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 2.0.0 Index]