DEploid (version 0.5.7)

plotAltVsRefPlotly: 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)