Nothing
context("DEploid tools")
vcfFileName <- system.file("extdata", "PG0390-C.test.vcf.gz",
package = "DEploid")
plafFileName <- system.file("extdata", "labStrains.test.PLAF.txt",
package = "DEploid")
panelFileName <- system.file("extdata", "labStrains.test.panel.txt",
package = "DEploid")
refFileName <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFileName <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390CoverageVcf <- extractCoverageFromVcf(vcfFileName)
plaf <- extractPLAF(plafFileName)
PG0390Deconv <- dEploid(paste("-vcf", vcfFileName, "-plaf", plafFileName,
"-noPanel"))
prop <- PG0390Deconv$Proportions[dim(PG0390Deconv$Proportions)[1], ]
expWSAF <- t(PG0390Deconv$Haps) %*% prop
test_that("Extracted coverage", {
PG0390CoverageTxt <- extractCoverageFromTxt(refFileName, altFileName)
expect_that(PG0390CoverageTxt, is_a("data.frame"))
expect_that(PG0390CoverageVcf, is_a("data.frame"))
expect_equal(PG0390CoverageTxt, PG0390CoverageVcf)
})
test_that("Extracted plaf", {
expect_that(plaf, is_a("numeric"))
})
test_that("computeObsWSAF", {
expect_equal(computeObsWSAF(0, 0), 0)
expect_equal(computeObsWSAF(0, 100), 0)
expect_equal(computeObsWSAF(1, 99), 0.01)
expect_equal(computeObsWSAF(99, 1), 0.99)
expect_equal(computeObsWSAF(50, 50), 0.5)
expect_equal(computeObsWSAF(50, 100), 0.3333333333333)
})
test_that("WSAF Related", {
obsWSAF <- computeObsWSAF(PG0390CoverageVcf$altCount,
PG0390CoverageVcf$refCount)
potentialOutliers <- c(5, 12, 25, 30, 35, 50)
expect_that(histWSAF(obsWSAF), is_a("histogram"))
png("histWSAF.png")
histWSAF(obsWSAF)
dev.off()
expect_that(inherits(plotHistWSAFPlotly(obsWSAF), "plotly"), is_true())
p <- plotHistWSAFPlotly(obsWSAF)
if (rmarkdown:::pandoc_available()) {
htmlwidgets::saveWidget(p, file = "histWSAFPlotly.html")
}
####
expect_null(plotWSAFvsPLAF(plaf, obsWSAF))
png("WSAFvsPLAF.png")
plotWSAFvsPLAF(plaf, obsWSAF)
dev.off()
expect_null(plotWSAFvsPLAF(plaf, obsWSAF, expWSAF))
expect_that(inherits(plotWSAFVsPLAFPlotly(plaf, obsWSAF,
PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount),
"plotly"), is_true())
p <- plotWSAFVsPLAFPlotly(plaf, obsWSAF,
PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount)
if (rmarkdown:::pandoc_available()) {
htmlwidgets::saveWidget(p, file = "WSAFvsPLAFPlotly.html")
}
###
expect_null(plotWSAFvsPLAF(plaf, obsWSAF,
potentialOutliers = potentialOutliers))
png("WSAFvsPLAFOutlier.png")
plotWSAFvsPLAF(plaf, obsWSAF, potentialOutliers = potentialOutliers)
dev.off()
expect_null(plotWSAFvsPLAF(plaf, obsWSAF, expWSAF,
potentialOutliers = potentialOutliers))
expect_that(inherits(plotWSAFVsPLAFPlotly(plaf, obsWSAF,
PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount,
potentialOutliers =
potentialOutliers),
"plotly"), is_true())
p <- plotWSAFVsPLAFPlotly(plaf, obsWSAF,
PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount,
potentialOutliers = potentialOutliers)
if (rmarkdown:::pandoc_available()) {
htmlwidgets::saveWidget(p, file = "WSAFvsPLAFPlotlyOutlier.html")
}
###
expect_null(plotObsExpWSAF(obsWSAF, expWSAF))
png("ObsExpWSAF.png")
plotObsExpWSAF(obsWSAF, expWSAF)
dev.off()
expect_that(inherits(plotObsExpWSAFPlotly(obsWSAF, expWSAF),
"plotly"), is_true())
p <- plotObsExpWSAFPlotly(obsWSAF, expWSAF)
if (rmarkdown:::pandoc_available()) {
htmlwidgets::saveWidget(p, file = "ObsExpWSAFPlotly.html")
}
})
test_that("plotAltVsRef", {
expect_null(plotAltVsRef(PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount))
png("AltVsRef.png")
plotAltVsRef(PG0390CoverageVcf$refCount, PG0390CoverageVcf$altCount)
dev.off()
expect_that(inherits(plotAltVsRefPlotly(PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount),
"plotly"), is_true())
p <- plotAltVsRefPlotly(PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount)
if (rmarkdown:::pandoc_available()) {
htmlwidgets::saveWidget(p, file = "plotAltVsRefPlotly.html")
}
})
test_that("plotAltVsRefWithOutliers", {
potentialOutliers <- c(1, 10, 20, 30, 40)
expect_null(plotAltVsRef(PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount,
potentialOutliers = potentialOutliers))
png("AltVsRefOutlier.png")
plotAltVsRef(PG0390CoverageVcf$refCount, PG0390CoverageVcf$altCount,
potentialOutliers = potentialOutliers)
dev.off()
expect_that(inherits(plotAltVsRefPlotly(PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount,
potentialOutliers = potentialOutliers),
"plotly"), is_true())
p <- plotAltVsRefPlotly(PG0390CoverageVcf$refCount,
PG0390CoverageVcf$altCount,
potentialOutliers = potentialOutliers)
if (rmarkdown:::pandoc_available()) {
htmlwidgets::saveWidget(p, file = "plotAltVsRefPlotlyOutlier.html")
}
})
test_that("plotProportion", {
expect_that(plotProportions(PG0390Deconv$Proportions, ""), is_a("numeric"))
})
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