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

Description Usage Arguments Value Examples

View source: R/vis_signature.R

Description

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

Usage

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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

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

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

HiLDA documentation built on Nov. 8, 2020, 11:09 p.m.