--- a/genomeview.r	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-
-caloffset = function(genome){
-    total_len = sum(as.numeric(genome[,2]))
-    offset = 0
-    for (i in 1:nrow(genome)) {
-        offset = c(offset,offset[i]+genome[i,2])        
-    }
-    offset    
-}
-
-coverage = function(intervals,genome,offset,resolution) {
-
-    nChr = length(offset) - 1
-    total_len = offset[nChr+1]
-    nbin = as.integer(total_len / resolution)
-    cov = numeric(nbin)#coverage
-    col = numeric(nbin)#color
-    for (i in 1:nChr) {
-        d = x[x[,1]==as.character(genome[i,1]),2:3]
-        d = ceiling(((d[,1]+d[,2])/2+offset[i])*nbin/total_len)
-        t = table(d)
-		pos = as.numeric(row.names(t)) 
-        cov[pos] = cov[pos] + as.numeric(t)
-        col[pos] = i
-    }
-    list(nbin=nbin,cov=cov,col=col)
-}
-
-# plot coverage
-# res = genomeView(x,genome,100000)
-plotcov = function(res,genome,offset,title,uselog) {
-	if (uselog == 'log'){
-		res$cov = log10(res$cov+1)
-	}
-    ymax = max(res$cov)
-    #print(ymax)
-	par(mar=c(5,5,5,1))
-    plot(seq(length(res$cov)),res$cov,type='h',cex=0.1,cex.axis=2,cex.lab=2,cex.main=3,col=res$col,xaxt='n',main=title,xlab='chromosome',ylab='coverage',frame.plot=F,ylim=c(0,ymax))
-    xticks = numeric(nrow(genome))
-    for (i in 1:nrow(genome)){
-       xticks[i] = (offset[i]+offset[i+1])/2*res$nbin/offset[length(offset)]
-    }
-    mtext(genome[,1],side=1,at=xticks,adj=1,las=2,col=seq(nrow(genome)))
-}
-
-union_correlation = function(x,y){
-	z = x>0 | y>0
-	cor(x[z],y[z])
-}
-
-
-heatmap2 = function(x,scale,sym,margins,labRow,labCol){
-    h = heatmap(x,scale=scale,sym=sym,margins=margins,labRow=labRow,labCol=labCol)
-    x = x[h$rowInd,h$colInd]
-    tx = numeric(0)
-    ty = numeric(0)
-    txt = character(0)
-    for (i in 1:nrow(x)){
-        for (j in 1:ncol(x)){
-            tx <- c(tx,i)
-            ty <- c(ty,ncol(x)-j+1)
-            txt <- c(txt,format(x[i,j],digits=2,nsmall=2))
-        }    
-    }
-    #heatmap(x,scale=scale,sym=sym,margins=margins,labRow=labRow[h$rowInd],labCol=labCol[h$colInd],add.expr=text(1:4,1:4,1:4))
-	cat(dim(tx))
-	text(tx,ty,txt)
-	heatmap(x,scale=scale,sym=sym,margins=margins,labRow=labRow[h$rowInd],labCol=labCol[h$colInd],add.expr=text(tx,ty,txt))
-
-}