plot_strand {MutationalPatterns} | R Documentation |
For each base substitution type and transcriptional strand the total number of mutations and the relative contribution within a group is returned.
plot_strand(strand_bias_df, mode = "relative", colors)
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 |
Barplot
mut_matrix_stranded
,
strand_occurrences
,
plot_strand_bias
## 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")