tests/testthat/test-BarPlot.R

In dtm2451/DittoSeq: User Friendly Single-Cell and Bulk RNA Sequencing Visualization

# Tests for dittoBarPlot function
# library(dittoSeq); library(testthat); source("setup.R"); source("test-BarPlot.R")

sce$number <- as.numeric(seq_along(colnames(sce)))
grp1 <- "groups"
grp2 <- "clusters"
grp3 <- "age"
cells.names <- colnames(sce)[1:40]
cells.logical <- c(rep(TRUE, 40), rep(FALSE,ncells-40))

test_that("dittoBarPlot can quantify clustering of groupings in percent or raw count", {
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3, scale = "count"),
        "ggplot")
})

test_that("dittoBarPlot works for bulk", {
    # bulk SCE
    expect_s3_class(
        dittoBarPlot(
            bulk, grp2, group.by = grp3),
        "ggplot")
})

test_that("dittoBarPlots can be subset to show only certain cells/samples with any cells.use method", {
    expect_s3_class(
        {c1 <- dittoBarPlot(
            sce, grp2, group.by = grp3,  data.out = TRUE,
            cells.use = cells.names)
        c1$p},
        "ggplot")
    expect_s3_class(
        {c2 <- dittoBarPlot(
            sce, grp2, group.by = grp3, data.out = TRUE,
            cells.use = cells.logical)
        c2$p},
        "ggplot")
    expect_equal(c1$data, c2$data)
    expect_s3_class(
        {c3 <- dittoBarPlot(
            sce, grp2, group.by = grp3, data.out = TRUE,
            cells.use = 1:40)
        c3$p},
        "ggplot")
    expect_equal(c1$data, c3$data)
    # And if we remove an entire X grouping...
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            cells.use = meta(grp3,sce)!=0),
        "ggplot")
    # And if we remove an entire var grouping...
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            cells.use = meta(grp2,sce)!=0),
        "ggplot")
})

test_that("dittoBarPlot main legend can be removed", {
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            legend.show = FALSE),
        "ggplot")
})

test_that("dittoBarPlots colors can be adjusted", {
    ### Manual check: These two should look the same.
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            color.panel = dittoColors()[5:1]),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            colors = 5:1),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            color.panel = c("red","blue","yellow")),
        "ggplot")
})

test_that("dittoBarPlots titles and theme can be adjusted", {
    ### Manual check: All titles should be adjusted.
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            main = "Gotta catch", sub = "em all",
            xlab = "Pokemon", ylab = "Pokedex #s",
            legend.title = "groups"),
        "ggplot")
    ### Manual check: plot should be boxed
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            theme = theme_bw()),
        "ggplot")
})

test_that("dittoBarPlots y-axis can be adjusted", {
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            y.breaks = seq(0,1,0.25)),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            min = -0.5, max = 2,
            y.breaks = seq(0,1,0.25)),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            scale = "count",
            y.breaks = seq(0,45,15)),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            scale = "count",
            min = -5, max = 55,
            y.breaks = seq(0,45,15)),
        "ggplot")
})

test_that("dittoBarPlot var-labels can be adjusted and reordered", {
    # Manual Check: groups changed to pikachu and libre.
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            var.labels.rename = c("pikachu", "squirtle", "ivysaur", "charizard")),
        "ggplot")
    # Manual Check: 1 on top of zero, with colors reversed too (orange still on top).
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            var.labels.reorder = 4:1),
        "ggplot")
})

test_that("dittoBarPlots x-labels can be adjusted", {
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            x.labels = 4:7),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            x.reorder = 4:1),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            x.labels.rotate = FALSE),
        "ggplot")
    ### Manual Check: L->R 4:7, with horizontal labels
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            scale = "count",
            x.labels = 4:7, x.reorder = 4:1, x.labels.rotate = FALSE),
        "ggplot")
    ### Manual Check: L->R 4:7, but order reversed compared to above
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            scale = "count",
            x.labels = 4:7, x.labels.rotate = FALSE),
        "ggplot")
})

test_that("dittoBarPlot can be faceted with 'split.by'", {
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            split.by = grp1),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            split.by = c(grp1,grp3)),
        "ggplot")
    
    # Work with cells.use
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            split.by = grp1,
            cells.use = sce$number<50),
        "ggplot")
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            split.by = c(grp1,grp3),
            cells.use = sce$number<50),
        "ggplot")
})

test_that("'split.by' can be given extra features", {
    # MANUAL: white space utilized fully
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3, scale = "count", split.ncol = 1,
            cells.use = meta(grp3,sce)==1,
            split.by = grp1,
            split.adjust = list(scales = "free"), max = NA
            ),
        "ggplot")
    # MANUAL: white space utilized fully
    expect_s3_class(
        dittoBarPlot(
            sce, grp2, group.by = grp3,
            split.by = c(grp1,grp3),
            split.adjust = list(scales = "free")),
        "ggplot")
})

test_that("dittoBarPlot, 'retain.factor.level' can be used to respect factor levels", {
    sce$var_factor <- factor(
        meta(grp2, sce),
        levels = rev(metaLevels(grp2, sce)))
    sce$grp_factor <- factor(
        meta(grp3, sce),
        levels = rev(metaLevels(grp3, sce)))
    
    # MANUAL: var and group.by ordering should be reverse of alpha-numeric
    #  & group.by-1 should remain.
    expect_s3_class(
        dittoBarPlot(
            sce, "var_factor", group.by = "grp_factor",
            retain.factor.levels = TRUE,
            cells.use = meta("grp_factor",sce)!=1),
        "ggplot")
})