plotSignatures: Plot Signatures with automated detection of type of mutations

In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib

Plot Signatures with automated detection of type of mutations

Description

This function checks the channels of the input matrix, determines the type of mutations and plots using the most appropriate signature plot.

Usage

plotSignatures(
  signature_data_matrix,
  output_file = NULL,
  plot_sum = TRUE,
  overall_title = "",
  add_to_titles = NULL,
  mar = NULL,
  howManyInOnePage = 100,
  ncolumns = 3
)

Arguments

signature_data_matrix	matrix of signatures, signatures as columns and channels as rows
output_file	set output file, should end with ".jpg", "png" or ".pdf". If output_file==null, output will not be to a file, but will still run the plot functions. The option output_file==null can be used to add this plot to a larger output file.
plot_sum	whether the sum of the channels should be plotted. If plotting signatures this should be FALSE, but if plotting sample catalogues, this can be set to TRUE to display the number of mutations in each sample.
overall_title	set the overall title of the plot
mar	set the option par(mar=mar)
howManyInOnePage	how many signatures or catalogues should be plotted on one page. Multiple pages are plotted if more signatures/catalogues to plot have been requested
ncolumns	how many columns should be used to arrange the signatures/catalogues to plot

Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.