DEploid (version 0.5.4)

plotAltVsRef: Plot coverage

Description

Plot alternative allele count vs reference allele count at each site.

Usage

plotAltVsRef(
  ref,
  alt,
  title = "Alt vs Ref",
  exclude.ref = c(),
  exclude.alt = c(),
  potentialOutliers = c(),
  cex.lab = 1,
  cex.main = 1,
  cex.axis = 1
)

Arguments

ref

Numeric array of reference allele count.

alt

Numeric array of alternative allele count.

title

Figure title, "Alt vs Ref" by default

exclude.ref

Numeric array of reference allele count at sites that are not deconvoluted.

exclude.alt

Numeric array of alternative allele count at sites that are not deconvoluted

potentialOutliers

Index of potential outliers.

cex.lab

Label size.

cex.main

Title size.

cex.axis

Axis text size.

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)
plotAltVsRef(PG0390CoverageT$refCount, PG0390CoverageT$altCount)

# Example 2
vcfFile = system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV = extractCoverageFromVcf(vcfFile)
plotAltVsRef(PG0390CoverageV$refCount, PG0390CoverageV$altCount)