AnnoUpsetPlot

AnnoUpsetPlot

Usage

AnnoUpsetPlot(LinkageObject, order_by = "freq")

Arguments

LinkageObject

An LinkageObject after the annottation.

order_by

How the intersections in the matrix should be ordered by. Options include frequency (entered as "freq"), degree, or both in any order.

Value

An upsetplot after the annottation.

Examples

library(Linkage)
data("SmallLinkageObject")
gene_list <- c("TSPAN6", "CD99", "KLHL13")
LinkageObject <-
  RegulatoryPeak(
    LinkageObject = SmallLinkageObject,
    gene_list = gene_list,
    genelist_idtype = "external_gene_name"
  )
peakAnno <- PeakAnnotation(LinkageObject, Species = "Homo")
#> Loading required package: org.Hs.eg.db
#> Loading required package: AnnotationDbi
#> Loading required package: stats4
#> Loading required package: BiocGenerics
#> 
#> Attaching package: 'BiocGenerics'
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#>     tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: IRanges
#> Loading required package: S4Vectors
#> 
#> Attaching package: 'S4Vectors'
#> The following object is masked from 'package:utils':
#> 
#>     findMatches
#> The following objects are masked from 'package:base':
#> 
#>     I, expand.grid, unname
#> 
#> Attaching package: 'IRanges'
#> The following object is masked from 'package:grDevices':
#> 
#>     windows
#> 
#> 'select()' returned 1:1 mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:1 mapping between keys and columns
AnnoUpsetPlot(LinkageObject = peakAnno)
#> Warning: `cols` is now required when using `unnest()`.
#> ℹ Please use `cols = c(res)`.