comparison shm_csr.r @ 24:9955b23db68c draft

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23:81453585dfc3

setwd(outputdir)

write.table(dat, input, sep="\t",quote=F,row.names=F,col.names=T)

base.order = data.frame(base=c("A", "T", "C", "G"), order=1:4)

calculate_result = function(i, gene, dat, matrx, f, fname, name){
	tmp = dat[grepl(paste("^", gene, ".*", sep=""), dat$best_match),]

	j = i - 1

		transition = transitionTable
		transition$id = names(transition)
		
		transition2 = melt(transition, id.vars="id")

		transition2 = merge(transition2, base.order, by.x="id", by.y="base")

		transition2 = merge(transition2, base.order, by.x="variable", by.y="base")

		transition2[is.na(transition2$value),]$value = 0
		
		if(any(transition2$value != 0)){ #having rows of data but a transition table filled with 0 is bad
			print("Plotting heatmap and 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=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()
			png(filename=paste("transitions_heatmap_", name, ".png", sep=""))
			p = ggplot(transition2, aes(factor(reorder(id, order.x)), factor(reorder(variable, order.y)))) + geom_tile(aes(fill = value)) + scale_fill_gradient(low="white", high="steelblue") #heatmap
			p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base")  + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black"))
			print(p)
			dev.off()
		} else {
			#print("No data to plot")
		}

24:9955b23db68c

setwd(outputdir)

write.table(dat, input, sep="\t",quote=F,row.names=F,col.names=T)

base.order.x = data.frame(base=c("A", "C", "G", "T"), order.x=1:4)
base.order.y = data.frame(base=c("T", "G", "C", "A"), order.y=1:4)

calculate_result = function(i, gene, dat, matrx, f, fname, name){
	tmp = dat[grepl(paste("^", gene, ".*", sep=""), dat$best_match),]

	j = i - 1

		transition = transitionTable
		transition$id = names(transition)
		
		transition2 = melt(transition, id.vars="id")

		transition2 = merge(transition2, base.order.x, by.x="id", by.y="base")

		transition2 = merge(transition2, base.order.y, by.x="variable", by.y="base")

		transition2[is.na(transition2$value),]$value = 0
		
		if(any(transition2$value != 0)){ #having a transition table filled with 0 is bad
			print("Plotting heatmap and 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("") + 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=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()
			png(filename=paste("transitions_heatmap_", name, ".png", sep=""))
			p = ggplot(transition2, aes(factor(reorder(variable, -order.y)), factor(reorder(id, -order.x)))) + geom_tile(aes(fill = value)) + scale_fill_gradient(low="white", high="steelblue") #heatmap
			p = p + xlab("To base") + ylab("From Base") + ggtitle("Mutations frequency from base to base")  + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=13, colour="black"))
			print(p)
			dev.off()
		} else {
			#print("No data to plot")
		}