venn.diagram: Make a Venn Diagram

Description

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

Usage

venn.diagram(x, filename, 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, ...)

Arguments

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

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

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

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

...

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

Value

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

Details

cccl{ 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) 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 external text placement. The elements allow for individual control of the areas in the order of the first area, second area and intersection area. ext.line.lwd 2 numeric lwd of line connecting to ext.text 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 }

Examples

Run this code

# Note: most examples are listed as dontrun to meet CRAN requirements, 
# but all should work as-is!

# compact and minimal notation
venn.plot <- venn.diagram(
	list(A = 1:150, B = 121:170), 
	"Venn_2set_simple.tiff"
	);
venn.plot <- venn.diagram(
	list(A = 1:150, B = 121:170, C = 101:200), 
	"Venn_3set_simple.tiff"
	);

# a more elaborate two-set Venn diagram with title and subtitle
venn.plot <- venn.diagram(
	x = list(
		"A" = 1:100,
		"B" = 96:140
		),
	filename = "Venn_2set_complex.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
	);

# 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 = "Euler_3set_simple.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 = "Euler_3set_scaled.tiff",
	cex = 2.5,
	cat.cex = 2.5,
	cat.pos = 0
	);

# 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 = "Venn_4set_pretty.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 = "Venn_5set_pretty.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 = 'Fig3-1_triple_labels_sub_and_superscripts.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 = "Fig3-2_Euler_3set_simple_with_subscripts.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
	);

# Example to print to screen
venn.plot <- venn.diagram(
	x = list(
			sample1 = c(1:40),
			sample2 = c(30:60)
			),
		filename = NULL
		);

# 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
	);

jpeg("venn_jpeg.jpg");
grid.draw(venn.plot);
dev.off();

#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.
# Figure 1A
venn.plot <- venn.diagram(
	x = list(
		Label = 1:100
		),
	filename = "1A-single_Venn.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 = "1B-double_Venn.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 = "1C-triple_Venn.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 = "1D-quadruple_Venn.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 = "2-1_special_case_ext-text.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 = "2-2_special_case_pairwise-inclusion.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 = "2-3_special_case_pairwise-exclusion.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 = "2-4_triple_special_case-001.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 = "2-5_triple_special_case-012AA.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 = "2-6_triple_special_case-022AAAO.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 = "2-7_triple_special_case-100.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 = "2-8_triple_special_case-011A.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 = "2-9_triple_special_case-121AO.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

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