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

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

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

Description

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

Usage

upsetSamples(
  MultiAssayExperiment,
  nsets = NULL,
  sets = names(MultiAssayExperiment),
  nintersects = NA_integer_,
  order.by = "freq",
  check.names = FALSE,
  ...
)

Arguments

MultiAssayExperiment	A MultiAssayExperiment object
nsets	numeric(1) The number of sets to analyze. If specified, sets will be ignored.
sets	character() A character vector of names in MultiAssayExperiment to use. If specified, nsets will be ignored.
nintersects	numeric(1) The number of intersections to plot. By default, 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.
check.names	logical(1) Whether to munge names as in the data.frame() constructor (default FALSE).
...	parameters passed to UpSetR::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 UpSetR::upset function requires data.frame input and has many parameters to tune appearance of the result. Assay name handling is important for interpretability.

Author(s)

Vincent J Carey

Examples

data(miniACC)
upsetSamples(miniACC)
upsetSamples(miniACC, nsets = 3, nintersects = 3)

waldronlab/MultiAssayExperiment documentation built on Nov. 4, 2024, 7:51 a.m.