--- a/pattern_plots.r	Mon Oct 31 05:05:26 2016 -0400
+++ b/pattern_plots.r	Tue Nov 01 10:15:37 2016 -0400
@@ -22,7 +22,7 @@
 
 
 
-classes = c("IGA", "IGA1", "IGA2", "IGG", "IGG1", "IGG2", "IGG3", "IGG4", "IGM")
+classes = c("IGA", "IGA1", "IGA2", "IGG", "IGG1", "IGG2", "IGG3", "IGG4", "IGM", "IGE")
 xyz = c("x", "y", "z")
 new.names = c(paste(rep(classes, each=3), xyz, sep="."), paste("un", xyz, sep="."), paste("all", xyz, sep="."))
 
@@ -45,7 +45,7 @@
 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 = p + theme(panel.background = element_rect(fill = "white", colour="black"),text = element_text(size=13, colour="black")) + scale_fill_manual(values=c("RGYW.WRCY" = "white", "TW.WA" = "blue4"))
+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)
 print(p)
@@ -79,7 +79,7 @@
 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 = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) + scale_fill_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "white"))
+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)
 print(p)
@@ -115,7 +115,7 @@
 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 = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) + scale_fill_manual(values=c("A/T" = "blue4", "G/C transversions" = "gray74", "G/C transitions" = "white"))
+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)
 print(p)