--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/baseline/comparePDFs.r	Thu Oct 13 10:52:24 2016 -0400
@@ -0,0 +1,225 @@
+options("warn"=-1)
+
+#from http://selection.med.yale.edu/baseline/Archive/Baseline%20Version%201.3/Baseline_Functions_Version1.3.r
+# Compute p-value of two distributions
+compareTwoDistsFaster <-function(sigma_S=seq(-20,20,length.out=4001), N=10000, dens1=runif(4001,0,1), dens2=runif(4001,0,1)){
+#print(c(length(dens1),length(dens2)))
+if(length(dens1)>1 & length(dens2)>1 ){
+	dens1<-dens1/sum(dens1)
+	dens2<-dens2/sum(dens2)
+	cum2 <- cumsum(dens2)-dens2/2
+	tmp<- sum(sapply(1:length(dens1),function(i)return(dens1[i]*cum2[i])))
+	#print(tmp)
+	if(tmp>0.5)tmp<-tmp-1
+	return( tmp )
+	}
+	else {
+	return(NA)
+	}
+	#return (sum(sapply(1:N,function(i)(sample(sigma_S,1,prob=dens1)>sample(sigma_S,1,prob=dens2))))/N)
+}  
+
+
+require("grid")
+arg <- commandArgs(TRUE)
+#arg <- c("300143","4","5")
+arg[!arg=="clonal"]
+input <- arg[1]
+output <- arg[2]
+rowIDs <- as.numeric(  sapply(arg[3:(max(3,length(arg)))],function(x){ gsub("chkbx","",x) } )  )
+
+numbSeqs = length(rowIDs)
+
+if ( is.na(rowIDs[1]) | numbSeqs>10 ) {
+  stop( paste("Error: Please select between one and 10 seqeunces to compare.") )
+}
+
+#load( paste("output/",sessionID,".RData",sep="") )
+load( input )
+#input
+
+xMarks = seq(-20,20,length.out=4001)
+
+plot_grid_s<-function(pdf1,pdf2,Sample=100,cex=1,xlim=NULL,xMarks = seq(-20,20,length.out=4001)){
+  yMax = max(c(abs(as.numeric(unlist(listPDFs[pdf1]))),abs(as.numeric(unlist(listPDFs[pdf2]))),0),na.rm=T) * 1.1
+
+  if(length(xlim==2)){
+    xMin=xlim[1]
+    xMax=xlim[2]
+  } else {
+    xMin_CDR = xMarks[listPDFs[pdf1][[1]][["CDR"]]>0.001][1]
+    xMin_FWR = xMarks[listPDFs[pdf1][[1]][["FWR"]]>0.001][1]
+    xMax_CDR = xMarks[listPDFs[pdf1][[1]][["CDR"]]>0.001][length(xMarks[listPDFs[pdf1][[1]][["CDR"]]>0.001])]
+    xMax_FWR = xMarks[listPDFs[pdf1][[1]][["FWR"]]>0.001][length(xMarks[listPDFs[pdf1][[1]][["FWR"]]>0.001])]
+  
+    xMin_CDR2 = xMarks[listPDFs[pdf2][[1]][["CDR"]]>0.001][1]
+    xMin_FWR2 = xMarks[listPDFs[pdf2][[1]][["FWR"]]>0.001][1]
+    xMax_CDR2 = xMarks[listPDFs[pdf2][[1]][["CDR"]]>0.001][length(xMarks[listPDFs[pdf2][[1]][["CDR"]]>0.001])]
+    xMax_FWR2 = xMarks[listPDFs[pdf2][[1]][["FWR"]]>0.001][length(xMarks[listPDFs[pdf2][[1]][["FWR"]]>0.001])]
+  
+    xMin=min(c(xMin_CDR,xMin_FWR,xMin_CDR2,xMin_FWR2,0),na.rm=TRUE)
+    xMax=max(c(xMax_CDR,xMax_FWR,xMax_CDR2,xMax_FWR2,0),na.rm=TRUE)
+  }
+
+  sigma<-approx(xMarks,xout=seq(xMin,xMax,length.out=Sample))$x
+  grid.rect(gp = gpar(col=gray(0.6),fill="white",cex=cex))
+  x <- sigma
+  pushViewport(viewport(x=0.175,y=0.175,width=0.825,height=0.825,just=c("left","bottom"),default.units="npc"))
