--- a/aa_histogram.r	Tue Jun 21 05:30:16 2016 -0400
+++ b/aa_histogram.r	Wed Jun 22 10:07:28 2016 -0400
@@ -4,6 +4,7 @@
 
 input = args[1]
 outfile = args[2]
+gene = args[3]
 
 print("---------------- read input ----------------")
 
@@ -40,12 +41,12 @@
 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("AA mutation frequency")
+m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency"))
 
 print("---------------- write/print ----------------")
 
 print("writing dat_dt") #need this
-write.table(dat_dt, paste(dirname(outfile), "/aa_histogram.txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
+write.table(dat_dt, paste(dirname(outfile), "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
 print("writing png") #also need this, file is haunted
 png(filename=outfile, width=1280, height=720)
 print(m)