Plot strand bias per base substitution type

Share:

Description

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

Usage

1
plot_strand_bias(strand_bias, colors)

Arguments

strand_bias

data.frame, result from strand_bias function

colors

Optional color vector for plotting with 6 values

Value

Barplot

See Also

mut_matrix_stranded, strand_occurrences, strand_bias_test plot_strand

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
## 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)

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.