Help for package VennDiagram

Version: 1.7.3

Type: Package

Title: Generate High-Resolution Venn and Euler Plots

Date: 2022年04月11日

Author: Hanbo Chen

Maintainer: Paul Boutros <pboutros@mednet.ucla.edu>

Imports: methods

Depends: R (≥ 3.5.0), grid (≥ 2.14.1), futile.logger

Description: A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.

License: GPL-2

LazyLoad: yes

Suggests: testthat

NeedsCompilation: no

Packaged: 2022年04月12日 00:04:33 UTC; root

Repository: CRAN

Date/Publication: 2022年04月12日 23:32:28 UTC

Venn diagram plotting

Description

Functions to plot high-resolution and highly-customizable Venn and Euler plots.

Details

Package: VennDiagram

Type: Package

Version: 1.6.0

Date: 2013年04月10日

License: GPL-2

LazyLoad: yes

Author(s)

Author: Hanbo Chen <Hanbert.Chen@mail.utoronto.ca>
Maintainer: Dr. Paul C. Boutros <Paul.Boutros@utoronto.ca>

Internal VennDiagram Functions

Description

Internal VennDiagram functions

Details

These are not to be called by the user (or in some cases are just waiting for proper documentation to be written :)

Calculate Overlap

Description

Determine the groupings of values as they would be presented in the venn diagram.

Usage

calculate.overlap(x)

Arguments

x

A list of vectors (e.g., integers, chars), with each component corresponding to a separate circle in the Venn diagram

Details

This function mostly complements the venn.diagram() function for the case where users want to know what values are grouped into the particular areas of the venn diagram.

Value

Returns a list of lists which contain the values assigned to each of the areas of a venn diagram.

Author(s)

Christopher Lalansingh

Examples

# A simple single-set diagram
cardiome <- letters[1:10]
superset <- letters[8:24]
overlap <- calculate.overlap(
	x = list(
		"Cardiome" = cardiome,
		"SuperSet" = superset
		)
	);

Draw a Venn Diagram with Two Sets

Description

Creates a Venn diagram with two sets. Creates Euler diagrams when the dataset meets certain conditions.

Usage

draw.pairwise.venn(area1, area2, cross.area, category = rep("", 2),
 euler.d = TRUE, scaled = TRUE, inverted = FALSE,
 ext.text = TRUE, ext.percent = rep(0.05, 3), lwd =
 rep(2, 2), lty = rep("solid", 2), col = rep("black",
 2), fill = NULL, alpha = rep(0.5, 2), label.col =
 rep("black", 3), cex = rep(1, 3), fontface =
 rep("plain", 3), fontfamily = rep("serif", 3), cat.pos
 = c(-50, 50), cat.dist = rep(0.025, 2), cat.cex =
 rep(1, 2), cat.col = rep("black", 2), cat.fontface =
 rep("plain", 2), cat.fontfamily = rep("serif", 2),
 cat.just = rep(list(c(0.5, 0.5)), 2), cat.default.pos
 = "outer", cat.prompts = FALSE, ext.pos = rep(0, 2),
 ext.dist = rep(0, 2), ext.line.lty = "solid",
 ext.length = rep(0.95, 2), ext.line.lwd = 1,
 rotation.degree = 0, rotation.centre = c(0.5, 0.5),
 ind = TRUE, sep.dist = 0.05, offset = 0, cex.prop =
 NULL, print.mode = "raw", sigdigs = 3, ...)

Arguments

area1

The size of the first set

area2

The size of the second set

cross.area

The size of the intersection between the sets

category

A vector (length 2) of strings giving the category names of the sets

euler.d

Boolean indicating whether to draw Euler diagrams when conditions are met or not (Venn Diagrams with moveable circles)

scaled

Boolean indicating whether to scale circle sizes in the diagram according to set sizes or not (euler.d must be true to enable this)

inverted

Boolean indicating whether the diagram should be mirrored long the vertical axis or not

ext.text

Boolean indicating whether to place area labels outside the circles in case of small partial areas or not

ext.percent

A vector (length 3) indicating the proportion that a partial area has to be smaller than to trigger external text placement. The elements allow for individual control of the areas in the order of area1, area2 and intersect area.

lwd

A vector (length 2) of numbers giving the line width of the circles' circumferences

lty

A vector (length 2) giving the line dash pattern of the circles' circumferences

col

A vector (length 2) giving the colours of the circles' circumferences

fill

A vector (length 2) giving the colours of the circles' areas

alpha

A vector (length 2) giving the alpha transparency of the circles' areas

label.col

A vector (length 3) giving the colours of the areas' labels

cex

A vector (length 3) giving the size of the areas' labels

fontface

A vector (length 3) giving the fontface of the areas' labels

fontfamily

A vector (length 3) giving the fontfamily of the areas' labels

cat.pos

A vector (length 2) giving the positions (in degrees) of the category names along the circles, with 0 (default) at the 12 o'clock location

cat.dist

A vector (length 2) giving the distances (in npc units) of the category names from the edges of the circles (can be negative)

cat.cex

A vector (length 2) giving the size of the category names

cat.col

A vector (length 2) giving the colours of the category names

cat.fontface

A vector (length 2) giving the fontface of the category names

cat.fontfamily

A vector (length 2) giving the fontfamily of the category names

cat.just

List of 2 vectors of length 2 indicating horizontal and vertical justification of each category name

cat.default.pos

One of c('outer', 'text') to specify the default location of category names (cat.pos and cat.dist are handled differently)

cat.prompts

Boolean indicating whether to display help text on category name positioning or not)

ext.pos

A vector (length 1 or 2) giving the positions (in degrees) of the external area labels along the circles, with 0 (default) at 12 o'clock

ext.dist

A vector (length 1 or 2) giving how far to place the external area labels relative to its anchor point

ext.line.lty

A vector (length 1 or 2) giving the dash pattern of the lines connecting the external area labels to their anchor points

ext.length

A vector (length 1 or 2) giving the proportion of the lines connecting the external area labels to their anchor points actually drawn

ext.line.lwd

A vector (length 1 or 2) giving the width of the lines connecting the external area labels to their anchor points

rotation.degree

Number of degrees to rotate the entire diagram

rotation.centre

A vector (length 2) indicating (x,y) of the rotation centre

ind

Boolean indicating whether the function is to automatically draw the diagram before returning the gList object or not

sep.dist

Number giving the distance between circles in case of an Euler diagram showing mutually exclusive sets

offset

Number between 0 and 1 giving the amount of offset from the centre in case of an Euler diagram showing inclusive sets

cex.prop

A function or string used to rescale areas

print.mode

Can be either 'raw' or 'percent'. This is the format that the numbers will be printed in. Can pass in a vector with the second element being printed under the first

sigdigs

If one of the elements in print.mode is 'percent', then this is how many significant digits will be kept

...

