UpSet plots are a data visualization method for showing set data with more than three intersecting sets. UpSet shows intersections in a matrix, with the rows of the matrix corresponding to the sets, and the columns to the intersections between these sets (or vice versa). The size of the sets and of the intersections are shown as bar charts.
An UpSet Plot showing how movie genres intersect. The largest intersection of two sets is the Comedy-Drama intersection.
UpSet plots were first proposed in 2014.[1] The first prototype was implemented as an interactive, web-based application.[2] UpSet plots are related to Mosaic Plots, although Mosaic plots are designed for categorical instead of set data.
UpSet plots became popular as they became available as an R-library based on ggplot2,[3] and were subsequently re-implemented in various programming languages, such as Python, and others.[4] As of January 2024, UpSetR has been downloaded from CRAN more than 1.5 million times.[5] UpSet plots are now frequently used instead of Venn diagrams, especially in life sciences.[6]
Usageedit
Illustration showing how the rows of an UpSet plot correspond to the segments of a Venn diagram.An UpSet plot showing three sets, and the corresponding venn diagram.
UpSet plots visualize intersections between sets in a matrix. In a vertical UpSet plot, the columns of the matrix correspond to the sets, the rows correspond to the intersections. For each row, the cells that are part of an intersection are filled in. If there are multiple filled-in cells, they are connected with a line, to emphasize the reading direction of the plot. As sets vary in size, the size of the set is plotted as bar charts on top of the columns. The size of the intersections are shown aligned with the rows, also as bar charts. This layout facilitates the comparison between the sizes of individual intersections, as the size of the bars is easy to compare. UpSets can be used horizontally and vertically.
UpSet plots can be sorted in various ways. A common sorting approach, for example, is to sort by cardinality (the size of an intersection), which places the biggest intersections on top. Alternative sortings are by the degree of the intersection, or by sets.
UpSet plots can also be used to visualize attributes about the intersections by placing attribute visualizations next to the bar charts.[7] Common choices for these attribute visualizations are compact visualization approaches for distributions, such as box plots, or violin plots.
Advanced features of UpSet plots include querying, grouping and aggregating data.[1] These features tend to be available only in interactive, web-based implementations of UpSet.[4]
Benefits and Limitationsedit
UpSet plots tend to perform better than Venn diagrams for larger numbers of sets and when it is desirable to also show contextual information about the set intersections.[8] For visualizing diagrams with less than three sets, or when there are only few intersections, Venn and Euler diagram are generally preferred, because they tend to be more familiar and intuitive to read.[9]
UpSet plots are limited to displaying 20-30 sets, though specifics depends on the actual data.[9] An alternative approach for larger datasets is to show a co-occurrence heat map, though these cannot show higher-order intersections[9]
^Conway, Jake R; Lex, Alexander; Gehlenborg, Nils (15 September 2017). "UpSetR: an R package for the visualization of intersecting sets and their properties". Bioinformatics. 33 (18): 2938–2940. doi:10.1093/bioinformatics/btx364. PMC5870712. PMID 28645171.
^ abLex, Alexander. "UpSet". upset.app. Retrieved 18 February 2022.
^Conway, Jake R; Gehlenborg, Nils (27 April 2022). "UpSetR". GitHub. Retrieved 28 April 2022.
^Gadhave, Kiran. ""UpSet 2: From Prototype to Tool"". Retrieved 28 April 2022.
^Laura, Ellis. "Set Analysis: A face off between Venn diagrams and UpSet plots". Little Miss Data. Retrieved 28 April 2022.
^ abcLex, Alexander; Gehlenborg, Nils (1 August 2014). "Sets and intersections". Nature Methods. 11 (8): 779. doi:10.1038/nmeth.3033. S2CID 39124565.
