visPMS: visualize probabisitic mutaiton signature for the independent...

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

Description

Generate visualization of mutation signatures for the model with substitution patterns and flanking bases represented by the indepenent representation.

Usage

visPMS(
  vF,
  numBases,
  baseCol = NA,
  trDir = FALSE,
  charSize = 5,
  isScale = FALSE,
  alpha = 2,
  charLimit = 0.25
)

Arguments

vF	a matrix for mutation signature
numBases	the number of flanking bases
baseCol	the colour of the bases (A, C, G, T, plus/minus strand)
trDir	the index whether the strand direction is plotted or not
charSize	the size of the character
isScale	the index whether the height of the flanking base is changed or not
alpha	the parameter for the Renyi entropy (applicable only if the isScale is TRUE)
charLimit	the limit of char size

Value

a plot of the input mutational signature

Examples

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

sig <- slot(Param, "signatureFeatureDistribution")[1,,]
visPMS(sig, numBases = 5, isScale = TRUE)

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