Additional arguments to be passed, including margin, which indicates amount of whitespace around the final diagram in npc units

Details

Euler diagrams are drawn for mutually exclusive sets (cross.area == 0), inclusive sets (area1 == 0 or area2 == 0), and coincidental sets (area1 == 0 and area2 == 0) if euler.d == TRUE. The function defaults to placing the larger set on the left. inverted or rotation.degree can be used to reverse this.

Value

Returns an object of class gList containing the grid objects that make up the diagram. Also displays the diagram in a graphical device unless specified with ind = FALSE. Grid::grid.draw can be used to draw the gList object in a graphical device.

Author(s)

Hanbo Chen

Examples

# A simple two-set diagram
venn.plot <- draw.pairwise.venn(100, 70, 30, c("First", "Second"));
grid.draw(venn.plot);
grid.newpage();
# Same diagram as above, but without scaling
venn.plot <- draw.pairwise.venn(100, 70, 30, c("First", "Second"), scaled = FALSE);
grid.draw(venn.plot);
grid.newpage();
# A more complicated diagram Demonstrating external area labels
venn.plot <- draw.pairwise.venn(
	area1 = 100,
	area2 = 70,
	cross.area = 68,
	category = c("First", "Second"),
	fill = c("blue", "red"),
	lty = "blank",
	cex = 2,
	cat.cex = 2,
	cat.pos = c(285, 105),
	cat.dist = 0.09,
	cat.just = list(c(-1, -1), c(1, 1)),
	ext.pos = 30,
	ext.dist = -0.05,
	ext.length = 0.85,
	ext.line.lwd = 2,
	ext.line.lty = "dashed"
	);
grid.draw(venn.plot);
grid.newpage();
# Demonstrating an Euler diagram
venn.plot <- draw.pairwise.venn(
	area1 = 100,
	area2 = 70,
	cross.area = 0,
	category = c("First", "Second"),
	cat.pos = c(0, 180),
	euler.d = TRUE,
	sep.dist = 0.03,
	rotation.degree = 45
	);
# Writing to file
tiff(
 filename = tempfile(
 pattern = 'Pairwise_Venn_diagram',
 fileext = '.tiff'
 ),
 compression = "lzw");
 
grid.draw(venn.plot);
dev.off();

Draw a Venn Diagram with Four Sets

Description

Creates a Venn diagram with four sets.

Usage

draw.quad.venn(area1, area2, area3, area4, n12, n13, n14, n23, n24,
 n34, n123, n124, n134, n234, n1234, category = rep("",
 4), lwd = rep(2, 4), lty = rep("solid", 4), col =
 rep("black", 4), fill = NULL, alpha = rep(0.5, 4),
 label.col = rep("black", 15), cex = rep(1, 15),
 fontface = rep("plain", 15), fontfamily = rep("serif",
 15), cat.pos = c(-15, 15, 0, 0), cat.dist = c(0.22,
 0.22, 0.11, 0.11), cat.col = rep("black", 4), cat.cex
 = rep(1, 4), cat.fontface = rep("plain", 4),
 cat.fontfamily = rep("serif", 4), cat.just =
 rep(list(c(0.5, 0.5)), 4), rotation.degree = 0,
 rotation.centre = c(0.5, 0.5), ind = TRUE, cex.prop =
 NULL, print.mode = "raw", sigdigs = 3, direct.area =
 FALSE, area.vector = 0, ...)

Arguments

area1

The size of the first set

area2

The size of the second set

area3

The size of the third set

area4

The size of the fourth set

n12

The size of the intersection between the first and the second set

n13

The size of the intersection between the first and the third set

n14

The size of the intersection between the first and the fourth set

n23

The size of the intersection between the second and the third set

n24

The size of the intersection between the second and the fourth set

n34

The size of the intersection between the third and the fourth set

n123

The size of the intersection between the first, second and third sets

n124

The size of the intersection between the first, second and fourth sets

n134

The size of the intersection between the first, third and fourth sets

n234

The size of the intersection between the second, third and fourth sets

n1234

The size of the intersection between all four sets

category

A vector (length 4) of strings giving the category names of the sets

lwd

A vector (length 4) of numbers giving the line width of the circles' circumferences

lty

A vector (length 4) giving the dash pattern of the circles' circumferences

col

A vector (length 4) giving the colours of the circles' circumferences

fill

A vector (length 4) giving the colours of the circles' areas

alpha

A vector (length 4) giving the alpha transparency of the circles' areas

label.col

A vector (length 15) giving the colours of the areas' labels

cex

A vector (length 15) giving the size of the areas' labels

fontface

A vector (length 15) giving the fontface of the areas' labels

fontfamily

A vector (length 15) giving the fontfamily of the areas' labels

cat.pos

A vector (length 4) giving the positions (in degrees) of the category names along the circles, with 0 (default) at 12 o'clock

cat.dist

A vector (length 4) giving the distances (in npc units) of the category names from the edges of the circles (can be negative)

cat.cex

A vector (length 4) giving the size of the category names

cat.col

A vector (length 4) giving the colours of the category names

cat.fontface

A vector (length 4) giving the fontface of the category names

cat.fontfamily

A vector (length 4) giving the fontfamily of the category names

cat.just

List of 4 vectors of length 2 indicating horizontal and vertical justification of each category name

rotation.degree

Number of degrees to rotate the entire diagram

rotation.centre

A vector (length 2) indicating (x,y) of the rotation centre

ind

Boolean indicating whether the function is to automatically draw the diagram before returning the gList object or not

cex.prop

A function or string used to rescale areas

print.mode

Can be either 'raw' or 'percent'. This is the format that the numbers will be printed in. Can pass in a vector with the second element being printed under the first

sigdigs

If one of the elements in print.mode is 'percent', then this is how many significant digits will be kept

direct.area

If this is equal to true, then the vector passed into area.vector will be directly assigned to the areas of the corresponding regions. Only use this if you know which positions in the vector correspond to which regions in the diagram

area.vector

An argument to be used when direct.area is true. These are the areas of the corresponding regions in the Venn Diagram

...

Additional arguments to be passed, including margin, which indicates amount of whitespace around the final diagram in npc units

Details

The function defaults to placing the ellipses so that area1 corresponds to lower left, area2 corresponds to lower right, area3 corresponds to middle left and area4 corresponds to middle right. Refer to the example below to see how the 31 partial areas are ordered. Arguments with length of 15 (label.col, cex, fontface, fontfamily) will follow the order in the example.

Value

Author(s)

Hanbo Chen

Examples

# Reference four-set diagram
venn.plot <- draw.quad.venn(
	area1 = 72,
	area2 = 86,
	area3 = 50,
	area4 = 52,
	n12 = 44,
	n13 = 27,
	n14 = 32,
	n23 = 38,
	n24 = 32,
	n34 = 20,
	n123 = 18,
	n124 = 17,
	n134 = 11,
	n234 = 13,
	n1234 = 6,
	category = c("First", "Second", "Third", "Fourth"),
	fill = c("orange", "red", "green", "blue"),
	lty = "dashed",
	cex = 2,
	cat.cex = 2,
	cat.col = c("orange", "red", "green", "blue")
	);
# Writing to file
tiff(
 filename = tempfile(
 pattern = 'Quad_Venn_diagram',
 fileext = '.tiff'
 ), 
 compression = "lzw"
 );
 
grid.draw(venn.plot);
dev.off();

Draw a Venn Diagram with Five Sets

Description

Creates a Venn diagram with five sets.

