plot_96_profile: Plot 96 trinucleotide profile

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

Plot 96 trinucleotide profile

Description

Plot relative contribution of 96 trinucleotides

Usage

plot_96_profile(mut_matrix, colors = NA, ymax = 0.2, condensed = FALSE)

Arguments

mut_matrix	96 trinucleotide profile matrix
colors	Optional 6 value color vector.
ymax	Y axis maximum value, default = 0.2
condensed	More condensed plotting format. Default = F.

Value

96 trinucleotide profile plot

See Also

mut_matrix, plot_profile_heatmap, plot_river

Examples

## See the 'mut_matrix()' example for how we obtained the
## mutation matrix information:
mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
  package = "MutationalPatterns"
))

## Plot the 96-profile of three samples
plot_96_profile(mut_mat[, c(1, 4, 7)])

## Plot a condensed profile
plot_96_profile(mut_mat[, c(1, 4, 7)], condensed = TRUE)

## It's also possible to plot signatures, for example signatures
## generated with NMF
## See 'extract_signatures()' on how we obtained these signatures.
nmf_res <- readRDS(system.file("states/nmf_res_data.rds",
  package = "MutationalPatterns"
))

## Optionally, provide signature names
colnames(nmf_res$signatures) <- c("Signature A", "Signature B")

## Generate the plot
plot_96_profile(nmf_res$signatures)

CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.