plot_strand_bias {MutationalPatterns}R Documentation

Plot strand bias per base substitution type per group

Description

Plot strand bias per base substitution type per group

Usage

plot_strand_bias(strand_bias, colors)

Arguments

strand_bias

data.frame, result from strand_bias function

colors

Optional color vector with 6 values for plotting

Value

Barplot

See Also

mut_matrix_stranded, strand_occurrences, strand_bias_test plot_strand

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")

## Perform the strand bias test.
strand_counts = strand_occurrences(mut_mat_s, by=tissue)
strand_bias = strand_bias_test(strand_counts)

## Plot the strand bias.
plot_strand_bias(strand_bias)
[Package MutationalPatterns version 1.4.3 Index]