--- a/RScript.r	Fri Nov 08 06:51:37 2013 -0500
+++ b/RScript.r	Fri Nov 08 06:54:21 2013 -0500
@@ -115,7 +115,7 @@
 	img = ggplot() + 
 	geom_tile(data=dat, aes(x=factor(reorder(Top.D.Gene, chr.orderD)), y=factor(reorder(Top.V.Gene, chr.orderV)), fill=log)) + 
 	theme(axis.text.x = element_text(angle = 90, hjust = 1)) + 
-	scale_fill_gradient(low="gold", high="blue", na.value="white", limits=c(0, maxVD)) + 
+	scale_fill_gradient(low="gold", high="blue", na.value="white") + 
 	ggtitle(paste(unique(dat$Sample), " (N=" , sum(dat[!is.na(dat[,4]),][4]) ,")", sep="")) + 
 	xlab("D genes") + 
 	ylab("V Genes")
@@ -126,16 +126,11 @@
 }
 
 VandDCount = data.frame(data.table(PRODF)[, list(Length=.N), by=c("Top.V.Gene", "Top.D.Gene", "Sample")])
-
-
-
-
 cartegianProductVD = expand.grid(Top.V.Gene = Vchain$v.name, Top.D.Gene = Dchain$v.name, Sample = unique(test$Sample))
 
 completeVD = merge(VandDCount, cartegianProductVD, all.y=TRUE)
 completeVD$Length = as.numeric(completeVD$Length)
 completeVD$log = log(completeVD$Length)
-maxVD = max(subset(completeVD, !is.na(completeVD$log), "log"))
 completeVD = merge(completeVD, Vchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
 completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
 #completeVD$log[is.na(completeVD$log)] = 0