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plot.venn <- function(x, y, ...,
small=0.7,
showSetLogicLabel=FALSE,
simplify=FALSE
)
{
drawVennDiagram(
data=x,
small=small,
showSetLogicLabel=showSetLogicLabel,
simplify=simplify
)
}
## data should be a matrix.
## - The first column of the matrix is the
## count of the number of objects with the specified pattern.
## - The second and subsequent columns contain 0-1 indicators
## giving the pattern of group membership
drawVennDiagram <-function(data,
small=0.7,
showSetLogicLabel=FALSE,
simplify=FALSE)
{
numCircles<-NA
data.colnames<-NULL
data.rownames<-NULL
if(is.matrix(data)) {
numCircles<-ncol(data)-1
data.colnames<-colnames(data)[2:(ncol(data))]
# Order is reverted since later indexing starts with
# the "lowest bit" and that is expected at the left
data.rownames<-rownames(data)
}
else {
if (is.list(data)) {
stop("gplots.drawVennDiagram: This internal function is used wrongly. ",
"Please call the function 'venn' with the same arguments, instead.\n")
}
warning("drawVennDiagram: Testing only, presuming first argument to specify",
"the number of circles to draw.\n")
numCircles<-data
}
m<-(0:(-1+2^numCircles))
if (! is.matrix(data)) {
##cat("prepare randomised data\n")
data<-t(sapply(X=m,FUN=function(v){
l<-baseOf(v,2,numCircles)
#print(l)
return(l)
}))
#print(data)
#data.names<-apply(data,1,function(X){
# return(paste(X),collapse="")
#})
for(i in m) {
n<-paste(data[i+1,],collapse="")
if (is.null(data.rownames)) {
data.rownames<-n
}
else {
data.rownames<-c(data.rownames,n)
}
}
#print(data.rownames)
data<-cbind(sample(1:100,size=2^numCircles,replace=TRUE),data)
#print(data)
rownames(data)<-data.rownames
data.colnames<-LETTERS[1:numCircles]
colnames(data)<-c("num",data.colnames)
}
plot.new()
h<-400
plot.window(c(0,h), c(0,h), ylab="", xlab="")
if ((2 <= numCircles && numCircles <= 3) || (4 == numCircles && simplify)) {
circle <- function(x,y=NULL,r=1) {
elps=cbind(r*cos(seq(0,2*pi,len=1000)), r*sin(seq(0,2*pi,len=1000)));
if (!is.null(y)) {
if (length(x) != length(y))
stop("circle: both x and y need to be of same length")
if (is.matrix(x) && ncol(x)>1)
stop("circle: if y is not NULL, then x must not be a matrix")
x<-cbind(x,y)
}
for(i in 1:nrow(x)) {
ax<-elps[,1]+rep(x[i,1],1000)
ay<-elps[,2]+rep(x[i,2],1000)
polygon(ax,ay)
}
}
#nolongerreguired#require(grid)
##cat("drawing circles\n")
# draw circles with radius 1.7 equally distributed
# with centers on a circle of radius 1
degrees<-2*pi/numCircles*(1:numCircles)
# scaling factor
s<-1/8*h
# radius for circles
r<-3/12*h
x<-sapply(degrees,FUN=sin)*s + 0.5*h
y<-sapply(degrees,FUN=cos)*s + 0.5*h
##cat("filling data\n")
circle(x,y,r)
distFromZero<-rep(NA,2^numCircles)
degrees<-rep(NA,2^numCircles)
degrees[(2^numCircles)]<-0
distFromZero[(2^numCircles)]<-0
for (i in 0:(numCircles-1)) {
distFromZero[2^i+1] <- r
degrees[2^i+1] <- 2*pi/numCircles*i
d<-degrees[2^i+1]
#print(data.colnames)
text(
# starting from the lowest bit, hence reading
# lables from the right
label=data.colnames[numCircles - i],
x=sin(d)*5/12*h+0.5*h,
y=cos(d)*5/12*h+0.5*h
)
}
if (4==numCircles) {
for (i in 0:(numCircles-1)) {
# Current set bit plus the bit left of it and the bit right of it
distFromZero[2^i
+2^((i+numCircles-1)%%numCircles)
+2^((i+1)%%numCircles)+1] <- 2/12*h
distFromZero[2^i+1] <- 3.5/12*h
degrees[2^i
+2^((i+numCircles-1)%%numCircles)
+2^((i+1)%%numCircles)+1] <- degrees[2^i+1]
}
}
#degrees[2^i+1] + degrees[2^((i+1)%%numCircles)+1])/2
if (3 <=numCircles) {
for (i in 0:(numCircles-1)) {
distFromZero[(2^i+2^((i+1)%%numCircles))+1]<- 2.2/12*h
distFromZero[2^i+1] <- 3/12*h
if (i == (numCircles-1)) {
degrees[(2^i+2^((i+1)%%numCircles))+1] <- (
degrees[2^i+1] + 2*pi+ degrees[1+1])/2
}
else {
degrees[(2^i+2^((i+1)%%numCircles))+1] <- (
degrees[2^i+1] + degrees[2^((i+1)%%numCircles)+1])/2
}
}
}
for(i in 1:2^numCircles) {
