R: Plot strand per base substitution type

plot_strand {MutationalPatterns}

R Documentation

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 = "relative", colors)

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

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")