Package 'ggVennDiagram'

Title: A 'ggplot2' Implement of Venn Diagram
Description: Easy-to-use functions to generate 2-7 sets Venn or upset plot in publication quality. 'ggVennDiagram' plot Venn or upset using well-defined geometry dataset and 'ggplot2'. The shapes of 2-4 sets Venn use circles and ellipses, while the shapes of 4-7 sets Venn use irregular polygons (4 has both forms), which are developed and imported from another package 'venn', authored by Adrian Dusa. We provided internal functions to integrate shape data with user provided sets data, and calculated the geometry of every regions/intersections of them, then separately plot Venn in four components, set edges/labels, and region edges/labels. From version 1.0, it is possible to customize these components as you demand in ordinary 'ggplot2' grammar. From version 1.4.4, it supports unlimited number of sets, as it can draw a plain upset plot automatically when number of sets is more than 7.
Authors: Chun-Hui Gao [aut, cre] , Guangchuang Yu [ctb] , Adrian Dusa [aut, cph] (<https://orcid.org/0000-0002-3525-9253>, Adrian Dusa is the author and copyright holder of venn, where ggVennDiagram imports the polygon coordinates enabling 5 - 7 sets Venn diagram.), Turgut Yigit Akyol [ctb]
Maintainer: Chun-Hui Gao <[email protected]>
License: GPL-3
Version: 1.5.3
Built: 2024-11-22 03:51:56 UTC
Source: https://github.com/gaospecial/ggvenndiagram

Help Index

All members of a list have the same elements

Description

All members of a list have the same elements

Usage

all_identical(list)

Arguments

list

a list

Value

TRUE or FALSE

all possible combinations of n sets

Description

all possible combinations of n sets

Usage

combinations(n)

Arguments

n

dim

Set difference.

Description

discern returns the difference between two group of sets selected from a Venn object. If multiple sets are chosen for the slices, union of those sets will be used.

Usage

discern(venn, slice1, slice2 = "all")

## S4 method for signature 'Venn'
discern(venn, slice1, slice2 = "all")

Arguments

venn

(Required) A Venn object.
slice1

(Required) The name or the index of the set of interest. Multiple sets can be selected.
slice2

(Optional) The name or the index of the set of interest. Multiple sets can be selected. Default is all the sets except the sets of slice1.

Value

A vector showing the difference between slice1 and slice2.

Author(s)

[email protected]

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
discern(venn, slice1 = 1)
discern(venn, slice1 = c(1, 2), slice2 = 3)

Calculate region of sets

Description

calculate the unique region defined by 'Venn' object and the parameter 'slice'.

Usage

discern_overlap(venn, slice = "all")

## S4 method for signature 'Venn'
discern_overlap(venn, slice = "all")

Arguments

venn

a Venn object
slice

index of Venn members, default is "all"

Value

region items

Author(s)

[email protected]

Examples

library(ggVennDiagram)
venn <- Venn(list(A=1:3,B=2:5,C=c(1L,3L,5L)))

discern_overlap(venn, slice = "all")
# is equal to
overlap(venn, slice = "all")

# however, `discern_overlap()` only contains specific region
discern_overlap(venn, slice = 1:2)
# is different from
overlap(venn, slice = 1:2)

Specifying a shape

Description

Specifying a shape

Usage

get_shape_by_id(id)

Arguments

id

shape id

Value

a shape

Examples

get_shape_by_id("401f")

get applicable shape data for Venn object

Description

ggVennDiagram stores shapes as internal data. You may see all the shapes by using 'plot_shapes()' or 'get_shapes()'.

Usage

get_shape_data(nsets, type = NULL, shape_id = NULL)

Arguments

nsets

number of sets
type

type of shape
shape_id

shape id

Value

a tibble describing specific shape

Examples

get_shape_data(nsets = 4, type = "polygon")

Get all shapes

Description

Get all shapes

Usage

get_shapes()

Value

a tibble

Examples

get_shapes()

ggVennDiagram main parser

Description

ggVennDiagram main parser

Usage

ggVennDiagram(
  x,
  category.names = names(x),
  show_intersect = FALSE,
  set_color = "black",
  set_size = NA,
  label = c("both", "count", "percent", "none"),
  label_alpha = 0.5,
  label_geom = c("label", "text"),
  label_color = "black",
  label_size = NA,
  label_percent_digit = 0,
  label_txtWidth = 40,
  edge_lty = "solid",
  edge_size = 1,
  force_upset = FALSE,
  nintersects = 20,
  order.intersect.by = c("size", "name", "none"),
  order.set.by = c("size", "name", "none"),
  relative_height = 3,
  relative_width = 0.3,
  ...
)

