upsetplot in ChIPseeker

[This article was first published on YGC » R, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here)
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

ChIPseeker is an R package for ChIP peak annotation, comparison and visualization.

We have implemented several visualization methods, including vennpie that was designed for viewing annotation overlap as shown below:

Not all overlap information can be demonstrated in vennpie. Upset is an effective way to visualize sets and intersections. We import upset function from UpSetR package and implement upsetplot function, that can visualize ChIP annotation overlap directly with output of annotatePeak.

?View Code RSPLUS
peak_file <- getSampleFiles()[[4]]
x <- annotatePeak(peak_file)

We add a new parameter, vennpie=FALSE, in upsetplot. If vennpie=TRUE, a vennpie will be added as show below:

Although upset contains more information, vennpie is more intuitive and the final figure is more compact. More information is available at the online vignette.


1. Alexander Lex, and Nils Gehlenborg. “Points of View: Sets and Intersections.” Nature Methods 11, no. 8 (August 2014): 779–779. doi:10.1038/nmeth.3033.
2. Guangchuang Yu, Li-Gen Wang, and Qing-Yu He. “ChIPseeker: An R/Bioconductor Package for ChIP Peak Annotation, Comparison and Visualization.” Bioinformatics 31, no. 14 (July 15, 2015): 2382–83. doi:10.1093/bioinformatics/btv145.
3. Conway Jake, and Gehlenborg Nils, "UpSetR",

Related Posts

To leave a comment for the author, please follow the link and comment on their blog: YGC » R. offers daily e-mail updates about R news and tutorials about learning R and many other topics. Click here if you're looking to post or find an R/data-science job.
Want to share your content on R-bloggers? click here if you have a blog, or here if you don't.

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)