Mercurial > repos > davidvanzessen > report_clonality_tcell_igg

diff r_wrapper.sh @ 2:fd1b76816395 draft

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Uploaded
author davidvanzessen
date Thu, 27 Mar 2014 10:54:03 -0400
parents 1ba88ffd6f4e
children b850200d4335
line wrap: on
line diff
--- a/r_wrapper.sh	Tue Mar 11 11:13:33 2014 -0400
+++ b/r_wrapper.sh	Thu Mar 27 10:54:03 2014 -0400
@@ -4,15 +4,30 @@
 outputDir=$3
 outputFile=$3/index.html #$2
 clonalType=$4
-species=$5
 dir="$(cd "$(dirname "$0")" && pwd)"
 mkdir $3
-Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType $species 2>&1
+Rscript --verbose $dir/RScript.r $inputFile $outputDir $outputDir $clonalType 2>&1
 cp $dir/tabber.js $outputDir
 cp $dir/style.css $outputDir
 cp $dir/script.js $outputDir
+cp $dir/jquery-1.11.0.min.js $outputDir
+cp $dir/jquery.tablesorter.min.js $outputDir
+cp $dir/asc.gif $outputDir
+cp $dir/desc.gif $outputDir
+cp $dir/bg.gif $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>" > $2
-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 "<html<head>" >> $outputFile
+echo "<script type='text/javascript' src='jquery-1.11.0.min.js'></script>" >> $outputFile
+echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
+echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
+echo "<script type='text/javascript' src='jquery.tablesorter.min.js'></script>" >> $outputFile
+echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
+echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
+
+echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
+echo "<img src='VFPlot.png'/>" >> $outputFile
+echo "<img src='DFPlot.png'/>" >> $outputFile
+echo "<img src='JFPlot.png'/>" >> $outputFile
 echo "<img src='VPlot.png'/>" >> $outputFile
 echo "<img src='DPlot.png'/>" >> $outputFile
 echo "<img src='JPlot.png'/></div>" >> $outputFile
@@ -22,13 +37,9 @@
 echo "<div class='tabbertab' title='Heatmaps'><div class='tabber'>" >> $outputFile
 for sample in $samples; do
 	echo "<div class='tabbertab' title='$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>" >> $outputFile
+	echo "<td><img src='HeatmapVD_$sample.png'/></td>" >> $outputFile
+	echo "<td><img src='HeatmapVJ_$sample.png'/></td>" >> $outputFile
+	echo "<td><img src='HeatmapDJ_$sample.png'/></td></tr></table></div>" >> $outputFile
 	count=$((count+1))
 done
 echo "</div></div>" >> $outputFile
@@ -69,13 +80,15 @@
 	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>" >> $outputFile
+hasJunctionData="$(if head -n 1 $inputFile | grep -q '3V-REGION trimmed-nt nb'; then echo 'Yes'; else echo 'No'; fi)"
+
+if [[ "$hasJunctionData" == "Yes" ]] ; then
+	echo "<div class='tabbertab' title='Junction Analysis'><table border='1' id='junction_table'  class='tablesorter'><thead><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><thead></tr><tbody>" >> $outputFile
 	while IFS=, read Sample unique VHDEL P1 N1 P2 DELDH DHDEL P3 N2 P4 DELJH TotalDel TotalN TotalP
 	do
 		echo "<tr><td>$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
+	echo "</tbody></table></div>" >> $outputFile
 fi
 
 echo "<div class='tabbertab' title='Comparison'><table border='1'><tr><th>ID</th><th>Include</th></tr>" >> $outputFile
@@ -91,7 +104,24 @@
 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 "<tr><td>The dataset used to generate the frequency graphs and the heatmaps (Unique based on clonaltype, $clonalType)</td><td><a href='allUnique.csv'>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.csv'>Download</a></td></tr>" >> $outputFile
+
+echo "<tr><td>The dataset used to generate the CDR3 length frequency graph</td><td><a href='CDR3LengthPlot.csv'>Download</a></td></tr>" >> $outputFile
+
+echo "<tr><td>The dataset used to generate the V gene family frequency graph</td><td><a href='VFFrequency.csv'>Download</a></td></tr>" >> $outputFile
+echo "<tr><td>The dataset used to generate the D gene family frequency graph</td><td><a href='DFFrequency.csv'>Download</a></td></tr>" >> $outputFile
+echo "<tr><td>The dataset used to generate the J gene family frequency graph</td><td><a href='JFFrequency.csv'>Download</a></td></tr>" >> $outputFile
+
+echo "<tr><td>The dataset used to generate the V gene frequency graph</td><td><a href='VFrequency.csv'>Download</a></td></tr>" >> $outputFile
+echo "<tr><td>The dataset used to generate the D gene frequency graph</td><td><a href='DFrequency.csv'>Download</a></td></tr>" >> $outputFile
+echo "<tr><td>The dataset used to generate the J gene frequency graph</td><td><a href='JFrequency.csv'>Download</a></td></tr>" >> $outputFile
+
+for sample in $samples; do
+	echo "<tr><td>The data used to generate the VD heatmap for $sample.</td><td><a href='HeatmapVD_$sample.csv'>Download</a></td></tr>" >> $outputFile
+	echo "<tr><td>The data used to generate the VJ heatmap for $sample.</td><td><a href='HeatmapVJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
+	echo "<tr><td>The data used to generate the DJ heatmap for $sample.</td><td><a href='HeatmapDJ_$sample.csv'>Download</a></td></tr>" >> $outputFile
+done
+
 echo "</table>" >> $outputFile
-echo "</div>" >> $outputFile
+echo "</div></html>" >> $outputFile