+  #pushViewport(plotViewport(c(1.8, 1.8, 0.25, 0.25)*cex))
+  pushViewport(dataViewport(x, c(yMax,-yMax),gp = gpar(cex=cex),extension=c(0.05)))
+  grid.polygon(c(0,0,1,1),c(0,0.5,0.5,0),gp=gpar(col=grey(0.95),fill=grey(0.95)),default.units="npc")
+  grid.polygon(c(0,0,1,1),c(1,0.5,0.5,1),gp=gpar(col=grey(0.9),fill=grey(0.9)),default.units="npc")
+  grid.rect()
+  grid.xaxis(gp = gpar(cex=cex/1.1))
+  yticks = pretty(c(-yMax,yMax),8)
+  yticks = yticks[yticks>(-yMax) & yticks<(yMax)]
+  grid.yaxis(at=yticks,label=abs(yticks),gp = gpar(cex=cex/1.1))
+  if(length(listPDFs[pdf1][[1]][["CDR"]])>1){
+    ycdr<-approx(xMarks,listPDFs[pdf1][[1]][["CDR"]],xout=seq(xMin,xMax,length.out=Sample),yleft=0,yright=0)$y
+    grid.lines(unit(x,"native"), unit(ycdr,"native"),gp=gpar(col=2,lwd=2))
+  }
+  if(length(listPDFs[pdf1][[1]][["FWR"]])>1){
+    yfwr<-approx(xMarks,listPDFs[pdf1][[1]][["FWR"]],xout=seq(xMin,xMax,length.out=Sample),yleft=0,yright=0)$y
+    grid.lines(unit(x,"native"), unit(-yfwr,"native"),gp=gpar(col=4,lwd=2))
+   }
+
+  if(length(listPDFs[pdf2][[1]][["CDR"]])>1){
+    ycdr2<-approx(xMarks,listPDFs[pdf2][[1]][["CDR"]],xout=seq(xMin,xMax,length.out=Sample),yleft=0,yright=0)$y
+    grid.lines(unit(x,"native"), unit(ycdr2,"native"),gp=gpar(col=2,lwd=2,lty=2))
+  }
+  if(length(listPDFs[pdf2][[1]][["FWR"]])>1){
+    yfwr2<-approx(xMarks,listPDFs[pdf2][[1]][["FWR"]],xout=seq(xMin,xMax,length.out=Sample),yleft=0,yright=0)$y
+    grid.lines(unit(x,"native"), unit(-yfwr2,"native"),gp=gpar(col=4,lwd=2,lty=2))
+   }
+
+  grid.lines(unit(c(0,1),"npc"), unit(c(0.5,0.5),"npc"),gp=gpar(col=1))
+  grid.lines(unit(c(0,0),"native"), unit(c(0,1),"npc"),gp=gpar(col=1,lwd=1,lty=3))
+
+  grid.text("Density", x = unit(-2.5, "lines"), rot = 90,gp = gpar(cex=cex))
+  grid.text( expression(paste("Selection Strength (", Sigma, ")", sep="")) , y = unit(-2.5, "lines"),gp = gpar(cex=cex))
+  
+  if(pdf1==pdf2 & length(listPDFs[pdf2][[1]][["FWR"]])>1 & length(listPDFs[pdf2][[1]][["CDR"]])>1 ){
+    pCDRFWR = compareTwoDistsFaster(sigma_S=xMarks, N=10000, dens1=listPDFs[[pdf1]][["CDR"]], dens2=listPDFs[[pdf1]][["FWR"]])       
+    pval = formatC(as.numeric(pCDRFWR),digits=3)
+    grid.text( substitute(expression(paste(P[CDR/FWR], "=", x, sep="")),list(x=pval))[[2]] , x = unit(0.02, "npc"),y = unit(0.98, "npc"),just=c("left", "top"),gp = gpar(cex=cex*1.2))
+  }
+  grid.text(paste("CDR"), x = unit(0.98, "npc"),y = unit(0.98, "npc"),just=c("right", "top"),gp = gpar(cex=cex*1.5))
+  grid.text(paste("FWR"), x = unit(0.98, "npc"),y = unit(0.02, "npc"),just=c("right", "bottom"),gp = gpar(cex=cex*1.5))
+  popViewport(2)
+}
+#plot_grid_s(1)
+
+
+p2col<-function(p=0.01){
+  breaks=c(-.51,-0.1,-.05,-0.01,-0.005,0,0.005,0.01,0.05,0.1,0.51)
+  i<-findInterval(p,breaks)
