Package 'ComplexUpset'

defines proportion that should be calculated, relative to 'intersection', 'group', or 'all' observed values

number of digits to show (default=0)

separator separator between the digit and percent sign (no separator by default)

a dataframe including binary columns representing membership in sets

vector with names of columns representing membership in sets

the radius of the circle

the maximal number of iterations

should debugging notes be printed?

the multiplier defining the distance from the centre

should only sets be extracted?

should all unique regions be extracted?

repeat intersection k times where k is the number of sets it belongs to?

the starting size of the grid for placement of elements

a dataframe including binary columns representing membership in classes

which columns should be used to compose the intersection

the default test function; it is expected to accept formula and data parameters, and a list with p.value, statistic, and method

a named list with tests for specific variables, overwriting the default test

a list with names of variables to exclude from testing

whether the membership columns and size columns for all modes should be ignored

region selection mode; note that modes other than exclusive_intersection repeat observations in different test group, introducing dependencies. See get_size_mode() for accepted values.

passed to upset_data()

a dataframe including binary columns representing membership in sets

the aesthetics mapping

vector with names of columns representing membership in sets

the radius of the circle

the resolution of the circle rasterizer

width of the outline

the color of the outline

Arguments passed on to ggplot2::geom_polygon

stat

The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")

position

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

rule

Either "evenodd" or "winding". If polygons with holes are being drawn (using the subgroup aesthetic) this argument defines how the hole coordinates are interpreted. See the examples in grid::pathGrob() for an explanation.

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

a dataframe including binary columns representing membership in sets

the aesthetics mapping

vector with names of columns representing membership in sets

the multiplier defining the distance from the centre

the fill of the label

the text size

the size of the label outline

Arguments passed on to ggplot2::geom_label

stat

The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")

position

Position adjustment, either as a string, or the result of a call to a position adjustment function. Cannot be jointy specified with nudge_x or nudge_y.

parse

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

nudge_x,nudge_y

Horizontal and vertical adjustment to nudge labels by. Useful for offsetting text from points, particularly on discrete scales. Cannot be jointly specified with position.

label.padding

Amount of padding around label. Defaults to 0.25 lines.

label.r

Radius of rounded corners. Defaults to 0.15 lines.

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

a dataframe including binary columns representing membership in sets

the aesthetics mapping

vector with names of columns representing membership in sets

the multiplier defining the distance from the centre

the fill of the label

the text size

the size of the label outline

Arguments passed on to ggplot2::geom_label

stat

The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")

position

Position adjustment, either as a string, or the result of a call to a position adjustment function. Cannot be jointy specified with nudge_x or nudge_y.

parse

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

nudge_x,nudge_y

Horizontal and vertical adjustment to nudge labels by. Useful for offsetting text from points, particularly on discrete scales. Cannot be jointly specified with position.

label.padding

Amount of padding around label. Defaults to 0.25 lines.

label.r

Radius of rounded corners. Defaults to 0.15 lines.

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

a dataframe including binary columns representing membership in sets

the aesthetics mapping

vector with names of columns representing membership in sets

the resolution of the circle rasterizer

Arguments passed on to ggplot2::geom_polygon

stat

The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")

position

Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.

rule

Either "evenodd" or "winding". If polygons with holes are being drawn (using the subgroup aesthetic) this argument defines how the hole coordinates are interpreted. See the examples in grid::pathGrob() for an explanation.

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

the mode to use. Accepted values: exclusive_intersection (alias distinct), inclusive_intersection (alias intersect), inclusive_union (alias union), exclusive_union.

the column suffix in use as passed to upset_data()

a geom_point call, allowing to specify parameters (e.g. geom=geom_point(shape='square'))

a geom_segment call, allowing to specify parameters (e.g. segment=geom_segment(linetype='dotted'))

a named list with two colors for outlines of active and inactive dots

additional aesthetics for geom_bar()

whether to display count number labels above the bars

if less than one, labels for bars height greater than this threshold will be placed on (not above) the bars

a name vector of characters specifying the color when on_background and on_bar (see bar_number_threshold)

additional parameters passed to geom_text()

additional aesthetics for geom_text()

region selection mode, defines which intersection regions will be accounted for when computing the size. See get_size_mode() for accepted values.

region selection mode for computing the denominator in ratio. See get_size_mode() for accepted values.

