DEploid (version 0.5.4)

plotProportions: Plot 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

if (FALSE) {
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")
}