Help for package ComplexUpset

Type:

Package

Title:

Create Complex UpSet Plots Using 'ggplot2' Components

Version:

1.3.3

Description:

UpSet plots are an improvement over Venn Diagram for set overlap visualizations. Striving to bring the best of the 'UpSetR' and 'ggplot2', this package offers a way to create complex overlap visualisations, using simple and familiar tools, i.e. geoms of 'ggplot2'. For introduction to UpSet concept, see Lex et al. (2014) <doi:10.1109/TVCG.2014.2346248>.

License:

MIT + file LICENSE

Encoding:

UTF-8

URL:

https://github.com/krassowski/complex-upset, https://krassowski.github.io/complex-upset/

BugReports:

https://github.com/krassowski/complex-upset/issues

Suggests:

testthat (≥ 2.1.0), knitr, rmarkdown, covr, tibble, ggplot2movies, vdiffr, jsonlite, data.table

Imports:

ggplot2, patchwork, scales, colorspace

VignetteBuilder:

knitr

RoxygenNote:

7.1.1

NeedsCompilation:

Packaged:

2021-12-10 23:51:20 UTC; krassowski

Author:

Michał Krassowski

[aut, cre]

Maintainer:

Michał Krassowski <krassowski.michal+r@gmail.com>

Repository:

CRAN

Date/Publication:

2021-12-11 15:20:03 UTC

Generate mapping for labeling percentages

Description

Generate mapping for labeling percentages

Usage

aes_percentage(relative_to, digits = 0, sep = "")

Arguments

relative_to

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

digits

number of digits to show (default=0)

sep

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

Arrange points for Venn diagram

Description

Arrange points for Venn diagram

Usage

arrange_venn(
  data,
  sets = NULL,
  radius = 1.5,
  max_iterations = 10,
  verbose = FALSE,
  outwards_adjust = 1.3,
  extract_sets = FALSE,
  extract_regions = FALSE,
  repeat_in_intersections = FALSE,
  starting_grid_size = "auto"
)

Arguments

data

a dataframe including binary columns representing membership in sets

sets

vector with names of columns representing membership in sets

radius

the radius of the circle

max_iterations

the maximal number of iterations

verbose

should debugging notes be printed?

outwards_adjust

the multiplier defining the distance from the centre

extract_sets

should only sets be extracted?

extract_regions

should all unique regions be extracted?

repeat_in_intersections

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

starting_grid_size

the starting size of the grid for placement of elements

Compare covariates between intersections

Description

Compare covariates between intersections

Usage

compare_between_intersections(
  data,
  intersect,
  test = kruskal.test,
  tests = list(),
  ignore = list(),
  ignore_mode_columns = TRUE,
  mode = "exclusive_intersection",
  ...
)

Arguments

data

a dataframe including binary columns representing membership in classes

intersect

which columns should be used to compose the intersection

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.

...

passed to upset_data()

Create an example dataset with three sets: A, B and C

Description

Create an example dataset with three sets: A, B and C

Usage

create_upset_abc_example()

Circle for Venn diagram

Description

Circle for Venn diagram

Usage

geom_venn_circle(
  data,
  mapping = aes_(),
  sets = NULL,
  radius = 1.5,
  resolution = 100,
  size = 0.8,
  color = "black",
  ...
)

Arguments

data

a dataframe including binary columns representing membership in sets

mapping

the aesthetics mapping

sets

vector with names of columns representing membership in sets

radius

the radius of the circle

resolution

the resolution of the circle rasterizer

size

width of the outline

color

the color of the outline

...

Arguments passed on to ggplot2::geom_polygon

stat: The statistical transformation to use on the data for this layer, as a string.
position: Position adjustment, either as a string, or the result of a call to a position adjustment function.
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().

Label for a region of Venn diagram

Description

Label for a region of Venn diagram

Usage

geom_venn_label_region(
  data,
  mapping = aes_(),
  sets = NULL,
  outwards_adjust = 1.3,
  fill = alpha("white", 0.85),
  size = 5,
  label.size = 0,
  ...
)

Arguments

data

a dataframe including binary columns representing membership in sets

mapping

the aesthetics mapping

sets

vector with names of columns representing membership in sets

outwards_adjust

the multiplier defining the distance from the centre

fill

the fill of the label

size

the text size

label.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, as a string.
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: Horizontal and vertical adjustment to nudge labels by. Useful for offsetting text from points, particularly on discrete scales. Cannot be jointly specified with position.
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().

Label for a set of Venn diagram

Description

Label for a set of Venn diagram

Usage

geom_venn_label_set(
  data,
  mapping = aes_(),
  sets = NULL,
  outwards_adjust = 2.5,
  fill = alpha("white", 0.85),
  size = 5,
  label.size = 0,
  ...
)

Arguments

data

a dataframe including binary columns representing membership in sets

mapping

the aesthetics mapping

sets

vector with names of columns representing membership in sets

outwards_adjust

the multiplier defining the distance from the centre

fill

the fill of the label

size

the text size

label.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, as a string.
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: Horizontal and vertical adjustment to nudge labels by. Useful for offsetting text from points, particularly on discrete scales. Cannot be jointly specified with position.
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().

