generateCOSMICMutSigSimHeatmap: Computes and plot the cosine similarity of each individual...

In ashishjain1988/MAFDash: Create an HTML Dashboard to Visualize Data from MAF File

Computes and plot the cosine similarity of each individual signature is computed against each COSMIC signature from COMIC V3.2

Description

This function computes and plot the cosine similarity of each individual signature is computed against each COSMIC signature from COMIC V3.2. The cosine similarity is a value between 0 (distinct) and 1 (identical) and indicates how much two vectors are alike.

Usage

generateCOSMICMutSigSimHeatmap(
  mymaf,
  use_silent_mutations = FALSE,
  full_output = FALSE,
  show_broad_categories = TRUE,
  clin_data = NULL,
  clin_data_colors = NULL,
  add_sample_names = NULL,
  savename = NULL,
  fig_height = NULL,
  fig_width = NULL
)

Arguments

mymaf	mutation count matrix (dimensions: a mutation features X n samples)
use_silent_mutations	96 mutation count matrix (dimensions: a mutation features X m samples)
full_output	return full output including the etiology matrix and plot data
show_broad_categories	To show broad etiology categories
clin_data	Clinical data to be plotted in the heatmap
clin_data_colors	Clinical data colors
add_sample_names	Whether or not to add column labels; if set to NULL, will add labels only if # samples less than 10
savename	file name of the plot
fig_height	Output height (inches); set to NULL to size automatically; only used if savename is set.
fig_width	Output width (inches); set to NULL to size automatically; only used if savename is set.

Value

Complex Heatmap object. If full_output is TRUE it will consist of a list including heatmap object, etiology matrix and plot data.

Examples

library(MAFDash)
library(maftools)
library(ComplexHeatmap)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
val<-generateCOSMICMutSigSimHeatmap(read.maf(maf));draw(val)

ashishjain1988/MAFDash documentation built on Feb. 9, 2023, 9:54 p.m.