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 1.99.3 Index]