Usage

draw.quintuple.venn(area1, area2, area3, area4, area5, n12, n13, n14, n15,
 n23, n24, n25, n34, n35, n45, n123, n124, n125, n134,
 n135, n145, n234, n235, n245, n345, n1234, n1235,
 n1245, n1345, n2345, n12345, category = rep("", 5),
 lwd = rep(2, 5), lty = rep("solid", 5), col =
 rep("black", 5), fill = NULL, alpha = rep(0.5, 5),
 label.col = rep("black", 31), cex = rep(1, 31),
 fontface = rep("plain", 31), fontfamily = rep("serif",
 31), cat.pos = c(0, 287.5, 215, 145, 70), cat.dist =
 rep(0.2, 5), cat.col = rep("black", 5), cat.cex =
 rep(1, 5), cat.fontface = rep("plain", 5),
 cat.fontfamily = rep("serif", 5), cat.just =
 rep(list(c(0.5, 0.5)), 5), rotation.degree = 0,
 rotation.centre = c(0.5, 0.5), ind = TRUE, cex.prop =
 NULL, print.mode = "raw", sigdigs = 3, direct.area =
 FALSE, area.vector = 0, ...)

Arguments

area1

The size of the first set

area2

The size of the second set

area3

The size of the third set

area4

The size of the fourth set

area5

The size of the fifth set

n12

The size of the intersection between the first and the second set

n13

The size of the intersection between the first and the third set

n14

The size of the intersection between the first and the fourth set

n15

The size of the intersection between the first and the fifth set

n23

The size of the intersection between the second and the third set

n24

The size of the intersection between the second and the fourth set

n25

The size of the intersection between the second and the fifth set

n34

The size of the intersection between the third and the fourth set

n35

The size of the intersection between the third and the fifth set

n45

The size of the intersection between the fourth and the fifth set

n123

The size of the intersection between the first, second and third sets

n124

The size of the intersection between the first, second and fourth sets

n125

The size of the intersection between the first, second and fifth sets

n134

The size of the intersection between the first, third and fourth sets

n135

The size of the intersection between the first, third and fifth sets

n145

The size of the intersection between the first, fourth and fifth sets

n234

The size of the intersection between the second, third and fourth sets

n235

The size of the intersection between the second, third and fifth sets

n245

The size of the intersection between the second, fourth and fifth sets

n345

The size of the intersection between the third, fourth and fifth sets

n1234

The size of the intersection between the first, second, third and fourth sets

n1235

The size of the intersection between the first, second, third and fifth sets

n1245

The size of the intersection between the first, second, fourth and fifth sets

n1345

The size of the intersection between the first, third, fourth and fifth sets

n2345

The size of the intersection between the second, third, fourth and fifth sets

n12345

The size of the intersection between all five sets

category

A vector (length 5) of strings giving the category names of the sets

lwd

A vector (length 5) of numbers giving the line width of the circles' circumferences

lty

A vector (length 5) giving the dash pattern of the circles' circumferences

col

A vector (length 5) giving the colours of the circles' circumferences

fill

A vector (length 5) giving the colours of the circles' areas

alpha

A vector (length 5) giving the alpha transparency of the circles' areas

label.col

A vector (length 31) giving the colours of the areas' labels

cex

A vector (length 31) giving the size of the areas' labels

fontface

A vector (length 31) giving the fontface of the areas' labels

fontfamily

A vector (length 31) giving the fontfamily of the areas' labels

cat.pos

A vector (length 5) giving the positions (in degrees) of the category names along the circles, with 0 (default) at 12 o'clock

cat.dist

A vector (length 5) giving the distances (in npc units) of the category names from the edges of the circles (can be negative)

cat.cex

A vector (length 5) giving the size of the category names

cat.col

A vector (length 5) giving the colours of the category names

cat.fontface

A vector (length 5) giving the fontface of the category names

cat.fontfamily

A vector (length 5) giving the fontfamily of the category names

cat.just

List of 5 vectors of length 2 indicating horizontal and vertical justification of each category name

rotation.degree

Number of degrees to rotate the entire diagram

rotation.centre

A vector (length 2) indicating (x,y) of the rotation centre

ind

Boolean indicating whether the function is to automatically draw the diagram before returning the gList object or not

cex.prop

A function or string used to rescale areas

print.mode

Can be either 'raw' or 'percent'. This is the format that the numbers will be printed in. Can pass in a vector with the second element being printed under the first

sigdigs

If one of the elements in print.mode is 'percent', then this is how many significant digits will be kept

direct.area

area.vector

An argument to be used when direct.area is true. These are the areas of the corresponding regions in the Venn Diagram

...

Additional arguments to be passed, including margin, which indicates amount of whitespace around the final diagram in npc units

Details

The function defaults to placing the ellipses representing the areas 1 to 5 in a counterclockwise fashion. Refer to the example below to see how the 31 partial areas are ordered. Arguments with length of 31 (label.col, cex, fontface, fontfamily) will follow the order in the example.

Value

Author(s)

Hanbo Chen

Examples

# Reference five-set diagram
venn.plot <- draw.quintuple.venn(
	area1 = 301,
	area2 = 321,
	area3 = 311,
	area4 = 321,
	area5 = 301,
	n12 = 188,
	n13 = 191,
	n14 = 184,
	n15 = 177,
	n23 = 194,
	n24 = 197,
	n25 = 190,
	n34 = 190,
	n35 = 173,
	n45 = 186,
	n123 = 112,
	n124 = 108,
	n125 = 108,
	n134 = 111,
	n135 = 104,
	n145 = 104,
	n234 = 111,
	n235 = 107,
	n245 = 110,
	n345 = 100,
	n1234 = 61,
	n1235 = 60,
	n1245 = 59,
	n1345 = 58,
	n2345 = 57,
	n12345 = 31,
	category = c("A", "B", "C", "D", "E"),
	fill = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
	cat.col = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
	cat.cex = 2,
	margin = 0.05,
	cex = c(1.5, 1.5, 1.5, 1.5, 1.5, 1, 0.8, 1, 0.8, 1, 0.8, 1, 0.8, 1, 0.8, 
	1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 1, 1, 1, 1, 1.5),
	ind = TRUE
	);
# Writing to file
tiff(
 filename = tempfile(
 pattern = 'Quintuple_Venn_diagram', 
 fileext = '.tiff'
 ),
 compression = "lzw"
 );
 
grid.draw(venn.plot);
dev.off();

Draw a Venn Diagram with a Single Set

Description

Creates a Venn diagram with a single set.

