tests/testthat/test_plotting.R

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

context("Testing plot functions: ")

test_that("plotting", {
    set.seed(42)
    ods <- makeExampleOutriderDataSet(n=40, m=40)
    
    mcols(ods)[['basepairs']] <- rnbinom(nrow(ods), mu=1e4, size=2)
    ods <- filterExpression(ods, filterGenes=FALSE, fpkmCutoff=1e3)
    genesOfInterest <- list("sample_1"=sample(rownames(ods), 10),
                            "sample_3"=sample(rownames(ods), 8),
                            "sample_10"=sample(rownames(ods), 20))
    ods <- OUTRIDER(ods, implementation='pca', q=2, 
                    subsets=list("testSet"=genesOfInterest))
    sex <- sample(c("female", "male"), dim(ods)[2], replace=TRUE)
    colData(ods)$Sex <- sex
    
    
    expect_is(plotAberrantPerSample(ods), "ggplot")
    expect_is(plotAberrantPerSample(ods, subsetName="testSet"), "ggplot")
    
    expect_equal(class(plotVolcano(ods, 30)), c("plotly", "htmlwidget"))
    expect_is(plotVolcano(ods, "sample_10", basePlot=TRUE), "ggplot")
    expect_is(plotVolcano(ods, "sample_10", subsetName="testSet", 
                            basePlot=TRUE), "ggplot")
    expect_is(plotVolcano(ods, "sample_10", label="feature_3", basePlot=TRUE), 
                "ggplot")
    
    
    expect_equal(class(plotExpressionRank(ods, 23)), c("plotly", "htmlwidget"))
    expect_is(plotExpressionRank(ods, "feature_13", normalized=FALSE,
            log=FALSE, basePlot=TRUE), 'ggplot')
    expect_is(plotExpressionRank(ods, "feature_13", normalized=TRUE,
                                 subsetName="testSet", basePlot=TRUE), 'ggplot')
    expect_is(plotExpressionRank(ods, "feature_13", normalized=FALSE,
                                 label=c("sample_1", "sample_5"),
                                 log=FALSE, basePlot=TRUE), 'ggplot')
    
    
    expect_equal(class(plotExpectedVsObservedCounts(ods, 39)), 
            c("plotly", "htmlwidget"))
    expect_is(plotExpectedVsObservedCounts(ods, "feature_32", basePlot=TRUE),
            "ggplot")
    expect_is(plotExpectedVsObservedCounts(ods, "feature_32", 
                                subsetName="testSet", basePlot=TRUE), "ggplot")
    expect_is(plotExpectedVsObservedCounts(ods, "feature_32", label="aberrant",
                                           basePlot=TRUE), "ggplot")
    
    
    expect_is(plotExpressedGenes(ods), "ggplot")
    
    expect_null(plotQQ(ods, 1))
    expect_null(plotQQ(ods, "feature_20"))
    expect_null(plotQQ(ods, "feature_20", subsetName="testSet"))
    expect_null(plotQQ(ods, global=TRUE))
    expect_null(plotQQ(ods, global=TRUE, outlierRatio=0.001))
    expect_null(plotQQ(ods, global=TRUE, outlierRatio=NULL))
    
    
    expect_is(plotCountCorHeatmap(ods, colGroup="Sex", basePlot=FALSE),
            'plotly')
    ods <- plotCountCorHeatmap(ods)
    expect_invisible(plotCountCorHeatmap(ods, colGroup="Sex", normalized=FALSE))
    expect_invisible(plotCountCorHeatmap(ods, rowGroup="sampleID"))
    expect_true("clusterNumber_4" %in% colnames(colData(ods)))
    expect_is(ods, "OutriderDataSet")
    
    
    expect_invisible(
            plotCountGeneSampleHeatmap(ods, normalized=FALSE, bcvQuantile=0.5))
    expect_invisible(plotCountGeneSampleHeatmap(ods, rowGroups="theta", 
            rowColSet=list(c("white", "darkgreen"))))
    
    pass <- mcols(ods)$passedFilter
    # don't use mcols(ods)$XXX <- NULL since this is broken in R < 3.5
    mcols(ods) <- mcols(ods)[,!colnames(mcols(ods)) %in% "passedFilter"]
    expect_message(plotFPKM(ods), "To see the difference .*")
    mcols(ods)[,'passedFilter'] <- pass
    expect_is(plotFPKM(ods), 'ggplot')
    
    
    plotPowerAnalysis(ods)
    
    expect_error(plotManhattan(ods, "sample_1"))
    gr <- GRanges(
            seqnames=sample(paste0("chr", 1:22), nrow(ods), replace=TRUE),
            ranges=IRanges(start=runif(nrow(ods), min=0, max=1e5), width=100))
    expect_is(plotManhattan(ods, "sample_1", featureRanges=gr), "GGbio")
    expect_is(plotManhattan(ods, "sample_1", featureRanges=gr, chr=10), "GGbio")
    expect_is(plotManhattan(ods, "sample_26", featureRanges=gr, 
                            subsetName="testSet"), "GGbio")
    
})