Nothing
context("PlotCatalogToPdf.SBS1536Catalog")
test_that("PlotCatalogToPdf.SBS1536Catalog function", {
skip_if("" == system.file(package = "BSgenome.Hsapiens.1000genomes.hs37d5"))
stopifnot(requireNamespace("BSgenome.Hsapiens.1000genomes.hs37d5"))
catalog.counts <- ReadCatalog("testdata/regress.cat.sbs.1536.csv",
ref.genome = "GRCh37",
region = "genome", catalog.type = "counts")
colnames(catalog.counts) <- paste0("HepG2_", 1 : 4)
out <-
PlotCatalogToPdf(catalog.counts,
file = file.path(tempdir(), "PlotCatSBS1536.counts.test.pdf"))
expect_equal(out$plot.success, TRUE)
catalog.density <-
TransformCatalog(catalog.counts, target.ref.genome = "GRCh37",
target.region = "genome",
target.catalog.type = "density")
out <-
PlotCatalogToPdf(catalog.density, file = file.path(tempdir(), "PlotCatSBS1536.density.test.pdf"))
expect_equal(out$plot.success, TRUE)
catalog.counts.signature <-
TransformCatalog(catalog.counts, target.ref.genome = "GRCh37",
target.region = "genome",
target.catalog.type = "counts.signature")
out <-
PlotCatalogToPdf(catalog.counts.signature,
file = file.path(tempdir(), "PlotCatSBS1536.counts.signature.test.pdf"))
expect_equal(out$plot.success, TRUE)
catalog.density.signature <-
TransformCatalog(catalog.counts, target.ref.genome = "GRCh37",
target.region = "genome",
target.catalog.type = "density.signature")
out <-
PlotCatalogToPdf(catalog.density.signature,
file = file.path(tempdir(), "PlotCatSBS1536.density.signature.test.pdf"))
expect_equal(out$plot.success, TRUE)
unlink(file.path(tempdir(), "PlotCatSBS1536.counts.test.pdf"))
unlink(file.path(tempdir(), "PlotCatSBS1536.density.test.pdf"))
unlink(file.path(tempdir(), "PlotCatSBS1536.counts.signature.test.pdf"))
unlink(file.path(tempdir(), "PlotCatSBS1536.density.signature.test.pdf"))
graphics.off()
})
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