upsetSamples {MultiAssayExperiment} | R Documentation |
UpSetR
Create a generalized Venn Diagram analog for sample membership in multiple
assays, using the upset algorithm in UpSetR
upsetSamples(MultiAssayExperiment, nsets = length(MultiAssayExperiment), nintersects = 24, order.by = "freq", nameFilter = force, check.names = FALSE, ...)
MultiAssayExperiment |
instance of
|
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 |
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
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.
Vincent J Carey
data(miniACC) upsetSamples(miniACC) upsetSamples(miniACC, nameFilter = function(x) substr(x, 1, 5))