--- a/aa_histogram.r	Tue Dec 20 09:03:15 2016 -0500
+++ b/aa_histogram.r	Thu Dec 22 09:39:27 2016 -0500
@@ -15,9 +15,12 @@
 absent.aa.by.id = read.table(absent.aa.by.id.file, sep="\t", fill=T, header=T, quote="")
 
 for(gene in genes){
+	graph.title = paste(gene, "AA mutation frequency")
 	if(gene == ""){
 		mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),]
 		absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),]
+		
+		graph.title = "AA mutation frequency all"
 	} else {
 		mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),]
 		absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),]
@@ -33,6 +36,7 @@
 	dat_freq = mutations.at.position / aa.at.position
 	dat_freq[is.na(dat_freq)] = 0
 	dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq)
+	
 
 	print("---------------- plot ----------------")
 
@@ -43,7 +47,7 @@
 	m = m + annotate("segment", x = 38.5, y = -0.05, xend=55.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 47, y = -0.1, label="FR2")
 	m = m + annotate("segment", x = 55.5, y = -0.07, xend=65.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 60.5, y = -0.15, label="CDR2")
 	m = m + annotate("segment", x = 65.5, y = -0.05, xend=104.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 85, y = -0.1, label="FR3")
-	m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency")) 
+	m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(graph.title) 
 	m = m + theme(panel.background = element_rect(fill = "white", colour="black"), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank())
 	#m = m + scale_colour_manual(values=c("black"))