Mercurial > repos > md-anderson-bioinformatics > heat_map_creation

comparison heatmap.sh @ 42:2f57ac512f46 draft

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Uploaded
author insilico-bob
date Mon, 06 Jul 2020 14:23:38 -0400
parents 8acca16f3921
children
comparison
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41:8acca16f3921 42:2f57ac512f46
130 fi 130 fi
131 done 131 done
132 classJson=$classJson']' 132 classJson=$classJson']'
133 #END: Construct JSON for classification files 133 #END: Construct JSON for classification files
134 134
135 parmJson=$parmJson$matrixJson$rowConfigJson$colConfigJson$classJson 135 #Add build platform JSON for distinction between GenePattern and Galaxy Builders
136 platformJson='"build_platform": "Galaxy",'
137
138 parmJson=$parmJson$matrixJson$rowConfigJson$colConfigJson$platformJson$classJson
136 parmJson=$parmJson'}' 139 parmJson=$parmJson'}'
137 #echo "HEATMAP PARAMETERS JSON: "$parmJson 140 #echo "HEATMAP PARAMETERS JSON: "$parmJson
138 141
139 #run R to cluster matrix 142 #run R to cluster matrix
140 output="$(R --slave --vanilla --file=$tooldir/CHM.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)" 143 output="$(R --slave --vanilla --file=$tooldir/CHM.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)"