Mercurial > repos > davidvanzessen > mutation_analysis

comparison sequence_overview.r @ 106:074ae1e30e8f draft

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author davidvanzessen
date Wed, 29 Jun 2016 05:13:25 -0400
parents 603a10976e9c
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105:e4957ad476a2 106:074ae1e30e8f
70 cat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T) 70 cat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
71 cat("<tr>", file=main.html, append=T) 71 cat("<tr>", file=main.html, append=T)
72 cat("<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><th>un</th>", file=main.html, append=T) 72 cat("<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><th>un</th>", file=main.html, append=T)
73 cat("<th>total CA</th><th>total CG</th><th>number of subclasses</th><th>present in both Ca and Cg</th><th>Ca1+Ca2</th>", file=main.html, append=T) 73 cat("<th>total CA</th><th>total CG</th><th>number of subclasses</th><th>present in both Ca and Cg</th><th>Ca1+Ca2</th>", file=main.html, append=T)
74 cat("<th>Cg1+Cg2</th><th>Cg1+Cg3</th><th>Cg1+Cg4</th><th>Cg2+Cg3</th><th>Cg2+Cg4</th><th>Cg3+Cg4</th>", file=main.html, append=T) 74 cat("<th>Cg1+Cg2</th><th>Cg1+Cg3</th><th>Cg1+Cg4</th><th>Cg2+Cg3</th><th>Cg2+Cg4</th><th>Cg3+Cg4</th>", file=main.html, append=T)
75 cat("<th>Cg1+Cg2+Cg3</th><th>Cg2+Cg3+Cg4</th><th>Cg1+Cg2+Cg4</th><th>Cg1+Cg3+Cg4</th>", file=main.html, append=T) 75 cat("<th>Cg1+Cg2+Cg3</th><th>Cg2+Cg3+Cg4</th><th>Cg1+Cg2+Cg4</th><th>Cg1+Cg3+Cg4</th><th>Cg1+Cg2+Cg3+Cg4</th>", file=main.html, append=T)
76 cat("</tr>", file=main.html, append=T) 76 cat("</tr>", file=main.html, append=T)
77 77
78 78
79 79
80 single.sequences=0 #sequence only found once, skipped 80 single.sequences=0 #sequence only found once, skipped
210 in.cg1.cg2.cg3 = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0) 210 in.cg1.cg2.cg3 = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0)
211 in.cg2.cg3.cg4 = (cg2.n > 0 & cg3.n > 0 & cg4.n > 0) 211 in.cg2.cg3.cg4 = (cg2.n > 0 & cg3.n > 0 & cg4.n > 0)
212 in.cg1.cg2.cg4 = (cg1.n > 0 & cg2.n > 0 & cg4.n > 0) 212 in.cg1.cg2.cg4 = (cg1.n > 0 & cg2.n > 0 & cg4.n > 0)
213 in.cg1.cg3.cg4 = (cg1.n > 0 & cg3.n > 0 & cg4.n > 0) 213 in.cg1.cg3.cg4 = (cg1.n > 0 & cg3.n > 0 & cg4.n > 0)
214 214
215 in.cg.all = (cg1.n > 0 & cg2.n > 0 & cg3.n > 0 & cg4.n > 0)
216
215 217
216 218
217 219
218 #rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html) 220 #rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html)
219 rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html) 221 rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, un.html)
220 rw = c(rw, ca.n, cg.n, in.classes, in.ca.cg, in.ca1.ca2, in.cg1.cg2, in.cg1.cg3, in.cg1.cg4, in.cg2.cg3, in.cg2.cg4, in.cg3.cg4, in.cg1.cg2.cg3, in.cg2.cg3.cg4, in.cg1.cg2.cg4, in.cg1.cg3.cg4) 222 rw = c(rw, ca.n, cg.n, in.classes, in.ca.cg, in.ca1.ca2, in.cg1.cg2, in.cg1.cg3, in.cg1.cg4, in.cg2.cg3, in.cg2.cg4, in.cg3.cg4, in.cg1.cg2.cg3, in.cg2.cg3.cg4, in.cg1.cg2.cg4, in.cg1.cg3.cg4, in.cg.all)
221 223
222 cat(tr(rw), file=main.html, append=T) 224 cat(tr(rw), file=main.html, append=T)
223 225
224 226
225 for(i in 1:nrow(allc)){ #generate html by id 227 for(i in 1:nrow(allc)){ #generate html by id