--- a/aa_histogram.r	Wed Jun 22 10:07:28 2016 -0400
+++ b/aa_histogram.r	Thu Jun 23 03:58:03 2016 -0400
@@ -20,20 +20,8 @@
 dat_freq = mutations.at.position / aa.at.position
 dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq)
 
-print("---------------- weird stuff ----------------")
-
-options(width=220)
-
-print(dat[,20:40])
-
-print(dat_dt) #need this or it will fail????
-
 print("---------------- plot ----------------")
 
-#also need these two, I don't even know...
-print(paste("dat_freq", length(dat_freq)))
-print(paste("dat_dt", nrow(dat_dt)))
-
 m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1))
 m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=1:length(dat_freq), labels=1:length(dat_freq))
 m = m + annotate("segment", x = 0.5, y = -0.05, xend=26.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 13, y = -0.1, label="FR1")
@@ -45,9 +33,7 @@
 
 print("---------------- write/print ----------------")
 
-print("writing dat_dt") #need this
 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)
 dev.off()