Mercurial > repos > davidvanzessen > mutation_analysis

comparison sequence_overview.r @ 76:becea91089ed draft

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author davidvanzessen
date Mon, 09 May 2016 03:45:39 -0400
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children c5c86d15cb94
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75:14749ced7ff2 76:becea91089ed
1 library(reshape2)
2
3 args <- commandArgs(trailingOnly = TRUE)
4
5 gene.matches = args[1]
6 sequence.file = args[2]
7 outputdir = args[3]
8 main.html = "index.html"
9
10 setwd(outputdir)
11
12 genes = read.table(gene.matches, header=T, sep="\t", fill=T)
13 sequences = read.table(sequence.file, header=T, sep="\t", fill=T, stringsAsFactors=F, quote="")
14
15 dat = merge(sequences, genes, by="Sequence.ID")
16
17 dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT, dat$FR2.IMGT, dat$FR3.IMGT)
18
19 IDs = dat[,c("Sequence.ID", "seq_conc", "best_match")]
20 IDs$best_match = as.character(IDs$best_match)
21
22 #dat = data.frame(data.table(dat)[, list(freq=.N), by=c("best_match", "seq_conc")])
23
24 dat = data.frame(table(dat$best_match, dat$seq_conc))
25
26 dat = dat[dat$Freq > 1,]
27
28 names(dat) = c("best_match", "seq_conc", "Freq")
29
30 dat$seq_conc = factor(dat$seq_conc)
31
32 dat = dat[order(nchar(as.character(dat$seq_conc))),]
33
34 #writing html from R...
35 td = function(val) { paste("<td>", val, "</td>", sep="") }
36 tr = function(val) { capture.output(cat("<tr>", td(val), "</tr>", sep="")) }
37 make.link = function(id, clss, val) { paste("<a href='", clss, "_", id, ".html'>", val, "</a>", sep="") }
38 tbl = function(df) { res = "<table border='1'>"; for(i in 1:nrow(df)){ res = paste(res, tr(df[i,]), sep=""); }; res = paste(res, "</table>"); }
39
40 cat("<table border='1'>", file=main.html, append=F)
41 cat("<tr><th>Sequence</th><th>ca1</th><th>ca2</th><th>cg1</th><th>cg2</th><th>cg3</th><th>cg4</th><th>cm</th></tr>", file=main.html, append=T)
42
43 for(i in 1:nrow(dat)){
44 ca1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca1",]
45 ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca2",]
46
47 cg1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg1",]
48 cg2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg2",]
49 cg3 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg3",]
50 cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg4",]
51
52 cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cm",]
53
54 id = as.numeric(dat[i,"seq_conc"])
55
56 if(nrow(ca1) > 0){
57 cat(tbl(ca1), file=paste("ca1_", id, ".html", sep=""))
58 }
59
60 if(nrow(ca2) > 0){
61 cat(tbl(ca2), file=paste("ca2_", id, ".html", sep=""))
62 }
63
64 if(nrow(cg1) > 0){
65 cat(tbl(cg1), file=paste("cg1_", id, ".html", sep=""))
66 }
67
68 if(nrow(cg2) > 0){
69 cat(tbl(cg2), file=paste("cg2_", id, ".html", sep=""))
70 }
71
72 if(nrow(cg3) > 0){
73 cat(tbl(cg3), file=paste("cg3_", id, ".html", sep=""))
74 }
75
76 if(nrow(cg4) > 0){
77 cat(tbl(cg4), file=paste("cg4_", id, ".html", sep=""))
78 }
79
80 if(nrow(cm) > 0){
81 cat(tbl(cm), file=paste("cm_", id, ".html", sep=""))
82 }
83
84 ca1.html = make.link(id, "ca1", nrow(ca1))
85 ca2.html = make.link(id, "ca2", nrow(ca2))
86
87 cg1.html = make.link(id, "cg1", nrow(cg1))
88 cg2.html = make.link(id, "cg2", nrow(cg2))
89 cg3.html = make.link(id, "cg3", nrow(cg3))
90 cg4.html = make.link(id, "cg4", nrow(cg4))
91
92 cm.html = make.link(id, "cm", nrow(cm))
93
94 rw = c(as.character(dat[i,"seq_conc"]), ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html)
95
96 cat(tr(rw), file=main.html, append=T)
97 }
98
99 cat("</table>", file=main.html, append=T)