plot_indel_contexts: Plot the indel contexts

In CuppenResearch/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

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)

CuppenResearch/MutationalPatterns documentation built on Nov. 23, 2022, 4:13 a.m.