Mercurial > repos > davidvanzessen > plotting_merged

comparison r_wrapper.sh @ 48:dea2d3353a42 draft

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author davidvanzessen
date Mon, 02 Dec 2013 10:56:47 -0500
parents 1b3ef7b2f4a0
children e6209052aaf4
comparison
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47:33ebd6f0d256 48:dea2d3353a42
15 echo "<img src='DPlot.png'/>" >> $2 15 echo "<img src='DPlot.png'/>" >> $2
16 echo "<img src='JPlot.png'/>" >> $2 16 echo "<img src='JPlot.png'/>" >> $2
17 17
18 samples=`cat $outputDir/samples.txt` 18 samples=`cat $outputDir/samples.txt`
19 count=1 19 count=1
20 echo "<table border='1'><caption><h3>$clonalType</h3><caption>" >> $outputFile 20 echo "<table border='1'><caption><h3>$clonalType</h3></caption>" >> $outputFile
21 for sample in $samples; do 21 for sample in $samples; do
22 echo "<tr><td colspan='3' height='100'></td>" >> $outputFile 22 clonalityScore="$(cat $outputDir/ClonalityScore_$sample.csv)"
23 echo "<tr><td colspan='3' height='100'></td></tr>" >> $outputFile
23 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile 24 echo "<tr><td colspan='3'><h1>$sample</h1></td></tr>" >> $outputFile
25
26 #if its a 'new' merged file with replicate info
27 if head -n 1 $inputFile | grep -q "Replicate"
28 then
29 echo "<tr><td colspan='3'><h2>Clonality Score: $clonalityScore</h2></td></tr>" >> $outputFile
30
31 #replicate,reads,squared
32 echo "<tr><td colspan='3'><table border='1'><tr><th>Replicate ID</th><th>Number of Reads</th><th>Reads Squared</th></tr>" >> $outputFile
33 while IFS=, read replicate reads squared
34 do
35
36 echo "<tr><td>$replicate</td><td>$reads</td><td>$squared</td></tr>" >> $outputFile
37 done < $outputDir/ReplicateReads_$sample.csv
38
39 #sum of reads and reads squared
40 while IFS=, read readsSum squaredSum
41 do
42 echo "<tr><td>Sum</td><td>$readsSum</td><td>$squaredSum</td></tr>" >> $outputFile
43 done < $outputDir/ReplicateSumReads_$sample.csv
44
45 echo "</table></td></tr>" >> $outputFile
46
47 #overview
48 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>" >> $outputFile
49 while IFS=, read type count weight weightedCount
50 do
51 echo "<tr><td>$type</td><td>$count</td><td>$weight</td><td>$weightedCount</td></tr>" >> $outputFile
52 done < $outputDir/ClonalityOverView_$sample.csv
53 echo "</table></td></tr>" >> $outputFile
54 fi
55
24 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 56 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>" >> $outputFile
25 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png" 57 mv "$outputDir/HeatmapVD_$sample.png" "$outputDir/VD_$sample.png"
26 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile 58 echo "<td><img src='VD_$sample.png'/></td>" >> $outputFile
27 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png" 59 mv "$outputDir/HeatmapVJ_$sample.png" "$outputDir/VJ_$sample.png"
28 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile 60 echo "<td><img src='VJ_$sample.png'/></td>" >> $outputFile