plot_spectrum {MutationalPatterns}R Documentation

Plot point mutation spectrum

Description

Plot point mutation spectrum

Usage

plot_spectrum(type_occurrences, CT = FALSE, by, colors, legend = TRUE)

Arguments

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

Value

Spectrum plot

See Also

read_vcfs_as_granges, mut_type_occurrences

Examples

## 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)
[Package MutationalPatterns version 1.12.0 Index]