bar width, by default set to 90%

Arguments passed on to intersection_size

position

position passed to geom_bar()

additional aesthetics for geom_bar()

whether to display count number labels above the bars

if less than one, labels for bars height greater than this threshold will be placed on (not above) the bars

a name vector of characters specifying the color when on_background and on_bar (see bar_number_threshold)

additional parameters passed to geom_text()

additional aesthetics for geom_text()

region selection mode, defines which intersection regions will be accounted for when computing the size. See get_size_mode() for accepted values.

position passed to geom_bar()

bar width, by default set to 90%

Arguments passed on to ggplot2::geom_bar

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

just

Adjustment for column placement. Set to 0.5 by default, meaning that columns will be centered about axis breaks. Set to 0 or 1 to place columns to the left/right of axis breaks. Note that this argument may have unintended behaviour when used with alternative positions, e.g. position_dodge().

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

orientation

The orientation of the layer. The default (NA) automatically determines the orientation from the aesthetic mapping. In the rare event that this fails it can be given explicitly by setting orientation to either "x" or "y". See the Orientation section for more detail.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

logarithm base (default 10)

a dataframe including binary columns representing membership in sets

vector with names of columns representing membership in sets

named list of colors for sets (one set=one color)

value for elements not belonging to any of the sets

which regions of the diagram to highlight

color for highlight

color for lack of highlight

the base scale (default=scale_color_manual())

Arguments passed on to ggplot2::scale_color_manual

values

a set of aesthetic values to map data values to. The values will be matched in order (usually alphabetical) with the limits of the scale, or with breaks if provided. If this is a named vector, then the values will be matched based on the names instead. Data values that don't match will be given na.value.

aesthetics

Character string or vector of character strings listing the name(s) of the aesthetic(s) that this scale works with. This can be useful, for example, to apply colour settings to the colour and fill aesthetics at the same time, via aesthetics = c("colour", "fill").

breaks

One of:

• NULL for no breaks

• waiver() for the default breaks (the scale limits)

• A character vector of breaks

• A function that takes the limits as input and returns breaks as output

Arguments passed on to scale_color_venn_mix

data

a dataframe including binary columns representing membership in sets

sets

vector with names of columns representing membership in sets

colors

named list of colors for sets (one set=one color)

highlight

which regions of the diagram to highlight

active_color

color for highlight

inactive_color

color for lack of highlight

scale

the base scale (default=scale_color_manual())

value for elements not belonging to any of the known sets

a dataframe including binary columns representing membership in classes

which columns should be used to compose the intersection

a named list with default annotations (i.e. the intersection size barplot)

the label shown below the intersection matrix

a named list of annotations, each being a list with: ⁠list(aes=mapping, geom=geom or list of geoms)⁠;

• (optional) ⁠highlight_geom=list of geoms⁠ geoms which can be highlighted with queries,

• (optional) ⁠top_geom=list of geoms⁠ which should show up on top of highlighted queries.

a named list of themes for components and annotations, see upset_default_themes()/upset_modify_themes()

specification of the stripes appearance created with upset_stripes()

function modifying the names of the sets (rows in the matrix)

ratio of the intersection matrix to intersection size height

ratio of the overall set size width to intersection matrix width

whether the plot should be wrapped into a group (makes adding a tile/combining with other plots easier)

the overall set sizes plot, e.g. from upset_set_size() (FALSE to hide)

region selection mode for computing the number of elements in intersection fragment. See get_size_mode() for accepted values.

a list of queries generated with upset_query()

action for legends aggregation and placement ('keep', 'collect', 'over' the set sizes)

whether set names (column in input data) should be encoded as numbers (set to TRUE to overcome R limitations of max 10 kB for variable names for datasets with huge numbers of sets); default TRUE for upset() and FALSE for upset_data().

the intersection matrix plot

Arguments passed on to upset_data

min_size

minimal number of observations in an intersection for it to be included

max_size

maximal number of observations in an intersection for it to be included

min_degree

minimal degree of an intersection for it to be included

max_degree

maximal degree of an intersection for it to be included

n_intersections

the exact number of the intersections to be displayed; n largest intersections that meet the size and degree criteria will be shown

keep_empty_groups

whether empty sets should be kept (including sets which are only empty after filtering by size)

warn_when_dropping_groups

whether a warning should be issued when empty sets are being removed

warn_when_converting

whether a warning should be issued when input is not boolean

sort_sets

whether to sort the rows in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE

sort_intersections

whether to sort the columns in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE

sort_intersections_by

the mode of sorting, the size of the intersection (cardinality) by default; one of: 'cardinality', 'degree', 'ratio', or any combination of these (e.g. c('degree', 'cardinality'))

sort_ratio_numerator

the mode for numerator when sorting by ratio

sort_ratio_denominator

the mode for denominator when sorting by ratio

group_by

the mode of grouping intersections; one of: 'degree', 'sets'

size_columns_suffix

suffix for the columns to store the sizes (adjust if conflicts with your data)

intersections

whether only the intersections present in data (observed, default), or all intersections (all) should be computed; using all intersections for a high number of sets is not computationally feasible - use min_degree and max_degree to narrow down the selection; this is only useful for modes different from the default exclusive intersection. You can also provide a list with a custom selection of intersections (order is respected when you set sort_intersections=FALSE)

max_combinations_datapoints_n

a fail-safe limit preventing accidental use of intersections='all' with a high number of sets and observations

A string with the name of the y aesthetic

A geom to be used as an annotation

a dataframe including binary columns representing membership in classes

which columns should be used to compose the intersection

minimal number of observations in an intersection for it to be included

maximal number of observations in an intersection for it to be included

minimal degree of an intersection for it to be included

maximal degree of an intersection for it to be included

the exact number of the intersections to be displayed; n largest intersections that meet the size and degree criteria will be shown

whether empty sets should be kept (including sets which are only empty after filtering by size)

whether a warning should be issued when empty sets are being removed

whether a warning should be issued when input is not boolean

whether to sort the rows in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE

whether to sort the columns in the intersection matrix (descending sort by default); one of: 'ascending', 'descending', FALSE

the mode of sorting, the size of the intersection (cardinality) by default; one of: 'cardinality', 'degree', 'ratio', or any combination of these (e.g. c('degree', 'cardinality'))

the mode for numerator when sorting by ratio

the mode for denominator when sorting by ratio

the mode of grouping intersections; one of: 'degree', 'sets'

region selection mode for sorting and trimming by size. See get_size_mode() for accepted values.

suffix for the columns to store the sizes (adjust if conflicts with your data)

whether set names (column in input data) should be encoded as numbers (set to TRUE to overcome R limitations of max 10 kB for variable names for datasets with huge numbers of sets); default TRUE for upset() and FALSE for upset_data()

a fail-safe limit preventing accidental use of intersections='all' with a high number of sets and observations

whether only the intersections present in data (observed, default), or all intersections (all) should be computed; using all intersections for a high number of sets is not computationally feasible - use min_degree and max_degree to narrow down the selection; this is only useful for modes different from the default exclusive intersection. You can also provide a list with a custom selection of intersections (order is respected when you set sort_intersections=FALSE)

arguments passed to theme()

region selection mode, defines which mode data will be made available for the annotation. See get_size_mode() for accepted values.

a named list of themes to be used to modify themes of specific components; see names(upset_themes) for components names.

name of the set to highlight

a vector of names for the intersection to highlight; pass NA to select the empty intersection

name of the set to highlight when using group_by='sets'

which components to modify; by default all eligible components will be modified; the available components are 'overall_sizes', 'intersections_matrix', 'Intersection size', and any annotations specified

• passed to geoms in modified components

additional aesthetics

a geom to use

on which side of the plot should the set sizes be displayed ('left' or 'right')

whether the intersections filters (e.g. n_intersections or min_size) should influence displayed set sizes

additional aesthetics

a geom to use, should accept x, y, xend, yend and color aesthetics

a vector of colors to repeat as many times as needed for the fill of stripes, or a named vector specifying colors for values of the variable mapped to the color aesthetics in the mapping argument

the dataset describing the sets with a column named set and any other columns as needed for mapping

a dataframe including binary columns representing membership in classes

which columns should be used to compose the intersection

Arguments passed on to compare_between_intersections

test

the default test function; it is expected to accept formula and data parameters, and a list with p.value, statistic, and method

tests

a named list with tests for specific variables, overwriting the default test

ignore

a list with names of variables to exclude from testing

ignore_mode_columns

whether the membership columns and size columns for all modes should be ignored

mode

region selection mode; note that modes other than exclusive_intersection repeat observations in different test group, introducing dependencies. See get_size_mode() for accepted values.

How many digits to show when rounding the percentage?

set to space (' ') if you prefer a whitespace between the number and the ⁠\%⁠ sign.

region selection mode for computing the numerator in ratio. See get_size_mode() for accepted values.