--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mlmm/source_library/plot_MLMM.Ago.r	Thu Jul 02 05:42:38 2015 -0400
@@ -0,0 +1,36 @@
+## fonction ###########################################################################
+plot_MLMM.Ago<-function(x) {
+	output1 <-x$out[order(x$out$Pos),]
+	output_ok<-output1[order(output1$Chr),]
+
+	maxpos<-c(0,cumsum(as.numeric(aggregate(output_ok$Pos,list(output_ok$Chr),max)$x+max(cumsum(as.numeric(aggregate(output_ok$Pos,list(output_ok$Chr),max)$x)))/200)))
+	plot_col<-rep(c('gray10','gray60'),ceiling(max(unique(output_ok$Chr))/2))
+#	plot_col<-c('blue','darkgreen','red','cyan','purple')
+	size<-aggregate(output_ok$Pos,list(output_ok$Chr),length)$x
+	a<-rep(maxpos[1],size[1])
+	b<-rep(plot_col[1],size[1])
+		for (i in 2:max(unique(output_ok$Chr))){
+	a<-c(a,rep(maxpos[i],size[i]))
+	b<-c(b,rep(plot_col[i],size[i]))}
+
+	output_ok$xpos<-output_ok$Pos+a
+	output_ok$col<-b
+	output_ok$col[output_ok$mk=='qtl']<-'cyan'
+	output_ok$col[output_ok$SNP %in% x$cof]<-'red'
+
+	d<-(aggregate(output_ok$xpos,list(output_ok$Chr),min)$x+aggregate(output_ok$xpos,list(output_ok$Chr),max)$x)/2
+
+	plot(output_ok$xpos,-log10(output_ok$pval),col=output_ok$col,pch=20,ylab='-log10(pval)',xaxt='n',xlab='chromosome')
+	axis(1,tick=FALSE,at=d,labels=c(1:max(unique(output_ok$Chr))))
+  xline(output_ok$xpos[output_ok$mk=='qtl'], col='cyan', lwd=0.1)
+	abline(h=x$bonf_thresh,lty=3,col='black')
+
+
+    if (length(output_ok$pval[-log10(output_ok$pval) > x$bonf_thresh]) > 0) {
+      text(output_ok$xpos[-log10(output_ok$pval) > x$bonf_thresh], -log10(output_ok$pval[-log10(output_ok$pval) > x$bonf_thresh]), output_ok$SNP[-log10(output_ok$pval) > x$bonf_thresh], pos=3, cex=0.7)
+      legend("topright", lty=3, paste("bonf thresh :", x$bonf_thresh ,sep=" "))
+      } else {
+      legend("topright", lty=3, paste("bonf thresh :", x$bonf_thresh ,sep=" "))
+      }
+
+}