Combined scores into a single Triangulation Score.

Code for UI to be integrated shortly.

src/edu/uconn/tripoint/export/PathwayGeneCytoscapeNode.java

@@ -39,7 +39,11 @@ public String toJSON(){
 		sb.append("\"impact_pval\" : "+_tg.getImpactPValue(_pathway)+",\n");
 		sb.append("\"impact_qval\" : "+_tg.getImpactFDR(_pathway)+",\n");
 		sb.append("\"noncoding_count\" : "+_noncodingcount+",\n");
-		sb.append("\"noncoding_count_pval\" : "+_ncp+"\n");
+		sb.append("\"noncoding_count_pval\" : "+_ncp+",\n");
+		sb.append("\"triangulation\" : "+_tg.getTriangulationScore(_pathway)+",\n");
+		sb.append("\"triangulation_pval\" : "+_tg.getTriangulationPValue(_pathway)+",\n");
+		sb.append("\"triangulation_qval\" : "+_tg.getTriangulationFDR(_pathway)+"\n");
+
 		sb.append("}\n");
 		sb.append("}\n");
 		return sb.toString();

src/edu/uconn/tripoint/export/TriangulationExport.java

@@ -32,9 +32,9 @@ public void ExportTriangulation(Map<Gene, List<Pathway>> genepathways, Collectio
 				"Support Score"+"\t"+"Support p-value"+"\t"+"Support q-value"+"\t"+
 				"Consistency Score"+"\t"+"Consistency p-value"+"\t"+"Consistency q-value"+"\t"+
 				"Impact Score"+"\t"+"Impact p-value"+"\t"+"Impact q-value"+"\t"+
-				//"Supporting Triangulation Score"+"\t"+"Supporting Triangulation p-value"+"\t"+"Supporting Triangulation q-value"+"\t"+
-				//"Inconsistent Triangulation Score"+"\t"+"Inconsistent Triangulation p-value"+"\t"+"Inconsistent Triangulation q-value"+"\t"+
-				"Number of NonCoding Targets"+"\t"+"NonCoding Poisson p-value"+"\n");
+				"Number of NonCoding Targets"+"\t"+"NonCoding Poisson p-value"+"\t"+
+				"Triangulation Score"+"\t"+"Triangulation p-value"+"\t"+"Triangulation q-value"+"\t"+"\n");
+
 		for(Iterator<TriangulatedGene> it = genes.iterator(); it.hasNext();){
 			TriangulatedGene next = it.next();
 			for(Iterator<Pathway> it2 = genepathways.get(next.getGene()).iterator(); it2.hasNext();){
@@ -70,13 +70,9 @@ private void writeLine(BufferedWriter bw, Pathway p, TriangulatedGene g, Map<Gen
 		double imp = g.getImpactPValue(pid);
 		double imfdr = g.getImpactFDR(pid);
 
-		//double stris = g.getSupportTriangulationScore(pid);
-		//double strip = g.getSupportTriangulationPValue(pid);
-		//double strifdr = g.getSupportingTriangulationFDR(pid);
-
-		//double itris = g.getInconsistentTriangulationScore(pid);
-		//double itrip = g.getInconsistentTriangulationPValue(pid);
-		//double itrifdr = g.getInconsistentTriangulationFDR(pid);
+		double tris = g.getTriangulationScore(pid);
+		double trip = g.getTriangulationPValue(pid);
+		double trifdr = g.getTriangulationFDR(pid);
 
 		List<Location> l = noncoding.get(gene);
 		int nccount = l != null ? l.size() : 0;
@@ -88,9 +84,8 @@ private void writeLine(BufferedWriter bw, Pathway p, TriangulatedGene g, Map<Gen
 				ss+"\t"+sp+"\t"+sfdr+"\t"+
 				cs+"\t"+cp+"\t"+cfdr+"\t"+
 				ims+"\t"+imp+"\t"+imfdr+"\t"+
-				//stris+"\t"+strip+"\t"+strifdr+"\t"+
-				//itris+"\t"+itrip+"\t"+itrifdr+"\t"+
-				nccount+"\t"+ncp+"\n");
+				nccount+"\t"+ncp+"\t"+
+				tris+"\t"+trip+"\t"+trifdr+"\n");
 	}
 
