Venn Diagram

Method 1:
A=LETTERS[1:15];B=LETTERS[5:20]
C=LETTERS[12:18];D=LETTERS[7:17]
All = unique(c(A, B, C, D))
Distribution = matrix(0, ncol=4, nrow=length(All));
colnames(Distribution)<-c('A','B','C','D');
rownames(Distribution)<-All;
Distribution[A, 1] = 1;
Distribution[B, 2] = 1;
Distribution[C, 3] = 1;
Distribution[D, 4] = 1;
library(limma);
par(mfrow=c(2, 2))
a <- vennCounts(Distribution[ ,c(1, 3,4)]); vennDiagram(a, main="", mar=c(0.5, 0.5, 0.5, 0.5), cex=0.9, lwd=1);
a <- vennCounts(Distribution[ ,c(1, 2,4)]); vennDiagram(a, main="", mar=c(0.5, 0.5, 0.5, 0.5), cex=0.9, lwd=1);
a <- vennCounts(Distribution[ ,c(2, 3,4)]); vennDiagram(a, main="", mar=c(0.5, 0.5, 0.5, 0.5), cex=0.9, lwd=1);

#########################
Method 2:

circle <- function(x, y, r, ...) {
    ang <- seq(0, 2*pi, length = 100)
    xx <- x + r * cos(ang)
    yy <- y + r * sin(ang)
    polygon(xx, yy, ...)
}

venndia <- function(A, B, C, getdata=FALSE, ...){
    cMissing <- missing(C)
    if(cMissing){ C <- c() }

    unionAB <- union(A, B)
    unionAC <- union(A, C)
    unionBC <- union(B, C)
    uniqueA <- setdiff(A, unionBC)
    uniqueB <- setdiff(B, unionAC)
    uniqueC <- setdiff(C, unionAB)
    intersAB <- setdiff(intersect(A, B), C)
    intersAC <- setdiff(intersect(A, C), B)
    intersBC <- setdiff(intersect(B, C), A)
    intersABC <- intersect(intersect(A, B), intersect(B, C))

    nA <- length(uniqueA)       
    nB <- length(uniqueB)
    nC <- length(uniqueC)

    nAB <- length(intersAB)
    nAC <- length(intersAC)
    nBC <- length(intersBC)

    nABC <- length(intersABC)   

    par(mar=c(2, 2, 0, 0))
    plot(-10, -10, ylim=c(0, 9), xlim=c(0, 9), axes=FALSE, ...)
    circle(x=3, y=6, r=3, col=rgb(1,0,0,.5), border=NA)
    circle(x=6, y=6, r=3, col=rgb(0,.5,.1,.5), border=NA)
    circle(x=4.5, y=3, r=3, col=rgb(0,0,1,.5), border=NA)

    text( x=c(1.2, 7.7, 4.5), y=c(7.8, 7.8, 0.8), c("A", "B", "C"), cex=3, col="gray90" )

    text(
        x=c(2, 7, 4.5, 4.5, 3, 6, 4.5), 
        y=c(7, 7, 2  , 7  , 4, 4, 5), 
        c(nA, nB, nC, nAB, nAC, nBC, nABC), 
        cex=2
    )

    if(getdata){
        list(A=uniqueA, B=uniqueB, C=uniqueC, 
                AB=intersAB , AC=intersAC , BC=intersBC , 
                ABC=intersABC
        )
    }
}

 venndia(A=LETTERS[1:15], B=LETTERS[5:20])

vd <- venndia(A=LETTERS[1:15], B=LETTERS[5:20], getdata=TRUE)

It is from 

http://stackoverflow.com/questions/1428946/venn-diagrams-with-r