Arguments

x

list of items
category.names

default is names(x)
show_intersect

if TRUE the text can be visualized by 'plotly'
set_color

color of set labels ("black")
set_size

size of set labels (NA)
label

format of region labels, select one from c("count","percent","both","none")
label_alpha

set 0 to remove the background of region labels
label_geom

layer of region labels, choose from c("label", "text")
label_color

color of region labels ("black")
label_size

size of region labels (NA)
label_percent_digit

number of digits when formatting percent label (0)
label_txtWidth

width of text used in showing intersect members, will be ignored unless show_intersection is TRUE (40)
edge_lty

line type of set edges ("solid")
edge_size

line width of set edges (1)
force_upset

if TRUE, will always produce Upset plot no matter how many sets have (FALSE)
nintersects

number of intersects. If NULL, all intersections will show.
order.intersect.by

'size', 'name', or "none"
order.set.by

'size', 'name', or "none"
relative_height

the relative height of top panel in upset plot
relative_width

the relative width of left panel in upset plot
...

useless

Details

From version 1.4.4, 'ggVennDiagram' will plot a upset plot when the number of sets is more than 7. Besides, user can switch to a upset plot with 'upset_plot()' function. Please check the document of this function.

Value

A ggplot object

Examples

library(ggVennDiagram)
x = list(A=1:5,B=2:7,C=3:6,D=4:9)
ggVennDiagram(x)  # 4d venn
ggVennDiagram(x[1:3])  # 3d venn
ggVennDiagram(x[1:2])  # 2d venn

Launch Reactor Data Shiny App

Description

Launch Reactor Data Shiny App

Usage

launch_app()

Value

a shiny app

Intersection of many sets.

Description

overlap returns the same elements of the sets in a Venn object.

Usage

overlap(venn, slice = "all")

## S4 method for signature 'Venn'
overlap(venn, slice = "all")

Arguments

venn

(Required) A Venn object.
slice

(Optional) The names or the indices of sets of interest. Default is "all", meaning the intersection will be calculated for all the sets.

Value

A vector showing the intersection of the sets.

Author(s)

[email protected]

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
overlap(venn)
overlap(venn, slice = c(1, 2))

Plot the set edge of a VennPlotData

Description

This is for viewing the shape id and appearance of the shape.

Usage

plot_shape_edge(x)

Arguments

x

a VennPlotData object

Value

a ggplot object

Examples

shape = get_shape_by_id("301")
  plot_shape_edge(shape)

plot all shapes provided by internal dataset

Description

These shapes are mainly collected from the package venn, and VennDiagram. For Venn plot with more than 4 sets, it is usually impossible to plot with simple circle or ellipse. So we need to use a predefined coordinates in plot.

Usage

plot_shapes()

Details

  • Shape 101, 201, 301, 401, 402, 501, 502, 601 and 701 are from venn

  • Shape 401f is from VennDiagram

see data-raw/shapes.R to find how we incorporate these data.

Examples

plot_shapes()

plot codes

Description

plot codes

Usage

plot_venn(
  data,
  show_intersect = FALSE,
  set_color = "black",
  set_size = NA,
  label = "both",
  label_geom = "label",
  label_alpha = 0.5,
  label_color = "black",
  label_size = NA,
  label_percent_digit = 0,
  label_txtWidth = 40,
  edge_lty = "solid",
  edge_size = 1,
  ...
)

Arguments

data

plot data
show_intersect

if TRUE the text can be visualized by 'plotly'
set_color

color of set labels ("black")
set_size

size of set labels (NA)
label

format of region labels, select one from c("count","percent","both","none")
label_geom

layer of region labels, choose from c("label", "text")
label_alpha

set 0 to remove the background of region labels
label_color

color of region labels ("black")
label_size

size of region labels (NA)
label_percent_digit

number of digits when formatting percent label (0)
label_txtWidth

width of text used in showing intersect members, will be ignored unless show_intersection is TRUE (40)
edge_lty

line type of set edges ("solid")
edge_size

line width of set edges (1)
...

