Use correct data set and color for PA edges

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/style/EMStyleBuilder.java

@@ -34,6 +34,7 @@
 import org.baderlab.csplugins.enrichmentmap.model.EMSignatureDataSet;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.cytoscape.event.CyEventHelper;
+import org.cytoscape.model.CyEdge;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.model.CyNode;
 import org.cytoscape.view.model.CyNetworkView;
@@ -112,6 +113,7 @@ public static class Columns {
 		public static final ColumnDescriptor<String> EDGE_DATASET = new ColumnDescriptor<>("Data Set", String.class);
 		public static final String EDGE_DATASET_VALUE_COMPOUND = "compound"; 
 		public static final String EDGE_DATASET_VALUE_SIG = "signature"; // post-analysis edges
+		public static final String EDGE_INTERACTION_VALUE_SIG = "sig"; // post-analysis edges
 
 		// Post-analysis Edge Attributes
 		public static final ColumnDescriptor<Double> EDGE_HYPERGEOM_PVALUE = new ColumnDescriptor<>("Overlap_Hypergeom_pVal", Double.class);
@@ -324,13 +326,14 @@ private void setEdgeWidth(VisualStyle vs, EMStyleOptions options) {
 	}
 
 	private void setEdgeLineType(VisualStyle vs, EMStyleOptions options) {
-		String prefix = options.getAttributePrefix();
-		String col = Columns.EDGE_DATASET.with(prefix, null);
+//		String prefix = options.getAttributePrefix();
+		String col = CyEdge.INTERACTION;
+//		String col = Columns.EDGE_DATASET.with(prefix, null);
 
 		DiscreteMapping<String, LineType> dm = (DiscreteMapping<String, LineType>) dmFactory
 				.createVisualMappingFunction(col, String.class, EDGE_LINE_TYPE);
 		dm.putMapValue(Columns.EDGE_DATASET_VALUE_COMPOUND, LineTypeVisualProperty.SOLID);
-		dm.putMapValue(Columns.EDGE_DATASET_VALUE_SIG, LineTypeVisualProperty.DOT);
+		dm.putMapValue(Columns.EDGE_INTERACTION_VALUE_SIG, LineTypeVisualProperty.DOT);
 
 		vs.addVisualMappingFunction(dm);
 	}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/CreateDiseaseSignatureTask.java

@@ -116,7 +116,6 @@ public class CreateDiseaseSignatureTask extends AbstractTask implements Observab
 	private Map<String, GenesetSimilarity> geneSetSimilarities;
 
 	private EMSignatureDataSet signatureDataSet;
-	private boolean createSeparateEdges;
 
 	private CreateDiseaseSignatureTaskResult.Builder taskResult = new CreateDiseaseSignatureTaskResult.Builder();
 
@@ -139,11 +138,6 @@ private EMSignatureDataSet getSignatureDataSet() {
 		return signatureDataSet;
 	}
 
-	public void setCreateSeparateEdges(boolean createSeparateEdges) {
-		this.createSeparateEdges = createSeparateEdges;
-	}
-	
-	
 	@Inject
 	public CreateDiseaseSignatureTask(@Assisted EnrichmentMap map, @Assisted PostAnalysisParameters params, @Assisted String dataSetName) {
 		this.map = map;
@@ -485,7 +479,7 @@ private void createEdge(String edgeName, CyNetwork network, CyNetworkView netVie
 
 		GenesetSimilarity genesetSimilarity = geneSetSimilarities.get(edgeName);
 		CyEdge edge = null;
-		if(!createSeparateEdges)
+		if(!map.getParams().getCreateDistinctEdges())
 			edge = NetworkUtil.getEdgeWithValue(network, edgeTable, CyNetwork.NAME, edgeName);
 
 		if (edge == null) {
@@ -497,7 +491,8 @@ private void createEdge(String edgeName, CyNetwork network, CyNetworkView netVie
 					return;
 
 				edge = network.addEdge(hubNode, geneSet, false);
-				sigDataSet.addEdgeSuid(edge.getSUID());
+//				sigDataSet.addEdgeSuid(edge.getSUID());
+				map.getDataSet(dataSetName).addEdgeSuid(edge.getSUID());
 				taskResult.addNewEdge(edge);
 			} else {
 				return; // edge does not exist and does not pass cutoff, do nothing
@@ -528,7 +523,7 @@ private void createEdge(String edgeName, CyNetwork network, CyNetworkView netVie
 		Columns.EDGE_OVERLAP_GENES.set(row, prefix, null, geneList);
 		Columns.EDGE_OVERLAP_SIZE.set(row, prefix, null, genesetSimilarity.getSizeOfOverlap());
 		Columns.EDGE_SIMILARITY_COEFF.set(row, prefix, null, genesetSimilarity.getSimilarityCoeffecient());
-		Columns.EDGE_DATASET.set(row, prefix, null, Columns.EDGE_DATASET_VALUE_SIG);
+		Columns.EDGE_DATASET.set(row, prefix, null, dataSetName /* Columns.EDGE_DATASET_VALUE_SIG */);
 
 		if (passedCutoff)
 			Columns.EDGE_CUTOFF_TYPE.set(row, prefix, null, params.getRankTestParameters().getType().display);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/PostAnalysisPanelMediator.java

@@ -133,7 +133,6 @@ private void addGeneSets(CyNetworkView netView, PostAnalysisParameters params) {
 			for(EMDataSet dataset : map.getDataSetList()) {
 				CreateDiseaseSignatureTask task = signatureTaskFactory.create(map, params, dataset.getName());
 				task.setSignatureDataSet(sigDataSet);
-				task.setCreateSeparateEdges(true);
 				tasks.append(task);
 			}