# HG changeset patch
# User davidvanzessen
# Date 1464617480 14400
# Node ID d57c624a9aa9551b5234884bd41b6d038a5cbae0
# Parent  fd63f5307962175f6c989dfdcb367f1bdec3201e
Uploaded

diff -r fd63f5307962 -r d57c624a9aa9 sequence_overview.r
--- a/sequence_overview.r	Mon May 30 06:49:13 2016 -0400
+++ b/sequence_overview.r	Mon May 30 10:11:20 2016 -0400
@@ -23,8 +23,8 @@
 
 dat = dat[dat$Sequence.ID %in% merged$Sequence.ID,]
 
-#dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT, dat$FR2.IMGT, dat$FR3.IMGT)
-dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT)
+dat$seq_conc = paste(dat$CDR1.IMGT, dat$FR2.IMGT, dat$CDR2.IMGT, dat$FR3.IMGT, dat$CDR3.IMGT)
+#dat$seq_conc = paste(dat$CDR1.IMGT, dat$CDR2.IMGT, dat$CDR3.IMGT)
 
 IDs = dat[,c("Sequence.ID", "seq_conc", "best_match", "Functionality")]
 IDs$best_match = as.character(IDs$best_match)
@@ -48,7 +48,7 @@
 tbl = function(df) { res = "<table border='1'>"; for(i in 1:nrow(df)){ res = paste(res, tr(df[i,]), sep=""); }; res = paste(res, "</table>"); }
 
 cat("<table border='1'>", file=main.html, append=F)
-cat("<caption>CDR1+CDR2+CDR3+FR2+FR3 sequences that show up more than once</caption>", file=main.html, append=T)
+cat("<caption>CDR1+FR2+CDR2+FR3+CDR3 sequences that show up more than once</caption>", file=main.html, append=T)
 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)
 
 for(i in 1:nrow(dat)){
@@ -125,7 +125,7 @@
 
 
 NToverview = genes[,c("Sequence.ID", "best_match")]
-sequences$seq = paste(sequences$CDR1.IMGT, sequences$CDR2.IMGT, sequences$FR2.IMGT, sequences$FR3.IMGT, sep="_")
+sequences$seq = paste(sequences$CDR1.IMGT, sequences$FR2.IMGT, sequences$CDR2.IMGT, sequences$FR3.IMGT, sep="_")
 
 NToverview = merge(NToverview, sequences[,c("Sequence.ID", "seq")], by="Sequence.ID")