--- a/pattern_plots.r	Tue Dec 20 09:03:15 2016 -0500
+++ b/pattern_plots.r	Thu Dec 22 09:39:27 2016 -0500
@@ -56,10 +56,10 @@
 
 write.table(data1, plot1.txt, quote=F, sep="\t", na="", row.names=F, col.names=T)
 
-p = ggplot(data1, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of mutations") + guides(fill=guide_legend(title=NULL))
+p = ggplot(data1, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of mutations") + guides(fill=guide_legend(title=NULL)) + ggtitle("Percentage of mutations in AID and pol eta motives")
 p = p + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_manual(values=c("RGYW.WRCY" = "white", "TW.WA" = "blue4"))
 #p = p + scale_colour_manual(values=c("RGYW.WRCY" = "black", "TW.WA" = "blue4"))
-png(filename=plot1.png, width=480, height=300)
+png(filename=plot1.png, width=510, height=300)
 print(p)
 dev.off()
 
@@ -93,7 +93,7 @@
 
 write.table(data2, plot2.txt, quote=F, sep="\t", na="", row.names=F, col.names=T)
 
-p = ggplot(data2, aes(x=Class, y=value, fill=Type)) + geom_bar(position="fill", stat="identity", colour = "black") + scale_y_continuous(labels=percent_format()) + guides(fill=guide_legend(title=NULL)) + ylab("% of mutations")
+p = ggplot(data2, aes(x=Class, y=value, fill=Type)) + geom_bar(position="fill", stat="identity", colour = "black") + scale_y_continuous(labels=percent_format()) + guides(fill=guide_legend(title=NULL)) + ylab("% of mutations") + ggtitle("Relative mutation patterns")
 p = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "white"))
 #p = p + scale_colour_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "black"))
 png(filename=plot2.png, width=480, height=300)
@@ -122,7 +122,7 @@
 data3 = melt(t(data3[8:10,]))
 names(data3) = c("Class", "Type", "value")
 
-chk = is.na(data1$data3)
+chk = is.na(data3$value)
 if(any(chk)){
 	data3[chk, "value"] = 0
 }
@@ -131,7 +131,7 @@
 
 write.table(data3, plot3.txt, quote=F, sep="\t", na="", row.names=F, col.names=T)
 
-p = ggplot(data3, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of nucleotides") + guides(fill=guide_legend(title=NULL))
+p = ggplot(data3, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge", colour = "black") + ylab("% of nucleotides") + guides(fill=guide_legend(title=NULL)) + ggtitle("Absolute mutation patterns")
 p = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=15, colour="black"), axis.text.x = element_text(angle = 45, hjust = 1)) + scale_fill_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "white"))
 #p = p + scale_colour_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "black"))
 png(filename=plot3.png, width=480, height=300)