Sample to sample distances — plotBarcodeDistance • bartools

Plot sample distances between barcode sets / samples

Usage

plotBarcodeDistance(
  dgeObject,
  method = "euclidean",
  upper = TRUE,
  clustered = TRUE,
  title = "Sample Distances"
)

plotBarcodeDistance(
  dgeObject,
  method = "euclidean",
  upper = TRUE,
  clustered = TRUE,
  title = "Sample Distances"
)

Arguments

dgeObject: DGEList object with barcode counts.
method: Distance metric to use (string). One of "euclidean", "maximum", "manhattan", "canberra", "binary" or "minkowski". Refer to stats::dist for details. Default = `euclidean`.
upper: Plot only the upper half of the matrix (boolean). Default = `TRUE`.
clustered: Cluster rows and columns of matrix (boolean). Default = `TRUE`.
title: Title of plot (string). Default = `Sample Distances - method`.
counts: matrix/dataframe containing raw or normalised counts
name: title of plot

Value

Returns a heatmap of sample distances using desired clustering

Examples

plotBarcodeDistance(test.dge$counts)
#> Error in plotBarcodeDistance(test.dge$counts): Please supply a valid DGEList object as input
data(test.dge)
plotBarcodeDistance(test.dge)