Basic User Interface

Note: The input data will be described in more detail in the next section

example of list input (list of named vectors, each having a list of contained elements)

listInput <- list(one = c("a", "b", "c", "e", "g", "h", "k", "l", "m"), two = c("a", 
    "b", "d", "e", "j"), three = c("a", "e", "f", "g", "h", "i", "j", "l", "m"))

w <- upsetjs() %>% fromList(listInput) %>% interactiveChart()
w

An UpSet plot consists of three areas:

• The bottom left area shows the list of sets as a vertical bar chart. The length of the bar corresponds to the cardinality of the set, i.e., the number of elements in this set.
• The top right area shows the list of set intersections as a horizontal bar chart. Again the length corresponds to the cardinality of the set
• The bottom right area shows which intersection consists of which sets. A dark dot indicates that the set is part of this set intersection. The line connecting the dots is just to visually group the dots.

Moving the mouse over a bar or a dot will automatically highlight the corresponding set or set intersection in orange. In addition, the number elements which are shared with the highlighted sets are also highlighted. This gives a quick overview how sets and set intersections are related to each other. More details, in the Interaction section.

Input Formats

In the current version the UpSet.js wrapper supports three input data formats: list, expression, and through a data.frame.

upsetjs() %>% fromList(list(one = c("a", "b", "c", "e", "g", "h", "k", "l", "m"), 
    two = c("a", "b", "d", "e", "j"), three = c("a", "e", "f", "g", "h", "i", "j", 
        "l", "m")))

# example of expression input
expressionInput <- list(one = 9, two = 5, three = 9, `one&two` = 3, `one&three` = 6, 
    `two&three` = 3, `one&two&three` = 2)


upsetjs() %>% fromExpression(expressionInput)

# boolean table with rows = elements, columns = sets, cell = is row part of this
# set
dataFrame <- as.data.frame(list(one = c(1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1), two = c(1, 
    1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0), three = c(1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 
    0, 1, 1)), row.names = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", 
    "l", "m"))


upsetjs() %>% fromDataFrame(dataFrame)

Data Intersections

In case of an expressionInput the combinations of sets are directly given.

generateIntersections, generateDistinctIntersections, and generateUnions let you customize the generation of the set combinations

• min … minimum number of sets in a set combination
• max … maximum number of sets in a set combination, NULL means no limit
• empty … include empty set combinations with no elements. By default they are not included
• order.by … sort set combinations either by cardinality (number of elements) or by degree (number of sets
• limit … show only the first limit set combinations

upsetjs() %>% fromList(listInput) %>% generateDistinctIntersections()

upsetjs() %>% fromList(listInput) %>% generateIntersections(min = 2, max = NULL, 
    empty = T, order.by = "cardinality", limit = NULL)

upsetjs() %>% fromList(listInput) %>% generateUnions(min = 0, max = 2, empty = T, 
    order.by = "degree", limit = NULL)

Interaction

upsetjs() %>% fromList(listInput) %>% interactiveChart()

upsetjs() %>% fromList(listInput) %>% setSelection("one")

upsetjs() %>% fromList(listInput) %>% setSelection(c("one", "two"))

Queries

besides the selection UpSet.js supports defining queries. A query can be a list of elements or a set that should be highlighted. A query consists of a name, a color, and either the list of elements or the set (combination) to highlight.

upsetjs() %>% fromList(listInput) %>% addQuery("Q1", color = "red", elems = c("a", 
    "b", "c")) %>% addQuery("Q2", color = "blue", set = "two")

Attributes

UpSet.js supports rendering boxplots as aggregations for numerical attributes of elements and mosaic plots for categorical attributes. The are given as part of the data frame. The attributes element has to be a list or a data frame.

dataFrame <- as.data.frame(list(one = c(1, 1, 1, 0, 1, 0, 1, 1, 0, 0, 1, 1, 1), two = c(1, 
    1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0, 0), three = c(1, 0, 0, 0, 1, 1, 1, 1, 1, 1, 
    0, 1, 1)), row.names = c("a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", 
    "l", "m"))

upsetjs() %>% fromDataFrame(dataFrame, attributes = list(attr = runif(nrow(dataFrame))))

Styling

upsetjs() %>% fromList(listInput) %>% chartTheme("dark")

upsetjs() %>% fromList(listInput) %>% chartLabels(title = "Chart Title", description = "this is a long chart description")

upsetjs() %>% fromList(listInput) %>% chartLabels(combination.name = "Combination Label", 
    set.name = "Set Label")

upsetjs() %>% fromList(listInput) %>% chartLayout(numerical.scale = "log")