SomaticSignatures (version 2.8.4)

signature-plots: Plot Mutational Signatures

Description

Visualize estimated signatures, sample contribution, and mutational spectra.

Usage

plotObservedSpectrum(s, colorby = c("sample", "alteration"))
plotFittedSpectrum(s, colorby = c("sample", "alteration"))
plotMutationSpectrum(vr, group, colorby = c("sample", "alteration"), normalize = TRUE)
plotSignatureMap(s)
plotSignatures(s, normalize = FALSE, percent = FALSE)
plotSampleMap(s)
plotSamples(s, normalize = FALSE, percent = FALSE)

Arguments

s

MutationalSignatures object [required]

vr

VRanges object

colorby

Which variable to use for the coloring in the spectra representation.

normalize

Plot relative constributions (TRUE) instead of absolute (FALSE) ones.

percent

Display the results as fraction (FALSE) or percent (TRUE)

group

Charactering string that represents the variable name used for grouping.

Value

A 'ggplot' object, whose properties can further be changed

Details

With the plotting function, the obtained signatures and their occurrance in the samples can be visualized either as a heatmap ('plotSignatureMap', 'plotSampleMap') or a barchart ('plotSignature', 'plotSamples').

Since the plotting is based on the 'ggplot2' framework, all properties of the plots can be fully controlled by the user after generating the plots. Please see the examples for some customizations and the 'ggplot2' documentation for the entire set of options.

See Also

See the 'ggplot2' package for customizing the plots.

Examples

data("sca_sigs", package = "SomaticSignatures")

plotSamples(sigs_nmf)

plotSignatures(sigs_nmf, normalize = TRUE)

## customize the plots ##
p = plotSamples(sigs_nmf)

library(ggplot2)
## (re)move the legend
p = p + theme(legend.position = "none")
## change the axis labels
p = p + xlab("Studies")
## add a title
p = p + ggtitle("Somatic Signatures in TGCA WES Data")
## change the color scale
p = p + scale_fill_brewer(palette = "Blues")
## decrease the size of x-axis labels
p = p + theme(axis.text.x = element_text(size = 9))

p