Mercurial > repos > davidvanzessen > imgt_immunerepertoire_igg

diff combined.sh @ 3:8b026af4b298 draft default tip

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Uploaded
author davidvanzessen
date Tue, 11 Mar 2014 10:39:04 -0400
parents 3cce6e04b1e8
children
line wrap: on
line diff
--- a/combined.sh	Tue Mar 11 09:21:57 2014 -0400
+++ b/combined.sh	Tue Mar 11 10:39:04 2014 -0400
@@ -44,63 +44,94 @@
 
 
 inputFile=$PWD/merged.txt
-outputFile=$html
 outputDir=$imageDir
+outputFile=$outputDir/index.html
 mkdir $outputDir
 Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
-echo "<html>" > $outputFile
+cp $dir/tabber.js $outputDir
+cp $dir/style.css $outputDir
+cp $dir/script.js $outputDir
+echo "<html><center><h1><a href='index.html'>Click here for the results</a></h1>Tip: Open it in a new tab (middle mouse button or right mouse button -> 'open in new tab' on the link above)</center></html>" > $html
+echo "<html><script type='text/javascript' src='tabber.js'></script><script type='text/javascript' src='script.js'></script><link rel='stylesheet' type='text/css' href='style.css'><div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
 echo "<img src='VPlot.png'/>" >> $outputFile
 echo "<img src='DPlot.png'/>" >> $outputFile
-echo "<img src='JPlot.png'/>" >> $outputFile
+echo "<img src='JPlot.png'/></div>" >> $outputFile
 
 samples=`cat $outputDir/samples.txt`
 count=1
-echo "<table border='1'><caption><a href='allUnique.tsv'><h3>$clonalType</h3></a></caption>" >> $outputFile
-hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
+echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
 for sample in $samples; do
-	clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
-	echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
-	echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
+	echo "<div class='tabbertab' title='$sample'><table border='1'><tr>" >> $outputFile
+	
+	mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
+	echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
+	mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
+	echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
+	mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
+	echo "<td><img src='DJ_$sample.png'/></td></tr></table></div>" >> $outputFile
+	count=$((count+1))
+done
+echo "</div></div>" >> $outputFile
 
-	echo "$hasReplicateColumn"
-	#if its a 'new' merged file with replicate info
-	if [[ "$hasReplicateColumn" == "Yes" ]] ; then
-		echo "<tr><td colspan='3'><a href='clonality_$sample.tsv'><h2>Clonality Score: $clonalityScore</h2></a></td></tr>" >> $outputFile
+
+hasReplicateColumn="$(if head -n 1 $inputFile | grep -q 'Replicate'; then echo 'Yes'; else echo 'No'; fi)"
+echo "$hasReplicateColumn"
+#if its a 'new' merged file with replicate info
+if [[ "$hasReplicateColumn" == "Yes" ]] ; then
+	echo "<div class='tabbertab' title='Clonality'><div class='tabber'>" >> $outputFile
+	for sample in $samples; do
+		clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
+		echo "<div class='tabbertab' title='$sample'><table border='1'>" >> $outputFile
+		echo "<tr><td colspan='4'>Clonality Score: $clonalityScore</td></tr>" >> $outputFile
 
 		#replicate,reads,squared
-		echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
+		echo "<tr><td>Replicate ID</td><td>Number of Reads</td><td>Reads Squared</td><td></td></tr>" >> $outputFile
 		while IFS=, read replicate reads squared
 		do
-
-			echo "<tr><td><a href='clonality_${sample}_$replicate.tsv'>$replicate</a></td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
+			
+			echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td><td></td></tr>" >> $outputFile
 		done < $outputDir/ReplicateReads_$sample.csv
-
+		
 		#sum of reads and reads squared
 		while IFS=, read readsSum squaredSum
 			do
 				echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
 		done < $outputDir/ReplicateSumReads_$sample.csv
-
-		echo "</table></td></tr>" >> $outputFile
-
+		
 		#overview
-		echo "<tr><td colspan='3'><table border='1'><tr><th>Coincidence Type</th><th>Raw Coincidence Freq</th><th>Coincidence Weight</th><th>Coincidences, Weighted</th></tr>" >> $outputFile
+		echo "<tr><td>Coincidence Type</td><td>Raw Coincidence Freq</td><td>Coincidence Weight</td><td>Coincidences, Weighted</td></tr>" >> $outputFile
 		while IFS=, read type count weight weightedCount
 		do
 			echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
 		done < $outputDir/ClonalityOverView_$sample.csv
-		echo "</table></td></tr>" >> $outputFile
-	fi
+		echo "</table></div>" >> $outputFile
+	done
+	echo "</div></div>" >> $outputFile
+fi
+
+if [[ "$hasReplicateColumn" == "Yes" ]] ; then
+	echo "<div class='tabbertab' title='Junction Analysis'><table border='1'><tr><th>Sample</th><th>unique</th><th>VH.DEL</th><th>P1</th><th>N1</th><th>P2</th><th>DEL.DH</th><th>DH.DEL</th><th>P3</th><th>N2</th><th>P4</th><th>DEL.JH</th><th>Total.Del</th><th>Total.N</th><th>Total.P</th></tr>" >> $outputFile
+	while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
+	do
+		echo "<tr><td>$Sample</td><td>$unique</td><td>$VHDEL</td><td>$P1</td><td>$N1</td><td>$P2</td><td>$DELDH</td><td>$DHDEL</td><td>$P3</td><td>$N2</td><td>$P4</td><td>$DELJH</td><td>$TotalDel</td><td>$TotalN</td><td>$TotalP</td></tr>" >> $outputFile
+	done < $outputDir/junctionAnalysis.csv
+	echo "</table></div>" >> $outputFile
+fi
 
-	echo "<tr><td><h2>V-D Heatmap:</h2></td><td><h2>V-J Heatmap:</h2></td><td><h2>D-J Heatmap:</h2></td></tr><tr>" >> $outputFile
-	mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
-	echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
-	mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
-	echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile
-	mv "$outputDir/HeatmapDJ_$sample.png" "$outputDir/DJ_$sample.png"
-	echo "<td><img src='DJ_$sample.png'/></td></tr>" >> $outputFile
-	count=$((count+1))
+echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
+for sample in $samples; do
+	echo "<tr><td>$sample</td><td><input type='checkbox' onchange=\"javascript:compareAdd('$sample')\" id='compare_checkbox_$sample'/></td></tr>" >> $outputFile
 done
-echo "</table>" >> $outputFile
+echo "</table><div name='comparisonarea'>" >> $outputFile
+echo "<table><tr id='comparison_table_vd'></tr></table>" >> $outputFile
+echo "<table><tr id='comparison_table_vj'></tr></table>" >> $outputFile
+echo "<table><tr id='comparison_table_dj'></tr></table>" >> $outputFile
+echo "</div></div>" >> $outputFile
 
-echo "</html>" >> $outputFile
+echo "<div class='tabbertab' title='Downloads'>" >> $outputFile
+echo "<table border='1'>" >> $outputFile
+echo "<tr><th>Description</th><th>Link</th></tr>" >> $outputFile
+echo "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.tsv'>Download</a></td></tr>" >> $outputFile
+echo "<tr><td>The dataset used to calculate clonality score (Unique based on clonaltype, $clonalType)</td><td><a href='clonalityComplete.tsv'>Download</a></td></tr>" >> $outputFile
+echo "</table>" >> $outputFile
+echo "</div>" >> $outputFile