plot_strand_bias {MutationalPatterns} | R Documentation |
Plot strand bias per base substitution type per group
plot_strand_bias(strand_bias, colors)
strand_bias |
data.frame, result from strand_bias function |
colors |
Optional color vector with 6 values for plotting |
Barplot
mut_matrix_stranded
,
strand_occurrences
,
strand_bias_test
plot_strand
## 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)