--- a/shm_csr.r	Mon Oct 31 05:05:26 2016 -0400
+++ b/shm_csr.r	Tue Nov 01 10:15:37 2016 -0400
@@ -280,15 +280,13 @@
 		transition2 = merge(transition2, base.order, by.x="variable", by.y="base")
 
 		transition2[is.na(transition2$value),]$value = 0
-		
-		print(transition2)
 
 		if(any(transition2$value != 0)){ #having rows of data but a transition table filled with 0 is bad
 			print("Plotting stacked transition")
 			png(filename=paste("transitions_stacked_", name, ".png", sep=""))
 			p = ggplot(transition2, aes(factor(reorder(id, order.x)), y=value, fill=factor(reorder(variable, order.y)))) + geom_bar(position="fill", stat="identity", colour="black") #stacked bar
 			p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base") + guides(fill=guide_legend(title=NULL))
-			p = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black")) + scale_fill_manual(values=c("A" = "blue4", "G" = "lightblue1", "C" = "olivedrab3", "T" = "olivedrab4"))
+			p = p + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black")) + scale_fill_manual(values=c("A" = "blue4", "G" = "lightblue1", "C" = "olivedrab3", "T" = "olivedrab4"))
 			#p = p + scale_colour_manual(values=c("A" = "black", "G" = "black", "C" = "black", "T" = "black"))
 			print(p)
 			dev.off()
@@ -374,7 +372,7 @@
 	pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=Gene))
 	pc = pc + geom_bar(width = 1, stat = "identity") + scale_fill_manual(labels=genesForPlot$label, values=c("IGA1" = "lightblue1", "IGA2" = "blue4"))
 	pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL)
-	pc = pc + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black"))
+	pc = pc + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black"), axis.title=element_blank(), axis.text=element_blank(), axis.ticks=element_blank())
 	pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGA subclasses", "( n =", sum(genesForPlot$Freq), ")"))
 	write.table(genesForPlot, "IGA_pie.txt", sep="\t",quote=F,row.names=F,col.names=T)
 
@@ -395,7 +393,7 @@
 	pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=Gene))
 	pc = pc + geom_bar(width = 1, stat = "identity") + scale_fill_manual(labels=genesForPlot$label, values=c("IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred"))
 	pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL)
-	pc = pc + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black"))
+	pc = pc + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black"), axis.title=element_blank(), axis.text=element_blank(), axis.ticks=element_blank())
 	pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGG subclasses", "( n =", sum(genesForPlot$Freq), ")"))
 	write.table(genesForPlot, "IGG_pie.txt", sep="\t",quote=F,row.names=F,col.names=T)
 
@@ -415,7 +413,7 @@
 
 p = ggplot(dat.clss, aes(best_match, percentage_mutations))
 p = p + geom_point(aes(colour=best_match), position="jitter") + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA)
-p = p + xlab("Subclass") + ylab("Frequency") + ggtitle("Frequency scatter plot") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black"))
+p = p + xlab("Subclass") + ylab("Frequency") + ggtitle("Frequency scatter plot") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black"))
 p = p + scale_fill_manual(values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet", "all" = "blue4"))
 p = p + scale_colour_manual(values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet", "all" = "blue4"))
 
@@ -442,7 +440,7 @@
 frequency_bins_data$frequency = round(frequency_bins_data$frequency_count / frequency_bins_data$class_sum * 100, 2)
 
 p = ggplot(frequency_bins_data, aes(frequency_bins, frequency))
-p = p + geom_bar(aes(fill=best_match_class), stat="identity", position="dodge") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black"))
+p = p + geom_bar(aes(fill=best_match_class), stat="identity", position="dodge") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black"))
 p = p + xlab("Frequency ranges") + ylab("Frequency") + ggtitle("Mutation Frequencies by class") + scale_fill_manual(values=c("IGA" = "blue4", "IGG" = "olivedrab3", "IGM" = "black", "all" = "blue4"))
 
 png(filename="frequency_ranges.png")