plotMutationDistribution {decompTumor2Sig} | R Documentation

## Plot mutation frequency data of a mutational signature or tumor genome.

### Description

'plotMutationDistribution()' plots a single signature or the mutation frequency data for a single genome. This works for signatures or genome data of both the Shiraishi and the Alexandrov type.

### Usage

    plotMutationDistribution(mutData, colors = NULL, strip = NULL)

### Arguments

`mutData` | (Mandatory) The signature or genome mutation frequency data to be plotted. This can either be a matrix (Shiraishi model) or a numeric vector (Alexandrov model).
`colors` | Vector of colors to be used for the base change data. For Alexandrov-type data, this vector must contain six elements (one per base change). For Shiraishi-type data, this vector must contain four elements (one per base). If `NULL` (default), for Alexandrov-type data, the colors are set to those used by the COSMIC website; for Shiraishi-type data, the consensus base colors for sequence logos will be used.
`strip` | Background color for strip labels; used only for Alexandrov-type data. If `NULL` (default), "papayawhip" will be used.

### Value

Returns (or draws) a plot according to the Alexandrov or Shiraishi model of mutational signatures.

### Author(s)

Rosario M. Piro
Politecnico di Milano
Maintainer: Rosario M. Piro
E-Mail: <rmpiro@gmail.com> or <rosariomichael.piro@polimi.it>

### References

http://rmpiro.net/decompTumor2Sig/
Krueger, Piro (2019) decompTumor2Sig: Identification of mutational signatures active in individual tumors. BMC Bioinformatics 20(Suppl 4):152.

### See Also

`decompTumor2Sig`

### Examples

    ### Attention: using plotMutationDistribution requires the package
    ### pmsignature to be installed!

    ### get Alexandrov signatures from COSMIC
    signatures <- readAlexandrovSignatures()

    ### plot the first Alexandrov signature
    plotMutationDistribution(signatures[[1]])

    ### read four Shiraishi signatures for breast cancer genomes from
    ### Nik-Zainal et al (PMID: 22608084) from flat files
    sigfiles <- system.file("extdata",
             paste0("Nik-Zainal_PMID_22608084-pmsignature-sig",1:4,".tsv"),
             package="decompTumor2Sig")
    signatures <- readShiraishiSignatures(sigfiles)

    ### plot the first Shiraishi signature
    plotMutationDistribution(signatures[[1]])

[Package decompTumor2Sig version 2.8.0 Index]