plot_spectrum {MutationalPatterns} | R Documentation |
Plot point mutation spectrum
plot_spectrum(type_occurrences, CT = FALSE, by, colors, legend = TRUE)
type_occurrences |
Type occurrences matrix |
CT |
Distinction between C>T at CpG and C>T at other sites, default = FALSE |
by |
Optional grouping variable |
colors |
Optional color vector with 7 values |
legend |
Plot legend, default = TRUE |
Spectrum plot
read_vcfs_as_granges
,
mut_type_occurrences
## See the 'read_vcfs_as_granges()' example for how we obtained the ## following data: vcfs <- readRDS(system.file("states/read_vcfs_as_granges_output.rds", package="MutationalPatterns")) ## Load a reference genome. ref_genome = "BSgenome.Hsapiens.UCSC.hg19" library(ref_genome, character.only = TRUE) ## Get the type occurrences for all VCF objects. type_occurrences = mut_type_occurrences(vcfs, ref_genome) ## Plot the point mutation spectrum over all samples plot_spectrum(type_occurrences) ## Or with distinction of C>T at CpG sites plot_spectrum(type_occurrences, CT = TRUE) ## Or without legend plot_spectrum(type_occurrences, CT = TRUE, legend = FALSE) ## Or plot spectrum per tissue tissue <- c("colon", "colon", "colon", "intestine", "intestine", "intestine", "liver", "liver", "liver") plot_spectrum(type_occurrences, by = tissue, CT = TRUE) ## You can also set custom colors. my_colors = c("pink", "orange", "blue", "lightblue", "green", "red", "purple") ## And use them in a plot. plot_spectrum(type_occurrences, CT = TRUE, legend = TRUE, colors = my_colors)