plotAltVsRef {DEploid} | R Documentation |
Plot alternative allele count vs reference allele count at each site.
plotAltVsRef(
ref,
alt,
title = "Alt vs Ref",
exclude.ref = c(),
exclude.alt = c(),
potentialOutliers = c(),
cex.lab = 1,
cex.main = 1,
cex.axis = 1
)
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. |
# 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)