visPMS {HiLDA} | R Documentation

## visualize probabisitic mutaiton signature for the independent model

### 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)

[Package HiLDA version 1.2.0 Index]