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

By J. R. Conway, Alexander Lex, Nils Gehlenborg. bioRxiv, 2017

2,990 citations recorded by the source corpus.

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. 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. UpSetR is available at https://cran.r-project.org/package=UpSetR and released under the MIT License. A Shiny app is available at https://gehlenborglab.shinyapps.io/upsetr/.

Subfields: Computer Vision and Pattern Recognition, Food Science, Information Systems

View Paper: https://www.semanticscholar.org/paper/05d59234186a4c4d568f403b87b81405faffb817

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Citations in the corpus

Dark Patterns after the GDPR: Scraping Consent Pop-ups and Demonstrating their Influence (2020, background): “UpSet diagram [16, 36] of sites by adherence to three core conditions of EU law.”
MIENTURNET: an interactive web tool for microRNA-target enrichment and network-based analysis (2019, methodology): “The performance of shiny package was widely tested and validated by several successful web applications [18–21].”
Intervene: a tool for intersection and visualization of multiple gene or genomic region sets (2017, methodology): “The accompanying web interface is developed using Shiny (version 1.0.0), a web application framework for R. Intervene uses pybedtools [6] to perform genomic region set intersections and Seaborn (https://sea-born.pydata.org/), Matplotlib [7], UpSetR [8], and Corrplot [9] to generate figures.”
MIBiG 2.0: a repository for biosynthetic gene clusters of known function (2019, methodology): “The intersection diagram is generated using the UpSetR tool (14).”
Complex heatmap visualization (2022, methodology): “The function UpSet() in ComplexHeatmap provides an enhanced implementation of the original tool [32].”
Accuracy assessment of fusion transcript detection via read-mapping and de novo fusion transcript assembly-based methods (2019, methodology): “…cancer cell lines BT474, KPL4, MCF7, and SKBR3. a All fusions identified by at least three different methods are shown and ranked from being predicted by fewest to most methods in an UpSetR [61] style plot (UpSetR code forked and modified to show individual fusion group memberships here [62]).”
Make Interactive Complex Heatmaps in R (2021, methodology): “This is an enhanced version of package UpSetR (Conway, Lex, and Gehlenborg 2017).”
Scalable Open Science Approach for Mutation Calling of Tumor Exomes Using Multiple Genomic Pipelines (2018, neutral): “(B) Variant counts in the open-access MAF by filter were processed using an UpSetR plot (Conway et al., 2017).”
Comprehensive Characterization of Cancer Driver Genes and Mutations (2018, background): “Hypermutators Exhibit Multiple Signatures, Microsatellite Instability, and Immune Infiltration Expression (A) UpSetR (Conway et al., 2017) plot highlights the intersection of multiple signatures and phenotypes with hypermutated samples.”
ggVennDiagram: An Intuitive, Easy-to-Use, and Highly Customizable R Package to Generate Venn Diagram (2021, methodology): “To date, there are three major methods to display set relationships: Venn diagram, Euler diagram, and UpSet plot (Conway et al., 2017).”