n<-paste(baseOf((i-1),2,numCircles),collapse="")
v<-data[n,1]
d<-degrees[i]
if (1 == length(d) && is.na(d)) {
if (v>0) warning("Not shown: ",n," contains ",v,"\n")
}
else {
l<-distFromZero[i]
x<-sin(d)*l+0.5*h
y<-cos(d)*l+0.5*h
#cat("i=",i," x=",x," y=",y," label=",n,"\n")
l<-v
if (showSetLogicLabel) l<-paste(n,"\n",v,sep="")
text(label=l,x=x,y=y)
}
}
}
else if ( (4 == numCircles && !simplify) || numCircles <= 5 ) {
# Function to turn and move ellipses/circles
relocate_elp <- function(e, alpha, x, y){
phi=(alpha/180)*pi;
xr=e[,1]*cos(phi)+e[,2]*sin(phi)
yr=-e[,1]*sin(phi)+e[,2]*cos(phi)
xr=x+xr;
yr=y+yr;
return(cbind(xr, yr))
}
lab<-function (identifier, data, showLabel=showSetLogicLabel) {
r<-data[identifier,1]
if (showLabel) {
return(paste(identifier,r,sep="\n"))
}
else {
return(r)
}
}
if (4 == numCircles) {
elps=cbind(162*cos(seq(0,2*pi,len=1000)), 108*sin(seq(0,2*pi,len=1000)));
#plot(c(0, 400), c(0, 400), type="n", axes=F, ylab="", xlab="");
polygon(relocate_elp(elps, 45,130,170));
polygon(relocate_elp(elps, 45,200,200));
polygon(relocate_elp(elps,135,200,200));
polygon(relocate_elp(elps,135,270,170));
text( 35, 315, data.colnames[1],cex=1.5)
text(138, 347, data.colnames[2],cex=1.5)
text(262, 347, data.colnames[3],cex=1.5)
text(365, 315, data.colnames[4],cex=1.5)
elps <- cbind(130*cos(seq(0,2*pi,len=1000)),
80*sin(seq(0,2*pi,len=1000)))
text( 35, 250, lab("1000",data));
text(140, 315, lab("0100",data));
text(260, 315, lab("0010",data));
text(365, 250, lab("0001",data));
text( 90, 280, lab("1100",data), cex=small)
text( 95, 110, lab("1010",data) )
text(200, 50, lab("1001",data), cex=small)
text(200, 290, lab("0110",data))
text(300, 110, lab("0101",data))
text(310, 280, lab("0011",data), cex=small)
text(130, 230, lab("1110",data))
text(245, 75, lab("1101",data),cex=small)
text(155, 75, lab("1011",data),cex=small)
text(270, 230, lab("0111",data))
text(200,150,lab("1111",data))
}
else if (5 == numCircles) {
elps <- cbind(150*cos(seq(0,2*pi,len=1000)),
60*sin(seq(0,2*pi,len=1000)))
polygon(relocate_elp(elps, 90,200, 250))
polygon(relocate_elp(elps, 162,250, 220))
polygon(relocate_elp(elps, 234,250, 150))
polygon(relocate_elp(elps, 306,180, 125))
polygon(relocate_elp(elps, 378,145, 200))
text( 20, 295, data.colnames[1],cex=1.5)
text(140, 380, data.colnames[2],cex=1.5)
text(350, 318, data.colnames[3],cex=1.5)
text(350, 2, data.colnames[4],cex=1.5)
text( 50, 10, data.colnames[5],cex=1.5)
text( 61, 228, lab("10000",data));
text(194, 329, lab("01000",data));
text(321, 245, lab("00100",data));
text(290, 81, lab("00010",data));
text(132, 69, lab("00001",data));
text(146, 250, lab("11000",data), cex=small)
text(123, 188, lab("10100",data), cex=small)
text(275, 152, lab("10010",data), cex=small)
text(137, 146, lab("10001",data), cex=small)
text(243, 268, lab("01100",data), cex=small)
text(175, 267, lab("01010",data), cex=small)
text(187, 117, lab("01001",data), cex=small)
text(286, 188, lab("00110",data), cex=small)
text(267, 235, lab("00101",data), cex=small)
text(228, 105, lab("00011",data), cex=small)
text(148, 210, lab("11100",data),cex=small)
text(159, 253, lab("11010",data),cex=small)
text(171, 141, lab("11001",data),cex=small)
text(281, 175, lab("10110",data),cex=small)
text(143, 163, lab("10101",data),cex=small)
text(252, 145, lab("10011",data),cex=small)
text(205, 255, lab("01110",data),cex=small)
text(254, 243, lab("01101",data),cex=small)
text(211, 118, lab("01011",data),cex=small)
text(267, 211, lab("00111",data),cex=small)
text(170, 231,lab("11110",data),cex=small)
text(158, 169,lab("11101",data),cex=small)
text(212, 139,lab("11011",data),cex=small)
text(263, 180,lab("10111",data),cex=small)
text(239, 232,lab("01111",data),cex=small)
text(204,190,lab("11111",data))
}
}
else {
stop(paste("Venn diagrams for ",numCircles," dimensions are not yet supported.\n"))
}
}
|
