upsetPeaks: upsetPeaks

In amitjavilaventura/seqViewR: Visualization of Omics And Sequencing Data In R

upsetPeaks

Description

This function calls 'getVennCounts()' and draws and UpSet plot using the UpSetR package.

Usage

upsetPeaks(
  peaks,
  conds = names(peaks),
  conds_order = conds,
  order.by = "freq",
  mainbar.y.label = "Intersect size",
  sets.x.label = "Set size",
  ...
)

Arguments

peaks	List of dataframes with the genomic coordinates of the regions to overlap. Dataframes must contain the columns seqnames, start, end.
conds	Character with the same length as the 'peaks' list. The names that are given to the diferente objects in the 'peaks' list. Default: 'names(peaks)'
conds_order	Character of the same length as 'conds'. Same values as in 'conds' but with the desired order of priority. Default: 'conds'.
order.by	Same as in UpSetR::upset(). One of "freq", "degree" or both.
mainbar.y.label	Same as in UpSetR::upset().
sets.x.label	Same as in UpSetR::upset().
...	Further arguments to be passed through 'UpSetR::upset()'.
title	(Not available yet) Character of length 1 or NULL. Title of the plot shown at the top. Passed through grid.arrange(). If NULL, title is not shown. Default: NULL

Author(s)

amitjavilaventura

See Also

plyranges

UpSetR

amitjavilaventura/seqViewR documentation built on Nov. 21, 2023, 10:12 a.m.