plotWSAFVsPLAFPlotly: Plot WSAF vs PLAF

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

Plot WSAF vs PLAF

Description

Plot allele frequencies within sample against population level.

Usage

plotWSAFVsPLAFPlotly(
  plaf,
  obsWSAF,
  ref,
  alt,
  title = "WSAF vs PLAF",
  potentialOutliers = c()
)

Arguments

plaf	Numeric array of population level allele frequency.
obsWSAF	Numeric array of observed altenative allele frequencies within sample.
ref	Numeric array of reference allele count.
alt	Numeric array of alternative allele count.
title	Figure title, "WSAF vs PLAF" by default
potentialOutliers	Index of potential outliers.

Examples

# Example 1
refFile <- system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFile <- system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390CoverageT <- extractCoverageFromTxt(refFile, altFile)
obsWSAF <- computeObsWSAF(PG0390CoverageT$altCount, PG0390CoverageT$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
  package = "DEploid"
)
plaf <- extractPLAF(plafFile)
plotWSAFVsPLAFPlotly(
  plaf, obsWSAF, PG0390CoverageT$refCount,
  PG0390CoverageT$altCount
)

# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
obsWSAF <- computeObsWSAF(PG0390CoverageV$altCount, PG0390CoverageV$refCount)
plafFile <- system.file("extdata", "labStrains.test.PLAF.txt",
  package = "DEploid"
)
plaf <- extractPLAF(plafFile)
plotWSAFVsPLAFPlotly(
  plaf, obsWSAF, PG0390CoverageV$refCount,
  PG0390CoverageV$altCount
)

DEploid documentation built on April 4, 2025, 2:16 a.m.