getdata("runEscape", "pbmc_small_ssGSEA")
  
  enriched <- .makeDFfromSCO(seuratObj, 
                             assay = "escape", 
                             group.by = NULL,
                             split.by = "groups",
                             gene.set = "Tcells")
  
  expect_equal(enriched,
               getdata("utils", "makeDFfromSCO_data.frame"))
})


test_that(".grabMeta works", {
  seuratObj <- getdata("runEscape", "pbmc_small_ssGSEA")
  seurat.meta<- .grabMeta(seuratObj)
  
  expect_equal(seurat.meta,
               cbind.data.frame(seuratObj@meta.data, ident = seuratObj@active.ident), 
               tolerance = 1e-3)
  
  sce <- Seurat::as.SingleCellExperiment(seuratObj)
  sce.meta <- .grabMeta(sce)
  
  expect_equal(sce.meta,
               as.data.frame(SummarizedExperiment::colData(sce)))
})