tests/testthat/test-plotCounts.R

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

test_that("default", {
    x <- plotCounts(
        object = object,
        genes = genes,
        line = "median"
    )
    expect_s3_class(x, "ggplot")
    expect_identical(
        object = x[["labels"]],
        expected = list(
            x = NULL,
            y = "counts",
            colour = "condition",
            fill = "condition",
            title = NULL,
            subtitle = NULL
        )
    )
    expect_s3_class(
        object = x[["layers"]][[1L]][["geom"]],
        class = "GeomPoint"
    )
    expect_s3_class(
        object = x[["layers"]][[2L]][["geom"]],
        class = "GeomCrossbar"
    )
})

test_that("Gene IDs or names", {
    for (genes in list(geneIds, geneNames)) {
        x <- plotCounts(object = object, genes = genes)
        expect_s3_class(x, "ggplot")
    }
})

trans <- eval(formals(`plotCounts,SE`)[["trans"]])
test_that("trans", {
    Map(
        trans = trans,
        ylab = c(
            identity = "counts",
            log2 = "log2 counts",
            log10 = "log10 counts"
        ),
        f = function(trans, ylab) {
            x <- plotCounts(object, genes = genes, trans = trans)
            expect_s3_class(x, "ggplot")
            expect_identical(
                object = x[["labels"]][["y"]],
                expected = ylab
            )
        }
    )
})

style <- eval(formals(`plotCounts,SE`)[["style"]])
test_that("style", {
    Map(
        style = style,
        facetClass = c(
            facet = "FacetWrap",
            wide = "FacetNull"
        ),
        f = function(style, facetClass) {
            x <- plotCounts(object, genes = genes, style = style)
            expect_s3_class(x, "ggplot")
            expect_s3_class(x[["facet"]], facetClass)
        }
    )
})



test_that("'geom' support", {
    data(
        SingleCellExperiment_Seurat,
        package = "AcidTest",
        envir = environment()
    )
    object <- SingleCellExperiment_Seurat
    genes <- head(rownames(object))
    ## Dots.
    p <- plotCounts(
        object = object,
        genes = genes,
        geom = "dots"
    )
    expect_s3_class(p, "ggplot")
    p <- plotDots(object, genes = genes)
    expect_s3_class(p, "ggplot")
    ## Violin.
    p <- plotCounts(
        object = object,
        genes = genes,
        geom = "violin"
    )
    expect_s3_class(p, "ggplot")
    p <- plotViolin(object, genes = genes)
    expect_s3_class(p, "ggplot")
})