plot_spectrum: Plot point mutation spectrum

In MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

Description

Plot point mutation spectrum

Usage

plot_spectrum(
  type_occurrences,
  CT = FALSE,
  by = NA,
  indv_points = FALSE,
  error_bars = c("95%_CI", "stdev", "SEM", "none"),
  colors = NA,
  legend = TRUE,
  condensed = FALSE
)

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
indv_points	Whether to plot the individual samples as points, default = FALSE
error_bars	The type of error bars to plot. * '95 * 'stdev' for standard deviations; * 'SEM' for the standard error of the mean (NOT recommended); * 'none' Do not plot any error bars;
colors	Optional color vector with 7 values
legend	Plot legend, default = TRUE
condensed	More condensed plotting format. Default = F.

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)

## You can also include individual sample points.
plot_spectrum(type_occurrences, CT = TRUE, indv_points = TRUE)

## You can also change the type of error bars
plot_spectrum(type_occurrences, error_bars = "stdev")

## Or plot spectrum per tissue
tissue <- c(
  "colon", "colon", "colon",
  "intestine", "intestine", "intestine",
  "liver", "liver", "liver"
)

plot_spectrum(type_occurrences, by = tissue, CT = TRUE)

## Or plot the spectrum per sample. Error bars are set to 'none', because they can't be plotted.
plot_spectrum(type_occurrences, by = names(vcfs), CT = TRUE, error_bars = "none")

## Plot it in a more condensed manner, 
## which is is ideal for publications.
plot_spectrum(type_occurrences, 
by = names(vcfs), 
CT = TRUE, 
error_bars = "none",
condensed = 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
)

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