repository·master·Indexed 21 days ago
https://github.com/hms-dbmi/upsetrAn R package for visualizing intersecting sets and their properties using the UpSet technique. It provides a matrix-based layout to represent set intersections, aggregates, and summary statistics, featuring the core `upset()` function and support for attribute plots and queries.
You can install the stable version of UpSetR from CRAN or the latest development version from GitHub.
To install from CRAN:
install.packages("UpSetR")To install the development version using devtools:
devtools::install_github("hms-dbmi/UpSetR")install.packages("UpSetR")You can use the queries argument to highlight specific intersections or subsets within the UpSet plot. This is often used in conjunction with attribute.plots to compare specific groups (e.g., comparing 'War' movies vs 'Noir' movies).
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"))))UpSetR includes built-in sample datasets for testing and demonstration. You can load them using system.file to locate the files within the installed package.
Available datasets:
movies.csv: Movie data curated by GroupLens Lab.mutations.csv: Mutation data for the 100 most mutated genes in a glioblastoma multiforme cohort.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 core function for creating visualizations is upset(). It visualizes set intersections in a matrix layout.
Example: Creating an UpSet plot for mutations with specific sets and ordering.
upset(mutations, sets = c("PTEN", "TP53", "EGFR", "PIK3R1", "RB1"), sets.bar.color = "#56B4E9",
order.by = "freq", empty.intersections = "on")upset(mutations, sets = c("PTEN", "TP53", "EGFR", "PIK3R1", "RB1"), sets.bar.color = "#56B4E9",
order.by = "freq", empty.intersections = "on")UpSetR allows you to add additional plots (like scatter plots or histograms) that represent attributes of the elements within the intersections using the attribute.plots argument.
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))