AmpliconHeatmap {umiAnalyzer}

Amplicon heatmap

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)