upsetSamples {MultiAssayExperiment} | R Documentation

## 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 = 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))

[Package MultiAssayExperiment version 1.12.6 Index]