pmBarplot: Plot both mutation signatures and their mutational exposures...

In USCbiostats/HiLDA: Conducting statistical inference on comparing the mutational exposures of mutational signatures by using hierarchical latent Dirichlet allocation

Description

Plot both mutation signatures and their mutational exposures from pmsignature output

Usage

pmBarplot(
  inputG,
  inputParam,
  sigOrder = NULL,
  refGroup = NULL,
  sortSampleNum = TRUE,
  refName = "Control",
  altName = "Case",
  charSize = 3
)

Arguments

inputG	a MutationFeatureData S4 class output by the pmsignature.
inputParam	a estimatedParameters S4 class output by the pmsignature.
sigOrder	the order of signatures if needed (default: NULL).
refGroup	the samples in the reference group (default: NULL).
sortSampleNum	whether to sort by number of mutations (default: TRUE).
refName	the name of reference group (default: Control).
altName	the name of the other group (default: Case).
charSize	the size of the character on the signature plot (default: 3).

Value

a list of a signature plot and a barplot of mutational exposures

Examples

load(system.file("extdata/sample.rdata", package="HiLDA"))
Param <- pmgetSignature(G, K = 3)

pmPlots <- pmBarplot(G, Param, refGroup=1:4)
cowplot::plot_grid(pmPlots$sigPlot, pmPlots$propPlot, rel_widths = c(1,3))

USCbiostats/HiLDA documentation built on Oct. 15, 2021, 10:22 a.m.