tests/testthat/test_plotAssays.R

In steveped/extraChIPs: Additional functions for working with ChIP-Seq data

nrows <- 200
ncols <- 4
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
df <- DataFrame(treat = c("A", "A", "B", "B"))
se <- SummarizedExperiment(
  assays = SimpleList(counts = counts),
  colData = df
)
se$totals <- colSums(counts)

test_that("Assay Density plots behave correctly", {

  expect_error(plotAssayDensities(se, colour = "col"))
  p <- plotAssayDensities(se)
  expect_equal(dim(p$data), c(512*4, 3))
  expect_equal(colnames(p$data), c("colnames", "x", "y"))
  expect_equal(
    unlist(lapply(p$labels, as.character)),
    c(x = "counts", y = "Density", group = "colnames")
  )
  p <- plotAssayDensities(se, colour = "treat", linetype = "treat")
  expect_equal(
    unlist(lapply(p$labels, as.character)),
    c(
      x = "counts", y = "Density", colour = "treat", linetype = "treat",
      group = "colnames"
    )
  )
  p <- plotAssayPCA(se, n_max = 10)
  expect_true(is(p, "gg"))

})

test_that("Assay Density transformations error", {
  expect_error(plotAssayDensities(se, trans = ""))
  p <- plotAssayDensities(se, trans = "log2")
  expect_true(median(p$data$x) < log2(1e4))
  expect_equal(p$labels$x, "log2 counts")
  expect_error(plotAssayDensities(se, trans = "max"), "This transformation")
})


test_that("Assay PCA plots error correctly", {
  expect_error(plotAssayPCA(se, colour = "col"))
  expect_error(plotAssayPCA(se, shape = "col"))
  expect_error(plotAssayPCA(se, label = "col"))
})

test_that("show_points behaves as expected", {
  p <- plotAssayPCA(se)
  expect_equal(length(p$layers), 1)
  expect_true(is(p$layers[[1]]$geom, "GeomPoint"))
  expect_null(p$mapping$colour)
  p <- plotAssayPCA(se, show_points = FALSE)
  expect_equal(length(p$layers), 0)
})

test_that("colours/size are added correctly", {
  p <- plotAssayPCA(se, colour = "treat", size = "totals")
  expect_equal(rlang::as_label(p$mapping$colour), "treat")
  expect_equal(
    grepl("PC", unlist(p$labels))[1:4], c(TRUE, TRUE, FALSE, FALSE)
  )
  expect_equal(p$labels$colour, "treat")
  expect_equal(p$labels$size, "totals")
})

test_that("labels repel correctly", {
  p <- plotAssayPCA(se, label = "treat")
  expect_equal(length(p$layers), 2)
  expect_s3_class(p$layers[[2]]$geom, "GeomTextRepel")
  p <- plotAssayPCA(se, label = "treat", show_points = FALSE)
  expect_equal(length(p$layers), 1)
  expect_s3_class(p$layers[[1]]$geom, "GeomText")
})

test_that("data is transformed correctly", {
    expect_error(plotAssayPCA(se, trans = ""))
    expect_error(plotAssayPCA(se, trans = "max"), "This transformation is not")
    expect_true(is(plotAssayPCA(se, trans = "log2"), "gg"))
})

test_that("plotAssayRle errors correctly", {
  err <- "'arg' should be one of .+"
  expect_error(plotAssayRle(se, "counts", colour = "a"), err)
  expect_error(plotAssayRle(se, "counts", fill = "a"), err)
  expect_error(plotAssayRle(se, "counts", rle_group = "a"), err)
  expect_error(plotAssayRle(se, "counts", by_x = "a"), err)
  expect_error(
    plotAssayRle(se, "counts", trans = "a"),
    "object 'a' of mode 'function' was not found"
  )
  expect_error(
    plotAssayRle(se, "counts", trans = "mean"),
    "This transformation is not applicable"
  )

})

test_that("plotAssayRle creates a plot", {
  p <- plotAssayRle(se, "counts", fill = "treat", n_max = 100)
  expect_true(is(p, "gg"))
  expect_equal(dim(p$data), c(100*ncols, 5))
  expect_equal(
    unlist(p$labels),
    c(x = "Sample", y = "RLE (counts)", fill = "treat", colour = "colour")
  )
  p <- plotAssayRle(se, "counts", by_x = "treat")
  expect_equal(unlist(p$labels)[["x"]], "treat")
})

test_that("plotAssayHeatmap creates a plot", {

    p <- plotAssayHeatmap(se[1:10,], trans = "log10")
    expect_equal(c("index", "colnames", "value", "treat", "totals"), colnames(p$data))
    expect_equal(dim(p$data), c(40, 5))
    rowRanges(se) <- GRanges(paste0("chr:", seq_len(nrow(se))))
    p <- plotAssayHeatmap(se[1:10,], trans = "log10")
    expect_equal(c("range", "colnames", "value", "treat", "totals"), colnames(p$data))
    expect_true(is(p, "gg"))
    p <- plotAssayHeatmap(se[1:10,], trans = "log10", ysideline = TRUE)
    expect_true(is(p, "ggside"))
    expect_error(
        plotAssayHeatmap(se, n_max = 1),
        "Only 1 ranges can be drawn. Please change the n_max parameter if you wish to draw more."
    )

})