Mercurial > repos > md-anderson-bioinformatics > heat_map_creation_advanced
comparison heatmap_advanced.sh @ 8:c1be063b2454 draft
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author | insilico-bob |
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date | Mon, 06 Jul 2020 14:26:14 -0400 |
parents | c5489978071a |
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7:c5489978071a | 8:c1be063b2454 |
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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)" |