+  cols = c( rgb(0.8,1,0.8), rgb(0.6,1,0.6), rgb(0.4,1,0.4), rgb(0.2,1,0.2) , rgb(0,1,0),
+            rgb(1,0,0), rgb(1,.2,.2), rgb(1,.4,.4), rgb(1,.6,.6) , rgb(1,.8,.8) )
+  return(cols[i])
+}
+
+
+plot_pvals<-function(pdf1,pdf2,cex=1,upper=TRUE){
+  if(upper){
+    pCDR1FWR2 = compareTwoDistsFaster(sigma_S=xMarks, N=10000, dens1=listPDFs[[pdf1]][["CDR"]], dens2=listPDFs[[pdf2]][["FWR"]])       
+    pFWR1FWR2 = compareTwoDistsFaster(sigma_S=xMarks, N=10000, dens1=listPDFs[[pdf1]][["FWR"]], dens2=listPDFs[[pdf2]][["FWR"]])
+    pFWR1CDR2 = compareTwoDistsFaster(sigma_S=xMarks, N=10000, dens2=listPDFs[[pdf2]][["CDR"]], dens1=listPDFs[[pdf1]][["FWR"]])       
+    pCDR1CDR2 = compareTwoDistsFaster(sigma_S=xMarks, N=10000, dens2=listPDFs[[pdf2]][["CDR"]], dens1=listPDFs[[pdf1]][["CDR"]])
+    grid.polygon(c(0.5,0.5,1,1),c(0,0.5,0.5,0),gp=gpar(col=p2col(pFWR1FWR2),fill=p2col(pFWR1FWR2)),default.units="npc")
+    grid.polygon(c(0.5,0.5,1,1),c(1,0.5,0.5,1),gp=gpar(col=p2col(pCDR1FWR2),fill=p2col(pCDR1FWR2)),default.units="npc")
+    grid.polygon(c(0.5,0.5,0,0),c(1,0.5,0.5,1),gp=gpar(col=p2col(pCDR1CDR2),fill=p2col(pCDR1CDR2)),default.units="npc")
+    grid.polygon(c(0.5,0.5,0,0),c(0,0.5,0.5,0),gp=gpar(col=p2col(pFWR1CDR2),fill=p2col(pFWR1CDR2)),default.units="npc")
+         
+    grid.lines(c(0,1),0.5,gp=gpar(lty=2,col=gray(0.925)))
+    grid.lines(0.5,c(0,1),gp=gpar(lty=2,col=gray(0.925)))
+
+    grid.text(formatC(as.numeric(pFWR1FWR2),digits=3), x = unit(0.75, "npc"),y = unit(0.25, "npc"),just=c("center", "center"),gp = gpar(cex=cex))
+    grid.text(formatC(as.numeric(pCDR1FWR2),digits=3), x = unit(0.75, "npc"),y = unit(0.75, "npc"),just=c("center", "center"),gp = gpar(cex=cex))
+    grid.text(formatC(as.numeric(pCDR1CDR2),digits=3), x = unit(0.25, "npc"),y = unit(0.75, "npc"),just=c("center", "center"),gp = gpar(cex=cex))
+    grid.text(formatC(as.numeric(pFWR1CDR2),digits=3), x = unit(0.25, "npc"),y = unit(0.25, "npc"),just=c("center", "center"),gp = gpar(cex=cex))
+    
+           
+ #   grid.text(paste("P = ",formatC(pCDRFWR,digits=3)), x = unit(0.5, "npc"),y = unit(0.98, "npc"),just=c("center", "top"),gp = gpar(cex=cex))
+ #   grid.text(paste("P = ",formatC(pFWRFWR,digits=3)), x = unit(0.5, "npc"),y = unit(0.02, "npc"),just=c("center", "bottom"),gp = gpar(cex=cex))
+  }
+  else{
+  }
+}
+
+
+##################################################################################
+################## The whole OCD's matrix ########################################
+##################################################################################
+
+#pdf(width=4*numbSeqs+1/3,height=4*numbSeqs+1/3)
+pdf( output ,width=4*numbSeqs+1/3,height=4*numbSeqs+1/3) 
+