Usage

draw.single.venn(area, category = "", lwd = 2, lty = "solid", col = "black", fill = NULL,
	alpha = 0.5, label.col = "black", cex = 1, 
	fontface = "plain", fontfamily = "serif",
	cat.pos = 0, cat.dist = 0.025, cat.cex = 1, cat.col = "black",
	cat.fontface = "plain", cat.fontfamily = "serif",
	cat.just = list(c(0.5, 0.5)),
	cat.default.pos = "outer", cat.prompts = FALSE, rotation.degree = 0,
	rotation.centre = c(0.5, 0.5), ind = TRUE, ...)

Arguments

area

The size of the set

category

The category name of the set

lwd

width of the circle's circumference

lty

dash pattern of the circle's circumference

col

Colour of the circle's circumference

fill

Colour of the circle's area

alpha

Alpha transparency of the circle's area

label.col

Colour of the area label

cex

size of the area label

fontface

fontface of the area label

fontfamily

fontfamily of the area label

cat.pos

The position (in degrees) of the category name along the circle, with 0 (default) at 12 o'clock

cat.dist

The distance (in npc units) of the category name from the edge of the circle (can be negative)

cat.cex

size of the category name

cat.col

Colour of the category name

cat.fontface

fontface of the category name

cat.fontfamily

fontfamily of the category name

cat.just

List of 1 vector of length 2 indicating horizontal and vertical justification of the category name

cat.default.pos

One of c('outer', 'text') to specify the default location of category names (cat.pos and cat.dist are handled differently)

cat.prompts

Boolean indicating whether to display help text on category name positioning or not)

rotation.degree

Number of degrees to rotate the entire diagram

rotation.centre

A vector (length 2) indicating (x,y) of the rotation centre

ind

Boolean indicating whether the function is to automatically draw the diagram in the end or not

...

Additional arguments to be passed, including margin, which indicates amount of whitespace around the final diagram in npc units

Details

This function mostly complements other functions in the VennDiagram package that draws multi-set diagrams by providing a function that draws single-set diagrams with similar graphical options.

Value

Author(s)

Hanbo Chen

Examples

# A simple single-set diagram
venn.plot <- draw.single.venn(100, "First");
grid.draw(venn.plot);
grid.newpage();
# A more complicated diagram
venn.plot <- draw.single.venn(
	area = 365,
	category = "All\nDays",
	lwd = 5,
	lty = "blank",
	cex = 3,
	label.col = "orange",
	cat.cex = 4,
	cat.pos = 180,
	cat.dist = -0.20,
	cat.col = "white",
	fill = "red",
	alpha = 0.15
	);
grid.draw(venn.plot);
grid.newpage();
# Writing to file
tiff(
 filename = tempfile(
 pattern = 'Single_Venn_diagram',
 fileext = '.tiff'
 ),
 compression = "lzw"
 );
 
venn.plot <- draw.single.venn(100, "First", ind = FALSE);
grid.draw(venn.plot);
dev.off();

Draw a special Venn Diagram with Three Sets. These are the non scaled cases

Description

Special case of draw.triple.venn. Internal use only.

Value

See draw.triple.venn

Author(s)

Zhiyuan Wang

Examples

venn.plot <- draw.triple.venn(
	area1 = 4,
	area2 = 3,
	area3 = 4,
	n12 = 2,
	n23 = 2,
	n13 = 2,
	n123 = 1,
	category = c('A', 'B', 'C'),
	fill = c('red', 'blue', 'green'),
	cat.col = c('red', 'blue', 'green'),
	cex = c(1/2,2/2,3/2,4/2,5/2,6/2,7/2),
	cat.cex = c(1,2,3),
	euler = TRUE,
	scaled = FALSE
	);
dev.off();

Draw a special Venn Diagram with Three Sets. These are the scaled cases

Description

Special case of draw.triple.venn. Internal use only.

Value

See draw.triple.venn

Author(s)

Zhiyuan Wang

Examples

venn.plot <- draw.triple.venn(
	area1 = 2,
	area2 = 1,
	area3 = 3,
	n12 = 1,
	n23 = 1,
	n13 = 2,
	n123 = 1,
	category = c('A', 'B', 'C'),
	fill = c('red', 'blue', 'green'),
	cat.col = c('red', 'blue', 'green'),
	cex = c(1/2,2/2,3/2,4/2,5/2,6/2,7/2),
	cat.cex = c(1,2,3),
	euler = TRUE,
	scaled = FALSE
	);
dev.off();

Draw a Venn Diagram with Three Sets

Description

Creates a Venn diagram with three sets. Creates Euler diagrams when the dataset meets certain conditions.

Usage

draw.triple.venn(area1, area2, area3, n12, n23, n13, n123, category =
 rep("", 3), rotation = 1, reverse = FALSE, euler.d =
 TRUE, scaled = TRUE, lwd = rep(2, 3), lty =
 rep("solid", 3), col = rep("black", 3), fill = NULL,
 alpha = rep(0.5, 3), label.col = rep("black", 7), cex
 = rep(1, 7), fontface = rep("plain", 7), fontfamily =
 rep("serif", 7), cat.pos = c(-40, 40, 180), cat.dist =
 c(0.05, 0.05, 0.025), cat.col = rep("black", 3),
 cat.cex = rep(1, 3), cat.fontface = rep("plain", 3),
 cat.fontfamily = rep("serif", 3), cat.just =
 list(c(0.5, 1), c(0.5, 1), c(0.5, 0)), cat.default.pos
 = "outer", cat.prompts = FALSE, rotation.degree = 0,
 rotation.centre = c(0.5, 0.5), ind = TRUE, sep.dist =
 0.05, offset = 0, cex.prop = NULL, print.mode = "raw",
 sigdigs = 3, direct.area = FALSE, area.vector = 0,
 ...)

Arguments

area1

The size of the first set

area2

The size of the second set

area3

The size of the third set

n12

The size of the intersection between the first and the second set

n23

The size of the intersection between the second and the third set

n13

The size of the intersection between the first and the third set

n123

The size of the intersection between all three sets

category

A vector (length 3) of strings giving the category names of the sets

rotation

1 (default), 2, or 3 indicating clockwise rotation of the three sets from the default arrangement

reverse

Boolean indicating whether the diagram should be mirrored long the vertical axis or not

euler.d

Boolean indicating whether to draw Euler diagrams when conditions are met or not (Venn Diagrams with moveable circles)

scaled

Boolean indicating whether to scale circle sizes in certain Euler diagrams according to set sizes or not (euler.d must be true to enable this)

lwd

A vector (length 3) of numbers giving the width of the circles' circumferences

lty

A vector (length 3) giving the dash pattern of the circles' circumferences

col

A vector (length 3) giving the colours of the circles' circumferences

fill

A vector (length 3) giving the colours of the circles' areas

alpha

A vector (length 3) giving the alpha transparency of the circles' areas

label.col

A vector (length 7) giving the colours of the areas' labels

cex

A vector (length 7) giving the size of the areas' labels

fontface

A vector (length 7) giving the fontface of the areas' labels

fontfamily

A vector (length 7) giving the fontfamily of the areas' labels

cat.pos

A vector (length 3) giving the positions (in degrees) of the category names along the circles, with 0 (default) at 12 o'clock

