plotDecomposedContribution {decompTumor2Sig} | R Documentation

## 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: <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`
`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)

[Package decompTumor2Sig version 2.4.1 Index]