ssvFeatureUpset: ssvFeatureUpset

In jrboyd/seqsetvis: Set Based Visualizations for Next-Gen Sequencing Data

ssvFeatureUpset

Description

Uses the UpSetR package to create an UpSetR::upset plot of region overlaps.

Usage

ssvFeatureUpset(
  object,
  return_UpSetR = FALSE,
  nsets = NULL,
  nintersects = 15,
  order.by = "freq",
  ...
)

Arguments

object	will be passed to ssvMakeMembTable for conversion to membership matrix
return_UpSetR	If TRUE, return the UpSetR object, The default is FALSE and results in a ggplotified version compatible with cowplot etc.
nsets	Number of sets to look at
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.
...	Additional parameters passed to upset in the UpSetR package.

Value

ggplot version of UpSetR plot

Examples

data(CTCF_in_10a_overlaps_gr)
ssvFeatureUpset(list(1:3, 2:6))
ssvFeatureUpset(CTCF_in_10a_overlaps_gr)
ssvFeatureUpset(S4Vectors::mcols(CTCF_in_10a_overlaps_gr)[,2:3])

jrboyd/seqsetvis documentation built on Dec. 10, 2024, 11:23 a.m.