 }

src/edu/uconn/tripoint/integration/PoissonNonCoding.java

@@ -26,16 +26,25 @@ public Map<Gene,Double> getPoissonPValues(Map<Gene,List<Location>> m){
 			average += size;
 			max = Math.max(max, size);
 		}
-		average /= m.size();
 
-		BigDecimal[] distr = getCumulativePoisson(max,average);
-
-		Map<Gene,Double> rv = new TreeMap<Gene, Double>();
-		for(Iterator<Entry<Gene, List<Location>>> it = m.entrySet().iterator(); it.hasNext();){
-			Entry<Gene, List<Location>> e = it.next();
-			rv.put(e.getKey(), getPoissonPValue(distr, e.getValue().size(), average));
+		if(max == 0){
+			Map<Gene,Double> rv = new TreeMap<Gene, Double>();
+			for(Iterator<Entry<Gene, List<Location>>> it = m.entrySet().iterator(); it.hasNext();){
+				Entry<Gene, List<Location>> e = it.next();
+				rv.put(e.getKey(), 1d);
+			}
+			return rv;
+		}
+		else{
+			average /= m.size();
+			BigDecimal[] distr = getCumulativePoisson(max,average);
+			Map<Gene,Double> rv = new TreeMap<Gene, Double>();
+			for(Iterator<Entry<Gene, List<Location>>> it = m.entrySet().iterator(); it.hasNext();){
+				Entry<Gene, List<Location>> e = it.next();
+				rv.put(e.getKey(), getPoissonPValue(distr, e.getValue().size(), average));
+			}
+			return rv;
 		}
-		return rv;
 	}
 
 	/**

src/edu/uconn/tripoint/triangulation/ProgramParameters.java

@@ -7,7 +7,7 @@
 
 public class ProgramParameters {
 
-	public final double VERSION = 1.0;
+	public final double VERSION = 1.1;
 	//required
 	private String _expfile;
 	private String _db;
@@ -28,7 +28,50 @@ public class ProgramParameters {
 	private String _chrinter;
 	private String _nct;
 	private int _prox = 50000;
+
 
+	public ProgramParameters(String expfile, String db, String outdir, 
+			String nct, String ci, String refflat, Integer prox,
+			double down, double up, double w, double p, double r, int perm, long rstate){
+		_down = -0.05;
+		_up = 0.05;
+		_w = 0.2;
+		_p = 0.25;
+		_r = 0.25;
+		_gid = "SYMBOL";
+		_perm = 10000;
+		_rstate = System.currentTimeMillis();
+
+
+		_expfile = expfile;
+		_db = db;
+		_outdir = outdir;
+
+		if(nct != null && !nct.equals("")){
+			_nct = nct;
+		}
+
+		if(ci != null && !ci.equals("")){
+			_chrinter = ci;
+		}
+
+		if(refflat != null && !refflat.equals("")){
+			_refflat = refflat;
+		}
+
+		if(prox != null){
+			_prox = prox;
+		}
+
+		_down = down;
+		_up = up;
+		_w = w;
+		_p = p;
+		_r = r;
+		_perm = perm;
+		_rstate = rstate;
+	}
+
 
 	public ProgramParameters(String[] args){
 		//set default values;
@@ -172,13 +215,13 @@ public boolean hasNonCoding(){
 	public String getConsoleManual(){
 		StringBuilder sb = new StringBuilder();
 		sb.append("Version: "+VERSION+"\n");
-		sb.append("Usage:\t\t\tjava -jar tripoint.jar <expression file> -db <pathway database> -o <output directory>\n\n");
+		sb.append("Usage:\t\t\tjava -jar tripoint.jar <expression file> -db <pathway database> -o <entire output directory path>\n\n");
 		sb.append("-db\t\t\tSets pathway database to import pathways from GRAPHITE.  Values available: \"kegg\", \"reactome\", \"biocarta\", \"humancyc\", \"nci\", \"panther\" \n\n");
 		sb.append("-o\t\t\tSets output directory for saving result files.  REQUIRED\n\n");
 		sb.append("-gid\t\t\tSets the conversion method for gene identifiers.  Refer to 'convertIdentifiers' in GRAPHITE. Default: \"SYMBOL\" (Currently other identifiers are not recommended)\n\n");
 		sb.append("-up\t\t\tSets the up-regulated gene threshold.  Default: 0.05\n\n");
 		sb.append("-down\t\t\tSets the down-regulated gene threshold.  Default: -0.05\n\n");
-		sb.append("-w\t\t\tSets the weak activation/inhibition factor.  Default: 0.5\n\n");
+		sb.append("-w\t\t\tSets the weak activation/inhibition factor.  Default: 0.2\n\n");
 		sb.append("-p\t\t\tControls the impact of gene expression when calculating measures.  Default: 0.25\n\n");
 		sb.append("-r\t\t\tControls the rate of exponential decay to control edge distance in impact score calculation.  Default: 0.25\n\n");
 		sb.append("-perm\t\t\tSets the number of permutations for p-value calculations.  Default: 10000\n\n");

