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. 2017 Sep 15;33(18):2938-2940.
doi: 10.1093/bioinformatics/btx364.

UpSetR: an R package for the visualization of intersecting sets and their properties

Jake R Conway  1 , Alexander Lex  2 , Nils Gehlenborg  1
Affiliations

UpSetR: an R package for the visualization of intersecting sets and their properties

Jake R Conway et al. Bioinformatics. .

Abstract

Motivation: Venn and Euler diagrams are a popular yet inadequate solution for quantitative visualization of set intersections. A scalable alternative to Venn and Euler diagrams for visualizing intersecting sets and their properties is needed.

Results: We developed UpSetR, an open source R package that employs a scalable matrix-based visualization to show intersections of sets, their size, and other properties.

Availability and implementation: UpSetR is available at https://github.com/hms-dbmi/UpSetR/ and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/ .

Contact: nils@hms.harvard.edu.

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Fig. 1
Fig. 1
An UpSetR plot of variants across eight ICGC cancer studies with three intersection queries, one element query, four attribute plots, and two set metadata plots. Data for LUSC-KR and LAML-KR are based on whole-genome sequencing, all others on whole-exome sequencing. The three intersection queries are the one-way intersections of LUSC-US (blue) and THCA-SA (purple), and the two-way intersection of LUSC-KR and LAML-KR (green). The element query (yellow) selects mutations classified as deletions. Three custom transition/transversion plots display the relative frequency of substitution events for the intersection queries. The bar plot attribute plot displays the contribution of variants unique to the THCA-SA cohort (purple) to each mutation type. Set metadata is plotted to the left of the set size bar (charts)
See this image and copyright information in PMC

References

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MeSH terms