AmpliconHeatmap: Amplicon heatmap

In umiAnalyzer: Tools for Analyzing Sequencing Data with Unique Molecular Identifiers

Description

Generates a heatmap of mutations with sample clustering using pheatmap.

Usage

AmpliconHeatmap(
  object,
  filter.name = "default",
  cut.off = 5,
  left.side = "columns",
  amplicons = NULL,
  samples = NULL,
  abs.count = FALSE,
  font.size = 10
)

Arguments

object	Requires a UMI sample or UMI experiment object
filter.name	Name of the filter to be plotted.
cut.off	How many variant reads are necessary to consider a variant above background? Default is 5 reads.
left.side	Show assays or sample on the left side of the heatmap. Default is assays
amplicons	(Optional) character vector of amplicons to be plotted.
samples	(Optional) character vector of samples to be plotted.
abs.count	Logical. Should absolute counts be used instead of frequencies?
font.size	Font size to use for sample labels

Value

A graphics object

Examples

## Not run: 
library(umiAnalyzer)

main = system.file('extdata', package = 'umiAnalyzer')
samples <- list.dirs(path = main, full.names = FALSE, recursive = FALSE)
simsen <- createUmiExperiment(experimentName = 'example',mainDir = main,sampleNames = samples)
simsen <- filterUmiObject(simsen)

hmap <- AmpliconHeatmap(simsen)

## End(Not run)

umiAnalyzer documentation built on Nov. 25, 2021, 9:07 a.m.