A More Scalable Alternative to Venn and Euler Diagrams for Visualizing Intersecting Sets

Creates visualizations of intersecting sets using a novel matrix design, along with visualizations of several common set, element and attribute related tasks.


UpSetR generates static UpSet plots. The UpSet technique 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.

For further details about the original technique see the UpSet website. You can also check out the UpSetR shiny app. Here is the source code for the shiny wrapper

Sample data sets for UpSetR are included in the package and can be loaded like this:

movies <- read.csv( system.file("extdata", "movies.csv", package = "UpSetR"), header=T, sep=";" )
mutations <- read.csv( system.file("extdata", "mutations.csv", package = "UpSetR"), header=T, sep = ",")

The movie data set created by the GroupLens Lab and curated by Bilal Alsallakh and the mutations data set was originally created by the TCGA Consortium and represents mutations for the 100 most mutated genes in a glioblastoma multiforme cohort.

There are currently four vignettes that explain how to use the features included in the UpSetR package:

A view of the UpSet plot with additional plots based on elements in the intersections.

upset(movies,attribute.plots=list(gridrows=60,plots=list(list(plot=scatter_plot, x="ReleaseDate", y="AvgRating"),
list(plot=scatter_plot, x="ReleaseDate", y="Watches"),list(plot=scatter_plot, x="Watches", y="AvgRating"),
list(plot=histogram, x="ReleaseDate")), ncols = 2))

A view of UpSetR mimicking the plot published by Lex & Gehlenborg http://www.nature.com/nmeth/journal/v11/n8/abs/nmeth.3033.html

upset(mutations, sets = c("PTEN", "TP53", "EGFR", "PIK3R1", "RB1"), sets.bar.color = "#56B4E9",
order.by = "freq", empty.intersections = "on")

An example using two set queries (war movies and noir movies) along with attribute plots comparing the average rating (top) and average rating vs the number of times the movies have been watched (bottom).

upset(movies, attribute.plots=list(gridrows = 100, ncols = 1, 
plots = list(list(plot=histogram, x="AvgRating",queries=T),
list(plot = scatter_plot, y = "AvgRating", x = "Watches", queries = T))), 
sets = c("Action", "Adventure", "Children", "War", "Noir"),
queries = list(list(query = intersects, params = list("War"), active = T),
list(query = intersects, params = list("Noir"))))

Install the latest released version from CRAN

install.packages("UpSetR")

Download the latest development code of UpSetR from GitHub using devtools with

devtools::install_github("hms-dbmi/UpSetR")

If you use UpSetR in a paper, please cite:

UpSet: Visualization of Intersecting Sets,
IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), vol. 20, no. 12, pp. 1983–1992, 2014.
doi:10.1109/TVCG.2014.2346248

News

Release v1.3.1

  • Fixed log scale bugs
  • Allow users to label their own queries, which can be displayed in query legend
  • Fixed query legend positioning bug. Allows query legend to be placed on top or bottom of plot grid
  • Fixed warnings and notes from new ggplot2 release
  • Updated plot margin of intersection size bar plot

Release v1.3.0

  • Introduced text scales for all plot axis labels, tick labels, set names, and numbers above the bars
  • Removed names.size parameter and replaced it with a text scale
  • Fixed vignettes so plot size and text is appropriately scaled

Release v1.2.4

  • Fixed check.names bug so that it reorders the set size bar plot, not just the set labels
  • Show all intersections when nintersects is set to NA

Release v1.2.3

  • Allow user to keep order of sets entered when using sets parameter
  • Updated Basic Usage vignette with example on how to do this

Release v1.2.2

  • Support for log10 and log2 scale transformations

Release v1.2.1

  • Updated vignettes
  • Adjusted metadata plot text size for ggplot2 update
  • Default gray88 color if matrix_rows metadata attribute used and no colors supplied
  • Fixed metadata error so that matrix_rows may be used alone
  • New link to UpSetR Shiny app in README

Release v1.2.0

  • Options for set metadata heat map, boolean heat map, text, and bar plot
  • Allow for multiple set metadata plots
  • Option to color matrix background using metadata
  • Created set.metadata.plots vignette
  • Removed set metadata example from attribute.plots vignette
  • Size adjustment of geoms for ggplot2 version 2.1.0

Release v1.1.1

  • Added selective import from plyr package to avoid warning from gridExtra package update (Requested by CRAN)

Release v1.1.0

  • Added set metadata plot feature
  • Added intersections parameter to include only intersections specified
  • Reorder sets when using sets or intersections parameter
  • Add label option for intersection size and set size bar plots
  • Include boxplot summary example in attribute vignette
  • Added set metadata example in attribute vignette and label parameter examples to basic usage vignette

Release v1.0.3

  • Fixed overlapping between matrix and intersection size bar plot (caused by late changes to ggplot2 update)
  • Updated vignettes to regenerate plots from new code

Release v1.0.2

  • Updated vignettes to include examples of the fromExpression and fromList functions
  • Changed to selective imports from grid package

Release v1.0.1

  • Fixed matrix plot to correctly work with new ggplot2 update

Release v1.0.0

  • Added directionality when choosing sets (-1,0,+1)
  • Allowed for NA's in non-set columns
  • Added increasing/decreasing options for ordering intersections
  • Added fromList to convert a list of named vectors to an UpSetR data frame
  • Added fromExpression to convert a vector acting as an expression to an UpSetR data frame
  • Updated vignette for alternative input formats (list & expression)

Release v.0.0.5

  • Now plotting using the base grid package to make compatible with all versions of gridExtra package
  • Allowed for element query overlay of intersection size bars
  • Added vignettes of basic usage, queries, and attribute plots
  • Matched set size font with intersection size font
  • Added utils, stats, methods, grDevices to imports to be safe (usually pre-installed)
  • Added badges
  • Updated README
  • Bumped required R version up to 3.0

Release v.0.0.4

  • changed aes to aes_string for ggplot2 aesthetics

Release v0.0.3

  • Fixed all CRAN issues
  • changed all ggplot2 aesthetics to aes_string() to resort from using "hacky" methods to get around CRAN issues

Release v0.0.2

  • Renamed custom.plots as attribute.plots to better fit its purpose.
  • Re-added query legend option when user selects for attribute plots
  • Lowered minimum required R version.
  • Allowed for 360 degree rotation of intersection size bar labels
  • Changed default color of matrix shaing from dodgerblue to light gray

Release v0.0.1

  • First public release.

Reference manual

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install.packages("UpSetR")

1.3.3 by Jake Conway, 6 months ago


http://github.com/hms-dbmi/UpSetR


Report a bug at http://github.com/hms-dbmi/UpSetR/issues


Browse source code at https://github.com/cran/UpSetR


Authors: Jake Conway [cre], Nils Gehlenborg [aut]


Documentation:   PDF Manual  


MIT + file LICENSE license


Imports ggplot2, gridExtra, plyr, utils, stats, methods, grDevices, scales

Suggests knitr


See at CRAN