cat.dist

A vector (length 3) giving the distances (in npc units) of the category names from the edges of the circles (can be negative)

cat.cex

A vector (length 3) giving the size of the category names

cat.col

A vector (length 3) giving the colours of the category names

cat.fontface

A vector (length 3) giving the fontface of the category names

cat.fontfamily

A vector (length 3) giving the fontfamily of the category names

cat.just

List of 3 vectors of length 2 indicating horizontal and vertical justification of each category name

cat.default.pos

One of c('outer', 'text') to specify the default location of category names (cat.pos and cat.dist are handled differently)

cat.prompts

Boolean indicating whether to display help text on category name positioning or not)

rotation.degree

Number of degrees to rotate the entire diagram

rotation.centre

A vector (length 2) indicating (x,y) of the rotation centre

ind

Boolean indicating whether the function is to automatically draw the diagram before returning the gList object or not

sep.dist

Number between 0 and 1 giving the distance between circles in certain Euler diagrams with mutually exclusive sets

offset

Number giving the amount of offset from the centre in certain Euler diagrams with inclusive sets

cex.prop

A function or string used to rescale areas

print.mode

Can be either 'raw' or 'percent'. This is the format that the numbers will be printed in. Can pass in a vector with the second element being printed under the first

sigdigs

If one of the elements in print.mode is 'percent', then this is how many significant digits will be kept

direct.area

area.vector

An argument to be used when direct.area is true. These are the areas of the corresponding regions in the Venn Diagram

...

Additional arguments to be passed, including margin, which indicates amount of whitespace around the final diagram in npc units

Details

Euler diagrams are drawn for 19 special cases if euler.d == TRUE. Certain Euler diagrams make use of the scaled, sep.dist, or offset arguments specific to two-set Venn diagrams where appropriate. The function defaults to placing the three circles in a triangular arrangement with two sets on top and one set below. The circles correspond to area1, area2 and area3 in a clockwise fashion with area1 on the top left. N.B. General scaling for three-set Venn diagrams are disabled due to potentially misleading visual representation of the data. To re-enable, assign any value to variable overrideTriple.

Value

Author(s)

Hanbo Chen

Examples

# A simple three-set diagram
venn.plot <- draw.triple.venn(65, 75, 85,
 35, 15, 25, 5, c("First", "Second", "Third"));
grid.draw(venn.plot);
grid.newpage();
# A more complicated diagram
venn.plot <- draw.triple.venn(
	area1 = 65,
	area2 = 75,
	area3 = 85,
	n12 = 35,
	n23 = 15,
	n13 = 25,
	n123 = 5,
	category = c("First", "Second", "Third"),
	fill = c("blue", "red", "green"),
	lty = "blank",
	cex = 2,
	cat.cex = 2,
	cat.col = c("blue", "red", "green")
	);
grid.draw(venn.plot);
grid.newpage();
# Demonstrating an Euler diagram
venn.plot <- draw.triple.venn(20, 40, 60, 0, 0, 0, 0,
 c("First", "Second", "Third"), sep.dist = 0.1, rotation.degree = 30);
# Writing to file
tiff(
 filename = tempfile(
 pattern = 'Triple_Venn_diagram',
 fileext = '.tiff'
 ),
 compression = "lzw"
 );
 
grid.draw(venn.plot);
dev.off();

Get the size of individual partitions in a Venn diagram

Description

Partitions a list into Venn regions.

Usage

get.venn.partitions(x, force.unique = TRUE, keep.elements = TRUE,
 hierarchical = FALSE)

Arguments

x

A list of vectors.

force.unique

A logical value. Should only unique values be considered?

keep.elements

A logical value. Should the elements in each region be returned?

hierarchical

A logical value. Changed the way overlapping elements are treated if force.unique is TRUE.

Value

A data frame with length(x) columns and 2 ^ length(x) rows. The first length(x) columns are all logical; see make.truth.table for more details. There are three additional columns:

..set..: A set theoretical desription of the Venn region. (Note that in some locales under Windows, the data.frame print method fails to correctly display the Unicode symbols for set union and set intersection. This is a bug in R, not this function.)
..values..: A vector of values contained in the Venn region. Not returned if keep.elements is FALSE.
..count..: An integer of the number of values in the Venn region.

Details

If force.unique is FALSE, then there are two supported methods of grouping categories with duplicated elements in common. If hierarchical is FALSE, then any common elements are gathered into a pool. So if x <- list(a = c(1,1,2,2,3,3), b=c(1,2,3,4,4,5), c=c(1,4)) then (b intersect c)/(a) would contain three 4's. Since the 4's are pooled, (b)/(a union c) contains no 4's. If hierachical is TRUE, then (b intersect c)/(a) would contain one 4.Then (b)/(a union c) cotains one 4.

Author(s)

Richard Cotton.

Examples

# Compare force.unique options
x <- list(a = c(1, 1, 1, 2, 2, 3), b = c(2, 2, 2, 3, 4, 4))
get.venn.partitions(x)
get.venn.partitions(x, force.unique = FALSE)
# Figure 1D from ?venn.diagram
xFig1d = list(
 I = c(1:60, 61:105, 106:140, 141:160, 166:175, 176:180, 181:205,
 206:220),
 IV = c(531:605, 476:530, 336:375, 376:405, 181:205, 206:220, 166:175,
 176:180),
 II = c(61:105, 106:140, 181:205, 206:220, 221:285, 286:335, 336:375,
 376:405),
 III = c(406:475, 286:335, 106:140, 141:160, 166:175, 181:205, 336:375,
 476:530)
 )
get.venn.partitions(xFig1d)
grid.draw(VennDiagram::venn.diagram(x, NULL, disable.logging = TRUE))

Make a truth table

Description

Makes a truth table of the inputs.

Usage

make.truth.table(x)

Arguments

x

A short vector.

Value

A data frame with length(x) logical vector columns and 2 ^ length(x) rows.

Author(s)

Richard Cotton

Examples

## Not run: make.truth.table(c(a = 1, b = 2, c = 3, d = 4))

Make a Venn Diagram

Description

This function takes a list and creates a publication-quality TIFF Venn Diagram

Usage

venn.diagram(x, filename, disable.logging = FALSE, height = 3000, 
 width = 3000, resolution = 500, imagetype = "tiff", 
 units = "px", compression = "lzw", na = "stop", main = NULL, 
 sub = NULL, main.pos = c(0.5, 1.05), main.fontface = "plain",
 main.fontfamily = "serif", main.col = "black",
 main.cex = 1, main.just = c(0.5, 1), sub.pos = c(0.5,
 1.05), sub.fontface = "plain", sub.fontfamily =
 "serif", sub.col = "black", sub.cex = 1, sub.just =
 c(0.5, 1), category.names = names(x), force.unique =
 TRUE, print.mode = "raw", sigdigs = 3, direct.area =
 FALSE, area.vector = 0, hyper.test = FALSE, total.population = NULL, 
 lower.tail = TRUE, ...)

