tests/testthat/test_plotting.R

In leekgroup/derfinderPlot: Plotting functions for derfinder

context("Plotting functions")

# Setup
## Load data
library("derfinder")

## Annotate regions, first two regions only
regions <- genomeRegions$regions[1:2]
annotatedRegions <- annotateRegions(
    regions = regions,
    genomicState = genomicState$fullGenome, minoverlap = 1
)

## Find nearest annotation with bumphunter::matchGenes()
library("bumphunter")
library("TxDb.Hsapiens.UCSC.hg19.knownGene")
genes <- annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene)
nearestAnnotation <- matchGenes(x = regions, subject = genes)

## Obtain fullCov object
fullCov <- list("21" = genomeDataRaw$coverage)

## Assign chr lengths using hg19 information
library("GenomicRanges")
seqlengths(regions) <- seqlengths(getChromInfoFromUCSC("hg19",
    as.Seqinfo = TRUE
))[
    mapSeqlevels(names(seqlengths(regions)), "UCSC")
]

## Get the region coverage
regionCov <- getRegionCoverage(fullCov = fullCov, regions = regions)

test_that("Region plots", {
    expect_that(
        plotRegionCoverage(
            regions = regions, regionCoverage = regionCov,
            groupInfo = genomeInfo$pop, nearestAnnotation = nearestAnnotation,
            annotatedRegions = data.frame("fail" = 1), whichRegions = 1:2, ask = FALSE
        ),
        throws_error()
    )
    expect_that(
        plotRegionCoverage(
            regions = regions, regionCoverage = regionCov,
            groupInfo = genomeInfo$pop, nearestAnnotation = data.frame("fail" = 1),
            annotatedRegions = annotatedRegions, whichRegions = 1:2, ask = FALSE
        ),
        throws_error()
    )
    expect_that(
        plotRegionCoverage(
            regions = regions, regionCoverage = regionCov,
            groupInfo = genomeInfo$pop, nearestAnnotation = GRanges("chr1", IRanges(
                1,
                2
            ), "fail" = 1),
            annotatedRegions = annotatedRegions, whichRegions = 1:2, ask = FALSE
        ),
        throws_error()
    )
    expect_that(
        plotRegionCoverage(
            regions = regions, regionCoverage = regionCov,
            groupInfo = c("a", "b"), nearestAnnotation = nearestAnnotation,
            annotatedRegions = annotatedRegions, whichRegions = 1:2, ask = FALSE
        ),
        throws_error()
    )
    expect_that(
        plotRegionCoverage(
            regions = regions, regionCoverage = regionCov,
            groupInfo = genomeInfo$pop, nearestAnnotation = nearestAnnotation,
            annotatedRegions = annotatedRegions, whichRegions = 1:3, ask = FALSE
        ),
        gives_warning()
    )
})