plot_profile_region: Plot 96 trinucleotide profile per subgroup

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description

Plot relative contribution of 96 trinucleotides per subgroup. This can be genomic regions but could also be other subsets. The function uses a matrix generated by 'lengthen_mut_matrix()' as its input.

Usage

plot_profile_region(
  mut_matrix,
  mode = c("relative_sample", "relative_sample_feature", "absolute"),
  colors = NULL,
  ymax = 0.2,
  condensed = FALSE
)

Arguments

mut_matrix	Mutation matrix
mode	'relative_sample', 'relative_sample_feature' or 'absolute' When 'relative_sample', the number of variants will be shown divided by the total number of variants in that sample. When 'relative_sample_feature', the number of variants will be shown divided by the total number of variants in that sample. and genomic region.
colors	6 value color vector
ymax	Y axis maximum value, default = 0.2
condensed	More condensed plotting format. Default = FALSE.

Value

96 trinucleotide profile plot per region

See Also

mut_matrix

Other genomic_regions: bin_mutation_density(), lengthen_mut_matrix(), plot_spectrum_region(), split_muts_region()

Examples

## See the 'lengthen_mut_matrix()' example for how we obtained the
## mutation matrix information:
mut_mat_long <- readRDS(system.file("states/mut_mat_longregions.rds",
  package = "MutationalPatterns"
))

## Plot the 96-profile of three samples
plot_profile_region(mut_mat_long[, c(1, 4, 7)])

MutationalPatterns documentation built on Nov. 14, 2020, 2:03 a.m.