expdat <- read.table(file="gene2go.hs.09May06.txt",header=FALSE,sep="\t",quote="")
expterm <- unique(expdat$V3)
dat1 <- scan(file="correl.hs.09May06.txt")
dat1 <- matrix(dat1,nrow=length(expterm),ncol=length(expterm))
dat <- data.frame(x=expdat$V3,y=expdat$V8)
dat <- unique(dat,margin=1)
g1 <- lapply(unique(dat[dat$y=="Function",1]),function(a){which(dat$x==a)})
g1 <- unlist(g1)
g2 <- lapply(unique(dat[dat$y=="Component",1]),function(a){which(dat$x==a)})
g2 <- unlist(g2)
g3 <- lapply(unique(dat[dat$y=="Process",1]),function(a){which(dat$x==a)})
g3 <- unlist(g3)
test2 <- c(g1,g2,g3)
dat7 <- dat1[test2,test2]
dat7[lower.tri(dat7,diag=TRUE)] <- NA
dat9 <- dat7[1:length(g1),1:length(g1)]
dat10 <- dat7[1:length(g1),(length(g1)+1):(length(g1)+length(g2))]
dat11 <- dat7[1:length(g1),(length(g1)+length(g2)+1):length(expterm)]
dat12 <- dat7[(length(g1)+1):(length(g1)+length(g2)),(length(g1)+1):(length(g1)+length(g2))]
dat13 <- dat7[(length(g1)+1):(length(g1)+length(g2)),(length(g1)+length(g2)+1):length(expterm)]
dat14 <- dat7[(length(g1)+length(g2)+1):length(expterm),(length(g1)+length(g2)+1):length(expterm)]
dat9 <- as.vector(dat9)
dat9 <- na.omit(dat9)
dat10 <- as.vector(dat10)
dat10 <- na.omit(dat10)
dat11 <- as.vector(dat11)
dat11 <- na.omit(dat11)
dat12 <- as.vector(dat12)
dat12 <- na.omit(dat12)
dat13 <- as.vector(dat13)
dat13 <- na.omit(dat13)
dat14 <- as.vector(dat14)
dat14 <- na.omit(dat14)
dat15 <- c(dat9,dat12,dat14)
dat16 <- c(dat10,dat11,dat13)
par(mfrow=c(2,1))
hist(dat15[dat15>0.2],main=("Correlation coefficients within sub-ontologies"),xlab="Correlation coefficients",ylim=c(0,4000),labels=TRUE,nclass=10)
hist(dat16[dat16>0.2],main=("Correlation coefficients between sub-ontologies"),xlab="Correlation coefficients",ylim=c(0,4000),labels=TRUE,nclass=10)