plot_bootstrapped_exposure: Plot signature exposure estimation for several samples

In SigsPack: Mutational Signature Estimation for Single Samples

Description

Creates a boxplot illustrating the results of the signature estimation for several mutational catalogues (e.g. bootstrapped re-samples or a cohort). The plot shows the distribution of estimated signature exposure for all the catalogues, highlighting the one of the original mutational catalogue if one is provided.

Usage

plot_bootstrapped_exposure(bootstrapped_exposure,
  original_estimation = NULL, title = NULL, box_col = NULL,
  point_col = NULL, sig_names = NULL, sample_names = NULL)

Arguments

bootstrapped_exposure	matrix (n by k) containing the signature exposure of several mutational catalogues (bootstrapped re-samples) n is the amount of re-samples k is the amount of signature profiles that P contains
original_estimation	matrix (n by k) containing the signature exposure of one or several mutational catalogues (typically, the original sample) that will be diplayed on top of the boxplots
title	character, title of the plot
box_col	color option of the boxplot
point_col	color option of the points that indicate the exposure of the original profile(s). Should be a vector, if several original profiles are plotted
sig_names	character vector, names of the signatures to be displayed as x-axis labels
sample_names	character vector, names of the original profile(s)

Value

Diplays a boxplot

Note

The function can of course also be used to plot the distribution of estimated signature exposures in a cohort instead of one bootstrapped sample.

Examples

# prepare input
data(cosmicSigs)
mut_cat <- create_mut_catalogues(4,400)
exposures <- signature_exposure(bootstrap_mut_catalogues(
1000, mut_cat[['catalogues']][,1]))[['exposures']]
original_exposure <- signature_exposure(mut_cat[['catalogues']])[['exposures']]

plot_bootstrapped_exposure(exposures, as.matrix(original_exposure[,1]))

plot_bootstrapped_exposure(exposures, as.matrix(original_exposure), 
title='Example', box_col='grey')

SigsPack documentation built on Nov. 8, 2020, 6:57 p.m.