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comparison sequence_overview.r @ 79:0513b46178c4 draft

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Uploaded
author davidvanzessen
date Thu, 12 May 2016 07:35:07 -0400
parents b523ce95d857
children a778156dad3d
comparison
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78:b523ce95d857 79:0513b46178c4
19 IDs = dat[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")] 19 IDs = dat[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")]
20 IDs$best_match = as.character(IDs$best_match) 20 IDs$best_match = as.character(IDs$best_match)
21 21
22 #dat = data.frame(data.table(dat)[, list(freq=.N), by=c("best_match", "seq_conc")]) 22 #dat = data.frame(data.table(dat)[, list(freq=.N), by=c("best_match", "seq_conc")])
23 23
24 dat = data.frame(table(dat$best_match, dat$seq_conc)) 24 dat = data.frame(table(dat$best_match, dat$seq_conc, dat$Functionality))
25 25
26 dat = dat[dat$Freq > 1,] 26 dat = dat[dat$Freq > 1,]
27 27
28 names(dat) = c("best_match", "seq_conc", "Freq") 28 names(dat) = c("best_match", "seq_conc", "Functionality", "Freq")
29 29
30 dat$seq_conc = factor(dat$seq_conc) 30 dat$seq_conc = factor(dat$seq_conc)
31 31
32 dat = dat[order(nchar(as.character(dat$seq_conc))),] 32 dat = dat[order(nchar(as.character(dat$seq_conc))),]
33 33
37 make.link = function(id, clss, val) { paste("<a href='", clss, "_", id, ".html'>", val, "</a>", sep="") } 37 make.link = function(id, clss, val) { paste("<a href='", clss, "_", id, ".html'>", val, "</a>", sep="") }
38 tbl = function(df) { res = "<table border='1'>"; for(i in 1:nrow(df)){ res = paste(res, tr(df[i,]), sep=""); }; res = paste(res, "</table>"); } 38 tbl = function(df) { res = "<table border='1'>"; for(i in 1:nrow(df)){ res = paste(res, tr(df[i,]), sep=""); }; res = paste(res, "</table>"); }
39 39
40 cat("<table border='1'>", file=main.html, append=F) 40 cat("<table border='1'>", file=main.html, append=F)
41 cat("<caption>CDR1+CDR2+CDR3+FR2+FR3 sequences that show up more than once</caption>", file=main.html, append=T) 41 cat("<caption>CDR1+CDR2+CDR3+FR2+FR3 sequences that show up more than once</caption>", file=main.html, append=T)
42 cat("<tr><th>Sequence</th><th>ca1</th><th>ca2</th><th>cg1</th><th>cg2</th><th>cg3</th><th>cg4</th><th>cm</th></tr>", file=main.html, append=T) 42 cat("<tr><th>Sequence</th><th>Functionality</th><th>ca1</th><th>ca2</th><th>cg1</th><th>cg2</th><th>cg3</th><th>cg4</th><th>cm</th></tr>", file=main.html, append=T)
43 43
44 for(i in 1:nrow(dat)){ 44 for(i in 1:nrow(dat)){
45 ca1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca1",] 45 ca1 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca1",]
46 ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca2",] 46 ca2 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "ca2",]
47 47
51 cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg4",] 51 cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cg4",]
52 52
53 cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cm",] 53 cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & IDs$best_match == "cm",]
54 54
55 id = as.numeric(dat[i,"seq_conc"]) 55 id = as.numeric(dat[i,"seq_conc"])
56
57 functionality = dat[i,"Functionality"]
56 58
57 if(nrow(ca1) > 0){ 59 if(nrow(ca1) > 0){
58 cat(tbl(ca1), file=paste("ca1_", id, ".html", sep="")) 60 cat(tbl(ca1), file=paste("ca1_", id, ".html", sep=""))
59 } 61 }
60 62
90 cg3.html = make.link(id, "cg3", nrow(cg3)) 92 cg3.html = make.link(id, "cg3", nrow(cg3))
91 cg4.html = make.link(id, "cg4", nrow(cg4)) 93 cg4.html = make.link(id, "cg4", nrow(cg4))
92 94
93 cm.html = make.link(id, "cm", nrow(cm)) 95 cm.html = make.link(id, "cm", nrow(cm))
94 96
95 rw = c(as.character(dat[i,"seq_conc"]), ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html) 97 rw = c(as.character(dat[i,"seq_conc"]), as.character(functionality), ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html)
96 98
97 cat(tr(rw), file=main.html, append=T) 99 cat(tr(rw), file=main.html, append=T)
98 } 100 }
99 101
100 cat("</table>", file=main.html, append=T) 102 cat("</table>", file=main.html, append=T)