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RainBio: Proportional Visualization of Large Sets in Biology

Authors: Lamy, Jean-Baptiste; Tsopra, Rosy;

RainBio: Proportional Visualization of Large Sets in Biology

Abstract

Set visualization is a well-known task in information visualization. In biology, it is used for comparing visually sets of genes or proteins, typically using Venn diagrams. However, limitations of the Venn diagram are well-known: they are limited to 6 sets and difficult to read above 4. Many other set visualization techniques have been proposed, but they have never been widely used in biology. In this paper, we introduce RainBio, a technique for visualizing sets in biology and aimed at providing a global overview showing the size of the main intersections, in a proportional way, and the similarities between sets. We adapt rainbow boxes, a technique for visualizing small datasets, to the visualization of larger sets, using element aggregation and intersection clustering. We present the application of RainBio to three datasets, with 5, 6 and 12 sets. We also describe a small user study comparing RainBio with Venn diagrams, involving 30 students in biology. Results showed that RainBio led to significantly fewer errors on 6-set dataset, and that the majority of students preferred RainBio. RainBio is proposed as a web-based tool for up to 15 sets.

Keywords

MESH: Data Visualization, Bioinformatics, Set visualization, MESH: Databases, Gene set comparison, MESH: Software, Genetic, MESH: Musa, Neoplasms, Databases, Genetic, Computer Graphics, Cluster Analysis, Humans, MESH: Neoplasms, [INFO.INFO-HC]Computer Science [cs]/Human-Computer Interaction [cs.HC], [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], MESH: Humans, Data Visualization, Computational Biology, Musa, MESH: Cluster Analysis, 004, Venn diagram, [SDV.SPEE] Life Sciences [q-bio]/Santé publique et épidémiologie, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, MESH: Computer Graphics, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-HC] Computer Science [cs]/Human-Computer Interaction [cs.HC], Software, MESH: Computational Biology

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
11
Top 10%
Average
Top 10%
Green
hybrid