Mercurial > repos > davidvanzessen > shm_csr

comparison sequence_overview.r @ 32:4c5ba6b5d10d draft

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author davidvanzessen
date Thu, 15 Dec 2016 09:21:54 -0500
parents fe44a905aee9
children 22fabe161cf3
comparison
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31:fe44a905aee9 32:4c5ba6b5d10d
81 } else if(empty.region.filter == "FR2"){ 81 } else if(empty.region.filter == "FR2"){
82 cat("<caption>CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T) 82 cat("<caption>CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
83 } 83 }
84 84
85 cat("<tr>", file=main.html, append=T) 85 cat("<tr>", file=main.html, append=T)
86 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) 86 cat("<th>Sequence</th><th>Functionality</th><th>IGA1</th><th>IGA2</th><th>IGG1</th><th>IGG2</th><th>IGG3</th><th>IGG4</th><th>IGM</th><th>IGE</th><th>UN</th>", file=main.html, append=T)
87 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) 87 cat("<th>total IGA</th><th>total IGG</th><th>total IGE</th><th>total IGM</th><th>number of subclasses</th><th>present in both IGA and IGG</th><th>present in IGA, IGG and IGM</th><th>present in IGA, IGG and IGE</th><th>present in IGA, IGG, IGM and IGE</th><th>IGA1+IGA2</th>", file=main.html, append=T)
88 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) 88 cat("<th>IGG1+IGG2</th><th>IGG1+IGG3</th><th>IGG1+IGG4</th><th>IGG2+IGG3</th><th>IGG2+IGG4</th><th>IGG3+IGG4</th>", file=main.html, append=T)
89 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) 89 cat("<th>IGG1+IGG2+IGG3</th><th>IGG2+IGG3+IGG4</th><th>IGG1+IGG2+IGG4</th><th>IGG1+IGG3+IGG4</th><th>IGG1+IGG2+IGG3+IGG4</th>", file=main.html, append=T)
90 cat("</tr>", file=main.html, append=T) 90 cat("</tr>", file=main.html, append=T)
91 91
92 92
93 93
94 single.sequences=0 #sequence only found once, skipped 94 single.sequences=0 #sequence only found once, skipped
110 cg3 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG3", IDs$best_match),] 110 cg3 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG3", IDs$best_match),]
111 cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG4", IDs$best_match),] 111 cg4 = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGG4", IDs$best_match),]
112 112
113 cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGM", IDs$best_match),] 113 cm = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGM", IDs$best_match),]
114 114
115 ce = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^IGE", IDs$best_match),]
116
115 un = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^unmatched", IDs$best_match),] 117 un = IDs[IDs$seq_conc == dat[i,c("seq_conc")] & grepl("^unmatched", IDs$best_match),]
116 allc = rbind(ca1, ca2, cg1, cg2, cg3, cg4, cm, un) 118
119 allc = rbind(ca1, ca2, cg1, cg2, cg3, cg4, cm, ce, un)
117 120
118 ca1.n = nrow(ca1) 121 ca1.n = nrow(ca1)
119 ca2.n = nrow(ca2) 122 ca2.n = nrow(ca2)
120 123
121 cg1.n = nrow(cg1) 124 cg1.n = nrow(cg1)
123 cg3.n = nrow(cg3) 126 cg3.n = nrow(cg3)
124 cg4.n = nrow(cg4) 127 cg4.n = nrow(cg4)
125 128
126 cm.n = nrow(cm) 129 cm.n = nrow(cm)
127 130
131 ce.n = nrow(ce)
132
128 un.n = nrow(un) 133 un.n = nrow(un)
129 134
130 classes = c(ca1.n, ca2.n, cg1.n, cg2.n, cg3.n, cg4.n, cm.n, un.n) 135 classes = c(ca1.n, ca2.n, cg1.n, cg2.n, cg3.n, cg4.n, cm.n, ce.n, un.n)
131 136
132 classes.sum = sum(classes) 137 classes.sum = sum(classes)
133 138
134 if(classes.sum == 1){ 139 if(classes.sum == 1){
135 single.sequences = single.sequences + 1 140 single.sequences = single.sequences + 1
143 148
144 in.classes = sum(classes > 0) 149 in.classes = sum(classes > 0)
145 150
146 matched = matched + in.classes #count in how many subclasses the sequence occurs. 151 matched = matched + in.classes #count in how many subclasses the sequence occurs.