useless

Value

ggplot object, or plotly object if show_intersect is TRUE

join the shape data with set data

Description

join the shape data with set data

Usage

plotData_add_venn(plotData, venn)

Arguments

plotData

a VennPlot object that stores plot shapes
venn

a Venn object that stores set values

S3 method for upsetPlotData

Description

S3 method for upsetPlotData

S3 method for VennPlotData

Usage

## S3 method for class 'upsetPlotData'
print(x, ...)

## S3 method for class 'VennPlotData'
print(x, ...)

Arguments

x

a VennPlotData object
...

useless

get plot data

Description

get plot data

Usage

process_data(venn, nsets = NULL, shape_id = NULL, type = NULL)

## S4 method for signature 'Venn'
process_data(venn, nsets = length(venn@sets), shape_id = NULL, type = NULL)

Arguments

venn

a Venn object
nsets

This parameter will be set automatically.
shape_id

apply filter to internal shapes. i.e. shape_id = "601"
type

apply filter to internal shapes. i.e. type = "polygon"

Details

This function will conduct set operations and combine the outputs will stored shapes, thus produce a dataset for plot in next step.

Run 'get_shapes()' to show all the characteristics of available shapes. Run 'plot_shapes()' to view those shapes.

Examples

## Not run: 
 venn = Venn(list(A=1:3,B=2:5,C=4:8))
 data = process_data(venn)

## End(Not run)

process upset data

Description

process upset data

Usage

process_upset_data(
  venn,
  nintersects = 30,
  order.intersect.by = "size",
  order.set.by = "name",
  specific = TRUE
)

Arguments

venn

a class Venn object
nintersects

number of intersects. If NULL, all intersections will show.
order.intersect.by

'size', 'name', or "none"
order.set.by

'size', 'name', or "none"
specific

whether return ONLY specific items for a subset, default is TRUE

Details

ggVennDiagram, by default, only return the specific subsets of a region. However, sometimes, we want to show all the overlapping items for two or more sets. For example: https://github.com/gaospecial/ggVennDiagram/issues/64 Therefore, we add a 'specific' switch to this function. While 'specific = FALSE', the seperator will be changed from "/" to "~", and all the overlapping items will be returned. This feature is useful in plotting upset plot.

Value

a upsetPlotData object

Implement of tidyr::separate_longer_delim

Description

Implement of tidyr::separate_longer_delim

Usage

separate_longer_delim(df, col, delim)

Arguments

df

a data.frame
col

column
delim

delimeter

Value

a data.frame

shapes: shape data used to setup Venn plot

Description

a collection of geometric shapes, which defined the edge and label of sets in a Venn plot. use plot_shapes() to see some of them.

Format

a list with several slots see "?VennPlotData".

Source

check and format slice name

Description

check and format slice name

Usage

slice_idx(venn, slice)

Arguments

venn

a Venn object
slice

a numeric or character vector

Value

the index of Venn (numeric vector) or "all"

Union of many sets.

Description

unite returns the union of the sets in a Venn object.

Usage

unite(venn, slice = "all")

## S4 method for signature 'Venn'
unite(venn, slice = "all")

Arguments

venn

(Required) A Venn object.
slice

(Optional) The names or the indices of sets of interest. Default is "all", meaning the union will be calculated for all the sets.

Value

A vector showing the union of the sets.

Author(s)

[email protected]

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
  unite(venn)
  unite(venn, slice = c(1, 2))

Plot a upset plot

Description

This function generate a upset plot by creating a composite plot which contains subplots generated by ggplot2.

Usage

plot_upset(
  venn,
  nintersects = NULL,
  order.intersect.by = c("size", "name", "none"),
  order.set.by = c("size", "name", "none"),
  relative_height = 3,
  relative_width = 0.3,
  top.bar.color = "grey30",
  top.bar.y.label = NULL,
  top.bar.show.numbers = TRUE,
  top.bar.numbers.size = 3,
  sets.bar.color = "grey30",
  sets.bar.show.numbers = FALSE,
  sets.bar.x.label = "Set Size",
  intersection.matrix.color = "grey30",
  specific = TRUE,
  ...
)

