Mercurial > repos > davidvanzessen > shm_csr

comparison aa_histogram.r @ 23:81453585dfc3 draft

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Uploaded
author davidvanzessen
date Thu, 01 Dec 2016 09:32:06 -0500
parents 0bea8c187a90
children 80c4eebf7bc9
comparison
equal deleted inserted replaced
22:0bea8c187a90 23:81453585dfc3
13 13
14 mutations.by.id = read.table(mutations.by.id.file, sep="\t", fill=T, header=T, quote="") 14 mutations.by.id = read.table(mutations.by.id.file, sep="\t", fill=T, header=T, quote="")
15 absent.aa.by.id = read.table(absent.aa.by.id.file, sep="\t", fill=T, header=T, quote="") 15 absent.aa.by.id = read.table(absent.aa.by.id.file, sep="\t", fill=T, header=T, quote="")
16 16
17 for(gene in genes){ 17 for(gene in genes){
18 if(gene == ""){
19 mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),]
20 absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),]
21 } else {
22 mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),]
23 absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),]
24 }
25 print(paste("nrow", gene, nrow(absent.aa.by.id.gene)))
26 if(nrow(mutations.by.id.gene) == 0){
27 next
28 }
18 29
19 if(gene == ""){ 30 mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)])
20 mutations.by.id.gene = mutations.by.id[!grepl("unmatched", mutations.by.id$best_match),] 31 aa.at.position = colSums(absent.aa.by.id.gene[,-c(1,2,3,4)])
21 absent.aa.by.id.gene = absent.aa.by.id[!grepl("unmatched", absent.aa.by.id$best_match),]
22 } else {
23 mutations.by.id.gene = mutations.by.id[grepl(paste("^", gene, sep=""), mutations.by.id$best_match),]
24 absent.aa.by.id.gene = absent.aa.by.id[grepl(paste("^", gene, sep=""), absent.aa.by.id$best_match),]
25 }
26 print(paste("nrow", gene, nrow(absent.aa.by.id.gene)))
27 if(nrow(mutations.by.id.gene) == 0){
28 next
29 }
30 32
31 mutations.at.position = colSums(mutations.by.id.gene[,-c(1,2)]) 33 dat_freq = mutations.at.position / aa.at.position
32 aa.at.position = colSums(absent.aa.by.id.gene[,-c(1,2,3,4)]) 34 dat_freq[is.na(dat_freq)] = 0
35 dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq)
33 36
34 dat_freq = mutations.at.position / aa.at.position 37 print("---------------- plot ----------------")
35 dat_freq[is.na(dat_freq)] = 0
36 dat_dt = data.frame(i=1:length(dat_freq), freq=dat_freq)
37 38
38 print("---------------- plot ----------------") 39 m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1), text = element_text(size=13, colour="black"))
40 m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=dat_dt$i, labels=dat_dt$i)
41 m = m + annotate("segment", x = 0.5, y = -0.05, xend=26.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 13, y = -0.1, label="FR1")
42 m = m + annotate("segment", x = 26.5, y = -0.07, xend=38.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 32.5, y = -0.15, label="CDR1")
43 m = m + annotate("segment", x = 38.5, y = -0.05, xend=55.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 47, y = -0.1, label="FR2")
44 m = m + annotate("segment", x = 55.5, y = -0.07, xend=65.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 60.5, y = -0.15, label="CDR2")
45 m = m + annotate("segment", x = 65.5, y = -0.05, xend=104.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 85, y = -0.1, label="FR3")
46 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency"))
47 m = m + theme(panel.background = element_rect(fill = "white", colour="black"), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank())
48 #m = m + scale_colour_manual(values=c("black"))
39 49
40 m = ggplot(dat_dt, aes(x=i, y=freq)) + theme(axis.text.x = element_text(angle = 90, hjust = 1), text = element_text(size=13, colour="black")) 50 print("---------------- write/print ----------------")
41 m = m + geom_bar(stat="identity", colour = "black", fill = "darkgrey", alpha=0.8) + scale_x_continuous(breaks=dat_dt$i, labels=dat_dt$i)
42 m = m + annotate("segment", x = 0.5, y = -0.05, xend=26.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 13, y = -0.1, label="FR1")
43 m = m + annotate("segment", x = 26.5, y = -0.07, xend=38.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 32.5, y = -0.15, label="CDR1")
44 m = m + annotate("segment", x = 38.5, y = -0.05, xend=55.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 47, y = -0.1, label="FR2")
45 m = m + annotate("segment", x = 55.5, y = -0.07, xend=65.5, yend=-0.07, colour="darkblue", size=1) + annotate("text", x = 60.5, y = -0.15, label="CDR2")
46 m = m + annotate("segment", x = 65.5, y = -0.05, xend=104.5, yend=-0.05, colour="darkgreen", size=1) + annotate("text", x = 85, y = -0.1, label="FR3")
47 m = m + expand_limits(y=c(-0.1,1)) + xlab("AA position") + ylab("Frequency") + ggtitle(paste(gene, "AA mutation frequency"))
48 m = m + theme(panel.background = element_rect(fill = "white", colour="black"), panel.grid.major.y = element_line(colour = "black"), panel.grid.major.x = element_blank())
49 m = m + scale_colour_manual(values=c("black"))
50
51 print("---------------- write/print ----------------")
52 51
53 52
54 dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position) 53 dat.sums = data.frame(index=1:length(mutations.at.position), mutations.at.position=mutations.at.position, aa.at.position=aa.at.position)
55 54
56 write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 55 write.table(dat.sums, paste(outdir, "/aa_histogram_sum_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
57 write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 56 write.table(mutations.by.id.gene, paste(outdir, "/aa_histogram_count_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
58 write.table(absent.aa.by.id.gene, paste(outdir, "/aa_histogram_absent_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 57 write.table(absent.aa.by.id.gene, paste(outdir, "/aa_histogram_absent_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
59 write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T) 58 write.table(dat_dt, paste(outdir, "/aa_histogram_", gene, ".txt", sep=""), sep="\t",quote=F,row.names=F,col.names=T)
60 59
61 png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720) 60 png(filename=paste(outdir, "/aa_histogram_", gene, ".png", sep=""), width=1280, height=720)
62 print(m) 61 print(m)
63 dev.off() 62 dev.off()
64 } 63 }