changeset 5:021d293121bb draft

Uploaded
author davidvanzessen
date Mon, 14 Oct 2013 09:49:29 -0400
parents 10cfa5e9186e
children f9a657db7af5
files RScript.r
diffstat 1 files changed, 12 insertions(+), 3 deletions(-) [+]
line wrap: on
line diff
--- a/RScript.r	Mon Oct 14 08:12:41 2013 -0400
+++ b/RScript.r	Mon Oct 14 09:49:29 2013 -0400
@@ -108,8 +108,9 @@
 
 
 plotVD <- function(dat){
+	#dat = dat[order(dat[,8],dat[,9]),]
 	img = ggplot() + 
-	geom_tile(data=dat, aes(x=factor(Top.D.Gene), y=factor(Top.V.Gene), fill=log)) + 
+	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") + 
 	ggtitle(unique(dat$Sample)) + 
@@ -128,6 +129,8 @@
 completeVD = merge(VandDCount, cartegianProductVD, all.y=TRUE)
 completeVD$Length = as.numeric(completeVD$Length)
 completeVD$log = log(completeVD$Length)
+completeVD = merge(completeVD, Vchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
+completeVD = merge(completeVD, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
 #completeVD$log[is.na(completeVD$log)] = 0
 l = split(completeVD, f=completeVD[,"Sample"])
 
@@ -136,8 +139,9 @@
 
 
 plotVJ <- function(dat){
+	#dat = dat[order(dat[,8],dat[,9]),]
 	img = ggplot() + 
-	geom_tile(data=dat, aes(x=factor(Top.J.Gene), y=factor(Top.V.Gene), fill=log)) + 
+	geom_tile(data=dat, aes(x=factor(reorder(Top.J.Gene, chr.orderJ)), 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") + 
 	ggtitle(unique(dat$Sample)) + 
@@ -155,13 +159,16 @@
 completeVJ = merge(VandJCount, cartegianProductVJ, all.y=TRUE)
 completeVJ$Length = as.numeric(completeVJ$Length)
 completeVJ$log = log(completeVJ$Length)
+completeVJ = merge(completeVJ, Vchain, by.x="Top.V.Gene", by.y="v.name", all.x=TRUE)
+completeVJ = merge(completeVJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
 #completeVJ$log[is.na(completeVJ$log)] = 0
 l = split(completeVJ, f=completeVJ[,"Sample"])
 lapply(l, FUN=plotVJ)
 
 plotDJ <- function(dat){
+	#dat = dat[order(dat[,8],dat[,9]),]
 	img = ggplot() + 
-	geom_tile(data=dat, aes(x=factor(Top.J.Gene), y=factor(Top.D.Gene), fill=log)) + 
+	geom_tile(data=dat, aes(x=factor(reorder(Top.J.Gene, chr.orderJ)), y=factor(reorder(Top.D.Gene, chr.orderD)), fill=log)) + 
 	theme(axis.text.x = element_text(angle = 90, hjust = 1)) + 
 	scale_fill_gradient(low="gold", high="blue", na.value="white") + 
 	ggtitle(unique(dat$Sample)) + 
@@ -179,6 +186,8 @@
 completeDJ = merge(DandJCount, cartegianProductDJ, all.y=TRUE)
 completeDJ$Length = as.numeric(completeDJ$Length)
 completeDJ$log = log(completeDJ$Length)
+completeDJ = merge(completeDJ, Dchain, by.x="Top.D.Gene", by.y="v.name", all.x=TRUE)
+completeDJ = merge(completeDJ, Jchain, by.x="Top.J.Gene", by.y="v.name", all.x=TRUE)
 #completeDJ$log[is.na(completeDJ$log)] = 0
 l = split(completeDJ, f=completeDJ[,"Sample"])
 lapply(l, FUN=plotDJ)