plotAltVsRefPlotly: Plot coverage

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

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)

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