Mercurial > repos > davidvanzessen > shm_csr

comparison shm_csr.r @ 3:275ab5175fd6 draft

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Uploaded
author davidvanzessen
date Thu, 27 Oct 2016 09:40:45 -0400
parents e85fec274cde
children 477e95b098fd
comparison
equal deleted inserted replaced
2:e85fec274cde 3:275ab5175fd6
412 dat.clss = rbind(dat, dat.clss) 412 dat.clss = rbind(dat, dat.clss)
413 413
414 p = ggplot(dat.clss, aes(best_match, percentage_mutations)) 414 p = ggplot(dat.clss, aes(best_match, percentage_mutations))
415 p = p + geom_point(aes(colour=best_match), position="jitter") + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA) 415 p = p + geom_point(aes(colour=best_match), position="jitter") + geom_boxplot(aes(middle=mean(percentage_mutations)), alpha=0.1, outlier.shape = NA)
416 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")) 416 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"))
417 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")) 417 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"))
418 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")) 418 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"))
419 419
420 png(filename="scatter.png") 420 png(filename="scatter.png")
421 print(p) 421 print(p)
422 dev.off() 422 dev.off()
423 423
439 439
440 frequency_bins_data$frequency = round(frequency_bins_data$frequency_count / frequency_bins_data$class_sum * 100, 2) 440 frequency_bins_data$frequency = round(frequency_bins_data$frequency_count / frequency_bins_data$class_sum * 100, 2)
441 441
442 p = ggplot(frequency_bins_data, aes(frequency_bins, frequency)) 442 p = ggplot(frequency_bins_data, aes(frequency_bins, frequency))
443 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")) 443 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"))
444 p = p + xlab("Frequency ranges") + ylab("Frequency") + ggtitle("Mutation Frequencies by class") + scale_fill_manual(values=c("IGA" = "blue4", "IGG" = "olivedrab3", "IGM" = "black")) 444 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"))
445 445
446 png(filename="frequency_ranges.png") 446 png(filename="frequency_ranges.png")
447 print(p) 447 print(p)
448 dev.off() 448 dev.off()
449 449