Querying the Data

For all examples the movies data set contained in the package will be used.

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

queries Parameter Breakdown

Each list contained in the queries parameter takes 4 fields: query, params, color, and active.

query specifies which query is going to be run
params is a list of paramters for the query to work on
color is the color that will represent the query on the plot. If no color is provided, a color will be selected from the UpSetR default color palette.
active determines how the query will be represented on the plot. If active is TRUE, the intersection size bar will be overlayed by a bar representing the query. If active is FALSE, a jitter point will be placed on the intersection size bar.

To learn how queries can be explored and visualized on an element level see the Attribute Plots vignette.

Example 1: Built-in Intersection Query

This example shows how to use the built in intersection query, intersects, to find or display elements in specific intersections. In this example the color selected for the active query is from the default color palette.

upset(movies, queries = list(list(query = intersects, params = list("Drama", "Comedy",
    "Action"), color = "orange", active = T), list(query = intersects, params = list("Drama"),
    color = "red", active = F), list(query = intersects, params = list("Action",
    "Drama"), active = T)))

## Warning: `aes_string()` was deprecated in ggplot2 3.0.0.
## ℹ Please use tidy evaluation idioms with `aes()`.
## ℹ See also `vignette("ggplot2-in-packages")` for more information.
## ℹ The deprecated feature was likely used in the UpSetR package.
##   Please report the issue at <https://github.com/hms-dbmi/UpSetR/issues>.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## ℹ The deprecated feature was likely used in the UpSetR package.
##   Please report the issue at <https://github.com/hms-dbmi/UpSetR/issues>.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

## Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
## ℹ Please use the `linewidth` argument instead.
## ℹ The deprecated feature was likely used in the UpSetR package.
##   Please report the issue at <https://github.com/hms-dbmi/UpSetR/issues>.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.

Example 2: Built-In Elements Query

This example shows how to use the built in element query, elements, to visualize how certain elements are distributed amongst the intersections.

upset(movies, queries = list(list(query = elements, params = list("AvgRating", 3.5,
    4.1), color = "blue", active = T), list(query = elements, params = list("ReleaseDate",
    1980, 1990, 2000), color = "red", active = F)))

Example 3: Using Expression Parameter to Subset Intersection and Element Queries

This example shows how to use the expression parameter to subset the results of element and intersection queries.

upset(movies, queries = list(list(query = intersects, params = list("Action", "Drama"),
    active = T), list(query = elements, params = list("ReleaseDate", 1980, 1990,
    2000), color = "red", active = F)), expression = "AvgRating > 3 & Watches > 100")

Example 4: Creating Custom Queries on Set Elements and Attributes

Creating a custom query to operate on the rows of the data.

Myfunc <- function(row, release, rating) {
    data <- (row["ReleaseDate"] %in% release) & (row["AvgRating"] > rating)
}

Applying the created query to the queries parameter.

upset(movies, queries = list(list(query = Myfunc, params = list(c(1970, 1980, 1990,
    1999, 2000), 2.5), color = "blue", active = T)))

Example 5: Applying a query legend

To add a legend for the queries applied, the query.legend parameter can be used. The query.legend parameter takes the position where the legend should be displayed, either top or bottom. To apply a specific name to each query, the parameter query.name can be used when defining the query in the queries paramter. If no query.name is provided, a generic name will be used. The example below shows how to do this.

upset(movies, query.legend = "top", queries = list(list(query = intersects, params = list("Drama",
    "Comedy", "Action"), color = "orange", active = T, query.name = "Funny action"),
    list(query = intersects, params = list("Drama"), color = "red", active = F),
    list(query = intersects, params = list("Action", "Drama"), active = T, query.name = "Emotional action")))

Example 6: Applying Everything at Once

Combining pieces from all previous examples into one awesome query!

upset(movies, query.legend = "bottom", queries = list(list(query = Myfunc, params = list(c(1970,
    1980, 1990, 1999, 2000), 2.5), color = "orange", active = T), list(query = intersects,
    params = list("Action", "Drama"), active = F), list(query = elements, params = list("ReleaseDate",
    1980, 1990, 2000), color = "red", active = F, query.name = "Decades")), expression = "AvgRating > 3 & Watches > 100")