# HG changeset patch
# User davidvanzessen
# Date 1432651071 14400
# Node ID 45554fd15511dcaad82141f70489b82bd90a68ad
# Parent  5ab17bdf2530f9b4f8914933a3e9b0dffa88e46b
Uploaded

diff -r 5ab17bdf2530 -r 45554fd15511 RScript.r
--- a/RScript.r	Fri May 22 09:06:04 2015 -0400
+++ b/RScript.r	Tue May 26 10:37:51 2015 -0400
@@ -136,10 +136,10 @@
     patient2$merge = paste(patient2$V_Segment_Major_Gene, patient2$J_Segment_Major_Gene, patient2$CDR3_Sense_Sequence)
   }
   
-  scatterplot_data_columns = c("Patient", "Sample", "Clone_Sequence", "Frequency", "normalized_read_count", "V_Segment_Major_Gene", "J_Segment_Major_Gene")
+  scatterplot_data_columns = c("Patient", "Sample", "Frequency", "normalized_read_count", "V_Segment_Major_Gene", "J_Segment_Major_Gene", "merge")
   scatterplot_data = rbind(patient1[,scatterplot_data_columns], patient2[,scatterplot_data_columns])
-  scatterplot_data = scatterplot_data[!duplicated(scatterplot_data$Clone_Sequence),]
-  scatterplot_data$type = factor(x="In one", levels=c("In one", "In Both"))
+  scatterplot_data = scatterplot_data[!duplicated(scatterplot_data$merge),]
+  scatterplot_data$type = factor(x=oneSample, levels=c(oneSample, twoSample, "In Both"))
   scatterplot_data$on = onShort
   
   patientMerge = merge(patient1, patient2, by.x="merge", by.y="merge")
@@ -159,8 +159,8 @@
     J_Segment = paste(".*", as.character(product[iter,J_SegmentIndex]), ".*", sep="")
     #both = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,onx] > threshhold & patientMerge[,ony] > threshhold) #both higher than threshold
     both = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge$thresholdValue > threshhold) #highest of both is higher than threshold
-    one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$Clone_Sequence %in% patientMerge[both,]$merge))
-    two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$Clone_Sequence %in% patientMerge[both,]$merge))
+    one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$merge %in% patientMerge[both,]$merge))
+    two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$merge %in% patientMerge[both,]$merge))
     read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count))
     read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count))
     res1 = append(res1, sum(one))
@@ -187,9 +187,14 @@
       if(nrow(scatterplot_locus_data) > 0){
         scatterplot_locus_data$Rearrangement = product[iter, titleIndex]
       }
-      in_two = (scatterplot_locus_data$Clone_Sequence %in% patientMerge[both,]$Clone_Sequence.x)
-      if(any(in_two)){
-        scatterplot_locus_data[in_two,]$type = "In Both"
+      in_both = (scatterplot_locus_data$merge %in% patientMerge[both,]$merge)
+      if(any(in_both)){
+        scatterplot_locus_data[in_both,]$type = "In Both"
+      }
+      in_one = (scatterplot_locus_data$merge %in% patient1$merge)
+      not_in_one = !in_one
+      if(any(not_in_one)){
+				scatterplot_locus_data[not_in_one,]$type = twoSample
       }
       if(type == "single"){
         single_patients <<- rbind(single_patients, scatterplot_locus_data)
@@ -197,10 +202,10 @@
       p = NULL
       if(nrow(scatterplot_locus_data) != 0){
         if(on == "normalized_read_count"){
-          scales = 10^(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
-          p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales)
+          scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
+          p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,1000000))
         } else {
-          p = ggplot(scatterplot_locus_data, aes(type, Frequency)) 
+          p = ggplot(scatterplot_locus_data, aes(type, Frequency)) + scale_y_continuous(limits = c(0, 100)) + expand_limits(y=c(0,100))
         }
         p = p + geom_point(aes(colour=type), position="jitter")
         p = p + xlab("In one or both samples") + ylab(onShort) + ggtitle(paste(patient1[1,patientIndex], patient1[1,sampleIndex], patient2[1,sampleIndex], onShort, product[iter, titleIndex]))
@@ -343,9 +348,9 @@
   patientMerge23$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_columns = c("Clone_Sequence", "Frequency", "normalized_read_count", "V_Segment_Major_Gene", "J_Segment_Major_Gene", "merge")
   scatterplot_data = rbind(patient1[,scatterplot_data_columns], patient2[,scatterplot_data_columns], patient3[,scatterplot_data_columns])
-  scatterplot_data = scatterplot_data[!duplicated(scatterplot_data$Clone_Sequence),]
+  scatterplot_data = scatterplot_data[!duplicated(scatterplot_data$merge),]
   scatterplot_data$type = factor(x="In one", levels=c("In one", "In two", "In three", "In multiple"))
   
   res1 = vector()
@@ -369,13 +374,13 @@
     #all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge[,onx] > threshhold & patientMerge[,ony] > threshhold & patientMerge[,onz] > threshhold) 
     all = (grepl(V_Segment, patientMerge$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge$J_Segment_Major_Gene.x) & patientMerge$thresholdValue > threshhold)
     
