tests/testthat/test-VolcanoPlot.R

In iSEEu: iSEE Universe

# Tests the various bits and pieces of the VolcanoPlot.
# library(testthat); library(iSEEu); source("test-VolcanoPlot.R")

se <- SummarizedExperiment(list(counts=matrix(0, 10, 4)),
    rowData=DataFrame(PValue=runif(10), LogFC=rnorm(10), AveExpr=rnorm(10)))
dimnames(se) <- list(1:nrow(se), letters[seq_len(ncol(se))])

test_that("VolcanoPlot constructor works", {
    expect_s4_class(VolcanoPlot(), "VolcanoPlot")

    expect_error(VolcanoPlot(LogFCThreshold=numeric(0)), "should be a numeric scalar")

    expect_error(VolcanoPlot(PValueThreshold=numeric(0)), "should be a numeric scalar")

    expect_error(VolcanoPlot(PValueCorrection='stuff'), "should be one of")
})

test_that("VolcanoPlot refinement works correctly", {
    x <- VolcanoPlot()
    expect_identical(x[["XAxis"]], "None")
    expect_identical(x[["XAxisRowData"]], NA_character_)
    expect_identical(x[["YAxis"]], NA_character_)

    se2 <- .cacheCommonInfo(x, se)
    y <- .refineParameters(x, se2)
    expect_identical(y[["XAxis"]], "Row data")
    expect_identical(y[["XAxisRowData"]], "LogFC")
    expect_identical(y[["YAxis"]], "PValue")

    se3 <- se
    rowData(se3)$PValue <- NULL
    se3 <- .cacheCommonInfo(x, se3)
    expect_warning(out <- .refineParameters(x, se3), "no valid")
    expect_identical(out, NULL)

    # Works for the other field.
    se3 <- se
    rowData(se3)$LogFC <- NULL
    se3 <- .cacheCommonInfo(x, se3)
    expect_warning(out <- .refineParameters(x, se3), "no valid")
    expect_identical(out, NULL)
})

test_that("VolcanoPlot interface generation works correctly", {
    x <- VolcanoPlot()
    expect_error(.defineDataInterface(x, se, list()), NA)

    expect_true(.hideInterface(x, "XAxis")) 
    expect_false(.hideInterface(x, "random")) 

    expect_identical(.fullName(x), "Volcano plot")
    expect_is(.panelColor(x), "character")
})

test_that("VolcanoPlot dot plot generation works correctly", {
    x <- VolcanoPlot()
    se2 <- .cacheCommonInfo(x, se)
    y <- .refineParameters(x, se2)
    envir <- new.env()
    envir$se <- se2

    out <- .generateDotPlotData(y, envir)
    expect_identical(envir$plot.data$Y, -log10(rowData(se2)$PValue))
    expect_identical(envir$plot.data$X, rowData(se2)$LogFC)
    expect_identical(names(out), c("commands", "labels"))

    priority <- .prioritizeDotPlotData(y, envir)
    expect_identical(names(priority), c("commands", "rescaled"))

    expect_identical(.colorByNoneDotPlotField(y), "IsSig")
    expect_match(.colorByNoneDotPlotScale(y), "scale_color_manual")

    library(ggplot2)
    envir$plot.type <- "scatter"
    .generateDotPlot(y, out$labels, envir)
    expect_s3_class(envir$dot.plot, "ggplot")
})

test_that("VolcanoPlot generates a tour correctly", {
    tour <- .definePanelTour(VolcanoPlot())

    expect_s3_class(tour, "data.frame")

    expect_true(any(grepl("false discovery rate", tour$intro)))
})