upsetSamples | R Documentation |
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,
...
)
MultiAssayExperiment |
A |
nsets |
numeric(1) The number of sets to analyze. If specified,
|
sets |
character() A character vector of names in MultiAssayExperiment
to use. If specified, |
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
|
... |
parameters passed to |
Produces a visualization of set intersections using the UpSet matrix design
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.
Vincent J Carey
data(miniACC)
upsetSamples(miniACC)
upsetSamples(miniACC, nsets = 3, nintersects = 3)
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