generateOncoPlot: Function to generate a dashboard from a MAF file

In MAFDash: Create an HTML Dashboard to Visualize Data from MAF File

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.

Author(s)

Mayank Tandon, Ashish Jain

Examples

library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
generateOncoPlot(read.maf(maf))

MAFDash documentation built on April 1, 2022, 9:05 a.m.