April 13, 2024
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UpSet plots are a data visualization method for showing set data with more than three intersecting sets UpSet shows intersections in a matrix with the rows of the matrix corresponding to the sets and the columns to the intersections between these sets or vice versa The size of the sets and of the intersections are shown as bar charts An UpSet Plot showing how movie genres intersect The largest intersection of two sets is the Comedy Drama intersection Contents 1 History 2 Usage 3 Benefits and Limitations 4 See also 5 ReferencesHistory editUpSet plots were first proposed in 2014 1 The first prototype was implemented as an interactive web based application 2 UpSet plots are related to Mosaic Plots although Mosaic plots are designed for categorical instead of set data UpSet plots became popular as they became available as an R library based on ggplot2 3 and were subsequently re implemented in various programming languages such as Python and others 4 As of January 2024 UpSetR has been downloaded from CRAN more than 1 5 million times 5 UpSet plots are now frequently used instead of Venn diagrams especially in life sciences 6 Usage edit nbsp Illustration showing how the rows of an UpSet plot correspond to the segments of a Venn diagram nbsp An UpSet plot showing three sets and the corresponding venn diagram UpSet plots visualize intersections between sets in a matrix In a vertical UpSet plot the columns of the matrix correspond to the sets the rows correspond to the intersections For each row the cells that are part of an intersection are filled in If there are multiple filled in cells they are connected with a line to emphasize the reading direction of the plot As sets vary in size the size of the set is plotted as bar charts on top of the columns The size of the intersections are shown aligned with the rows also as bar charts This layout facilitates the comparison between the sizes of individual intersections as the size of the bars is easy to compare UpSets can be used horizontally and vertically UpSet plots can be sorted in various ways A common sorting approach for example is to sort by cardinality the size of an intersection which places the biggest intersections on top Alternative sortings are by the degree of the intersection or by sets UpSet plots can also be used to visualize attributes about the intersections by placing attribute visualizations next to the bar charts 7 Common choices for these attribute visualizations are compact visualization approaches for distributions such as box plots or violin plots Advanced features of UpSet plots include querying grouping and aggregating data 1 These features tend to be available only in interactive web based implementations of UpSet 4 Benefits and Limitations editUpSet plots tend to perform better than Venn diagrams for larger numbers of sets and when it is desirable to also show contextual information about the set intersections 8 For visualizing diagrams with less than three sets or when there are only few intersections Venn and Euler diagram are generally preferred because they tend to be more familiar and intuitive to read 9 UpSet plots are limited to displaying 20 30 sets though specifics depends on the actual data 9 An alternative approach for larger datasets is to show a co occurrence heat map though these cannot show higher order intersections 9 See also editVenn diagram Euler diagramReferences edit a b Lex Alexander Gehlenborg Nils Strobelt Hendrik Vuillemot Romain Pfister Hanspeter 31 December 2014 UpSet Visualization of Intersecting Sets IEEE Transactions on Visualization and Computer Graphics 20 12 1983 1992 doi 10 1109 TVCG 2014 2346248 PMC 4720993 PMID 26356912 Lex Alexander Gehlenborg Nils Strobelt Hendrik Vuillemot Romain Pfister Hanspeter UpSet Visualizing Intersecting Sets Conway Jake R Lex Alexander Gehlenborg Nils 15 September 2017 UpSetR an R package for the visualization of intersecting sets and their properties Bioinformatics 33 18 2938 2940 doi 10 1093 bioinformatics btx364 PMC 5870712 PMID 28645171 a b Lex Alexander UpSet upset app Retrieved 18 February 2022 Conway Jake R Gehlenborg Nils 27 April 2022 UpSetR GitHub Retrieved 28 April 2022 Gadhave Kiran UpSet 2 From Prototype to Tool Retrieved 28 April 2022 Gu Zuguang UpSet plot a href Template Cite book html title Template Cite book cite book a website ignored help Laura Ellis Set Analysis A face off between Venn diagrams and UpSet plots Little Miss Data Retrieved 28 April 2022 a b c Lex Alexander Gehlenborg Nils 1 August 2014 Sets and intersections Nature Methods 11 8 779 doi 10 1038 nmeth 3033 S2CID 39124565 Retrieved from https en wikipedia org w index php title UpSet Plot amp oldid 1195651026, wikipedia, wiki, book, books, library,
