Forest Plot.

Create a forest plot comparing mutation frequencies for a set of genes between two groups.

Usage

prettyForestPlot(
  maf,
  mutmat,
  metadata,
  genes,
  keepGeneOrder = FALSE,
  min_mutations = 1,
  comparison_column,
  rm_na_samples = FALSE,
  comparison_values = FALSE,
  separate_hotspots = FALSE,
  comparison_name = FALSE,
  custom_colours = FALSE,
  custom_labels = FALSE,
  max_q = 1,
  base_size = 10
)

Arguments

maf

A maf data frame. Minimum required columns are Hugo_Symbol and Tumor_Sample_Barcode.

mutmat

Optional argument for binary mutation matrix. If not supplied, function will generate this matrix from the file used in argument "maf".

metadata

Metadata for the comparisons. Minimum required columns are Tumor_Sample_Barcode and the column assigning each case to one of two groups.

genes

An optional vector of genes to restrict your plot to. If no gene-list is supplied, the function will extract all mutated genes from the incoming maf. See min_mutations parameter for more info.

keepGeneOrder

Set to TRUE if you want to preserve the gene order specified.

min_mutations

Optional parameter for when no `genes` is provided. This parameter ensures only genes with n mutations are kept in `genes`. Default value is 1, this means all genes in the incoming maf will be plotted.

comparison_column

Mandatory: the name of the metadata column containing the comparison values.

rm_na_samples

Set to TRUE to remove 0 mutation samples. Default is FALSE.

comparison_values

Optional: If the comparison column contains more than two values or is not a factor, specify a character vector of length two in the order you would like the factor levels to be set, reference group first.

separate_hotspots

Optional: If you would like to treat hotspots separately from other mutations in any gene. Requires that the maf file is annotated with [GAMBLR::annotate_hotspots].

comparison_name

Optional: Specify the legend title if different from the comparison column name.

custom_colours

Optional: Specify a named vector of colours that match the values in the comparison column.

custom_labels

Optional: Specify custom labels for the legend categories. Must be in the same order as comparison_values.

max_q

cut off for q values to be filtered in fish test

base_size

Numeric value to specify font size of the gene labels on the plot. Default is 10.

Value

A convenient list containing all the data frames that were created in making the plot, including the mutation matrix. It also produces (and returns) ggplot object with a side-by-side forest plot and bar plot showing mutation incidences across two groups.

Details

This function returns two types of plot (box plot and forest plot), the user can either view them separately or arranged on the same grob. In addition this function also lets the user control the mutation frequencies of the plotted genes. If no `genes` is provided, this function auto-defaults to all genes in the incoming maf. The user can then control the minimum number of mutations requirement for a gene to be included in the plot. This is done with the `min_mutations` parameter. For extended examples on how to use this function, refer to the example inside the function documentation or the vignettes.

Examples

library(GAMBLR.open)
suppressWarnings(
  suppressMessages({

metadata = get_gambl_metadata()
this_meta = dplyr::filter(metadata, pairing_status == "matched")
this_meta = dplyr::filter(this_meta, pathology %in% c("FL", "DLBCL")) %>%
            check_and_clean_metadata(.,duplicate_action="keep_first")

maf = get_coding_ssm(these_samples_metadata = this_meta)

plots = prettyForestPlot(maf = maf,
                 metadata = this_meta,
                 genes = c("ATP6V1B2",
                           "EZH2",
                           "TNFRSF14",
                           "RRAGC"),
                 comparison_column = "pathology",
                 comparison_values = c("DLBCL",
                                       "FL"),
                 separate_hotspots = FALSE,
                 comparison_name = "FL vs DLBCL")
plots$arranged

}))