# HG changeset patch
# User davidvanzessen
# Date 1506950665 14400
# Node ID bcf1469e8feb7968e1cb8e47060a387adbee715c
# Parent  89d80f086328259e763c7c546bd5348c267766ab
Uploaded

diff -r 89d80f086328 -r bcf1469e8feb RScript.r
--- a/RScript.r	Mon Sep 25 08:20:12 2017 -0400
+++ b/RScript.r	Mon Oct 02 09:24:25 2017 -0400
@@ -47,7 +47,7 @@
 cat("<tr><td>Calculating Frequency</td></tr>", file=logfile, append=T)
 
 dat$Frequency = ((10^dat$Log10_Frequency)*100)
-dat = dat[dat$Frequency <= 100,] #just in case
+dat = dat[dat$Frequency <= 100,] #just in case?
 
 dat = dat[dat$Frequency >= min_freq,]
 
@@ -169,7 +169,7 @@
     scatterplot_data = scatter_locus_data_list[[patient]]
     cat(paste("<td>", nrow(patient1), " in ", oneSample, " and ", nrow(patient2), " in ", twoSample, ", ", nrow(patientMerge), " in both (fetched from cache)</td></tr>", sep=""), file=logfile, append=T)
     
-    print(names(patient.merge.list))
+    #print(names(patient.merge.list))
   } else {
     #fuzzy matching here...
     
@@ -773,15 +773,15 @@
 
 		} else if(nrow(rows.1) > 1){
 			patient1 = patient1[!(patient1$Clone_Sequence %in% rows.1$Clone_Sequence),]
-			print(names(patient1)[names(patient1) %in% sum.1])
-			print(names(patient1)[!(names(patient1) %in% sum.1)])
-			print(names(patient1))
-			print(names(sum.1))
-			print(summary(sum.1))
-			print(summary(patient1))
-			print(dim(sum.1))
-			print(dim(patient1))
-			print(head(sum.1[,names(patient1)]))
+			#print(names(patient1)[names(patient1) %in% sum.1])
+			#print(names(patient1)[!(names(patient1) %in% sum.1)])
+			#print(names(patient1))
+			#print(names(sum.1))
+			#print(summary(sum.1))
+			#print(summary(patient1))
+			#print(dim(sum.1))
+			#print(dim(patient1))
+			#print(head(sum.1[,names(patient1)]))
 			patient1 = rbind(patient1, sum.1[,names(patient1)])
 			patient.fuzzy = patient.fuzzy[-match.filter.1,]
 		} else {
@@ -1042,7 +1042,7 @@
 	product = data.frame("Titles"=rep(Titles, each=length(interval)), "interval"=rep(interval, times=10), "V_Segments"=rep(V_Segments, each=length(interval)), "J_Segments"=rep(J_Segments, each=length(interval)))
 
 	triplets = split(triplets, triplets$Patient, drop=T)
-	print(nrow(triplets))
+	#print(nrow(triplets))
 	for(triplet in triplets){
 		samples = unique(triplet$Sample)
 		one = triplet[triplet$Sample == samples[1],]