MAFDash (version 0.2.1)

generateOncoPlot: Function to generate a dashboard from a MAF file

Description

This function created an HTML file containing the different figures and plots explaining the MAF dataset.

Usage

generateOncoPlot(
  maf,
  cohort_freq_thresh = 0.01,
  auto_adjust_cohort_freq = TRUE,
  genes_to_plot = NULL,
  include_all = FALSE,
  oncomat_only = FALSE,
  title_text = "",
  custom_column_order = NULL,
  add_clinical_annotations = FALSE,
  clin_data_colors = NULL
)

Arguments

maf

The MAF object

cohort_freq_thresh

Fraction of cohort that a gene must be mutated to select for display

auto_adjust_cohort_freq

Whether or not to automatically adjust the frequen

genes_to_plot

Character vector, data frame, or tab-delimited file name with genes to plot. Data frame or file should contain a column named "Hugo_Symbol" with gene symbols, and optionally, a column named "Reason" for labeling the plot

include_all

Flag to include all the samples including the missing one (Default: FALSE)

oncomat_only

Whether or not to return just the oncoplot matrix

title_text

The title of the plot

custom_column_order

A list containing the order of samples to show in the plot (Optional)

add_clinical_annotations

Whether or not to try to plot column annotations from the 'clinical.data' slot of the MAF object

clin_data_colors

Named list of colors for clinical annoations

Value

A ComplexHeatmap object if 'oncomat_only' is FALSE or a character matrix if 'oncomat_only' is TRUE.

Examples

# NOT RUN {
library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
generateOncoPlot(read.maf(maf))

# }