-    one_two = (grepl(V_Segment, patientMerge12$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge12$J_Segment_Major_Gene.x) & patientMerge12$thresholdValue > threshhold & !(patientMerge12$Clone_Sequence.x %in% patientMerge[all,]$merge))
-    one_three = (grepl(V_Segment, patientMerge13$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge13$J_Segment_Major_Gene.x) & patientMerge13$thresholdValue > threshhold & !(patientMerge13$Clone_Sequence.x %in% patientMerge[all,]$merge))
-    two_three = (grepl(V_Segment, patientMerge23$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge23$J_Segment_Major_Gene.x) & patientMerge23$thresholdValue > threshhold & !(patientMerge23$Clone_Sequence.x %in% patientMerge[all,]$merge))
+    one_two = (grepl(V_Segment, patientMerge12$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge12$J_Segment_Major_Gene.x) & patientMerge12$thresholdValue > threshhold & !(patientMerge12$merge %in% patientMerge[all,]$merge))
+    one_three = (grepl(V_Segment, patientMerge13$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge13$J_Segment_Major_Gene.x) & patientMerge13$thresholdValue > threshhold & !(patientMerge13$merge %in% patientMerge[all,]$merge))
+    two_three = (grepl(V_Segment, patientMerge23$V_Segment_Major_Gene.x) & grepl(J_Segment, patientMerge23$J_Segment_Major_Gene.x) & patientMerge23$thresholdValue > threshhold & !(patientMerge23$merge %in% patientMerge[all,]$merge))
     
-    one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$Clone_Sequence %in% patientMerge[all,]$merge) & !(patient1$Clone_Sequence %in% patientMerge12[one_two,]$merge) & !(patient1$Clone_Sequence %in% patientMerge13[one_three,]$merge))
-    two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$Clone_Sequence %in% patientMerge[all,]$merge) & !(patient2$Clone_Sequence %in% patientMerge12[one_two,]$merge) & !(patient2$Clone_Sequence %in% patientMerge23[two_three,]$merge))
-    three = (grepl(V_Segment, patient3$V_Segment_Major_Gene) & grepl(J_Segment, patient3$J_Segment_Major_Gene) & patient3[,on] > threshhold & !(patient3$Clone_Sequence %in% patientMerge[all,]$merge) & !(patient3$Clone_Sequence %in% patientMerge13[one_three,]$merge) & !(patient3$Clone_Sequence %in% patientMerge23[two_three,]$merge))
+    one = (grepl(V_Segment, patient1$V_Segment_Major_Gene) & grepl(J_Segment, patient1$J_Segment_Major_Gene) & patient1[,on] > threshhold & !(patient1$merge %in% patientMerge[all,]$merge) & !(patient1$merge %in% patientMerge12[one_two,]$merge) & !(patient1$merge %in% patientMerge13[one_three,]$merge))
+    two = (grepl(V_Segment, patient2$V_Segment_Major_Gene) & grepl(J_Segment, patient2$J_Segment_Major_Gene) & patient2[,on] > threshhold & !(patient2$merge %in% patientMerge[all,]$merge) & !(patient2$merge %in% patientMerge12[one_two,]$merge) & !(patient2$merge %in% patientMerge23[two_three,]$merge))
+    three = (grepl(V_Segment, patient3$V_Segment_Major_Gene) & grepl(J_Segment, patient3$J_Segment_Major_Gene) & patient3[,on] > threshhold & !(patient3$merge %in% patientMerge[all,]$merge) & !(patient3$merge %in% patientMerge13[one_three,]$merge) & !(patient3$merge %in% patientMerge23[two_three,]$merge))
     
