draw.quintuple.venn {VennDiagram}

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

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 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

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

# 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();