Arguments

venn

a class Venn object
nintersects

number of intersects. If NULL, all intersections will show.
order.intersect.by

'size', 'name', or "none"
order.set.by

'size', 'name', or "none"
relative_height

the relative height of top panel in upset plot
relative_width

the relative width of left panel in upset plot
top.bar.color

default is "grey30"
top.bar.y.label

default is NULL
top.bar.show.numbers

default is TRUE
top.bar.numbers.size

text size of numbers
sets.bar.color

default is "grey30"
sets.bar.show.numbers

default is FALSE
sets.bar.x.label

default is "Set Size"
intersection.matrix.color

default is "grey30"
specific

whether only include specific items in subsets, default is TRUE.
...

useless

Value

an upset plot

Examples

list = list(A = sample(LETTERS, 20),
             B = sample(LETTERS, 22),
             C = sample(LETTERS, 14),
             D = sample(LETTERS, 30, replace = TRUE))
 venn = Venn(list)
 plot_upset(venn)
 plot_upset(venn, order.intersect.by = "name")
 plot_upset(venn, nintersects = 6)

Prepare Venn data

Description

Prepare Venn data

Usage

process_set_data(venn)

process_region_data(venn, sep = "/", specific = TRUE)

Arguments

venn

a Venn object
sep

name and id separator for intersections
specific

whether return ONLY specific items for a subset, default is TRUE

Details

ggVennDiagram, by default, only return the specific subsets of a region. However, sometimes, we want to show all the overlapping items for two or more sets. For example: https://github.com/gaospecial/ggVennDiagram/issues/64 Therefore, we add a 'specific' switch to this function. While 'specific = FALSE', the seperator will be changed from "/" to "~", and all the overlapping items will be returned. This feature is useful in plotting upset plot.

Value

a tibble

Examples

x = list(
A = sample(letters, 8),
B = sample(letters, 8),
C = sample(letters, 8),
D = sample(letters, 8)
)

venn = Venn(x)
process_set_data(venn)
process_region_data(venn)

Get VennPlotData slot

Description

Get VennPlotData slot

Usage

venn_regionedge(obj)

venn_regionlabel(obj)

venn_setedge(obj)

venn_setlabel(obj)

venn_set(obj)

venn_region(obj)

Arguments

obj

a list that stores all the data from the S3 class 'VennPlotData' object

Value

a tibble

Examples

venn = Venn(list(A=1:5,B=2:7,C=3:6,D=4:9))
obj = process_data(venn)
venn_regionlabel(obj)  # return regionLabel data
venn_regionedge(obj)   # return regionEdge data
venn_setlabel(obj) # return setLabel data
venn_setedge(obj)  # return setEdge data
venn_set(obj)     # set items
venn_region(obj)  # region items

Venn is a S4 class to represent multiple sets.

Description

Print user-friendly information of a Venn object

Usage

Venn(sets, names = NULL)

## S4 method for signature 'ANY'
Venn(sets, names = NULL)

## S4 method for signature 'Venn'
show(object)

Arguments

sets

(Required) A list containing vectors in the same class. If a vector contains duplicates they will be discarded. If the list doesn't have names the sets will be named as "Set_1", "Set_2", "Set_3" and so on.
names

names of sets
object

a Venn class object

Value

A Venn object.

Slots

sets

A list object containing vectors in the same type.

names

The names of the sets if it has names. If the list doesn't have names, the sets will be named as "Set_1", "Set_2", "Set_3" and so on.

Examples

venn = Venn(list(letters[1:10], letters[3:12], letters[6:15]))
 print(venn)

An S3 class constructor of representing Venn plot components.

Description

An S3 class constructor of representing Venn plot components.

Usage

VennPlotData(x)

Arguments

x

data source of a VennPlotData object

Slots

shapeId

shape id

type

type of shape

nsets

number of sets

setEdge

a data.frame, the coordinates of set edges, can be retrieved by venn_setedge()

setLabel

a data.frame, the coordinates of set labels, can be retrieved by venn_setlabel()

regionEdge

a data.frame, the coordinates of different regions, can be retrieved by venn_regionedge()

regionLabel

a data.frame, the centroid of the regions, where region labels anchored, can be retrieved by venn_regionlabel()

setData

a data.frame, the set data provided by user, can be retrieved by venn_set()

regionData

a data.frame, the region data that calculated by ggVennDiagram, can be retrieved by venn_region()

Import venn shape coordinates

Description

Import venn shape coordinates

Usage

vensets()

Value

a data frame