     read1Count = append(read1Count, sum(patient1[one,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.x))
     read2Count = append(read2Count, sum(patient2[two,]$normalized_read_count) + sum(patientMerge[all,]$normalized_read_count.y))
@@ -427,11 +432,11 @@
       }
     } else { #scatterplot data
       scatterplot_locus_data = scatterplot_data[grepl(V_Segment, scatterplot_data$V_Segment_Major_Gene) & grepl(J_Segment, scatterplot_data$J_Segment_Major_Gene),]
-      in_two = (scatterplot_locus_data$Clone_Sequence %in% patientMerge12[one_two,]$Clone_Sequence.x) | (scatterplot_locus_data$Clone_Sequence %in% patientMerge13[one_three,]$Clone_Sequence.x) | (scatterplot_locus_data$Clone_Sequence %in% patientMerge23[two_three,]$Clone_Sequence.x)
+      in_two = (scatterplot_locus_data$merge %in% patientMerge12[one_two,]$merge) | (scatterplot_locus_data$merge %in% patientMerge13[one_three,]$merge) | (scatterplot_locus_data$merge %in% patientMerge23[two_three,]$merge)
       if(sum(in_two) > 0){
 				scatterplot_locus_data[in_two,]$type = "In two"
       }
-      in_three = (scatterplot_locus_data$Clone_Sequence %in% patientMerge[all,]$Clone_Sequence.x)
+      in_three = (scatterplot_locus_data$merge %in% patientMerge[all,]$merge)
       if(sum(in_three)> 0){
 				scatterplot_locus_data[in_three,]$type = "In three"
       }
diff -r 5ab17bdf2530 -r 45554fd15511 wrapper.sh
--- a/wrapper.sh	Fri May 22 09:06:04 2015 -0400
+++ b/wrapper.sh	Tue May 26 10:37:51 2015 -0400
@@ -52,7 +52,7 @@
 	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_freq'>" >> "$html"
 	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
-	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'>"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'><table border='0'><tr>"
 	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -86,7 +86,7 @@
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"
 		if [ "${cut_off_value}" == "0" ] ; then
-			scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /><br />"
+			scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_freq_${locus}_scatter.png' /></td>"
 		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
@@ -96,7 +96,7 @@
 	echo "<a href='${patient}_freq.png'><img src='${patient}_freq.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_freq_both.png'><img src='${patient}_freq_both.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_percent_freq.png'><img src='${patient}_percent_freq.png' width='1280' height='720' /></a></div>" >> "$html"
-	echo "${scatterplot_tab}</div>" >> "$html"
+	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
 	
 	tail -n+2 ${patient}_reads.txt | sed "s/>//" > tmp.txt
 	echo "<div class='tabbertab' title='Data reads'>" >> "$html"
@@ -104,7 +104,7 @@
 	echo "<table border = 1 class='result_table summary_table' id='summary_table_${patient}_reads'>" >> "$html"
 	echo "<thead><th>Ig/TCR gene rearrangement type</th><th>Proximal gene segment</th><th>Distal gene segment</th><th>Cut off value</th><th>Number of sequences ${patient}_Both</th><th>Number of sequences_$sample1</th><th>Read Count $sample1</th><th>Number of sequences_$sample2</th><th>Read Count $sample2</th><th>Sum number of sequences $patient</th><th>Percentage of sequences ${patient}_both</th></thead>" >> "$html"
 	echo "<tbody>" >> "$html"
-	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Frequency'>"
+	scatterplot_tab="<div class='tabbertab' title='Scatter Plots Reads'><table border='0'><tr>"
 	while read locus j_segment v_segment cut_off_value both one read_count1 two read_count2 sum percent locusreadsum1 locusreadsum2
 	do
 		if [ "$locus" != "$oldLocus" ] ; then
@@ -138,7 +138,7 @@
 		echo "</tr>" >> "$html"
 		oldLocus="$locus"
 		if [ "${cut_off_value}" == "0" ] ; then
-			scatterplot_tab="${scatterplot_tab}<img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /><br />"
+			scatterplot_tab="${scatterplot_tab}<td><img src='${patient}_${sample1}_${sample2}_reads_${locus}_scatter.png' /></td>"
 		fi
 	done < tmp.txt
 	echo "</tbody></table>" >> "$html"
@@ -148,7 +148,7 @@
 	echo "<a href='${patient}_reads.png'><img src='${patient}_reads.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_reads_both.png'><img src='${patient}_reads_both.png' width='1280' height='720' /></a><br />" >> "$html"
 	echo "<a href='${patient}_percent_reads.png'><img src='${patient}_percent_reads.png' width='1280' height='720' /></a></div>" >> "$html"
-	echo "${scatterplot_tab}</div>" >> "$html"
+	echo "${scatterplot_tab}</tr></table></div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</div>" >> "$html"
 	echo "</html>" >> "$html"