Pretty MAF summary — pretty_MAF_summary • GAMBLR.viz

Generates a visually appealling alternative to MAFtools `plotmafSummary“.

Usage

pretty_MAF_summary(
  maf_data,
  these_samples_metadata,
  base_size = 4,
  top_n = 10,
  point_size = 0.5,
  one_per_sample = FALSE,
  gene_sizes,
  returnEverything = FALSE
)

Arguments

maf_data: A data frame containing the mutation data.
base_size: Base size of fonts to use in Morons theme
top_n: Number of genes to show in top_n panel (default 10)
point_size: Size of points to use in ggbeeswarm plot (default 0.5)
returnEverything: Set to TRUE to get the underlying numbers and all panels as a list

Value

A plot

Details

This function reproduces the multi-panel MAF summary plot generated by MAFtools. The colour, plot aesthetics etc utilize GAMBLR colours and are consistent with other GAMBLR.viz plots such as prettyOncoplot.

Examples

suppressMessages(library(GAMBLR.open))
FL_meta <- GAMBLR.open::get_gambl_metadata() %>%
    dplyr::filter(pathology == "FL") %>%
    check_and_clean_metadata(.,duplicate_action="keep_first")
#> Using the bundled metadata in GAMBLR.data...
FL_coding <- GAMBLR.open::get_coding_ssm(these_samples_metadata = FL_meta)
#> Using the bundled SSM calls (.maf) calls in GAMBLR.data...
#> after linking with metadata, we have mutations from 215 samples

pretty_MAF_summary(FL_coding)


pretty_MAF_summary(FL_coding, top_n = 22, base_size = 6)