MAFDash (version 0.2.1)

getMAFDashboard: Function to generate a dashboard from a MAF file.

Description

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

Usage

getMAFDashboard(
  maf = NULL,
  plotList = NULL,
  outputFileName = "dashboard.html",
  outputFileTitle = "MAF Dash",
  outputFilePath = tempdir()
)

Arguments

maf

MAF object or MAF file path information in the MAF format

plotList

A named list denoting which plots to draw. List elements can be: - boolean, if the name matches one of built-in plots: "summary_plot","burden","oncoplot","cooccurence","heatmap" - ggplot, ComplexHeatmap, or plotly object - file path to image (must be absolute path) The default value (if set to NULL) is 'list("summary_plot"=TRUE,"burden"=TRUE,"oncoplot"=TRUE,"cooccurence"=TRUE,"heatmap"=TRUE)' The order of the list determines the order of the tabs, and list names are used as tab titles.

outputFileName

The name of the output html dashboard file

outputFileTitle

The title of the output html dashboard

outputFilePath

The path of the output html dashboard

Value

No return value, the MAF dashboard html file is created in the given output folder

Examples

# NOT RUN {
library(MAFDash)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
# }
# NOT RUN {
getMAFDashboard(maf = maf,outputFilePath=tempdir())
# }