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

被引：2183

作者：

Conway, Jake R. ^{[1
]}

Lex, Alexander ^{[2
]}

Gehlenborg, Nils ^{[1
]}

机构：

[1] Harvard Med Sch, Dept Biomed Informat, Boston, MA 02115 USA

[2] Univ Utah, Inst Sci, Sch Comp, Salt Lake City, UT 84112 USA

来源：

BIOINFORMATICS | 2017年 / 33卷 / 18期

基金：

美国国家卫生研究院;

关键词：

D O I：

10.1093/bioinformatics/btx364

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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.

引用

页码：2938 / 2940

页数：3

共 9 条

[1] The State-of-the-Art of Set Visualization [J].

Alsallakh, Bilal ;

Micallef, Luana ;

Aigner, Wolfgang ;

Hauser, Helwig ;

Miksch, Silvia ;

Rodgers, Peter .

COMPUTER GRAPHICS FORUM, 2016, 35 (01) :234-260

[2] VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R [J].

Chen, Hanbo ;

Boutros, Paul C. .

BMC BIOINFORMATICS, 2011, 12

[3] GRAPHICAL PERCEPTION - THEORY, EXPERIMENTATION, AND APPLICATION TO THE DEVELOPMENT OF GRAPHICAL METHODS [J].

CLEVELAND, WS ;

MCGILL, R .

JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 1984, 79 (387) :531-554

[4] The banana (Musa acuminata) genome and the evolution of monocotyledonous plants [J].

D'Hont, Angelique ;

Denoeud, France ;

Aury, Jean-Marc ;

Baurens, Franc-Christophe ;

Carreel, Francoise ;

Garsmeur, Olivier ;

Noel, Benjamin ;

Bocs, Stephanie ;

Droc, Gaetan ;

Rouard, Mathieu ;

Da Silva, Corinne ;

Jabbari, Kamel ;

Cardi, Celine ;

Poulain, Julie ;

Souquet, Marlene ;

Labadie, Karine ;

Jourda, Cyril ;

Lengelle, Juliette ;

Rodier-Goud, Marguerite ;

Alberti, Adriana ;

Bernard, Maria ;

Correa, Margot ;

Ayyampalayam, Saravanaraj ;

Mckain, Michael R. ;

Leebens-Mack, Jim ;

Burgess, Diane ;

Freeling, Mike ;

Mbeguie-A-Mbeguie, Didier ;

Chabannes, Matthieu ;

Wicker, Thomas ;

Panaud, Olivier ;

Barbosa, Jose ;

Hribova, Eva ;

Heslop-Harrison, Pat ;

Habas, Remy ;

Rivallan, Ronan ;

Francois, Philippe ;

Poiron, Claire ;

Kilian, Andrzej ;

Burthia, Dheema ;

Jenny, Christophe ;

Bakry, Frederic ;

Brown, Spencer ;

Guignon, Valentin ;

Kema, Gert ;

Dita, Miguel ;

Waalwijk, Cees ;

Joseph, Steeve ;

Dievart, Anne ;

Jaillon, Olivier .

NATURE, 2012, 488 (7410) :213-+

[5] UpSet: Visualization of Intersecting Sets [J].

Lex, Alexander ;

Gehlenborg, Nils ;

Strobelt, Hendrik ;

Vuillemot, Romain ;

Pfister, Hanspeter .

IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2014, 20 (12) :1983-1992

[6] POINTS OF VIEW Sets and intersections [J].

Lex, Alexander ;

Gehlenborg, Nils .

NATURE METHODS, 2014, 11 (08) :779-779

[7]

Wickham H, 2009, USE R, P1, DOI 10.1007/978-0-387-98141-3

[8] Exact and Approximate Area-Proportional Circular Venn and Euler Diagrams [J].

Wilkinson, Leland .

IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2012, 18 (02) :321-331

[9] A fast and accurate SNP detection algorithm for next-generation sequencing data [J].

Xu, Feng ;

Wang, Weixin ;

Wang, Panwen ;

Li, Mulin Jun ;

Sham, Pak Chung ;

Wang, Junwen .

NATURE COMMUNICATIONS, 2012, 3

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