Arguments

x

A list of vectors (e.g., integers, chars), with each component corresponding to a separate circle in the Venn diagram

filename

Filename for image output, or if NULL returns the grid object itself

disable.logging

Boolean to disable log file output and print to console instead

height

Integer giving the height of the output figure in units

width

Integer giving the width of the output figure in units

resolution

Resolution of the final figure in DPI

imagetype

Specification of the image format (e.g. tiff, png or svg)

units

Size-units to use for the final figure

compression

What compression algorithm should be applied to the final tiff

na

Missing value handling method: "none", "stop", "remove"

main

Character giving the main title of the diagram

sub

Character giving the subtitle of the diagram

main.pos

Vector of length 2 indicating (x,y) of the main title

main.fontface

Character giving the fontface (font style) of the main title

main.fontfamily

Character giving the fontfamily (font type) of the main title

main.col

Character giving the colour of the main title

main.cex

Number giving the cex (font size) of the main title

main.just

Vector of length 2 indicating horizontal and vertical justification of the main title

sub.pos

Vector of length 2 indicating (x,y) of the subtitle

sub.fontface

Character giving the fontface (font style) of the subtitle

sub.fontfamily

Character giving the fontfamily (font type) of the subtitle

sub.col

Character Colour of the subtitle

sub.cex

Number giving the cex (font size) of the subtitle

sub.just

Vector of length 2 indicating horizontal and vertical justification of the subtitle

category.names

Allow specification of category names using plotmath syntax

force.unique

Logical specifying whether to use only unique elements in each item of the input list or use all elements. Defaults to FALSE

print.mode

Can be either 'raw' or 'percent'. This is the format that the numbers will be printed in. Can pass in a vector with the second element being printed under the first

sigdigs

If one of the elements in print.mode is 'percent', then this is how many significant digits will be kept

direct.area

area.vector

An argument to be used when direct.area is true. These are the areas of the corresponding regions in the Venn Diagram

hyper.test

If there are only two categories in the venn diagram and total.population is not NULL, then perform the hypergeometric test and add it to the sub title.

total.population

An argument to be used when hyper.test is true. This is the total population size

lower.tail

logical; if TRUE (default), probabilities are P[X <= x], otherwise, P[X > x]

...

A series of graphical parameters tweaking the plot. See below for details

Details

Argument Venn Sizes Class Description

lwd 1,2,3,4,5 numeric Vector giving the width of each circle's circumference

lty 1,2,3,4,5 numeric Vector giving the dash pattern of each circle's circumference

col 1,2,3,4,5 character Vector giving the colour of each circle's circumference

fill 1,2,3,4,5 character Vector giving the colour of each circle's area

alpha 1,2,3,4,5 numeric Vector giving the alpha transparency of each circle's area

label.col 1,2,3,4,5 character Vector giving the colour for each area label (length =

1/3/7/15 based on set-number)

cex 1,2,3,4,5 numeric Vector giving the size for each area label (length =

1/3/7/15 based on set-number)

fontface 1,2,3,4,5 character Vector giving the fontface for each area label (length =

1/3/7/15 based on set-number)

fontfamily 1,2,3,4,5 character Vector giving the fontfamily for each area label (length =

1/3/7/15 based on set-number)

cat.pos 1,2,3,4,5 numeric Vector giving the position (in degrees) of each category

name along the circle, with 0 at 12 o'clock

cat.dist 1,2,3,4,5 numeric Vector giving the distance (in npc units) of each category

name from the edge of the circle (can be negative)

cat.cex 1,2,3,4,5 numeric Vector giving the size for each category name

cat.col 1,2,3,4,5 character Vector giving the colour for each category name

cat.fontface 1,2,3,4,5 character Vector giving the fontface for each category name

cat.fontfamily 1,2,3,4,5 character Vector giving the fontfamily for each category name

cat.just 1,2,3,4,5 numeric List (length = 1/2/3/4 based on set number) of Vectors

of length 2 indicating horizontal and vertical justification

for each category name

cat.default.pos 1,2,3 character One of c('outer', 'text') to specify the default location

of category names (cat.pos and cat.dist are handled differently)

cat.prompts 2 numeric Boolean indicating whether to display help text on category

name positioning or not

margin 1,2,3,4,5 numeric Number giving the amount of whitespace around the diagram

in grid units

rotation.degree 1,2,3,4,5 numeric Number of degrees to rotate the entire diagram

rotation.centre 1,2,3,4,5 numeric Vector of length 2 indicating (x,y) of the rotation

centre

rotation 3 numeric Number giving the clockwise rotation of a three-set Venn

diagram (1, 2, or 3)

reverse 3 logical Reflect the three-set Venn diagram along its central

vertical axis of symmetry. Use in combination with rotation

to generate all possible set orders

euler.d 2, 3 logical Enable Euler diagrams for two-set and three-set Venn

diagrams (Venn Diagrams with moveable circles)

scaled 2, 3 logical Enable scaling for two-set and certain three-set Euler

diagrams. (euler.d must be true to enable this)

sep.dist 2, 3 numeric Controls the separation between distinct circles in

certain two-set or three-set Euler diagrams.

offset 2, 3 numeric Number between 0 and 1 giving the amount to offset the

smaller circle by in the inclusion type of two-set Euler

diagram and certain similar three-set Euler diagrams.

inverted 2 logical Flip the two-set Venn diagram along its vertical

axis (distinguished from reverse)

ext.text 2 logical Allow external text labels when areas are small

ext.percent 2 numeric A vector (length 3) indicating the proportion that

a partial area has to be smaller than to trigger externa

l text placement. The elements allow for individual

control of the areas in the order of the first area,

second area and intersection area.

ext.pos 2 numeric A vector (length 1 or 2) giving the positions (in degrees)

of the external area labels along the

circles, with 0 (default) at 12 o'clock

ext.line.lwd 2 numeric Width of line connecting to ext.text

ext.line.lty 2 numeric The dash pattern of the lines connecting the external

area labels to their anchor points.

ext.dist 2 numeric Vector of length 1 or 2 indicating length of external

line (use negative values to shorten the line )

ext.length 2 numeric Vector of length 1 or 2 indicating the proportion of

the external line that is drawn from the anchor to the text

Value

Plots a figure to the file given by the filename argument.