+pushViewport(viewport(x=0.02,y=0.02,just = c("left", "bottom"),w =0.96,height=0.96,layout = grid.layout(numbSeqs+1,numbSeqs+1,widths=unit.c(unit(rep(1,numbSeqs),"null"),unit(4,"lines")),heights=unit.c(unit(4,"lines"),unit(rep(1,numbSeqs),"null")))))
+
+for( seqOne in 1:numbSeqs+1){
+  pushViewport(viewport(layout.pos.col = seqOne-1, layout.pos.row = 1))
+  if(seqOne>2){ 
+    grid.polygon(c(0,0,0.5,0.5),c(0,0.5,0.5,0),gp=gpar(col=grey(0.5),fill=grey(0.9)),default.units="npc")
+    grid.polygon(c(1,1,0.5,0.5),c(0,0.5,0.5,0),gp=gpar(col=grey(0.5),fill=grey(0.95)),default.units="npc")
+    grid.polygon(c(0,0,1,1),c(1,0.5,0.5,1),gp=gpar(col=grey(0.5)),default.units="npc")
+       
+    grid.text(y=.25,x=0.75,"FWR",gp = gpar(cex=1.5),just="center")
+    grid.text(y=.25,x=0.25,"CDR",gp = gpar(cex=1.5),just="center")
+  }
+  grid.rect(gp = gpar(col=grey(0.9)))
+  grid.text(y=.75,substr(paste(names(listPDFs)[rowIDs[seqOne-1]]),1,16),gp = gpar(cex=2),just="center")
+  popViewport(1)
+}
+
+for( seqOne in 1:numbSeqs+1){
+  pushViewport(viewport(layout.pos.row = seqOne, layout.pos.col = numbSeqs+1))
+  if(seqOne<=numbSeqs){   
+    grid.polygon(c(0,0.5,0.5,0),c(0,0,0.5,0.5),gp=gpar(col=grey(0.5),fill=grey(0.95)),default.units="npc")
+    grid.polygon(c(0,0.5,0.5,0),c(1,1,0.5,0.5),gp=gpar(col=grey(0.5),fill=grey(0.9)),default.units="npc")
+    grid.polygon(c(1,0.5,0.5,1),c(0,0,1,1),gp=gpar(col=grey(0.5)),default.units="npc")
+    grid.text(x=.25,y=0.75,"CDR",gp = gpar(cex=1.5),just="center",rot=270)
+    grid.text(x=.25,y=0.25,"FWR",gp = gpar(cex=1.5),just="center",rot=270)
+  }
+  grid.rect(gp = gpar(col=grey(0.9)))
+  grid.text(x=0.75,substr(paste(names(listPDFs)[rowIDs[seqOne-1]]),1,16),gp = gpar(cex=2),rot=270,just="center")
+  popViewport(1)
+}
+
+for( seqOne in 1:numbSeqs+1){
+  for(seqTwo in 1:numbSeqs+1){
+    pushViewport(viewport(layout.pos.col = seqTwo-1, layout.pos.row = seqOne))
+    if(seqTwo>seqOne){
+      plot_pvals(rowIDs[seqOne-1],rowIDs[seqTwo-1],cex=2)
+      grid.rect()
+    }    
+    popViewport(1)
+  }
+}
+   
+
+xMin=0
+xMax=0.01
+for(pdf1 in rowIDs){
+  xMin_CDR = xMarks[listPDFs[pdf1][[1]][["CDR"]]>0.001][1]
+  xMin_FWR = xMarks[listPDFs[pdf1][[1]][["FWR"]]>0.001][1]
+  xMax_CDR = xMarks[listPDFs[pdf1][[1]][["CDR"]]>0.001][length(xMarks[listPDFs[pdf1][[1]][["CDR"]]>0.001])]
+  xMax_FWR = xMarks[listPDFs[pdf1][[1]][["FWR"]]>0.001][length(xMarks[listPDFs[pdf1][[1]][["FWR"]]>0.001])]
+  xMin=min(c(xMin_CDR,xMin_FWR,xMin),na.rm=TRUE)
+  xMax=max(c(xMax_CDR,xMax_FWR,xMax),na.rm=TRUE)
+}
+
+
+
+for(i in 1:numbSeqs+1){
+  for(j in (i-1):numbSeqs){    
+    pushViewport(viewport(layout.pos.col = i-1, layout.pos.row = j+1))
+    grid.rect()
+    plot_grid_s(rowIDs[i-1],rowIDs[j],cex=1)
+    popViewport(1)
+  }
+}
+
+dev.off() 
+
+cat("Success", paste(rowIDs,collapse="_"),sep=":")
+