plot_profile_heatmap {MutationalPatterns} | R Documentation

## Plot a mutation matrix as a heatmap

### Description

Function to plot a SNV mutation matrix as a heatmap. This is especially usefull when looking at a wide mutational context.

### Usage

    plot_profile_heatmap(mut_matrix, by = NA, max = 0.02, condensed = FALSE)

### Arguments

`mut_matrix` | Matrix containing mutation counts.
`by` | Optional grouping variable
`max` | Maximum value used for plotting the relative contributions. Contributions that are higher will have the maximum colour. (Default: 0.02)
`condensed` | More condensed plotting format. Default = F.

### Value

A ggplot object

### See Also

`mut_matrix`, `plot_96_profile`, `plot_river`

### Examples

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

    ## Create heatmap of profile
    plot_profile_heatmap(mut_mat, max = 0.1)

    ## Get extended matrix
    mut_mat_extended <- readRDS(system.file("states/mut_mat_data_extended.rds",
      package = "MutationalPatterns"
    ))

    ## Create heatmap of extended profile
    plot_profile_heatmap(mut_mat_extended)

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

    plot_profile_heatmap(mut_mat_extended, by = tissue)

    ## Or plot the heatmap per sample.
    plot_profile_heatmap(mut_mat_extended,
      by = colnames(mut_mat_extended),
      max = 0.05
    )

    ## Create a condensed heatmap of extended profile
    plot_profile_heatmap(mut_mat_extended, condensed = TRUE)

[Package MutationalPatterns version 3.0.1 Index]