Author(s)

Hanbo Chen

Examples

# Note: most examples are listed as dontrun to meet CRAN requirements, 
# but all should work as-is!
# compact and minimal notation
## Not run: 
venn.plot <- venn.diagram(
	list(A = 1:150, B = 121:170), 
	filename = tempfile(
	 pattern = 'Venn_2set_simple',
	 fileext = '.tiff'
	 )
	);
venn.plot <- venn.diagram(
	list(A = 1:150, B = 121:170, C = 101:200), 
	filename = tempfile(
	 pattern = 'Venn_3set_simple',
	 fileext = '.tiff'
	 )
	);
## End(Not run)
# a more elaborate two-set Venn diagram with title and subtitle
venn.plot <- venn.diagram(
	x = list(
		"A" = 1:100,
		"B" = 96:140
		),
	filename = tempfile(
	 pattern = 'Venn_2set_complex',
	 fileext = '.tiff'
	 ),
	scaled = TRUE,
	ext.text = TRUE,
	ext.line.lwd = 2,
	ext.dist = -0.15,
	ext.length = 0.9,
	ext.pos = -4,
	inverted = TRUE,
	cex = 2.5,
	cat.cex = 2.5,
	rotation.degree = 45,
	main = "Complex Venn Diagram",
	sub = "Featuring: rotation and external lines",
	main.cex = 2,
	sub.cex = 1
	);
## Not run: 
# sample three-set Euler diagram
venn.plot <- venn.diagram(
	x = list(
		"Num A" = paste("Num", 1:100),
		"Num B" = c(paste("Num", 61:70), paste("Num", 71:100)),
		"Num C" = c(paste("Num", 41:60), paste("Num", 61:70))),
	euler.d = TRUE,
	filename = tempfile(
	 pattern = 'Euler_3set_simple',
	 fileext = '.tiff'
	 ),
	cat.pos = c(-20, 0, 20),
	cat.dist = c(0.05, 0.05, 0.02),
	cex = 2.5,
	cat.cex = 2.5,
	reverse = TRUE
	);
# sample three-set Euler diagram
venn.plot <- venn.diagram(
	x = list(
		A = c(1:10),
		B = c(11:90),
		C = c(81:90)
		),
	euler.d = TRUE,
	filename = tempfile(
	 pattern = 'Euler_3set_scaled',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.pos = 0
	);
## End(Not run)
# sample four-set Venn Diagram
A <- sample(1:1000, 400, replace = FALSE);
B <- sample(1:1000, 600, replace = FALSE);
C <- sample(1:1000, 350, replace = FALSE);
D <- sample(1:1000, 550, replace = FALSE);
E <- sample(1:1000, 375, replace = FALSE);
venn.plot <- venn.diagram(
	x = list(
		A = A,
		D = D,
		B = B,
		C = C
		),
	filename = tempfile(
	 pattern = 'Venn_4set_pretty', 
	 fileext = '.tiff'
	 ),
	col = "transparent",
	fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),
	alpha = 0.50,
	label.col = c("orange", "white", "darkorchid4", "white", 
	"white", "white", "white", "white", "darkblue", "white", 
	"white", "white", "white", "darkgreen", "white"),
	cex = 1.5,
	fontfamily = "serif",
	fontface = "bold",
	cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),
	cat.cex = 1.5,
	cat.pos = 0,
	cat.dist = 0.07,
	cat.fontfamily = "serif",
	rotation.degree = 270,
	margin = 0.2
	);
# sample five-set Venn Diagram
venn.plot <- venn.diagram(
	x = list(
		A = A,
		B = B,
		C = C,
		D = D,
		E = E
		),
	filename = tempfile(
	 pattern = 'Venn_5set_pretty',
	 fileext = '.tiff'
	 ),
	col = "black",
	fill = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
	alpha = 0.50,
	cex = c(1.5, 1.5, 1.5, 1.5, 1.5, 1, 0.8, 1, 0.8, 1, 0.8, 1, 0.8,
	 1, 0.8, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 0.55, 1, 1, 1, 1, 1, 1.5),
	cat.col = c("dodgerblue", "goldenrod1", "darkorange1", "seagreen3", "orchid3"),
	cat.cex = 1.5,
	cat.fontface = "bold",
	margin = 0.05
	);
# Complex three-way Venn with labels & sub-/super-scripts	
venn.plot <- venn.diagram(
	x = list(
		I = c(1:60, 61:105, 106:140, 141:160, 166:175, 176:180, 181:205, 
		206:220),
		II = c(531:605, 476:530, 336:375, 376:405, 181:205, 206:220, 166:175, 
		176:180),
		III = c(61:105, 106:140, 181:205, 206:220, 221:285, 286:335, 336:375, 
		376:405)
		),
	category.names = c(
		expression( bold('A'['1: subscript']) ),
		expression( bold('B'^'2: going up') ),
		expression( paste(bold('C'^'3'), bold('X'['i' <= 'r'^'2']^'2') ) )
		),
	filename = tempfile(
	 pattern = 'Fig3-1_triple_labels_sub_and_superscripts',
	 fileext = '.tiff'
	 ),
	output = TRUE,
	height = 3000,
	width = 3000,
	resolution = 300,
	compression = 'lzw',
	units = 'px',
	lwd = 6,
	lty = 'blank',
	fill = c('yellow', 'purple', 'green'),
	cex = 3.5,
	fontface = "bold",
	fontfamily = "sans",
	cat.cex = 3,
	cat.fontface = "bold",
	cat.default.pos = "outer",
	cat.pos = c(-27, 27, 135),
	cat.dist = c(0.055, 0.055, 0.085),
	cat.fontfamily = "sans",
	rotation = 1
	);
# Complex 3-way Venn using expressions
venn.plot <- venn.diagram(
 x = list(
		"Num A" = paste("Num", 1:100),
		"Num B" = c(paste("Num", 61:70), paste("Num", 71:100)),
		"Num C" = c(paste("Num", 41:60), paste("Num", 61:70))),
	category.names = c(
		expression( bold('A'['1']) ),
		expression( bold('A'['2']) ),
		expression( bold('A'['3']) )
		),
	euler.d = TRUE,
	filename = tempfile(
	 pattern = 'Fig3-2_Euler_3set_simple_with_subscripts',
	 fileext = '.tiff'
	 ),
	cat.pos = c(-20, 0, 20),
	cat.dist = c(0.05, 0.05, 0.02),
	cex = 2.5,
	cat.cex = 2.5,
	reverse = TRUE
	);
## Not run: 
# Example to print to screen
venn.plot <- venn.diagram(
	x = list(
			sample1 = c(1:40),
			sample2 = c(30:60)
			),
		filename = NULL,
		disable.logging = TRUE
		);
# Save picture to non-TIFF file type
# currently working on adding this functionality directly into venn.diagram
venn.plot <- venn.diagram(
	x = list (
		A = 1:10,
		B = 6:25
		),
	filename = NULL,
	disable.logging = TRUE
	);
jpeg(tempfile(pattern = 'venn_jpeg', fileext = '.jpg'));
grid.draw(venn.plot);
dev.off();
## End(Not run)
#dontrun-starts-here
### NB: All figures from the paper can be run, but are turned off from
### automatic execution to reduce burden on CRAN computing resources.
## Not run: 
# Figure 1A
venn.plot <- venn.diagram(
	x = list(
		Label = 1:100
		),
	filename = tempfile(
	 pattern = '1A-single_Venn',
	 fileext = '.tiff'
	 ),
	col = "black",
	lwd = 9,
	fontface = "bold",
	fill = "grey",
	alpha = 0.75,
	cex = 4,
	cat.cex = 3,
	cat.fontface = "bold",
	);
# Figure 1B
venn.plot <- venn.diagram(
	x = list(
		X = 1:150,
