Bubble plot function!

bubblePlot.R

bubblePlot<-function(yvector,xvector,sigvector=NULL,nbreaks=10,ret=FALSE,scale=1,...){
	#if(names(yvector)%in%names(xvector)){
	#	stop("Name the y and x vectors -- ideally the same name ;-)")
	#}
	ybreaks = cut(yvector,breaks=quantile(yvector,p=seq(0,1,length.out=nbreaks)),include.lowest=T)
	xbreaks = cut(xvector,breaks=quantile(xvector,p=seq(0,1,length.out=nbreaks)),include.lowest=T)
	numFeatures = lapply(levels(xbreaks),function(i){
		k = which(xbreaks==i)
		sapply(levels(ybreaks),function(j){
			length(which(ybreaks[k]==j))
			})
		})
	names(numFeatures) = levels(xbreaks)
	yvec = 1:length(levels(ybreaks))
	nc = length(yvec)

	if(!is.null(sigvector)){
		# I am calculating numFeatures twice if sigvector==TRUE
		# This can be changed to if else statement to return two rows
		numSig = lapply(levels(xbreaks),function(i){
			k = which(xbreaks==i)
			sapply(levels(ybreaks),function(j){
				x = sum(names(yvector[k])[which(ybreaks[k]==j)]%in%names(sigvector))/length(which(ybreaks[k]==j))
				if(is.na(x)) x = 0
				x
			})
		})
	}
	medianSizes = median(unlist(numFeatures))
	plot(y=yvec,x=rep(1,nc),cex=scale*numFeatures[[1]]/medianSizes,
		xlim=c(-0.25,nc+.25),ylim=c(-0.25,nc+.25),bty="n",xaxt="n",yaxt="n",
		xlab="",ylab="",pch=21,...,bg=rgb(blue=1,red=0,green=0,alpha=numSig[[1]]))
	for(i in 2:length(numFeatures)){
		points(y=yvec,x=rep(i,nc),cex =scale*numFeatures[[i]]/medianSizes,pch=21,bg=rgb(blue=1,red=0,green=0,alpha=numSig[[i]]))
	}
	axis(1,at = 1:nc,labels=levels(xbreaks),las=2,cex.axis=.5)
	axis(2,at = 1:nc,labels=levels(ybreaks),las=2,cex.axis=.5)
	if(ret == TRUE){
		return(cbind(xbreaks,ybreaks))
	}
}

xlabel and ylabel?

What do you mean xlabel and ylabel? Currently the function takes two ordered vectors and breaks each separately into nbreaks. The breaks are turned into tick marks and displayed on the respective x,y axis. The ... in the function allows for sending a ylab and xlab.

I'm not sure if I should change the function to allow n1 breaks for y and n2 breaks for x; automatically size circles, etc. any suggestions are greatly appreciated!