#' Basic plot of binned vectors.
 #' 
 #' This function plots takes two vectors, calculates the contingency table and 
 #' plots circles sized by the contingency table value. Optional significance vectors
 #' of the values significant will shade the circles by proportion of significance.
 #' 
 #' 
 #' @param yvector A vector of values represented along y-axis.
 #' @param xvector A vector of values represented along x-axis.
 #' @param sigvector A vector of the names of significant features (names should match x/yvector).
 #' @param nbreaks Number of bins to break yvector and xvector into.

 #' @param ybreak The values to break the yvector at.
 #' @param xbreak The values to break the xvector at.
 #' @param scale Scaling of circle bin sizes.
 #' @param local Boolean to shade by signficant bin numbers (TRUE) or overall proportion (FALSE).

 #' @param ... Additional plot arguments.

 #' @return A matrix of features along rows, and the group membership along columns.

 #' @seealso \code{\link{plotMRheatmap}}
 #' @examples
 #' 
 #' data(mouseData)
 #' mouseData = mouseData[which(rowSums(mouseData)>139),]
 #' sparsity = rowMeans(MRcounts(mouseData)==0)
 #' lor = log(fitPA(mouseData,cl=pData(mouseData)[,3])$oddsRatio)
 #' plotBubble(lor,sparsity,main="lor ~ sparsity")

 #' # Example 2
 #' x = runif(100000)
 #' y = runif(100000)
 #' plotBubble(y,x)
 #'
 plotBubble<-function(yvector,xvector,sigvector=NULL,nbreaks=10, ybreak=quantile(yvector,p=seq(0,1,length.out=nbreaks)),

     xbreak=quantile(xvector,p=seq(0,1,length.out=nbreaks)),scale=1,local=FALSE,...){

     ybreaks = cut(yvector,breaks=ybreak,include.lowest=TRUE)
     xbreaks = cut(xvector,breaks=xbreak,include.lowest=TRUE)

     contTable = lapply(levels(xbreaks),function(i){
         k = which(xbreaks==i)
         sapply(levels(ybreaks),function(j){
             length(which(ybreaks[k]==j))
             })
         })
     names(contTable) = levels(xbreaks)
     yvec = 1:length(levels(ybreaks))
     nc = length(yvec)
 
     if(!is.null(sigvector)){
         # I am calculating contTable twice if sigvector==TRUE
         # This can be changed to if else statement to return two rows
         contSig = lapply(levels(xbreaks),function(i){
             k = which(xbreaks==i)
             sapply(levels(ybreaks),function(j){
                 x = sum(names(yvector[k])[which(ybreaks[k]==j)]%in%sigvector)/length(which(ybreaks[k]==j))
                 if(is.na(x)) x = 0
                 x
             })
         })

         if(local==TRUE){
             contSigTable = sapply(contSig,function(i){i})
             linMap <- function(x, a, b) approxfun(range(x), c(a, b))(x)

             if(length(levels(ybreak))!=length(levels(xbreak))) {

                 warning("Not square matrix - this is not implemented currently")
             }

             contSigTable = matrix(linMap(contSigTable,a=0,b=1),nrow=length(levels(ybreaks)))
             for(i in 1:length(levels(ybreaks))){

                     contSig[[i]] = contSigTable[,i]
             }
         }

     } else {
         contSig = lapply(levels(xbreaks),function(i){
             k = which(xbreaks==i)
             sapply(levels(ybreaks),function(j){
                 1
             })
         })
     }

     medianSizes = median(unlist(contTable))
     plot(y=yvec,x=rep(1,nc),cex=scale*contTable[[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=contSig[[1]]))
     for(i in 2:length(contTable)){
         points(y=yvec,x=rep(i,nc),cex =scale*contTable[[i]]/medianSizes,pch=21,bg=rgb(blue=1,red=0,green=0,alpha=contSig[[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)

     res = cbind(as.character(ybreaks),as.character(xbreaks))
     colnames(res) = c("yvector","xvector")
     rownames(res) = names(yvector)
     if(is.null(sigvector)){
         sig = rep(0,nrow(res))
         sig[which(rownames(res)%in%sigvector)] = 1
         res = cbind(res,sig)

     }

     invisible(res)

 }