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.
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 three 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 mimicing 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")