Mercurial > repos > davidvanzessen > argalaxy_tools

comparison report_clonality/r_wrapper.sh @ 8:8cbc1a8d27ae draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author davidvanzessen
date Mon, 19 Dec 2016 08:50:31 -0500
parents bcec7bb4e089
children 5f5d29c5e711
comparison
equal deleted inserted replaced
7:54f6756bacb1 8:8cbc1a8d27ae
104 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile 104 echo "<script type='text/javascript' src='tabber.js'></script>" >> $outputFile
105 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile 105 echo "<script type='text/javascript' src='script.js'></script>" >> $outputFile
106 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile 106 echo "<link rel='stylesheet' type='text/css' href='style.css'></head>" >> $outputFile
107 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile 107 echo "<div class='tabber'><div class='tabbertab' title='Gene frequencies'>" >> $outputFile
108 108
109 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile 109
110 echo "<img src='VFPlot.png'/>" >> $outputFile 110 echo "<img src='VFPlot.png'/>" >> $outputFile
111 if [[ "$useD" == "true" ]] ; then 111 if [[ "$useD" == "true" ]] ; then
112 echo "<img src='DFPlot.png'/>" >> $outputFile 112 echo "<img src='DFPlot.png'/>" >> $outputFile
113 fi 113 fi
114 echo "<img src='VPlot.png'/>" >> $outputFile 114 echo "<img src='VPlot.png'/>" >> $outputFile
115 if [[ "$useD" == "true" ]] ; then 115 if [[ "$useD" == "true" ]] ; then
116 echo "<img src='DPlot.png'/>" >> $outputFile 116 echo "<img src='DPlot.png'/>" >> $outputFile
117 fi 117 fi
118 echo "<img src='JPlot.png'/>" >> $outputFile 118 echo "<img src='JPlot.png'/>" >> $outputFile
119 echo "</div>" >> $outputFile
120
121 echo "<div class='tabbertab' title='CDR3 Characteristics'>" >> $outputFile
122 echo "<img src='CDR3LengthPlot.png'/><br />" >> $outputFile
119 echo "<img src='AAComposition.png'/>" >> $outputFile 123 echo "<img src='AAComposition.png'/>" >> $outputFile
120 echo "<img src='DReadingFrame.png'/>" >> $outputFile 124 echo "<img src='DReadingFrame.png'/>" >> $outputFile
125
126 echo "<table class='pure-table pure-table-striped'>" >> $outputFile
127 echo "<thead><tr><th>Sample</th><th>Median CDR3 Length</th></tr></thead>" >> $outputFile
128 while IFS=, read Sample median
129 do
130 echo "<tr><td>$Sample</td><td>$median</td></tr>" >> $outputFile
131 done < $outputDir/AAMedianBySample.csv
132 echo "</table>" >> $outputFile
133
121 echo "</div>" >> $outputFile 134 echo "</div>" >> $outputFile
122 135
123 #Heatmaps 136 #Heatmaps
124 137
125 count=1 138 count=1