plot_contribution {MutationalPatterns} | R Documentation |
Plot contribution of signatures
plot_contribution(contribution, signatures, index = c(), coord_flip = FALSE, mode = "relative", palette = c())
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. |
Stacked barplot with contribution of each signature for each sample
extract_signatures
,
mut_matrix
## 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)