UpSetR Plot

Visualization of set intersections using novel UpSet matrix design.

upset(data, nsets = 5, nintersects = 40, sets = NULL,
  keep.order = F, set.metadata = NULL, intersections = NULL,
  matrix.color = "gray23", = "gray23",
  mainbar.y.label = "Intersection Size", mainbar.y.max = NULL, = "gray23", sets.x.label = "Set Size",
  point.size = 2.2, line.size = 0.7, mb.ratio = c(0.7, 0.3),
  expression = NULL, att.pos = NULL, att.color =, = c("freq", "degree"), decreasing = c(T, F),
  show.numbers = "yes", number.angles = 0, = "degree",
  cutoff = NULL, queries = NULL, query.legend = "none",
  shade.color = "gray88", shade.alpha = 0.25, = 0.5,
  empty.intersections = NULL, color.pal = 1, boxplot.summary = NULL,
  attribute.plots = NULL, scale.intersections = "identity",
  scale.sets = "identity", text.scale = 1, set_size.angles = 0, = FALSE, set_size.numbers_size = NULL,
  set_size.scale_max = NULL)

Data set


Number of sets to look at


Number of intersections to plot. If set to NA, all intersections will be plotted.


Specific sets to look at (Include as combinations. Ex: c("Name1", "Name2"))


Keep sets in the order entered using the sets parameter. The default is FALSE, which orders the sets by their sizes.


Metadata that offers insight to an attribute of the sets. Input should be a data frame where the first column is set names, and the remaining columns are attributes of those sets. To learn how to use this parameter it is highly suggested to view the set metadata vignette. The link can be found on the package's GitHub page.


Specific intersections to include in plot entered as a list of lists. Ex: list(list("Set name1", "Set name2"), list("Set name1", "Set name3")). If data is entered into this parameter the only data shown on the UpSet plot will be the specific intersections listed.


Color of the intersection points

Color of the main bar plot


The y-axis label of the intersection size bar plot


The maximum y value of the intersection size bar plot scale. May be useful when aligning multiple UpSet plots horizontally.

Color of set size bar plot


The x-axis label of the set size bar plot


Size of points in matrix plot


Width of lines in matrix plot


Ratio between matrix plot and main bar plot (Keep in terms of hundredths)


Expression to subset attributes of intersection or element query data. Enter as string (Ex: "ColName > 3")


Position of attribute plot. If NULL or "bottom" the plot will be at below UpSet plot. If "top" it will be above UpSet plot


Color of attribute histogram bins or scatterplot points for unqueried data represented by main bars. Default set to color of main bars.

How the intersections in the matrix should be ordered by. Options include frequency (entered as "freq"), degree, or both in any order.


How the variables in should be ordered. "freq" is decreasing (greatest to least) and "degree" is increasing (least to greatest)


Show numbers of intersection sizes above bars


The angle of the numbers atop the intersection size bars

How the data should be grouped ("degree" or "sets")


The number of intersections from each set (to cut off at) when aggregating by sets


Unified query of intersections, elements, and custom row functions. Entered as a list that contains a list of queries. query is the type of query being conducted. params are the parameters of the query (if any). color is the color of the points on the plot that will represent the query. If no color is selected one will be provided automatically. active takes TRUE or FALSE, and if TRUE, it will overlay the bars present with the results from the query. If FALSE a tick mark will indicate the intersection size. See examples section on how to do this.


Position query legend on top or bottom of UpSet plot


Color of row shading in matrix


Transparency of shading in matrix

Transparency of the empty intersections points in the matrix


Additionally display empty sets up to nintersects


Color palette for attribute plots


Boxplots representing the distribution of a selected attribute for each intersection. Select attributes by entering a character vector of attribute names (e.g. c("Name1", "Name2")). The maximum number of attributes that can be entered is 2.


