plotSpectraCaterpillar: generates caterpillar plot of signature weights for...

In juliancandia/mutSigMapper: Mapping Spectra to Mutational Signatures Based on Shot-Noise Modeling

Description

For each chosen sample, this function generates a caterpillar plot of signature weights. By default, signatures are ordered by p-value and those below the significance threshold are marked with an asterisk. Weights from the input sample are shown as red crosses, whereas weights from the generated random spectra are shown as blue circles (median values) and bars (confidence interval ranges). Options are provided to customize signature selection and display.

Usage

plotSpectraCaterpillar(x, spectra.set=NULL, sig.set=NULL, order_sig_by_pval=TRUE, 
signif=TRUE, pval=0.05, CI=0.95, xlab=NULL, ylab=NULL, cexRow=NULL, cex.lab=0.95, 
main.title=NULL, col.title="black", line.title=1.5, cex.title=0.85, subtitle=NULL, 
col.subtitle="darkgray", line.subtitle=0.5, cex.subtitle=0.55, legend=TRUE)

Arguments

x	mutSigMapper object.
spectra.set	Vector of samples names. If NULL, all samples are included.
sig.set	Vector of signature names. If NULL, all signatures are included.
order_sig_by_pval	Logical to order signatures by p-value. Default is TRUE.
signif	Logical to display asterisks in statistically significant signature labels. Default is TRUE.
pval	P-value threshold for statistical significance. Default is 0.05.
CI	Confidence interval (normalized to 1) around the median for random spectra (shown as blue bars). Default is 0.95.
xlab	Label for x axis.
ylab	Label for y axis.
cexRow	Size of row labels.
cex.lab	Axis label size.
main.title	Custom title.
col.title	Title color.
line.title	Title line position.
cex.title	Title size.
subtitle	Custom subtitle.
col.subtitle	Subtitle color.
line.subtitle	Subtitle line position.
cex.subtitle	Subtitle size.
legend	Logical to display legend. Default is TRUE.

Value

None.

Author(s)

Julian Candia
Maintainer: Julian Candia [e-mail]

See Also

mutSigMapper, plotSpectraHeatmap

Examples

data(spectra)
map = mutSigMapper(spectra)
plotSpectraCaterpillar(map, spectra.set="colon1")

juliancandia/mutSigMapper documentation built on Oct. 19, 2020, 3:58 a.m.