147 152
148 if(any(classes == classes.sum)){ 153 if(any(classes == classes.sum)){
149 multiple.in.one = multiple.in.one + 1 154 multiple.in.one = multiple.in.one + 1
150 } else if (un.n > 0) { 155 } else if (un.n > 0) {
151 some.unmatched = some.unmatched + 1 156 some.unmatched = some.unmatched + 1
152 } else { 157 } else {
153 in.multiple = in.multiple + 1 158 in.multiple = in.multiple + 1
185 190
186 if(cm.n > 0){ 191 if(cm.n > 0){
187 cat(tbl(cm), file=paste("IGM_", id, ".html", sep="")) 192 cat(tbl(cm), file=paste("IGM_", id, ".html", sep=""))
188 } 193 }
189 194
195 if(ce.n > 0){
196 cat(tbl(ce), file=paste("IGE_", id, ".html", sep=""))
197 }
198
190 if(un.n > 0){ 199 if(un.n > 0){
191 cat(tbl(un), file=paste("un_", id, ".html", sep="")) 200 cat(tbl(un), file=paste("un_", id, ".html", sep=""))
192 } 201 }
193 202
194 ca1.html = make.link(id, "IGA1", ca1.n) 203 ca1.html = make.link(id, "IGA1", ca1.n)
199 cg3.html = make.link(id, "IGG3", cg3.n) 208 cg3.html = make.link(id, "IGG3", cg3.n)
200 cg4.html = make.link(id, "IGG4", cg4.n) 209 cg4.html = make.link(id, "IGG4", cg4.n)
201 210
202 cm.html = make.link(id, "IGM", cm.n) 211 cm.html = make.link(id, "IGM", cm.n)
203 212
213 ce.html = make.link(id, "IGE", ce.n)
214
204 un.html = make.link(id, "un", un.n) 215 un.html = make.link(id, "un", un.n)
205 216
206 #extra columns 217 #extra columns
207 ca.n = ca1.n + ca2.n 218 ca.n = ca1.n + ca2.n
208 219
209 cg.n = cg1.n + cg2.n + cg3.n + cg4.n 220 cg.n = cg1.n + cg2.n + cg3.n + cg4.n
210 221
211 #in.classes 222 #in.classes
212 223
213 in.ca.cg = (ca.n > 0 & cg.n > 0) 224 in.ca.cg = (ca.n > 0 & cg.n > 0)
225
226 in.ca.cg.cm = (ca.n > 0 & cg.n > 0 & cm.n > 0)
227
228 in.ca.cg.ce = (ca.n > 0 & cg.n > 0 & ce.n > 0)
229
230 in.ca.cg.cm.ce = (ca.n > 0 & cg.n > 0 & cm.n > 0 & ce.n > 0)
214 231
215 in.ca1.ca2 = (ca1.n > 0 & ca2.n > 0) 232 in.ca1.ca2 = (ca1.n > 0 & ca2.n > 0)
216 233
217 in.cg1.cg2 = (cg1.n > 0 & cg2.n > 0) 234 in.cg1.cg2 = (cg1.n > 0 & cg2.n > 0)
218 in.cg1.cg3 = (cg1.n > 0 & cg3.n > 0) 235 in.cg1.cg3 = (cg1.n > 0 & cg3.n > 0)
230 247
231 248
232 249
233 250
234 #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) 251 #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)
235 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) 252 rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html, ce.html, un.html)
236 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) 253 rw = c(rw, ca.n, cg.n, cm.n, ce.n, in.classes, in.ca.cg, in.ca.cg.cm, in.ca.cg.ce, in.ca.cg.cm.ce, 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)
237 254
238 cat(tr(rw), file=main.html, append=T) 255 cat(tr(rw), file=main.html, append=T)
239 256
240 257
241 for(i in 1:nrow(allc)){ #generate html by id 258 for(i in 1:nrow(allc)){ #generate html by id