Makefile_annotationAndBiclustering

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# (C) 2016 Tyler W. H. Backman
# Tables and figures for annotation comparison and biclustering sections
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# perform comparison between bioassay and drugbank targets and store as matrix
# drug vs cluster object is called "drugComparisonMatrix"
working/drugComparisonMatrix.RData: src/comparisonMatrix.R $(databaseFile) working/highlyScreenedCids.txt working/curatedClusters.txt working/drug_target_uniprot_links.csv working/drugbank_links.csv
	$^ $@

# quantify results in drugComparisonMatrix
working/drugComparisonTable.tex: src/drugComparisonTable.R working/drugComparisonMatrix.RData working/clusterAnnotations.csv
	$^ $@

# perform biclustering to identify target/drug groups
working/biClusters.RData: src/biclusterMatrix.R working/drugComparisonMatrix.RData src/bicbin.R
	$^ $@ $(cores)

# analyze each bicluster one at a time
working/perClusterAnalysis: src/perClusterAnalysis.R \
							working/drugComparisonMatrix.RData \
							working/biClusters.RData \
							working/curatedClusters.txt \
							working/clusterAnnotations.csv \
							working/drugbank_links.csv \
							working/structureClusterDrugs.tab \
							working/combinedTargetDomainsTwoCols \
							working/Pfam-A.clans.tsv
	mkdir -p $@
	$^ $@ $(cores)

# make MDS plot of biclusters (color) vs structure (spatial)
working/biclusterMDS.pdf: src/biclusterMDS.R working/biClusters.RData working/drugbank.sdf working/drugbank_links.csv
	$^ $@	

# make heatmap of GO terms vs biclusters
working/biclusterGoScatter.pdf: src/biclusterGoScatter.R working/perClusterAnalysis working/clusterGOslimAnnotations.csv working/clusterAnnotations.csv working/drugComparisonMatrix.RData
	$^ $@

# make graph object of drug target matrix
working/drugComparisonGraph.gml: src/biclusterBipartiteGraph.R \
                                 working/drugComparisonMatrix.RData \
                                 working/biClusters.RData \
                                 working/clusterGOslimAnnotations.csv \
                                 working/clusterAnnotations.csv \
								 working/biclustergoids.RData
	$^ $@