plots: signeR plot functions
In signeR: Empirical Bayesian approach to mutational signature discovery

Description Usage Arguments Value Examples

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 barchart, with error bars according to the variation of individual entries along generated Gibbs samples.

SignHeat: Plot the mutations 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 generated Gibbs samples.

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

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=20, 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="", samplenames=TRUE, ...)
## S4 method for signature 'SignExp'
ExposureBoxplot(signexp_obj, plot_to_file=FALSE,
    file="Exposure_boxplot.pdf", col='tan2', threshold=0,
    plots_per_page=4, reord=NA, ...)
## S4 method for signature 'SignExp'
ExposureHeat(signexp_obj, plot_to_file=FALSE,
    file="Exposure_heatmap.pdf", nbins=20, pal="roh", distmethod="euclidean",
        clustermethod="complete", ...)

`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","roh".
`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 in 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 TRUE, thus generating a barplot of relative contributions of the signatures to mutation counts. Otherwise, absolute contributions to mutation counts will be displayed.
`title`	Main title added to the plot. Default is no title.
`samplenames`	Whether sample names will be shown in the plot. Default is TRUE, however sample names are not shown if there are more then 50 samples.
`...`	.

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.

# each plot function need 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")