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RainBio:生物学中大规模数据集的比例可视化。

RainBio: Proportional Visualization of Large Sets in Biology.

出版信息

IEEE Trans Vis Comput Graph. 2020 Nov;26(11):3285-3298. doi: 10.1109/TVCG.2019.2921544. Epub 2019 Jun 7.


DOI:10.1109/TVCG.2019.2921544
PMID:31180862
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.

摘要

集可视化是信息可视化中的一个著名任务。在生物学中,它用于直观地比较基因或蛋白质集,通常使用韦恩图。然而,韦恩图的局限性是众所周知的:它们最多只能用于比较 6 个集,并且很难用于阅读超过 4 个集。已经提出了许多其他的集可视化技术,但它们从未在生物学中得到广泛应用。在本文中,我们介绍了 RainBio,这是一种用于生物学中集可视化的技术,旨在提供一种全局概述,以比例方式显示主要交集的大小,并显示集之间的相似性。我们将彩虹盒(一种用于可视化小数据集的技术)应用于更大的数据集,使用元素聚合和交集聚类。我们展示了 RainBio 在三个数据集(5、6 和 12 个集)上的应用。我们还描述了一项涉及 30 名生物学学生的小型用户研究,将 RainBio 与韦恩图进行了比较。结果表明,RainBio 在 6 个数据集上显著减少了错误,而且大多数学生更喜欢 RainBio。RainBio 被提议作为一个基于网络的工具,最多可用于 15 个集。

相似文献

[1]
RainBio: Proportional Visualization of Large Sets in Biology.

IEEE Trans Vis Comput Graph. 2020-11

[2]
Venn diagrams in bioinformatics.

Brief Bioinform. 2021-9-2

[3]
InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams.

BMC Bioinformatics. 2015-5-22

[4]
VennPainter: A Tool for the Comparison and Identification of Candidate Genes Based on Venn Diagrams.

PLoS One. 2016-4-27

[5]
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams.

BMC Genomics. 2008-10-16

[6]
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R.

BMC Bioinformatics. 2011-1-26

[7]
Drawing area-proportional Euler diagrams representing up to three sets.

IEEE Trans Vis Comput Graph. 2014-1

[8]
VennDiagramWeb: a web application for the generation of highly customizable Venn and Euler diagrams.

BMC Bioinformatics. 2016-10-3

[9]
Generalized Venn diagrams: a new method of visualizing complex genetic set relations.

Bioinformatics. 2005-4-15

[10]
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets.

BMC Bioinformatics. 2017-5-31

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