Plot UpSet diagram of orthogroup sharing — plot_upset • paneffectR

Creates an UpSet plot showing intersections of orthogroups across assemblies. Useful for visualizing core, accessory, and unique orthogroups.

Usage

plot_upset(pa, min_size = 1, max_sets = NULL, order_by = "freq", ...)

Arguments

pa: A pa_matrix object.
min_size: Integer. Minimum intersection size to show (default: 1).
max_sets: Integer. Maximum number of sets to display. If NULL (default), all assemblies are shown.
order_by: Character. How to order intersections: "freq" (by size, default) or "degree" (by number of sets in intersection).
...: Additional arguments passed to UpSetR::upset().

Value

An UpSetR plot object (can be printed to display).

Examples

if (FALSE) { # \dontrun{
plot_upset(pa)
plot_upset(pa, min_size = 2)
plot_upset(pa, order_by = "degree")
} # }