plot_contribution {MutationalPatterns}R Documentation

Plot signature contribution barplot

Description

Plot contribution of signatures

Usage

plot_contribution(contribution, signatures, index = c(), coord_flip = FALSE,
  mode = "relative", palette = c())

Arguments

contribution

Signature contribution matrix

signatures

Signature matrix

index

optional sample subset parameter

coord_flip

Flip X and Y coordinates, default = FALSE

mode

"relative" or "absolute"; to plot the relative contribution or absolute number of mutations, default = "relative"

palette

A color palette like c("#FF0000", "#00FF00", "9999CC") that will be used as colors in the plot. By default, ggplot2's colors are used to generate a palette.

Value

Stacked barplot with contribution of each signature for each sample

See Also

extract_signatures, mut_matrix

Examples

## See the 'mut_matrix()' example for how we obtained the following
## mutation matrix.
mut_mat <- readRDS(system.file("states/mut_mat_data.rds",
                                package="MutationalPatterns"))

## Extracting signatures can be computationally intensive, so
## we use pre-computed data generated with the following command:
# nmf_res <- extract_signatures(mut_mat, rank = 2)

nmf_res <- readRDS(system.file("states/nmf_res_data.rds",
                    package="MutationalPatterns"))

## Optionally set column and row names.
colnames(nmf_res$signatures) = c("Signature A", "Signature B")
rownames(nmf_res$contribution) = c("Signature A", "Signature B")

## The following are examples of contribution plots.
plot_contribution(nmf_res$contribution,
                    nmf_res$signature,
                    mode = "relative")

plot_contribution(nmf_res$contribution,
                    nmf_res$signature,
                    mode = "absolute")

plot_contribution(nmf_res$contribution,
                    nmf_res$signature,
                    mode = "absolute",
                    index = c(1,2))

plot_contribution(nmf_res$contribution,
                    nmf_res$signature,
                    mode = "absolute",
                    coord_flip = TRUE)
[Package MutationalPatterns version 1.12.0 Index]