Region of Venn diagram

Description

Region of Venn diagram

Usage

geom_venn_region(data, mapping = aes_(), sets = NULL, resolution = 250, ...)

Arguments

data

a dataframe including binary columns representing membership in sets

mapping

the aesthetics mapping

sets

vector with names of columns representing membership in sets

resolution

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, as a string.
position: Position adjustment, either as a string, or the result of a call to a position adjustment function.
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().

Retrieve symbol for given mode that can be used in aesthetics mapping with double bang (`⁠!!⁠`)

Description

Retrieve symbol for given mode that can be used in aesthetics mapping with double bang (⁠!!⁠)

Usage

get_size_mode(mode, suffix = "_size")

Arguments

mode

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

suffix

the column suffix in use as passed to upset_data()

Prepare layers for sets sizes plot

Description

Prepare layers for sets sizes plot

Usage

intersection_matrix(
  geom = geom_point(size = 3),
  segment = geom_segment(),
  outline_color = list(active = "black", inactive = "grey70")
)

Arguments

geom

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

segment

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

outline_color

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

Barplot annotation of relative intersections sizes

Description

A large intersection size can be driven by a large number of members in a group; to account for that, one can divide the intersection size by the size of a union of the same groups. This cannot be calculated for the null intersection (observations which do not belong to either of the groups).

Usage

intersection_ratio(
  mapping = aes(),
  counts = TRUE,
  bar_number_threshold = 0.75,
  text_colors = c(on_background = "black", on_bar = "white"),
  text = list(),
  text_mapping = aes(),
  mode = "distinct",
  denominator_mode = "union",
  ...
)

Arguments

mapping

additional aesthetics for geom_bar()

counts

whether to display count number labels above the bars

bar_number_threshold

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

text_colors

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

text

additional parameters passed to geom_text()

text_mapping

additional aesthetics for geom_text()

mode

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

denominator_mode

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

...

Arguments passed on to intersection_size

position: position passed to geom_bar()

Barplot annotation of intersections sizes

Description

Barplot annotation of intersections sizes

Usage

intersection_size(
  mapping = aes(),
  counts = TRUE,
  bar_number_threshold = 0.85,
  text_colors = c(on_background = "black", on_bar = "white"),
  text = list(),
  text_mapping = aes(),
  mode = "distinct",
  position = position_stack(),
  ...
)

Arguments

mapping

additional aesthetics for geom_bar()

counts

whether to display count number labels above the bars

bar_number_threshold

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

text_colors

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

text

additional parameters passed to geom_text()

text_mapping

additional aesthetics for geom_text()

mode

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

position

position passed to geom_bar()

...

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)).

width

Bar width. By default, set to 90% of the resolution of the data.

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().

stat

Override the default connection between geom_bar() and stat_count().

Logarithmic scale for use with `upset_set_size()`

Description

Inspired by Brian Diggs' answer which is CC-BY-SA 4.0.

Usage

reverse_log_trans(base = 10)

Arguments

base

logarithm base (default 10)

Color scale for Venn diagram

Description

Color scale for Venn diagram

Usage

scale_color_venn_mix(
  data,
  sets = NULL,
  colors = c("red", "blue", "green"),
  na.value = "grey40",
  highlight = NULL,
  active_color = "orange",
  inactive_color = "NA",
  scale = scale_color_manual,
  ...
)

Arguments

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)

na.value

value for elements not belonging to any of the sets

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())

...

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

Fill scale for Venn diagram

Description

Fill scale for Venn diagram

Usage

scale_fill_venn_mix(..., na.value = "NA")

Arguments

...

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())

na.value

value for elements not belonging to any of the known sets

Compose an UpSet plot

Description

Compose an UpSet plot

Usage

upset(
  data,
  intersect,
  base_annotations = "auto",
  name = "group",
  annotations = list(),
  themes = upset_themes,
  stripes = upset_stripes(),
  labeller = identity,
  height_ratio = 0.5,
  width_ratio = 0.3,
  wrap = FALSE,
  set_sizes = upset_set_size(),
  mode = "distinct",
  queries = list(),
  guides = NULL,
  encode_sets = TRUE,
  matrix = intersection_matrix(),
  ...
)

Arguments

data

a dataframe including binary columns representing membership in classes

intersect

which columns should be used to compose the intersection

base_annotations

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

name

the label shown below the intersection matrix

annotations

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.

themes

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

stripes

specification of the stripes appearance created with upset_stripes()

labeller

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

height_ratio

ratio of the intersection matrix to intersection size height

width_ratio

ratio of the overall set size width to intersection matrix width

wrap

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

set_sizes

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

mode

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

queries

a list of queries generated with upset_query()

guides

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

encode_sets

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().

matrix

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

Annotation panel shorthand

Description

Simplifies creation of annotation panels, automatically building aesthetics mappings, at a cost of lower flexibility than when providing a custom mapping; aes(x=intersection) is prespecified.

