plotUpset: UpSet plot

In acidgenomics/minimalism: Acid Genomics Plot Functions and Themes

UpSet plot

Description

UpSet plot

Usage

plotUpset(object, ...)

## S4 method for signature 'DFrame'
plotUpset(object, ...)

## S4 method for signature 'data.frame'
plotUpset(object, ...)

## S4 method for signature 'list'
plotUpset(object, ...)

## S4 method for signature 'matrix'
plotUpset(
  object,
  minSize = 0L,
  maxSize = Inf,
  nIntersections = 40L,
  orderBySize = c(intersections = TRUE, sets = TRUE),
  labels = list(title = NULL, subtitle = NULL)
)

Arguments

object	Object.
...	Additional arguments.
minSize, maxSize	Non-negative integer(1) or Inf. Minimal/maximal number of observations in an intersection for it to be included. Defaults to all observations. Note that maxSize must be greater than minSize.
nIntersections	integer(1) or Inf. Maximum number of intersections to plot. Set Inf to plot all intersections.
orderBySize	logical. Whether to order main bar plot and/or intersection matrix by set size. "intersection": refers to main intersection bar plot. "sets": refers to set intersection matrix, shown as connected dots. When TRUE, orders by the set size (see plot to the left). Can pass in TRUE/FALSE boolean flag and both "intersection" and "sets" settings will inherit.
labels	list. ggplot2 labels. See ggplot2::labs() for details.

Details

S4 wrapper for ComplexUpset::upset() with improved default aesthetics.

Value

Plot.

Note

Updated 2022-04-05.

See Also

• intersectionMatrix().

• ComplexUpset::upset().

• ComplexUpset::upset_themes.

• UpSetR package (legacy approach).

Examples

## list ====
list <- list(
    "aaa" = c("a", "b", "c", "d", "e", "f"),
    "bbb" = c("b", "c", "d", "e", "f", "g"),
    "ccc" = c("c", "d", "e", "f", "g", "h"),
    "ddd" = c("d", "e", "f", "g", "h", "i")
)
print(list)
plotUpset(list)

## matrix ====
mat <- AcidBase::intersectionMatrix(list)
print(mat)
plotUpset(mat)

acidgenomics/minimalism documentation built on April 1, 2024, 10:34 a.m.