tests/testthat/test-SCE-functions.R

In Oshlack/splatter: Simple Simulation of Single-cell RNA Sequencing Data

context("SCE functions")

sce <- simpleSimulate()

test_that("addFeatureStats works with counts", {
    ss <- addFeatureStats(sce)
    expect_true(all(c(
        "MeanCounts", "VarCounts", "CVCounts", "MedCounts",
        "MADCounts"
    ) %in% colnames(rowData(ss))))
    ss <- addFeatureStats(sce, log = TRUE)
    expect_true(all(c(
        "MeanLogCounts", "VarLogCounts", "CVLogCounts",
        "MedLogCounts", "MADLogCounts"
    ) %in%
        colnames(rowData(ss))))
    ss <- addFeatureStats(sce, no.zeros = TRUE)
    expect_true(all(c(
        "MeanCountsNo0", "VarCountsNo0", "CVCountsNo0",
        "MedCountsNo0", "MADCountsNo0"
    ) %in%
        colnames(rowData(ss))))
    ss <- addFeatureStats(sce, log = TRUE, no.zeros = TRUE)
    expect_true(all(c(
        "MeanLogCountsNo0", "VarLogCountsNo0", "CVLogCountsNo0",
        "MedLogCountsNo0", "MADLogCountsNo0"
    ) %in%
        colnames(rowData(ss))))
})

test_that("addGeneLengths generate method works", {
    expect_silent(addGeneLengths(sce))
    expect_error(addGeneLengths("a"))
    expect_error(addGeneLengths(sce, loc = "a"))
    expect_error(addGeneLengths(sce, scale = "a"))
    expect_error(addGeneLengths(sce, scale = -1))
})

test_that("addGeneLength sample method works", {
    lens <- round(runif(100, 100, 10000))
    expect_silent(addGeneLengths(sce, method = "sample", lengths = lens))
    expect_error(addGeneLengths(sce, method = "sample"))
    expect_error(addGeneLengths(sce, method = "sample"), lengths = 0)
    expect_error(addGeneLengths(sce, method = "sample"), lengths = "a")
})

test_that("minimiseSCE works", {
    min_sce <- minimiseSCE(sce)
    expect_s4_class(min_sce, "SingleCellExperiment")
})

test_that("minimiseSCE keep arguments work", {
    min_sce <- minimiseSCE(sce, rowData.keep = "Gene", verbose = FALSE)
    expect_true("Gene" %in% colnames(rowData(min_sce)))
    min_sce <- minimiseSCE(sce, colData.keep = "Cell", verbose = FALSE)
    expect_true("Cell" %in% colnames(colData(min_sce)))
    min_sce <- minimiseSCE(sce, metadata.keep = "Params", verbose = FALSE)
    expect_true("Params" %in% names(metadata(min_sce)))
    min_sce <- minimiseSCE(sce, assays.keep = FALSE, verbose = FALSE)
    expect_true(length(assays(min_sce)) == 0)
})