upsetSamples: Create a generalized Venn Diagram analog for sample...

In MultiAssayExperiment: Software for the integration of multi-omics experiments in Bioconductor

Description

Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR

Usage

upsetSamples(
  MultiAssayExperiment,
  nsets = length(MultiAssayExperiment),
  nintersects = 24,
  order.by = "freq",
  nameFilter = force,
  check.names = FALSE,
  ...
)

Arguments

MultiAssayExperiment	A MultiAssayExperiment instance
nsets	integer number of sets to analyze
nintersects	Number of intersections to plot. If set to NA, all intersections will be plotted.
order.by	How the intersections in the matrix should be ordered by. Options include frequency (entered as "freq"), degree, or both in any order.
nameFilter	function, defaulting to force, to manipulate colnames of incidence matrix
check.names	logical(1) used when incidence matrix is coerced to data.frame for use in UpSetR::upset
...	parameters passed to upset

Value

Produces a visualization of set intersections using the UpSet matrix design

Note

This function is intended to provide convenient visualization of assay availability configurations in MultiAssayExperiment instances. The upset function requires data.frame input and has many parameters to tune appearance of the result. Assay name handling is important for interpretability, and the nameFilter parameter may be useful to simplify resulting outputs.

Author(s)

Vincent J Carey

Examples

data(miniACC)
upsetSamples(miniACC)
upsetSamples(miniACC, nameFilter = function(x) substr(x, 1, 5))

MultiAssayExperiment documentation built on Nov. 8, 2020, 8:10 p.m.