vennplot (version 0.9.02)

vennplot: Draw Venn diagram in 2D or 3D

Description

Draw Venn diagram in 2D or 3D

Usage

vennplot(combinations = NULL, fit = 0.5, GRAM = T, main = NULL,
  arbitrary = NULL, mu = 2, NAME = NULL, ALPHA = 10^(-5),
  alpha.col = 0.3, disjoint = F, ThreeD = FALSE, delta = 0.01,
  mar = rep(1, 4), priority = 2, weight = rep(1, length(priority)))

Arguments

combinations

Named numeric vector or data.frame where each row is a logical vector indicating set membership. See Details.

fit

Scaling of semi-diameters; a scalar between 0.5 and 1.

GRAM

If TRUE, use the centralized GRAM matrix as the initial location. Otherwise use the center of an arbitrary circle.

main

Title of 2D plot.

arbitrary

When GRAM = FALSE, an integer designating which circle to use for inital location, or NULL to use a random circle. Argument is ignored when GRAM = TRUE.

mu

Generates defaults for unspecificed two-way intersections. See Details.

NAME

The name of each circle. See Examples.

ALPHA

Size of steepest descent.

alpha.col

Color darkness.

disjoint

If TRUE plots only the disjoint part of overlapping circles.

ThreeD

Draw Venn diagram in 3D. See Examples.

delta

Closeness betwen connected components.

mar

Plot margins.

priority

Scalar or vector specifying the fitting priority for intersections. See Examples.

weight

Priority weights. Must the the same length as priority. See Examples.

Value

An object of the class vennplot with following components:

center

centers of the circles (columns are (x, y) or (x, y, z) coordinates).

semidiameters

semi-diameters of the circles.

LOSS

total loss of vennplot.

weighted.least.square

Given specific priorities and weights, the weighted least square between input and lay-out.

Details

The names of data sets (circles) supplied to combination must be single letters, e.g., combination = c(A=1, B=2, AB=0.5). Here A means the whole data-set, so does B, which means AB can be no larger than min(A,B).

If a few two way intersections are unspecified, mu gives one way to generate them. For example, Suppose input combinations are c(a=1,b=2,c=1,abc = 0.2). Then default values for the two-way interserctions are ab = mu^(3-2)*abc = 0.2mu^(3-2), and bc = mu^(3-2)*abc = 0.2mu^(3-2), ac = mu^(3-2)*abc = 0.2mu^(3-2).

Examples

# NOT RUN {
# arbitray sets
combinations = c(A=1.8, B=0.9,C=1.3, D = 1.3,E = 1.6, AC=0.3,
                 AD= 0.3,BE = 0.3, AE = 0.4, f = 0.7,g =0.8,
                 h = 0.5, gf = 0.2, Bh = 0.1,i = 1,j = 0.4,
                 k=0.7,l = 1.4,kl = 0.2,m = 0.5,lm = 0.2,
                 o = 0.8,p = 0.9, op = 0.3)
ve = vennplot(combinations)

# named sets
# combinations = c(A=1, B=1,C=1, ABC = 0.1)
# ve = vennplot(combinations,NAME = c("Loon","Goose","Duck"))

# effect of parameter mu
# combinations = c(A=1, B=1, C=1, D=1, E=1, ABCDE = 0.1)
# par(mfrow = c(1,3))
# ve = vennplot(combinations)
# ve = vennplot(combinations,mu=2)
# ve = vennplot(combinations,mu=1.2)

# 3D Venn plot
combinations = c(A=803, B=304,C=1015, D = 1100,E = 1005,f = 967,H=3020,
                 CD = 1000,BC = 248,ABC = 185,ADE = 327,CDfH = 846,
                 I=800, J=760,K=1000, L = 1100,M = 900, IK=333,
                 JM = 251,IL= 289, KM = 412,JL = 213)
timestart <- Sys.time()
ve = vennplot(combinations, disjoint = TRUE,ThreeD = TRUE)
timeend <- Sys.time()
runningtime <- timeend-timestart
print(runningtime)

# effect of parameters priority and weight
# combinations = c(A = 79,B=29,C=58,AB = 25,AC = 44, BC=18,ABC = 1)
# par(mfrow = c(2,2))
# vennplot(combinations, priority = 2)
# vennplot(combinations, priority = 3)
# vennplot(combinations, priority = c(2,3), weight = c(30,1000))
# vennplot(combinations, priority = c(2,3), weight = c(30,10))

# binary data
# combinations = sharks[,c(1,3:5,8)]
# vennplot(combinations = combinations)
# }