Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced

comparison heatmap_advanced.sh @ 8:c1be063b2454 draft

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author insilico-bob
date Mon, 06 Jul 2020 14:26:14 -0400
parents c5489978071a
children
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7:c5489978071a 8:c1be063b2454
349 done 349 done
350 classJson=$classJson']' 350 classJson=$classJson']'
351 #END: Construct JSON for classification files 351 #END: Construct JSON for classification files
352 #echo "CLASSIFICATION JSON: "$classJson 352 #echo "CLASSIFICATION JSON: "$classJson
353 353
354 #Add build platform JSON for distinction between GenePattern and Galaxy Builders
355 platformJson='"build_platform": "Galaxy",'
356
354 #Complete construction of Parameter JSON file by adding all JSON sections created above 357 #Complete construction of Parameter JSON file by adding all JSON sections created above
355 parmJson=$parmJson$rowConfigJson$colConfigJson$attribJson$matrixJson$classJson 358 parmJson=$parmJson$rowConfigJson$colConfigJson$attribJson$matrixJson$platformJson$classJson
356 parmJson=$parmJson'}' 359 parmJson=$parmJson'}'
357 #echo "COMPLETED PARAMETER JSON: "$parmJson 360 #echo "COMPLETED PARAMETER JSON: "$parmJson
358 361
359 #run R to cluster matrix 362 #run R to cluster matrix
360 output="$(R --slave --vanilla --file=$tooldir/CHM_Advanced.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)" 363 output="$(R --slave --vanilla --file=$tooldir/CHM_Advanced.R --args $inputMatrix $rowOrder $rowDistance $rowAgglomeration $colOrder $colDistance $colAgglomeration $rowOrderFile $colOrderFile $rowDendroFile $colDendroFile $rowCuts $colCuts $rowLabels $colLabels 2>&1)"