plot_strand: Plot strand per base substitution type

Description Usage Arguments Value See Also Examples

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(strand_bias_df, mode = "relative", colors)

Arguments

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

Value

Barplot

See Also

mut_matrix_stranded, strand_occurrences, plot_strand_bias

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
## 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")


Search within the MutationalPatterns package
Search all R packages, documentation and source code

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.