		Y = 121:180
		),
	filename = tempfile(
	 pattern = '1B-double_Venn',
	 fileext = '.tiff'
	 ),
	lwd = 4,
	fill = c("cornflowerblue", "darkorchid1"),
	alpha = 0.75,
	label.col = "white",
	cex = 4,
	fontfamily = "serif",
	fontface = "bold",
	cat.col = c("cornflowerblue", "darkorchid1"),
	cat.cex = 3,
	cat.fontfamily = "serif",
	cat.fontface = "bold",
	cat.dist = c(0.03, 0.03),
	cat.pos = c(-20, 14)
	);
# Figure 1C
venn.plot <- venn.diagram(
	x = list(
		R = c(1:70, 71:110, 111:120, 121:140),
		B = c(141:200, 71:110, 111:120, 201:230),
		G = c(231:280, 111:120, 121:140, 201:230)
		),
	filename = tempfile(
	 pattern = '1C-triple_Venn',
	 fileext = '.tiff'
	 ),
	col = "transparent",
	fill = c("red", "blue", "green"),
	alpha = 0.5,
	label.col = c("darkred", "white", "darkblue", "white",
	 "white", "white", "darkgreen"),
	cex = 2.5,
	fontfamily = "serif",
	fontface = "bold",
	cat.default.pos = "text",
	cat.col = c("darkred", "darkblue", "darkgreen"),
	cat.cex = 2.5,
	cat.fontfamily = "serif",
	cat.dist = c(0.06, 0.06, 0.03),
	cat.pos = 0
	);
# Figure 1D
venn.plot <- venn.diagram(
	x = list(
		I = c(1:60, 61:105, 106:140, 141:160, 166:175, 176:180, 181:205, 
		206:220),
		IV = c(531:605, 476:530, 336:375, 376:405, 181:205, 206:220, 166:175, 
		176:180),
		II = c(61:105, 106:140, 181:205, 206:220, 221:285, 286:335, 336:375, 
		376:405),
		III = c(406:475, 286:335, 106:140, 141:160, 166:175, 181:205, 336:375, 
		476:530)
		),
	filename = tempfile(
	 pattern = '1D-quadruple_Venn',
	 fileext = '.tiff'
	 ),
	col = "black",
	lty = "dotted",
	lwd = 4,
	fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),
	alpha = 0.50,
	label.col = c("orange", "white", "darkorchid4", "white", "white", "white",
	 "white", "white", "darkblue", "white",
	 "white", "white", "white", "darkgreen", "white"),
	cex = 2.5,
	fontfamily = "serif",
	fontface = "bold",
	cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),
	cat.cex = 2.5,
	cat.fontfamily = "serif"
	);
# Figure 2-1
venn.plot <- venn.diagram(
	x = list(
		A = 1:105,
		B = 101:115
		),
	filename = tempfile(
	 pattern = '2-1_special_case_ext-text',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.pos = c(-20, 20),
	ext.line.lty = "dotted",
	ext.line.lwd = 2,
	ext.pos = 12,
	ext.dist = -0.12,
	ext.length = 0.85
	);
# Figure 2-2
venn.plot <- venn.diagram(
	x = list(
		A = 1:100,
		B = 1:10
		),
	filename = tempfile(
	 pattern = '2-2_special_case_pairwise-inclusion',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.pos = 0
	);
# Figure 2-3
venn.plot <- venn.diagram(
	x = list(
		A = 1:150,
		B = 151:250
		),
	filename = tempfile(
	 pattern = '2-3_special_case_pairwise-exclusion',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.pos = c(0, 0),
	cat.dist = 0.05
	);
# Figure 2-4
venn.plot <- venn.diagram(
	x = list(
		A = c(1:50, 101:140, 141:160, 161:170),
		B = c(171:230, 101:140, 161:170, 291:320),
		C = c(141:160, 161:170, 291:320)
		),
	filename = tempfile(
	 pattern = '2-4_triple_special_case-001',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.dist = c(0.05, 0.05, -0.1)
	);
# Figure 2-5
venn.plot <- venn.diagram(
	x = list(
		A = c(1:100),
		B = c(61:70, 71:100),
		C = c(41:60, 61:70)
		),
	filename = tempfile(
	 pattern = '2-5_triple_special_case-012AA',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.pos = c(-25, 0, 30),
	cat.dist = c(0.05, 0.05, 0.02)
	);
# Figure 2-6
venn.plot <- venn.diagram(
	x = list(
		A = c(1:90),
		B = c(1:25),
		C = c(1:5)
		),
	filename = tempfile(
	 pattern = '2-6_triple_special_case-022AAAO',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.pos = 0,
	cat.dist = c(0.03, 0.03, 0.01)
	);
# Figure 2-7
venn.plot <- venn.diagram(
	x = list(
		A = c(1:20),
		B = c(21:80),
		C = c(81:210)
		),
	filename = tempfile(
	 pattern = '2-7_triple_special_case-100',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.dist = 0.05
	);
# Figure 2-8
venn.plot <- venn.diagram(
	x = list(
		A = c(1:80),
		B = c(41:150),
		C = c(71:100)
		),
	filename = tempfile(
	 pattern = '2-8_triple_special_case-011A',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.dist = c(0.07, 0.07, 0.02),
	cat.pos = c(-20, 20, 20)
	);
# Figure 2-9
venn.plot <- venn.diagram(
	x = list(
		A = c(1:10),
		B = c(11:90),
		C = c(81:90)
		),
	filename = tempfile(
	 pattern = '2-9_triple_special_case-121AO',
	 fileext = '.tiff'
	 ),
	cex = 2.5,
	cat.cex = 2.5,
	cat.pos = 0,
	cat.dist = c(0.04, 0.04, 0.02),
	reverse = TRUE
	);
#dontrun-ends-here
## End(Not run)

A collection of venn diagram grob objects

Description

Examples of venn.diagram. For testing that the venn.diagrams are generated properly

Value

Depends on which file is loaded. Can be a list of one to five category Venn Diagrams

Author(s)

Zhiyuan Wang

Venn diagram plotting

Description

Details

Author(s)

Internal VennDiagram Functions

Description

Details

Calculate Overlap

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Draw a Venn Diagram with Two Sets

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Draw a Venn Diagram with Four Sets

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Draw a Venn Diagram with Five Sets

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Draw a Venn Diagram with a Single Set

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Draw a special Venn Diagram with Three Sets. These are the non scaled cases

Description

Value

Author(s)

Examples

Draw a special Venn Diagram with Three Sets. These are the scaled cases

Description

Value

Author(s)

Examples

Draw a Venn Diagram with Three Sets

Description

Usage

Arguments

Details

Value

Author(s)

Examples

Get the size of individual partitions in a Venn diagram

Description

Usage

Arguments

Value

Details

Author(s)

See Also

Examples

Make a truth table

Description

Usage

Arguments

Value

Author(s)