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

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

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() 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 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

Vincent J Carey

Examples


data(miniACC)
upsetSamples(miniACC)

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