src/edu/uconn/tripoint/triangulation/Run.java

@@ -28,6 +28,7 @@ public static void main(String[] args){
 	}
 
 	public void run(String[] args){
+		long timestart = System.currentTimeMillis();
 		ProgramParameters params = new ProgramParameters(args);
 		if(params.hasRequired()){
 			//Step 1: Import the pathways from Graphite (needs Rserve started to work)
@@ -53,18 +54,13 @@ public void run(String[] args){
 				e.printStackTrace();
 			}
 
-			//Step 3: Run Triangulation.
-			Triangulation t = new Triangulation();
-			t.runTriangulation(globalpathway, pathways, g.values(), params.getDownThresh(), params.getUpThresh(), params.getW(), params.getP(), params.getR());
-
-			System.out.println("Running permutations:");
-			//Step 4: Run Permutations
-			t.runPermutations(g.values(), params.getNumPermutations(), params.getRandomState(), globalpathway, pathways, params.getDownThresh(), params.getUpThresh(), params.getW(), params.getP(), params.getR());
-
 
 			//Optional & Output Steps:
 			Map<Gene,List<Location>> m = new TreeMap<Gene,List<Location>>();
+			Map<Gene,Double> ncp = new TreeMap<Gene,Double>();
+			PoissonNonCoding pnc = new PoissonNonCoding();
 			if(params.hasNonCoding()){
+
 				Util u = new Util();
 				Map<Gene, List<Location>> refflat = null;
 				try {
@@ -89,20 +85,28 @@ public void run(String[] args){
 					Proximal p = new Proximal(params.getNonCodingTargets(), params.getProximityDistance());
 					m = p.getNoncodingTargets(g.values(), refflat);
 				}
-				//Export Noncoding Targets
+			}
+
+
+			//Step 3: Run Triangulation.
+			Triangulation t = new Triangulation();
+			t.runTriangulation(globalpathway, pathways, g.values(), params.getDownThresh(), params.getUpThresh(), params.getW(), params.getP(), params.getR(), m);
+
+			System.out.println("Running permutations:");
+			//Step 4: Run Permutations
+			t.runPermutations(g.values(), params.getNumPermutations(), params.getRandomState(), globalpathway, pathways, params.getDownThresh(), params.getUpThresh(), params.getW(), params.getP(), params.getR(), m);
+
+			if(params.hasNonCoding()){
 				NonCodingRegulatorExport ncte = new NonCodingRegulatorExport();
 				try {
 					ncte.ExportNonCodingTargets(globalpathway, pathways, t.getTriangulatedGenes(), m, params.getOutputDirectory(), params.getPathwayDB());
 				} catch (IOException e) {
 					e.printStackTrace();
 				}
+				ncp = pnc.getPoissonPValues(m);
 			}
-
-
-			Map<Gene,Double> ncp = new TreeMap<Gene,Double>();
-			PoissonNonCoding pnc = new PoissonNonCoding();
-			ncp = pnc.getPoissonPValues(m);
-
+
+
 			//Export Triangulation
 			TriangulationExport te = new TriangulationExport();
 			try {
@@ -128,6 +132,7 @@ public void run(String[] args){
 		else{
 			System.out.println(params.getConsoleManual());
 		}
+		System.out.println(System.currentTimeMillis()-timestart+" milliseconds.");
 	}