# HG changeset patch
# User davidvanzessen
# Date 1432037629 14400
# Node ID a63ccc36f5a4829af8ce470f2eedfc03b6ff5ed4
# Parent  dd8518ea23dd6c3c1e5f7a4906c1984dce138a3a
Uploaded

diff -r dd8518ea23dd -r a63ccc36f5a4 RScript.r
--- a/RScript.r	Wed Feb 25 09:18:14 2015 -0500
+++ b/RScript.r	Tue May 19 08:13:49 2015 -0400
@@ -61,6 +61,9 @@
 TitlesOrder = data.frame("Title"=Titles, "TitlesOrder"=1:length(Titles))
 
 patientCountOnColumn <- function(x, product, interval, on, appendtxt=F){
+  if (!is.data.frame(x) & is.list(x)){
+    x = x[[1]]
+  }
   x$Sample = factor(x$Sample, levels=unique(x$Sample))
   onShort = "reads"
   if(on == "Frequency"){
@@ -255,9 +258,8 @@
   
   patientMerge = merge(patient1, patient2, by="merge")
   patientMerge = merge(patientMerge, patient3, by="merge")
-  colnames(patientMerge)[30:length(colnames(patientMerge))] = paste(colnames(patientMerge)[30:length(colnames(patientMerge))], ".z", sep="")
+  colnames(patientMerge)[which(!grepl("(\\.x$)|(\\.y$)|(merge)", names(patientMerge)))] = paste(colnames(patientMerge)[which(!grepl("(\\.x$)|(\\.y$)|(merge)", names(patientMerge), perl=T))], ".z", sep="")
   patientMerge$thresholdValue = pmax(patientMerge[,onx], patientMerge[,ony], patientMerge[,onz])
-  
   patientMerge12 = merge(patient1, patient2, by="merge")
   patientMerge12$thresholdValue = pmax(patientMerge12[,onx], patientMerge12[,ony])
   patientMerge13 = merge(patient1, patient3, by="merge")
@@ -265,6 +267,7 @@
   patientMerge23 = merge(patient2, patient3, by="merge")
   patientMerge23$thresholdValue = pmax(patientMerge23[,onx], patientMerge23[,ony])
   
+  
   scatterplot_data_columns = c("Clone_Sequence", "Frequency", "normalized_read_count", "V_Segment_Major_Gene", "J_Segment_Major_Gene")
   scatterplot_data = rbind(patient1[,scatterplot_data_columns], patient2[,scatterplot_data_columns], patient3[,scatterplot_data_columns])
   scatterplot_data = scatterplot_data[!duplicated(scatterplot_data$Clone_Sequence),]
@@ -358,7 +361,6 @@
 				scatterplot_locus_data[in_three,]$type = "In three"
       }
       not_in_one = scatterplot_locus_data$type != "In one"
-      print(not_in_one)
       if(sum(not_in_one) > 0){
 				scatterplot_locus_data[not_in_one,]$type = "In multiple"
       }
diff -r dd8518ea23dd -r a63ccc36f5a4 script.js
diff -r dd8518ea23dd -r a63ccc36f5a4 wrapper.sh