plotDecomposedContribution: Plot the decomposition (contributions/exposures) of a tumor...

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

Plot the decomposition (contributions/exposures) of a tumor genome.

Description

'plotDecomposedContribution()' plots the decomposition of a tumor genome, i.e., the contributions/exposures obtained from decomposeTumorGenomes for a set of signatures.

Usage

plotDecomposedContribution(decomposition, signatures=NULL,
removeNA=TRUE)

Arguments

decomposition	(Mandatory) A decomposition vector (exposure vector) obtained for a single tumor genome.
signatures	(Optional) A list object containing the signatures used to compute the decomposition. If specified, the signature labels used in the plot will be taken from the element names of the list; otherwise signature names will be taken from the exposure object (decomposition) or named from sign_1 to sign_N.
removeNA	(Optional) If TRUE (default), signatures with an NA as exposure will not be included on the x-axis of the the plot. Exposures can be NA if they have been determined with a greedy search.

Value

Returns (or draws) a plot of the decomposed tumor genome (i.e., contributions of the single 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
decomposeTumorGenomes

Examples

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

### load preprocessed breast cancer genomes (object 'genomes') from
### Nik-Zainal et al (PMID: 22608084) 
gfile <- system.file("extdata",
         "Nik-Zainal_PMID_22608084-genomes-Alexandrov_3bases.Rdata", 
         package="decompTumor2Sig")
load(gfile)

### compute exposures
exposures <- decomposeTumorGenomes(genomes, signatures, verbose=FALSE)

### plot signature composition of the first genome
plotDecomposedContribution(exposures[[1]], signatures=NULL)

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