plotProportions: Plot proportions

In DEploid: Deconvolute Mixed Genomes with Unknown Proportions

Description

Plot the MCMC samples of the proportion, indexed by the MCMC chain.

Usage

plotProportions(
  proportions,
  title = "Components",
  cex.lab = 1,
  cex.main = 1,
  cex.axis = 1
)

Arguments

proportions	Matrix of the MCMC proportion samples. The matrix size is number of the MCMC samples by the number of strains.
title	Figure title.
cex.lab	Label size.
cex.main	Title size.
cex.axis	Axis text size.

Examples

## Not run: 
plafFile = system.file("extdata", "labStrains.test.PLAF.txt",
    package = "DEploid")
panelFile = system.file("extdata", "labStrains.test.panel.txt",
    package = "DEploid")
refFile = system.file("extdata", "PG0390-C.test.ref", package = "DEploid")
altFile = system.file("extdata", "PG0390-C.test.alt", package = "DEploid")
PG0390CoverageT = extractCoverageFromTxt(refFile, altFile)
PG0390Coverage.deconv = dEploid(paste("-ref", refFile, "-alt", altFile,
    "-plaf", plafFile, "-noPanel"))
plotProportions(PG0390Coverage.deconv$Proportions, "PG0390-C proportions")

## End(Not run)

DEploid documentation built on April 22, 2020, 1:04 a.m.