plots: signeR plot functions

In rvalieris/signeR: Empirical Bayesian approach to mutational signature discovery

signeR plot functions

Description

BICboxplot: Plot the measured values of the Bayesian Information Criterion (BICs) for tested model dimensions.

Paths: Plot the convergence of the Gibbs sampler for signatures and exposures on separate charts.

SignPlot: Plot the mutational signatures in a bar chart, with error bars according to the variation of individual entries along the generated Gibbs samples.

SignHeat: Plot the mutation signatures in a heatmap.

ExposureBarplot: Barplot of estimated exposure values, showing the contribution of the signatures to the mutation counts of each genome sample.

ExposureBoxplot: Boxplot of exposure values, showing their variation along the generated Gibbs samples.

ExposureHeat: Plot a heatmap of the exposures, along with a dendrogram of the samples grouped by exposure levels.

Usage

BICboxplot(signeRout, plot_to_file=FALSE, file="Model_selection_BICs.pdf")
## S4 method for signature 'SignExp'
Paths(signexp_obj, plot_to_file=FALSE,
    file_suffix="plot.pdf", plots_per_page=4, ...)
## S4 method for signature 'SignExp'
SignPlot(signexp_obj, plot_to_file=FALSE,
    file="Signature_plot.pdf", pal="bcr1", threshold=0, plots_per_page=4,
    gap=1, reord=NA, ...)
## S4 method for signature 'SignExp'
SignHeat(signexp_obj, plot_to_file=FALSE,
    file="Signature_heatmap.pdf", nbins=50, pal="roh", ...)
## S4 method for signature 'SignExp'
ExposureBarplot(signexp_obj, plot_to_file=FALSE,
    file="Exposure_barplot.pdf", col='tan2', threshold=0, relative=FALSE,
    title="", show_samples=NA, ...)
## S4 method for signature 'SignExp'
ExposureBoxplot(signexp_obj, plot_to_file=FALSE,
    file="Exposure_boxplot.pdf", col='tan2', threshold=0, show_samples=NA,
    plots_per_page=4, reord=NA, ...)
## S4 method for signature 'SignExp'
ExposureHeat(signexp_obj, plot_to_file=FALSE,
    file="Exposure_heatmap.pdf", nbins=50, pal="roh", distmethod="euclidean",
        clustermethod="complete", show_samples=NA, ...)

Arguments

signexp_obj	A SignExp object returned by signeR function. e.g.: sig$SignExposures
signeRout	The list returned by the signeR function.
plot_to_file	Whether to save the plot to the file parameter. Default is FALSE.
file	Output pdf file of the plots.
pal	Color palette used. Options are: "brew","lba","bcr1", "bcr2","bw","rdh","roh","blh" or "bph".
threshold	Entries below this value will be rounded to 0. Default is 0 (all entries are kept).
plots_per_page	How many plots in a single page, default is 4.
gap	Distance between consecutive bars on the plot.
reord	Order of signatures for plotting. Should be a permutation of 1:nsig, where nsig is the number of signatures. By default, signatures are ordered by the total exposure, in decreasing order.
nbins	The range of signature entries is divided into this number of bins for plotting, each bin corresponding to a different color.
file_suffix	The suffix of the output file.
col	Single color name for boxplots.
distmethod	Distance measure used for grouping samples. Default is "euclidean", see the documentation of the dist function for other options.
clustermethod	Agglomeration method used for grouping samples. Default is "complete", see the documentation of the hclust function for other options.
relative	Whether to normalize exposures of each sample so that they sum up to one. Default is FALSE, thus generating a plot of absolute contributions of signatures to mutation counts. Otherwise, relative contributions will be displayed.
title	Main title added to the plot. Default is no title.
show_samples	Whether sample names will be shown in the plot. Default is NA, which leads to sample names being displayed only when there are less than 30 samples. However, even if show_samples=TRUE, due to display limitations sample names are not shown if there are more than 50 samples.
...	.

Value

The plot result is exported to the current graphic device. If plot_to_file=TRUE, the plot is saved in the file defined by the file argument.

Examples

# each plot function needs the SignExposures object
# which is part of the result of the signeR() call
SignPlot(signatures$SignExposures)
Paths(signatures$SignExposures)
# etc ...

# BICboxplot needs the returned list itself
BICboxplot(signatures)

# see also
vignette(package="signeR")

rvalieris/signeR documentation built on April 20, 2024, 2:08 p.m.