Mercurial > repos > davidvanzessen > mutation_analysis

comparison mutation_analysis.r @ 119:626a956f3811 draft

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author davidvanzessen
date Thu, 11 Aug 2016 10:35:52 -0400
parents ad7ca9c2b748
children 613278c1bde0
comparison
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118:ad7ca9c2b748 119:626a956f3811
274 transition2 = merge(transition2, base.order, by.x="id", by.y="base") 274 transition2 = merge(transition2, base.order, by.x="id", by.y="base")
275 transition2 = merge(transition2, base.order, by.x="variable", by.y="base") 275 transition2 = merge(transition2, base.order, by.x="variable", by.y="base")
276 276
277 transition2[is.na(transition2$value),]$value = 0 277 transition2[is.na(transition2$value),]$value = 0
278 278
279 png(filename=paste("transitions_stacked_", name, ".png", sep="")) 279 if(!all(transition2$value == 0)){ #having rows of data but a transition table filled with 0 is bad
280 p = ggplot(transition2, aes(factor(reorder(id, order.x)), y=value, fill=factor(reorder(variable, order.y)))) + geom_bar(position="fill", stat="identity") #stacked bar 280
281 p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base") + guides(fill=guide_legend(title=NULL)) 281 print("Plotting stacked transition")
282 print(p) 282
283 dev.off() 283 print(transition2)
284 284
285 png(filename=paste("transitions_heatmap_", name, ".png", sep="")) 285 png(filename=paste("transitions_stacked_", name, ".png", sep=""))
286 p = ggplot(transition2, aes(factor(reorder(id, order.x)), factor(reorder(variable, order.y)))) + geom_tile(aes(fill = value), colour="white") + scale_fill_gradient(low="white", high="steelblue") #heatmap 286 p = ggplot(transition2, aes(factor(reorder(id, order.x)), y=value, fill=factor(reorder(variable, order.y)))) + geom_bar(position="fill", stat="identity") #stacked bar
287 p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base") 287 p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base") + guides(fill=guide_legend(title=NULL))
288 print(p) 288 print(p)
289 dev.off() 289 dev.off()
290
291 print("Plotting heatmap transition")
292
293 png(filename=paste("transitions_heatmap_", name, ".png", sep=""))
294 p = ggplot(transition2, aes(factor(reorder(id, order.x)), factor(reorder(variable, order.y)))) + geom_tile(aes(fill = value), colour="white") + scale_fill_gradient(low="white", high="steelblue") #heatmap
295 p = p + xlab("From base") + ylab("To base") + ggtitle("Mutations frequency from base to base")
296 print(p)
297 dev.off()
298 } else {
299 print("No data to plot")
300 }
290 } 301 }
291 302
292 #print(paste("writing value file: ", name, "_", fname, "_value.txt" ,sep="")) 303 #print(paste("writing value file: ", name, "_", fname, "_value.txt" ,sep=""))
293 304
294 write.table(x=transitionTable, file=paste("transitions_", name ,"_", fname, ".txt", sep=""), sep=",",quote=F,row.names=T,col.names=NA) 305 write.table(x=transitionTable, file=paste("transitions_", name ,"_", fname, ".txt", sep=""), sep=",",quote=F,row.names=T,col.names=NA)