snv_plotSignatures: Plots decomposed mutational signatures

In ShixiangWang/VSHunter: Capture Variation Signatures from Genomic Data

Description

Takes results from extractSignatures and plots decomposed mutational signatures as a barplot.

Usage

snv_plotSignatures(nmfRes = NULL, contributions = FALSE,
  color = NULL, patient_order = NULL, font_size = 1.2,
  show_title = TRUE, axis_lwd = 2, title_size = 0.9,
  show_barcodes = FALSE, yaxisLim = 0.3, ...)

Arguments

nmfRes	results from extractSignatures
contributions	If TRUE plots contribution of signatures in each sample.
color	colors for each Ti/Tv conversion class. Default NULL
patient_order	User defined ordering of samples. Default NULL.
font_size	font size. Default 1.2
show_title	Default TRUE
axis_lwd	axis width. Default 2.
title_size	size of title. Default 1.3
show_barcodes	Default FALSE
yaxisLim	Default 0.3. If NA autoscales.
...	further plot options passed to barplot

Value

a base plot

See Also

Other SNV analysis functions: snv_extractSignatures, snv_readprofile, snv_signatureEnrichment, snv_trinucleotideMatrix

Examples

## Not run: 
laml.tnm <- snv_trinucleotideMatrix(maf = laml, ref_genome = 'BSgenome.Hsapiens.UCSC.hg19',
    prefix = 'chr', add = TRUE, useSyn = TRUE)
laml.sign <- snv_extractSignatures(mat = laml.tnm, plotBestFitRes = FALSE)

## End(Not run)

ShixiangWang/VSHunter documentation built on June 27, 2019, 4:56 p.m.