plot_strand: Plot strand per base substitution type

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

Plot strand per base substitution type

Description

For each base substitution type and transcriptional strand the total number of mutations and the relative contribution within a group is returned.

Usage

plot_strand(strand_bias_df, mode = c("relative", "absolute"), colors = NA)

Arguments

strand_bias_df	data.frame, result from strand_bias function
mode	Either "absolute" for absolute number of mutations, or "relative" for relative contribution, default = "relative"
colors	Optional color vector for plotting with 6 values

Value

Barplot

See Also

mut_matrix_stranded, strand_occurrences, plot_strand_bias

Examples

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

## Load a reference genome.
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)

tissue <- c(
  "colon", "colon", "colon",
  "intestine", "intestine", "intestine",
  "liver", "liver", "liver"
)

strand_counts <- strand_occurrences(mut_mat_s, by = tissue)

## Plot the strand in relative mode.
strand_plot <- plot_strand(strand_counts)

## Or absolute mode.
strand_plot <- plot_strand(strand_counts, mode = "absolute")

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