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      Speaking Stata: The joy of sets: Graphical alternatives to Euler and Venn diagrams

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          Abstract

          Membership of overlapping or intersecting sets may be recorded in a bundle of (0, 1) indicator variables. Annotated Euler or Venn diagrams may be used to show graphically the frequencies of subsets so defined, but beyond just a few sets such diagrams can be hard to draw and use effectively. This column presents two new commands for graphical alternatives: upsetplot and vennbar. Each command produces a bar chart by default, but there is scope to recast to different graphical forms. The differences between the new commands reflect the divide in Stata between twoway commands and other graph commands. They also provide some flexibility in graph design to match tastes and circumstances. The discussion includes many historical details and references.

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

          Abstract 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.
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            UpSet: Visualization of Intersecting Sets.

            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.
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              The B73 maize genome: complexity, diversity, and dynamics.

              We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

                Author and article information

                Journal
                The Stata Journal: Promoting communications on statistics and Stata
                The Stata Journal: Promoting communications on statistics and Stata
                SAGE Publications
                1536-867X
                1536-8734
                June 2024
                July 25 2024
                June 2024
                : 24
                : 2
                : 329-361
                Affiliations
                [1 ]Department of Geography, Durham University, Durham, U.K.
                [2 ]MRC Clinical Trials Unit, University College London, London, U.K.
                Article
                10.1177/1536867X241258010
                4a726875-7b0b-431f-b5d6-6973489a66de
                © 2024

                https://creativecommons.org/licenses/by-nc/4.0/

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