Create custom ggplot using intersection data represented in the main bar plot. Prior to adding custom plots, the UpSet plot is set up in a 100 by 100 grid. The attribute.plots parameter takes a list that contains the number of rows that should be allocated for the custom plot, and a list of plots with specified positions. nrows is the number of rows the custom plots should take up. There is already 100 allocated for the custom plot. plots takes a list that contains a function that returns a custom ggplot and the x and y aesthetics for the function. ncols is the number of columns that your ggplots should take up. See examples for how to add custom ggplots.


The scale to be used for the intersection sizes. Options: "identity", "log10", "log2"


The scale to be used for the set sizes. Options: "identity", "log10", "log2"


Numeric, value to scale the text sizes, applies to all axis labels, tick labels, and numbers above bar plot. Can be a universal scale, or a vector containing individual scales in the following format: c(intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers above bars)


Numeric, angle to rotate the set size plot x-axis text

Logical, display the set sizes on the set size bar chart


If is TRUE, adjust the size of the numbers


Increase the maximum of set size scale


Visualization of set data in the layout described by Lex and Gehlenborg in UpSet also allows for visualization of queries on intersections and elements, along with custom queries queries implemented using Hadley Wickham's apply function. To further analyze the data contained in the intersections, the user may select additional attribute plots to be displayed alongside the UpSet plot. The user also has the the ability to pass their own plots into the function to further analyze data belonging to queries of interest. Most aspects of the UpSet plot are customizable, allowing the user to select the plot that best suits their style. Depending on how the features are selected, UpSet can display between 25-65 sets and between 40-100 intersections.


Data set must be formatted as described on the original UpSet github page:


Lex et al. (2014). UpSet: Visualization of Intersecting Sets IEEE Transactions on Visualization and Computer Graphics (Proceedings of InfoVis 2014), vol 20, pp. 1983-1992, (2014).

Lex and Gehlenborg (2014). Points of view: Sets and intersections. Nature Methods 11, 779 (2014).

See Also

Original UpSet Website:

UpSetR github for additional examples:

  • upset
movies <- read.csv( system.file("extdata", "movies.csv", package = "UpSetR"), header=TRUE, sep=";" )

require(ggplot2); require(plyr); require(gridExtra); require(grid);

between <- function(row, min, max){
  newData <- (row["ReleaseDate"] < max) & (row["ReleaseDate"] > min)

plot1 <- function(mydata, x){
  myplot <- (ggplot(mydata, aes_string(x= x, fill = "color"))
            + geom_histogram() + scale_fill_identity()
            + theme(plot.margin = unit(c(0,0,0,0), "cm")))

plot2 <- function(mydata, x, y){
  myplot <- (ggplot(data = mydata, aes_string(x=x, y=y, colour = "color"), alpha = 0.5)
            + geom_point() + scale_color_identity()
            + theme_bw() + theme(plot.margin = unit(c(0,0,0,0), "cm")))

attributeplots <- list(gridrows = 55,
                  plots = list(list(plot = plot1, x= "ReleaseDate",  queries = FALSE),
                         list(plot = plot1, x= "ReleaseDate", queries = TRUE),
                         list(plot = plot2, x = "ReleaseDate", y = "AvgRating", queries = FALSE),
                         list(plot = plot2, x = "ReleaseDate", y = "AvgRating", queries = TRUE)),
                   ncols = 3)

upset(movies, nsets = 7, nintersects = 30, mb.ratio = c(0.5, 0.5), = c("freq", "degree"), decreasing = c(TRUE,FALSE))

upset(movies, sets = c("Drama", "Comedy", "Action", "Thriller", "Western", "Documentary"),
      queries = list(list(query = intersects, params = list("Drama", "Action")),
                list(query = between, params = list(1970, 1980), color = "red", active = TRUE)))

upset(movies, attribute.plots = attributeplots,
     queries = list(list(query = between, params = list(1920, 1940)),
                    list(query = intersects, params = list("Drama"), color= "red"),
                    list(query = elements, params = list("ReleaseDate", 1990, 1991, 1992))), = "yellow")

# }
Documentation reproduced from package UpSetR, version 1.4.0, License: MIT + file LICENSE

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