Literature DB >> 26356912

UpSet: Visualization of Intersecting Sets.

Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister.   

Abstract

Understanding relationships between sets is an important analysis task that has received widespread attention in the visualization community. The major challenge in this context is the combinatorial explosion of the number of set intersections if the number of sets exceeds a trivial threshold. In this paper we introduce UpSet, a novel visualization technique for the quantitative analysis of sets, their intersections, and aggregates of intersections. UpSet is focused on creating task-driven aggregates, communicating the size and properties of aggregates and intersections, and a duality between the visualization of the elements in a dataset and their set membership. UpSet visualizes set intersections in a matrix layout and introduces aggregates based on groupings and queries. The matrix layout enables the effective representation of associated data, such as the number of elements in the aggregates and intersections, as well as additional summary statistics derived from subset or element attributes. Sorting according to various measures enables a task-driven analysis of relevant intersections and aggregates. The elements represented in the sets and their associated attributes are visualized in a separate view. Queries based on containment in specific intersections, aggregates or driven by attribute filters are propagated between both views. We also introduce several advanced visual encodings and interaction methods to overcome the problems of varying scales and to address scalability. UpSet is web-based and open source. We demonstrate its general utility in multiple use cases from various domains.

Entities:  

Mesh:

Year:  2014        PMID: 26356912      PMCID: PMC4720993          DOI: 10.1109/TVCG.2014.2346248

Source DB:  PubMed          Journal:  IEEE Trans Vis Comput Graph        ISSN: 1077-2626            Impact factor:   4.579


  14 in total

1.  D³: Data-Driven Documents.

Authors:  Michael Bostock; Vadim Ogievetsky; Jeffrey Heer
Journal:  IEEE Trans Vis Comput Graph       Date:  2011-12       Impact factor: 4.579

2.  Context-preserving visual links.

Authors:  Markus Steinberger; Manuela Waldner; Marc Streit; Alexander Lex; Dieter Schmalstieg
Journal:  IEEE Trans Vis Comput Graph       Date:  2011-12       Impact factor: 4.579

3.  Design study of LineSets, a novel set visualization technique.

Authors:  Basak Alper; Nathalie Henry Riche; Gonzalo Ramos; Mary Czerwinski
Journal:  IEEE Trans Vis Comput Graph       Date:  2011-12       Impact factor: 4.579

4.  Untangling euler diagrams.

Authors:  Nathalie Henry Riche; Tim Dwyer
Journal:  IEEE Trans Vis Comput Graph       Date:  2010 Nov-Dec       Impact factor: 4.579

5.  Radial sets: interactive visual analysis of large overlapping sets.

Authors:  Bilal Alsallakh; Wolfgang Aigner; Silvia Miksch; Helwig Hauser
Journal:  IEEE Trans Vis Comput Graph       Date:  2013-12       Impact factor: 4.579

6.  Rethinking perceptual organization: The role of uniform connectedness.

Authors:  S Palmer; I Rock
Journal:  Psychon Bull Rev       Date:  1994-03

7.  Bubble sets: revealing set relations with isocontours over existing visualizations.

Authors:  Christopher Collins; Gerald Penn; Sheelagh Carpendale
Journal:  IEEE Trans Vis Comput Graph       Date:  2009 Nov-Dec       Impact factor: 4.579

8.  Exact and approximate area-proportional circular Venn and Euler diagrams.

Authors:  Leland Wilkinson
Journal:  IEEE Trans Vis Comput Graph       Date:  2012-02       Impact factor: 4.579

9.  The banana (Musa acuminata) genome and the evolution of monocotyledonous plants.

Authors:  Angélique D'Hont; France Denoeud; Jean-Marc Aury; Franc-Christophe Baurens; Françoise Carreel; Olivier Garsmeur; Benjamin Noel; Stéphanie Bocs; Gaëtan Droc; Mathieu Rouard; Corinne Da Silva; Kamel Jabbari; Céline Cardi; Julie Poulain; Marlène Souquet; Karine Labadie; Cyril Jourda; Juliette Lengellé; Marguerite Rodier-Goud; Adriana Alberti; Maria Bernard; Margot Correa; Saravanaraj Ayyampalayam; Michael R Mckain; Jim Leebens-Mack; Diane Burgess; Mike Freeling; Didier Mbéguié-A-Mbéguié; Matthieu Chabannes; Thomas Wicker; Olivier Panaud; Jose Barbosa; Eva Hribova; Pat Heslop-Harrison; Rémy Habas; Ronan Rivallan; Philippe Francois; Claire Poiron; Andrzej Kilian; Dheema Burthia; Christophe Jenny; Frédéric Bakry; Spencer Brown; Valentin Guignon; Gert Kema; Miguel Dita; Cees Waalwijk; Steeve Joseph; Anne Dievart; Olivier Jaillon; Julie Leclercq; Xavier Argout; Eric Lyons; Ana Almeida; Mouna Jeridi; Jaroslav Dolezel; Nicolas Roux; Ange-Marie Risterucci; Jean Weissenbach; Manuel Ruiz; Jean-Christophe Glaszmann; Francis Quétier; Nabila Yahiaoui; Patrick Wincker
Journal:  Nature       Date:  2012-08-09       Impact factor: 49.962

10.  Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies.

