plot_indel_contexts {MutationalPatterns} | R Documentation

## Plot the indel contexts

### Description

Plot the indel contexts

### Usage

    plot_indel_contexts(
      counts,
      same_y = FALSE,
      extra_labels = FALSE,
      condensed = FALSE
    )

### Arguments

`counts` | A tibble containing the number of indels per COSMIC context.
`same_y` | A boolean describing whether the same y axis should be used for all samples.
`extra_labels` | A boolean describing whether extra labels should be added. These can clarify the plot, but will shift when different plot widths are used. We recommend saving a plot with a width of 12, when using this argument.
`condensed` | More condensed plotting format. Default = F.

### Details

Plots the number of indels COSMIC context per sample. It takes a tibble with counts as its input. This tibble can be generated by 'count_indel_contexts()'. Each sample is plotted in a separate facet. The same y axis can be used for all samples or a separate y axis can be used. The facets at the top show the indel types. First the C and T deletions Then the C and T insertions. Next are the multi base deletions and insertions. Finally the deletions with microhomology (mh) are shown. The x-axis at the bottom shows the number of repeat units. For mh deletions the microhomology length is shown.

### Value

A ggplot figure.

### See Also

`count_indel_contexts`, `plot_main_indel_contexts`

Other Indels: `count_indel_contexts()`, `get_indel_context()`, `plot_compare_indels()`, `plot_main_indel_contexts()`

### Examples

    ## Get The indel counts
    ## See 'count_indel_contexts()' for more info on how to do this.
    indel_counts <- readRDS(system.file("states/blood_indel_counts.rds",
      package = "MutationalPatterns"
    ))

    ## Plot contexts
    plot_indel_contexts(indel_counts)

    ## Use the same y axis for all samples.
    plot_indel_contexts(indel_counts, same_y = TRUE)

    ## Add extra labels to make plot clearer
    plot_indel_contexts(indel_counts, extra_labels = TRUE)

    ## Create a more condensed plot
    plot_indel_contexts(indel_counts, condensed = TRUE)

[Package MutationalPatterns version 3.0.1 Index]