ggalign (version 1.0.1)

ggupset: Create an UpSet plot

Description

ggupset is a specialized version of quad_discrete(), which simplifies the creation of Upset plot.

Usage

ggupset(
  data = NULL,
  mapping = aes(),
  ...,
  direction = "h",
  point = NULL,
  line = NULL,
  rect = NULL,
  width = NA,
  height = NA,
  theme = NULL,
  active = NULL
)

Arguments

data

Data used to create the UpSet plot. fortify_matrix() will be used to convert the data to a matrix. Currently, only fortify_matrix.list_upset and fortify_matrix.matrix_upset are suitable for creating an UpSet plot.

mapping

Default list of aesthetic mappings to use for main plot in the layout. If not specified, must be supplied in each layer added to the main plot.

...

Additional arguments passed to fortify_matrix().

direction

A string indicating the direction of the UpSet plot, "h"(horizontal) or "v"(vertical). In a vertical UpSet plot, the columns of the matrix correspond to the sets, and the rows correspond to the intersections. By default, the horizontal UpSet plot is used, where the rows of the matrix correspond to the sets and the columns correspond to the intersections.

point

A list of parameters passed to geom_point().

line

A list of parameters passed to geom_line().

rect

A list of parameters passed to geom_rect().

width, height

The relative width/height of the main plot, can be a unit object.

theme

A theme() object used to customize various elements of the layout, including guides, title, subtitle, caption, margins, panel.border, and background. By default, the theme will inherit from the parent layout. It also controls the panel spacing for all plots in the layout.

active

A active() object that defines the context settings when added to a layout.

ggplot2 specification

The data input will be converted to a matrix using fortify_matrix(), and the data in the underlying main plot will contain the following columns:

• .panel_x and .panel_y: the column and row panel groups.

• .x and .y: an integer index of x and y coordinates

• .discrete_x and .discrete_y: a factor of the data labels (only applicable when .row_names and .column_names exists).

• .row_names and .column_names: A character of the row and column names of the original matrix (only applicable when names exist).

• .row_index and .column_index: the row and column index of the original matrix.

• value: the actual matrix value.

Examples

set.seed(123)
lt <- list(
    a = sample(letters, 5),
    b = sample(letters, 10),
    c = sample(letters, 15)
)
ggupset(tune(lt)) +
    scale_fill_manual(values = c("#F0F0F0", "white"), guide = "none") +
    scale_color_manual(values = c("grey", "black"), guide = "none") +
    anno_top() +
    ggalign(data = function(d) ggalign_attr(d, "intersection_sizes")) +
    ggplot2::geom_bar(aes(y = .data$value), stat = "identity") +
    anno_right() +
    ggalign(data = function(d) ggalign_attr(d, "set_sizes")) +
    ggplot2::geom_bar(aes(x = .data$value),
        stat = "identity",
        orientation = "y"
    )