plot_contribution_heatmap {MutationalPatterns}R Documentation

Plot signature contribution heatmap

Description

Plot relative contribution of signatures in a heatmap

Usage

plot_contribution_heatmap(contribution, sig_order, cluster_samples = TRUE,
  method = "complete", plot_values = FALSE)

Arguments

contribution

Signature contribution matrix

sig_order

Character vector with the desired order of the signature names for plotting. Optional.

cluster_samples

Hierarchically cluster samples based on eucledian distance. Default = T.

method

The agglomeration method to be used for hierarchical clustering. This should be one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC). Default = "complete".

plot_values

Plot relative contribution values in heatmap. Default = F.

Value

Heatmap with relative contribution of each signature for each sample

See Also

extract_signatures, mut_matrix, plot_contribution

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"))

## Set signature names as row names in the contribution matrix
rownames(nmf_res$contribution) = c("Signature A", "Signature B")

## Define signature order for plotting
sig_order = c("Signature B", "Signature A")


## Contribution heatmap with signatures in defined order
plot_contribution_heatmap(nmf_res$contribution, 
                          sig_order = c("Signature B", "Signature A"))

## Contribution heatmap without sample clustering
plot_contribution_heatmap(nmf_res$contribution, 
                          sig_order = c("Signature B", "Signature A"), 
                          cluster_samples = FALSE, method = "complete")
[Package MutationalPatterns version 1.6.1 Index]