plotMutationDistribution: Plot mutation frequency data of a mutational signature or...

In rmpiro/decompTumor2Sig: Decomposition of individual tumors into mutational signatures by signature refitting

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: <[e-mail]> or <[e-mail]>

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]])

rmpiro/decompTumor2Sig documentation built on May 15, 2022, 3:27 a.m.