Authors:  David B Neale; Jill L Wegrzyn; Kristian A Stevens; Aleksey V Zimin; Daniela Puiu; Marc W Crepeau; Charis Cardeno; Maxim Koriabine; Ann E Holtz-Morris; John D Liechty; Pedro J Martínez-García; Hans A Vasquez-Gross; Brian Y Lin; Jacob J Zieve; William M Dougherty; Sara Fuentes-Soriano; Le-Shin Wu; Don Gilbert; Guillaume Marçais; Michael Roberts; Carson Holt; Mark Yandell; John M Davis; Katherine E Smith; Jeffrey F D Dean; W Walter Lorenz; Ross W Whetten; Ronald Sederoff; Nicholas Wheeler; Patrick E McGuire; Doreen Main; Carol A Loopstra; Keithanne Mockaitis; Pieter J deJong; James A Yorke; Steven L Salzberg; Charles H Langley
Journal:  Genome Biol       Date:  2014-03-04       Impact factor: 13.583

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  434 in total

1.  Atlas of Subcellular RNA Localization Revealed by APEX-Seq.

Authors:  Furqan M Fazal; Shuo Han; Kevin R Parker; Pornchai Kaewsapsak; Jin Xu; Alistair N Boettiger; Howard Y Chang; Alice Y Ting
Journal:  Cell       Date:  2019-06-20       Impact factor: 41.582

2.  EDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure.

Authors:  Marius Alfred Dieckmann; Sebastian Beyvers; Rudel Christian Nkouamedjo-Fankep; Patrick Harald Georg Hanel; Lukas Jelonek; Jochen Blom; Alexander Goesmann
Journal:  Nucleic Acids Res       Date:  2021-07-02       Impact factor: 16.971

3.  Response to "Plotting intersections" by Lentini.

Authors:  Alexander Lex; Nils Gehlenborg
Journal:  Nat Methods       Date:  2015-04       Impact factor: 28.547

4.  Patterns of host use by brood parasitic Maculinea butterflies across Europe.

Authors:  András Tartally; Jeremy A Thomas; Christian Anton; Emilio Balletto; Francesca Barbero; Simona Bonelli; Markus Bräu; Luca Pietro Casacci; Sándor Csősz; Zsolt Czekes; Matthias Dolek; Izabela Dziekańska; Graham Elmes; Matthias A Fürst; Uta Glinka; Michael E Hochberg; Helmut Höttinger; Vladimir Hula; Dirk Maes; Miguel L Munguira; Martin Musche; Per Stadel Nielsen; Piotr Nowicki; Paula S Oliveira; László Peregovits; Sylvia Ritter; Birgit C Schlick-Steiner; Josef Settele; Marcin Sielezniew; David J Simcox; Anna M Stankiewicz; Florian M Steiner; Giedrius Švitra; Line V Ugelvig; Hans Van Dyck; Zoltán Varga; Magdalena Witek; Michal Woyciechowski; Irma Wynhoff; David R Nash
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2019-04-01       Impact factor: 6.237

5.  Evaluating the Calling Performance of a Rare Disease NGS Panel for Single Nucleotide and Copy Number Variants.

Authors:  P Cacheiro; A Ordóñez-Ugalde; B Quintáns; S Piñeiro-Hermida; J Amigo; M García-Murias; S I Pascual-Pascual; F Grandas; J Arpa; A Carracedo; M J Sobrido
Journal:  Mol Diagn Ther       Date:  2017-06       Impact factor: 4.074

6.  Addressing multi-label imbalance problem of surgical tool detection using CNN.

Authors:  Manish Sahu; Anirban Mukhopadhyay; Angelika Szengel; Stefan Zachow
Journal:  Int J Comput Assist Radiol Surg       Date:  2017-03-29       Impact factor: 2.924

7.  Extracellular vesicles in DLBCL provide abundant clues to aberrant transcriptional programming and genomic alterations.

Authors:  Sarah C Rutherford; Angela A Fachel; Sheng Li; Seema Sawh; Ashlesha Muley; Jennifer Ishii; Ashish Saxena; Pilar M Dominguez; Eloisi Caldas Lopes; Xabier Agirre; Nyasha Chambwe; Fabian Correa; Yanwen Jiang; Kristy L Richards; Doron Betel; Rita Shaknovich
Journal:  Blood       Date:  2018-07-02       Impact factor: 22.113

8.  Integrative analysis identifies DNMTs against immune-infiltrating neutrophils and dendritic cells in colorectal cancer.

Authors:  Qili Shi; Libing Shen; Jun Gan; Lirong He; Jing Lin; Shiyu Guo; Zi Xiong; Jie Lin; Shun Zhang
Journal:  Epigenetics       Date:  2019-03-16       Impact factor: 4.528

9.  Transcriptomic analysis of the development of skeletal muscle atrophy in cancer-cachexia in tumor-bearing mice.

Authors:  Thomas A Blackwell; Igor Cervenka; Bhuwan Khatri; Jacob L Brown; Megan E Rosa-Caldwell; David E Lee; Richard A Perry; Lemuel A Brown; Wesley S Haynie; Michael P Wiggs; Walter G Bottje; Tyrone A Washington; Byungwhi C Kong; Jorge L Ruas; Nicholas P Greene
Journal:  Physiol Genomics       Date:  2018-10-05       Impact factor: 3.107

10.  Pathfinder: Visual Analysis of Paths in Graphs.

Authors:  C Partl; S Gratzl; M Streit; A M Wassermann; H Pfister; D Schmalstieg; A Lex
Journal:  Comput Graph Forum       Date:  2016-07-04       Impact factor: 2.078

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