Usage

upset_annotate(y, geom)

Arguments

y

A string with the name of the y aesthetic

geom

A geom to be used as an annotation

Prepare data for UpSet plots

Description

Prepare data for UpSet plots

Usage

upset_data(
  data,
  intersect,
  min_size = 0,
  max_size = Inf,
  min_degree = 0,
  max_degree = Inf,
  n_intersections = NULL,
  keep_empty_groups = FALSE,
  warn_when_dropping_groups = FALSE,
  warn_when_converting = "auto",
  sort_sets = "descending",
  sort_intersections = "descending",
  sort_intersections_by = "cardinality",
  sort_ratio_numerator = "exclusive_intersection",
  sort_ratio_denominator = "inclusive_union",
  group_by = "degree",
  mode = "exclusive_intersection",
  size_columns_suffix = "_size",
  encode_sets = FALSE,
  max_combinations_datapoints_n = 10^10,
  intersections = "observed"
)

Arguments

data

a dataframe including binary columns representing membership in classes

intersect

which columns should be used to compose the intersection

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'

mode

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

size_columns_suffix

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

encode_sets

max_combinations_datapoints_n

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

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)

Default themes modified by specified arguments

Description

Return the default UpSet themes with all themes modified with provided arguments

Usage

upset_default_themes(...)

Arguments

...

arguments passed to theme()

Layer defining the intersection mode for the data to be displayed

Description

By default the annotations are given data corresponding to the same mode as the mode of the passed in the upset() call.

Usage

upset_mode(mode)

Arguments

mode

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

Default themes modified by specified component-specific arguments

Description

Return the default UpSet themes with specific themes modified with provided themes

Usage

upset_modify_themes(to_update)

Arguments

to_update

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

Highlight chosen sets or intersections

Description

Highlight sets or intersections matching specified query.

Usage

upset_query(
  set = NULL,
  intersect = NULL,
  group = NULL,
  only_components = NULL,
  ...
)

Arguments

set

name of the set to highlight

intersect

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

group

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

only_components

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

Examples

upset_query(intersect=c('Drama', 'Comedy'), color='red', fill='red')
upset_query(set='Drama', fill='blue')

Prepare layers for sets sizes plot

Description

Prepare layers for sets sizes plot

Usage

upset_set_size(
  mapping = aes(),
  geom = geom_bar(width = 0.6),
  position = "left",
  filter_intersections = FALSE
)

Arguments

mapping

additional aesthetics

geom

a geom to use

position

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

filter_intersections

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

Define appearence of the stripes

Description

Define appearence of the stripes

Usage

upset_stripes(
  mapping = aes(),
  geom = geom_segment(size = 7),
  colors = c("white", "grey95"),
  data = NULL
)

Arguments

mapping

additional aesthetics

geom

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

colors

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

data

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

Test for differences between intersections

Description

This is a wrapper around compare_between_intersections(), adding sorting by FDR, warnings, etc.

Usage

upset_test(data, intersect, ...)

Arguments

data

a dataframe including binary columns representing membership in classes

intersect

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.

Generate percentage label of the intersection/union sizes ratio

Description

For use together with intersection_size or intersection_ratio

Usage

upset_text_percentage(digits = 0, sep = "", mode = "distinct")

Arguments

digits

How many digits to show when rounding the percentage?

sep

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

mode

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

Examples

ggplot2::aes(label=!!upset_text_percentage())

List of default themes for upset components

Description

List of default themes for upset components

Usage

upset_themes

Format

An object of class list of length 4.

Generate mapping for labeling percentages

Description

Usage

Arguments

Arrange points for Venn diagram

Description

Usage

Arguments

Compare covariates between intersections

Description

Usage

Arguments

Create an example dataset with three sets: A, B and C

Description

Usage

Circle for Venn diagram

Description

Usage

Arguments

Label for a region of Venn diagram

Description

Usage

Arguments

Label for a set of Venn diagram

Description

Usage

Arguments

Region of Venn diagram

Description

Usage

Arguments

Retrieve symbol for given mode that can be used in aesthetics mapping with double bang (⁠!!⁠)

Description

Usage

Arguments

Prepare layers for sets sizes plot

Description

Usage

Arguments

Barplot annotation of relative intersections sizes

Description

Usage

Arguments

Barplot annotation of intersections sizes

Description

Usage

Arguments

Logarithmic scale for use with upset_set_size()

Description

Usage

Arguments

Color scale for Venn diagram

Description

Usage

Arguments

Fill scale for Venn diagram

Description

Usage

Arguments

Compose an UpSet plot

Description

Usage

Arguments

Annotation panel shorthand

Description

Usage

Arguments

Prepare data for UpSet plots

Description

Usage

Arguments

Default themes modified by specified arguments

Description

Usage

Arguments

Layer defining the intersection mode for the data to be displayed

Description

Usage

Arguments

Default themes modified by specified component-specific arguments

Retrieve symbol for given mode that can be used in aesthetics mapping with double bang (`⁠!!⁠`)

Logarithmic scale for use with `upset_set_size()`