plotSpectraHeatmap: generates heatmap plots of spectra vs mutational signatures

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

Description

This function generates a heatmap plot of associations between spectra (columns) and mutational signatures (rows), which may include statistical significance annotations based on shot noise modeling. By default, all spectra and signatures are plotted, but the user can provide custom subsets. Options are provided to plot only samples and/or signatures that satisfy statistical significance. A variety of association metrics can be chosen via type; numerical results are returned.

Usage

plotSpectraHeatmap(x, spectra.set=NULL, sig.set=NULL, 
type=c("weights","cosine","entropy","correlation"), 
cor.method = c("pearson","kendall","spearman"), signif=TRUE, pval=0.05, 
signif.sig.only=FALSE, signif.sample.only=FALSE, xlab=NULL, ylab=NULL, 
color=NULL, breaks=NULL, breaks.scale.adj=TRUE, 
breaks.scale.adj.max=c("q99","q95","max"), scale="none", Rowv=FALSE, Colv=TRUE, 
na.color=NULL, cexRow=NULL, srtRow=0, cexCol=NULL, srtCol=45, margins=c(5,5), 
key=TRUE, key.title=NA, dendrogram="none", trace="none", notecol="red", 
cor.notecol="white", notecex=1.5, main.title=NULL, col.title="black", 
line.title=1, cex.title=0.95, subtitle=NULL, col.subtitle="red", 
line.subtitle=-1, cex.subtitle=0.65, ...)

Arguments

x	mutSigMapper object.
spectra.set	Vector of sample names. If NULL, all samples are included.
sig.set	Vector of signature names. If NULL, all signatures are included.
type	Type of signature vs spectra matrix to show: "weights" (signature contributions calculated for each sample), "cosine" (cosine similarity), "entropy" (Jensen-Shannon divergence) and "correlation". Default is "weights".
cor.method	Correlation method (if type="correlation"). Default is "pearson".
signif	Logical to display statistical significance annotations. Default is TRUE.
pval	P-value threshold for statistical significance. Default is 0.05.
signif.sig.only	Logical to only display statistically significant signatures. Default is FALSE.
signif.sample.only	Logical to only display statistically significant samples. Default is FALSE.
xlab	Label for x axis.
ylab	Label for y axis.
color	Heatmap color vector. Length must be one less than number of breaks.
breaks	Color breaks vector.
breaks.scale.adj	(If breaks is NULL) Logical to automatically adjust the breaks scale to the data being plotted. Default is TRUE.
breaks.scale.adj.max	(If breaks is NULL and breaks.scale.adj is TRUE) Breaks maximum: "q99" (99-th percentile), "q95" (95-th percentile), or "max" (maximum). Default is "q99".
scale	Logical to scale the data for heatmap in either the row or column direction. Default is "none".
Rowv	Logical to reorder rows (signatures) by hierarchical clustering. Default is FALSE.
Colv	Logical to reorder columns (samples) by hierarchical clustering. Default is TRUE.
na.color	Color to use for missing values.
cexRow	Size of row labels.
srtRow	Angle of row labels, in degrees from horizontal.
cexCol	Size of column labels.
srtCol	Angle of column labels, in degrees from horizontal.
margins	Numeric vector of length 2 containing the margins for column and row names, respectively.
key	Logical to display key. Default is TRUE.
key.title	Main title of the color key.
dendrogram	To draw dendrograms. Default is "none".
trace	To display trace lines. Default is "none".
notecol	Color of statistical significance annotations for type="weights", "cosine" or "entropy".
cor.notecol	Color of statistical significance annotations for type="correlation".
notecex	Size of significance annotations.
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.
...	Additional plotting parameters to be passed to gplots::heatmap.2()

Value

A list with:

sig_spectra

Numerical data frame with the values plotted in the heatmap across signatures (rows) and samples (columns).

Author(s)

Julian Candia
Maintainer: Julian Candia [e-mail]

See Also

mutSigMapper, plotSpectraCaterpillar

Examples

data(spectra)
map = mutSigMapper(spectra)
weights = plotSpectraHeatmap(map)
cos_sim = plotSpectraHeatmap(map,type="cosine")

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