plot_192_profile {MutationalPatterns}R Documentation

Plot 192 trinucleotide profile

Description

Plot relative contribution of 192 trinucleotides

Usage

plot_192_profile(mut_matrix, colors, ymax = 0.2, condensed = FALSE)

Arguments

mut_matrix

192 trinucleotide profile matrix

colors

6 value color vector

ymax

Y axis maximum value, default = 0.2

condensed

More condensed plotting format. Default = F.

Value

192 trinucleotide profile plot

See Also

mut_matrix_stranded, extract_signatures

Examples

## See the 'mut_matrix_stranded()' example for how we obtained the
## mutation matrix with transcriptional strand information:
mut_mat_s <- readRDS(system.file("states/mut_mat_s_data.rds",
                                    package="MutationalPatterns"))

## Extract the signatures.
## This is a computationally intensive task, so we load a precomputed
## version instead.
# nmf_res_strand <- extract_signatures(mut_mat_s, rank = 2)
nmf_res_strand <- readRDS(system.file("states/nmf_res_strand_data.rds",
                                    package="MutationalPatterns"))

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

## Generate the plot
plot_192_profile(nmf_res_strand$signatures)
[Package MutationalPatterns version 1.12.0 Index]