tests/testthat/test-exposures.R

In oirot/tumorHeatmap: Visual comparison of mutational processes in a set of tumors

test_that("Heatmap with Shiarishi signatures", {
    ## read breast cancer genomes from Nik-Zainal et al (PMID: 22608084)
    gfile <-
        system.file("extdata", "Nik-Zainal_PMID_22608084-MPF.txt.gz",
            package="decompTumor2Sig"
        )

    ## get the filenames with the shiraishi signatures
    sigfiles <- system.file(
        "extdata",
        paste0(
            "Nik-Zainal_PMID_22608084-pmsignature-sig",
            1:4, ".tsv"
        ),
        package="decompTumor2Sig"
    )

    ## compute the exposure vectors and plot the heatmap
    exposures <- tumorHeatmap(gfile, sigfiles,
        signaturesType=signatureTypes$shiraishi
    )
    ## switch off the graphical device
    dev.off()
    expect_is(exposures, "matrix")
})

test_that("Heatmap with Alexandrov V3.2 signatures", {
    ## read breast cancer genomes from Nik-Zainal et al (PMID: 22608084)
    gfile <-
        system.file("extdata", "Nik-Zainal_PMID_22608084-MPF.txt.gz",
            package="decompTumor2Sig"
        )

    sigfile <- system.file("extdata", "COSMIC_v3.2_SBS_GRCh37.txt",
        package="tumorHeatmap"
    )
    exposures <- tumorHeatmap(
        gfile,
        sigfile,
        signaturesType=signatureTypes$alexandrov32,
        numBases=3,
        trDir=FALSE
    )
    ## switch off the graphical device
    dev.off()
    expect_is(exposures, "matrix")
})

test_that("Wrong signatures", {
    ## read breast cancer genomes from Nik-Zainal et al (PMID: 22608084)
    gfile <-
        system.file("extdata", "Nik-Zainal_PMID_22608084-MPF.txt.gz",
            package="decompTumor2Sig"
        )

    sigfiles <- system.file(
        "extdata",
        paste0(
            "Nik-Zainal_PMID_22608084-pmsignature-sig",
            1:4, ".tsv"
        ),
        package="decompTumor2Sig"
    )
    expect_error(
        tumorHeatmap(
            gfile,
            sigfiles,
            signaturesType=signatureTypes$alexandrov32,
            numBases=3,
            trDir=FALSE
        )
    )
})

test_that("Wrong parameters", {
    ## read breast cancer genomes from Nik-Zainal et al (PMID: 22608084)
    gfile <-
        system.file("extdata", "Nik-Zainal_PMID_22608084-MPF.txt.gz",
            package="decompTumor2Sig"
        )

    sigfile <- system.file("extdata", "COSMIC_v3.2_SBS_GRCh37.txt",
        package="tumorHeatmap"
    )
    expect_error(
        tumorHeatmap(
            gfile,
            sigfile,
            signaturesType=signatureTypes$alexandrov32,
            numBases=3,
            trDir=TRUE
        )
    )
})