Mercurial > repos > davidvanzessen > mutation_analysis

comparison sequence_overview.r @ 92:b869a126e2c4 draft

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author davidvanzessen
date Mon, 06 Jun 2016 08:26:54 -0400
parents 5e237c243088
children e39176ccddc8
comparison
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91:5e237c243088 92:b869a126e2c4
64 next 64 next
65 } 65 }
66 66
67 id = as.numeric(dat[i,"seq_conc"]) 67 id = as.numeric(dat[i,"seq_conc"])
68 68
69 functionality = paste(unique(allc[,"Functionality"], sep=",")) 69 functionality = paste(unique(allc[,"Functionality"]), collapse=",")
70 70
71 if(nrow(ca1) > 0){ 71 if(nrow(ca1) > 0){
72 cat(tbl(ca1), file=paste("ca1_", id, ".html", sep="")) 72 cat(tbl(ca1), file=paste("ca1_", id, ".html", sep=""))
73 } 73 }
74 74
104 cg3.html = make.link(id, "cg3", nrow(cg3)) 104 cg3.html = make.link(id, "cg3", nrow(cg3))
105 cg4.html = make.link(id, "cg4", nrow(cg4)) 105 cg4.html = make.link(id, "cg4", nrow(cg4))
106 106
107 cm.html = make.link(id, "cm", nrow(cm)) 107 cm.html = make.link(id, "cm", nrow(cm))
108 108
109 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) 109 rw = c(as.character(dat[i,"seq_conc"]), functionality, ca1.html, ca2.html, cg1.html, cg2.html, cg3.html, cg4.html, cm.html)
110 #print(rw)
111 110
112 cat(tr(rw), file=main.html, append=T) 111 cat(tr(rw), file=main.html, append=T)
113 } 112 }
114 113
115 cat("</table>", file=main.html, append=T) 114 cat("</table>", file=main.html, append=T)
116 115
117 116
118 #ACGT overview 117 #ACGT overview
119
120
121 118
122 NToverview = merged 119 NToverview = merged
123 NToverview$seq = paste(NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq, sep="_") 120 NToverview$seq = paste(NToverview$CDR1.IMGT.seq, NToverview$FR2.IMGT.seq, NToverview$CDR2.IMGT.seq, NToverview$FR3.IMGT.seq, sep="_")
124 121
125 NToverview$A = nchar(gsub("[^Aa]", "", NToverview$seq)) 122 NToverview$A = nchar(gsub("[^Aa]", "", NToverview$seq))