signature-plot-functions: Plot Mutational Signatures

Description Usage Arguments Details Value See Also Examples

Description

Visualize estimated signatures, sample contribution, and mutational spectra.

Usage

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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.

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.

Value

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

See Also

See the 'ggplot2' package for customizing the plots.

Examples

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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

SomaticSignatures documentation built on Nov. 1, 2018, 2:23 a.m.