plot_profile_region: Plot 96 trinucleotide profile per subgroup

In CuppenResearch/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Plot 96 trinucleotide profile per subgroup

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)])

CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.