Plot barcode heatmap

Takes a DGEList with barcode counts, selects the n most abundant barcodes per sample and plots a heatmap. Stars indicate the most abundant barcodes in the respective sample.

Usage

plotBarcodeHeatmap(
  dgeObject,
  topN = 5,
  name = "CPM",
  showBarcodes = FALSE,
  group = NULL,
  colAnnot = NULL,
  discrete = FALSE,
  discreteThreshold = 1,
  labelTopBarcodes = TRUE
)

Arguments

dgeObject

DGEList object with barcode counts.

topN

Number of top barcodes per sample to show (integer). Default = `5`.

name

String of the heatmap scale name (string). Default = `CPM`.

showBarcodes

Show barcode names on the heatmap (boolean). Default = `FALSE`.

group

Optional, column name in sample metadata to group samples by (string).

colAnnot

List of vectors assigning colours to each level of metadata.

discrete

Show presence/absence of barcodes instead of abundance (boolean). Default = `FALSE`.

discreteThreshold

Threshold for presence of barcode in samples (decimal). Default = `1`.

labelTopBarcodes

Label top barcodes within a sample (boolean). Default = `TRUE`.

Value

Returns a heatmap

Examples

data(test.dge)
plotBarcodeHeatmap(test.dge)