plot_bootstrapped_contribution: Plot the bootstrapped signature contributions

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Plot the bootstrapped signature contributions

Description

Plot the signature contributions retrieved with 'fit_to_signatures_bootstrapped'. The function can plot both the absolute or the relative signature contribution. The graph can be plotted as either a jitter plot or as a barplot.

Usage

plot_bootstrapped_contribution(
  contri_boots,
  mode = c("absolute", "relative"),
  plot_type = c("jitter", "barplot", "dotplot")
)

Arguments

contri_boots	matrix showing signature contributions across bootstrap iterations.
mode	Either "absolute" for absolute number of mutations, or "relative" for relative contribution, default = "absolute"
plot_type	Either "jitter" for a jitter plot, "barplot" for a barplot, or "dotplot" for a dotplot

Value

A ggplot2 graph

Examples

## Get the bootstrapped signature contributions
## See 'count_indel_contexts()' for more info on how to do this.
contri_boots <- readRDS(system.file("states/bootstrapped_snv_refit.rds",
  package = "MutationalPatterns"
))

## Plot bootstrapped contribution
plot_bootstrapped_contribution(contri_boots)

## Plot bootstrapped contribution with relative contributions
plot_bootstrapped_contribution(contri_boots, mode = "relative")

## Plot bootstrapped contribution with a barplot
plot_bootstrapped_contribution(contri_boots, plot_type = "barplot")

## Plot bootstrapped contribution with a dotplot
plot_bootstrapped_contribution(contri_boots, plot_type = "dotplot", mode = "absolute")

UMCUGenetics/MutationalPatterns documentation built on Nov. 24, 2022, 4:31 a.m.