UpSetR: an R package for the visualization of intersecting sets and their properties - PubMed (original) (raw)

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

Jake R Conway et al. Bioinformatics. 2017.

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.

© The Author(s) 2017. Published by Oxford University Press.

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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)

References

    1. Alsallakh B. et al. (2016) The State-of-the-Art of Set Visualization. Computer Graphics Forum, 35: 234–260.
    1. Chen H., Boutros P.C. (2011) VennDiagram: a package for the generation of highly-customizable Venn & Euler diagrams in R. BMC Bioinformatics, 12, 35.. -PMC -PubMed
    1. Cleveland W.S., McGill R. (1984) Graphical perception: Theory, experimentation, and application to the development of graphical methods. J. Am. Stat. Assoc, 79, 531–554.
    1. D’Hont A. et al. (2012) The banana (musa acuminata) genome and the evolution of monocotyledonous plants. Nature, 488, 213–217. -PubMed
    1. Lex A., Gehlenborg N. (2014) Sets & intersections. Nat. Methods, 11, 779. -PubMed

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