plotAltVsRefPlotly {DEploid} | R Documentation |
Plot coverage
Description
Plot alternative allele count vs reference allele count at each site.
Usage
plotAltVsRefPlotly(ref, alt, title = "Alt vs Ref", potentialOutliers = c())
Arguments
ref |
Numeric array of reference allele count. |
alt |
Numeric array of alternative allele count. |
title |
Figure title, "Alt vs Ref" 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)
plotAltVsRefPlotly(PG0390CoverageT$refCount, PG0390CoverageT$altCount)
# Example 2
vcfFile <- system.file("extdata", "PG0390-C.test.vcf.gz", package = "DEploid")
PG0390CoverageV <- extractCoverageFromVcf(vcfFile, "PG0390-C")
plotAltVsRefPlotly(PG0390CoverageV$refCount, PG0390CoverageV$altCount)
[Package DEploid version 0.5.7 Index]