Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.r @ 39:a24f8c93583a draft

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author davidvanzessen
date Thu, 22 Dec 2016 09:39:27 -0500
parents 8d1c4c75f81b
children 1cf60ae234b4
comparison
equal deleted inserted replaced
38:05c62efdc393 39:a24f8c93583a
300 300
301 if(any(transition2$value != 0)){ #having a transition table filled with 0 is bad 301 if(any(transition2$value != 0)){ #having a transition table filled with 0 is bad
302 print("Plotting heatmap and transition") 302 print("Plotting heatmap and transition")
303 png(filename=paste("transitions_stacked_", name, ".png", sep="")) 303 png(filename=paste("transitions_stacked_", name, ".png", sep=""))
304 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 304 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
305 p = p + xlab("From base") + ylab("") + ggtitle("Mutations frequency from base to base") + guides(fill=guide_legend(title=NULL)) 305 p = p + xlab("From base") + ylab("") + ggtitle("Bargraph transition information") + guides(fill=guide_legend(title=NULL))
306 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")) 306 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"))
307 #p = p + scale_colour_manual(values=c("A" = "black", "G" = "black", "C" = "black", "T" = "black")) 307 #p = p + scale_colour_manual(values=c("A" = "black", "G" = "black", "C" = "black", "T" = "black"))
308 print(p) 308 print(p)
309 dev.off() 309 dev.off()
310 png(filename=paste("transitions_heatmap_", name, ".png", sep="")) 310 png(filename=paste("transitions_heatmap_", name, ".png", sep=""))
311 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 311 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
312 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")) 312 p = p + xlab("To base") + ylab("From Base") + ggtitle("Heatmap transition information") + theme(panel.background = element_rect(fill = "white", colour="black"), text = element_text(size=16, colour="black"))
313 print(p) 313 print(p)
314 dev.off() 314 dev.off()
315 } else { 315 } else {
316 #print("No data to plot") 316 #print("No data to plot")
317 } 317 }
386 386
387 pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=Gene)) 387 pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=Gene))
388 pc = pc + geom_bar(width = 1, stat = "identity") + scale_fill_manual(labels=genesForPlot$label, values=c("IGA1" = "lightblue1", "IGA2" = "blue4")) 388 pc = pc + geom_bar(width = 1, stat = "identity") + scale_fill_manual(labels=genesForPlot$label, values=c("IGA1" = "lightblue1", "IGA2" = "blue4"))
389 pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL) 389 pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL)
390 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()) 390 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())
391 pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGA subclasses", "( n =", sum(genesForPlot$Freq), ")")) 391 pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGA subclass distribution", "( n =", sum(genesForPlot$Freq), ")"))
392 write.table(genesForPlot, "IGA_pie.txt", sep="\t",quote=F,row.names=F,col.names=T) 392 write.table(genesForPlot, "IGA_pie.txt", sep="\t",quote=F,row.names=F,col.names=T)
393 393
394 png(filename="IGA.png") 394 png(filename="IGA.png")
395 print(pc) 395 print(pc)
396 dev.off() 396 dev.off()
407 407
408 pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=Gene)) 408 pc = ggplot(genesForPlot, aes(x = factor(1), y=Freq, fill=Gene))
409 pc = pc + geom_bar(width = 1, stat = "identity") + scale_fill_manual(labels=genesForPlot$label, values=c("IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred")) 409 pc = pc + geom_bar(width = 1, stat = "identity") + scale_fill_manual(labels=genesForPlot$label, values=c("IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred"))
410 pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL) 410 pc = pc + coord_polar(theta="y") + scale_y_continuous(breaks=NULL)
411 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()) 411 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())
412 pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGG subclasses", "( n =", sum(genesForPlot$Freq), ")")) 412 pc = pc + xlab(" ") + ylab(" ") + ggtitle(paste("IGG subclass distribution", "( n =", sum(genesForPlot$Freq), ")"))
413 write.table(genesForPlot, "IGG_pie.txt", sep="\t",quote=F,row.names=F,col.names=T) 413 write.table(genesForPlot, "IGG_pie.txt", sep="\t",quote=F,row.names=F,col.names=T)
414 414
415 png(filename="IGG.png") 415 png(filename="IGG.png")
416 print(pc) 416 print(pc)
417 dev.off() 417 dev.off()
428 428
429 p = ggplot(dat.clss, aes(best_match, percentage_mutations)) 429 p = ggplot(dat.clss, aes(best_match, percentage_mutations))
430 p = p + geom_point(aes(colour=best_match), position="jitter") + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA) 430 p = p + geom_point(aes(colour=best_match), position="jitter") + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA)
431 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")) 431 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"))
432 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", "IGE" = "darkorange", "all" = "blue4")) 432 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", "IGE" = "darkorange", "all" = "blue4"))
433 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", "IGE" = "darkorange", "all" = "blue4")) 433 p = p + scale_colour_manual(guide = guide_legend(title = "Subclass"), values=c("IGA" = "blue4", "IGA1" = "lightblue1", "IGA2" = "blue4", "IGG" = "olivedrab3", "IGG1" = "olivedrab3", "IGG2" = "red", "IGG3" = "gold", "IGG4" = "darkred", "IGM" = "darkviolet", "IGE" = "darkorange", "all" = "blue4"))
434 434
435 png(filename="scatter.png") 435 png(filename="scatter.png")
436 print(p) 436 print(p)
437 dev.off() 437 dev.off()
438 438
452 452
453 frequency_bins_data$frequency = round(frequency_bins_data$frequency_count / frequency_bins_data$class_sum * 100, 2) 453 frequency_bins_data$frequency = round(frequency_bins_data$frequency_count / frequency_bins_data$class_sum * 100, 2)
454 454
455 p = ggplot(frequency_bins_data, aes(frequency_bins, frequency)) 455 p = ggplot(frequency_bins_data, aes(frequency_bins, frequency))
456 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")) 456 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"))
457 p = p + xlab("Frequency ranges") + ylab("Frequency") + ggtitle("Mutation Frequencies by class") + scale_fill_manual(values=c("IGA" = "blue4", "IGG" = "olivedrab3", "IGM" = "darkviolet", "IGE" = "darkorange", "all" = "blue4")) 457 p = p + xlab("Frequency ranges") + ylab("Frequency") + ggtitle("Mutation Frequencies by class") + scale_fill_manual(guide = guide_legend(title = "Class"), values=c("IGA" = "blue4", "IGG" = "olivedrab3", "IGM" = "darkviolet", "IGE" = "darkorange", "all" = "blue4"))
458 458
459 png(filename="frequency_ranges.png") 459 png(filename="frequency_ranges.png")
460 print(p) 460 print(p)
461 dev.off() 461 dev.off()
462 462