plot_signature_strand_bias: Plot signature strand bias

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

Plot signature strand bias

Description

Plot strand bias per mutation type for each signature.

Usage

plot_signature_strand_bias(signatures_strand_bias)

Arguments

signatures_strand_bias

Signature matrix with 192 features

Value

Barplot

See Also

link{extract_signatures}, link{mut_matrix}

Examples

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

## Extracting signatures can be computationally intensive, so
## we use pre-computed data generated with the following command:
# nmf_res_strand <- extract_signatures(mut_mat_s, rank = 2)

nmf_res_strand <- readRDS(system.file("states/nmf_res_strand_data.rds",
  package = "MutationalPatterns"
))

## Provide column names for the plot.
colnames(nmf_res_strand$signatures) <- c("Signature A", "Signature B")

## Creat figure
plot_signature_strand_bias(nmf_res_strand$signatures)

## You can also plot the bias of samples
plot_signature_strand_bias(mut_mat_s[, c(1, 2)])

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