tests/testthat/test1.R

In Przemol/seqplots-release: An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.

bw1 <- system.file("extdata", "GSM1208360_chrI_100Kb_q5_sample.bw", package="seqplots")
bed1 <- system.file("extdata", "Transcripts_ce10_chrI_100Kb.bed", package="seqplots")
bed2 <- system.file("extdata", "GSM1208361_chrI_100Kb_PeakCalls.bed", package="seqplots")

test_that("Test BSgenome package installation", {
    context("Testing BSgenome package installation")    
    if(!"BSgenome.Celegans.UCSC.ce10" %in% BSgenome::installed.genomes()) {
        if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
            source("http://bioconductor.org/biocLite.R")
            biocLite("BSgenome.Celegans.UCSC.ce10")
        }
    }
    expect_true("BSgenome.Celegans.UCSC.ce10" %in% BSgenome::installed.genomes())
})

test_that("Test getPlotSetArray function and plotting interfaces", {
    
    tmp <- file.path(tempdir(), 'SeqPlots')
    context("Testing getPlotSetArray")
    if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
         psa <- getPlotSetArray(bw1, c(bed1, bed2), 'ce10')
    } else {
        psa <- get(load(system.file(
            "extdata", "precalc_plotset.Rdata", package="seqplots"))[[1]])
    }
    expect_that(psa, is_a("PlotSetArray"))
    
    context("Testing utils")
    expect_is(capture.output(show(psa)),    'character', info = NULL, label = NULL)
    expect_is(unlist(psa), 'PlotSetList', info = NULL, label = NULL)
    expect_is(psa[1],      'PlotSetList', info = NULL, label = NULL)
    expect_is(psa[2,1],    'PlotSetArray', info = NULL, label = NULL)
    expect_is(psa[[2]],    'PlotSetPair', info = NULL, label = NULL)
    
    context("Testing graphics")
    expect_error(plot(psa, what='h'))
    expect_null(plot(psa, what='a'))
    expect_is(plot(psa[2], what='h'), 'data.frame')
    expect_is(plot(psa[2,1], what='h'), 'data.frame')
    
})

test_that("Test motifs", {
    
    
    ms <- MotifSetup()
    ms$addMotif('GAGA')
    ms$addMotif('TATA')
    ms$addBigWig(bw1)
    expect_is(ms, 'MotifSetup', info = NULL, label = NULL)
    expect_equal(ms$nmotifs(), 3, info = NULL, label = NULL)

    context("Testing getPlotSetArray with motifs")
    if(.Platform$OS.type != "windows" || .Machine$sizeof.pointer != 4) {
        psa <- getPlotSetArray(ms, c(bed1, bed2), 'ce10')
    } else {
        psa <- get(load(system.file(
            "extdata", "precalc_plotset.Rdata", package="seqplots"))[[2]])
    }
    expect_that(psa, is_a("PlotSetArray"))
    
    context("Testing utils with motifs")
    expect_is(capture.output(show(psa)),    'character', info = NULL, label = NULL)
    expect_is(unlist(psa), 'PlotSetList', info = NULL, label = NULL)
    expect_is(psa[1],      'PlotSetList', info = NULL, label = NULL)
    expect_is(psa[2,1],    'PlotSetArray', info = NULL, label = NULL)
    expect_is(psa[[2]],    'PlotSetPair', info = NULL, label = NULL)
    
    context("Testing graphics with motifs")
    expect_error(plot(psa, what='h'))
    expect_null(plot(psa, what='a'))
    expect_is(plot(psa[2,1], what='h'), 'data.frame')
    expect_is(plot(psa[c(1,3,5)], what='h'), 'data.frame')
    
    context("Testing heatmap options")
    expect_is(plotHeatmap(psa[1,], indi = FALSE), 'data.frame')
    
    context("Testing heatmap cluster report")
    expect_true( all(is.na( psa[1,]$plot('h', clusters=0)$ClusterID )) )
    expect_true( all(is.na( plotHeatmap(psa[1,], clstmethod='none' )$ClusterID )) )
    
})