Create a generalized Venn Diagram analog for sample membership in multiple assays, using the upset algorithm in UpSetR
Source: R/upsetSamples.R
upsetSamples.Rd
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 thedata.frame()
constructor (default FALSE).- ...
parameters passed to
UpSetR::upset
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.
Examples
data(miniACC)
upsetSamples(miniACC)
upsetSamples(miniACC, nsets = 3, nintersects = 3)