Filter HeatMap based on data set of selected node/edge. Refs #396

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/PropertyManager.java

@@ -36,6 +36,7 @@ public interface PropertyListener<T> {
 	public static final Property<Boolean>  HEATMAP_AUTOFOCUS    = Property.of("heatmapAutofocus", false);
 	public static final Property<Boolean>  HEATMAP_DATASET_SYNC = Property.of("heatmapDatasetSync", true);
 	public static final Property<Boolean>  HEATMAP_AUTO_SORT    = Property.of("heatmapAutoSort", true);
+	public static final Property<Boolean>  HEATMAP_SELECT_SYNC  = Property.of("heatmapSelectSync", true);
 	public static final Property<Double>   P_VALUE              = Property.of("default.pvalue", 1.0);
 	public static final Property<Double>   Q_VALUE              = Property.of("default.qvalue", 0.1);
 	public static final Property<Boolean>  CREATE_WARN          = Property.of("create.warn", true);
@@ -98,6 +99,10 @@ public <T> T getValue(Property<T> property) {
 		}
 	}
 
+	public boolean isTrue(Property<Boolean> property) {
+		return Boolean.TRUE.equals(getValue(property));
+	}
+	
 	@SuppressWarnings("rawtypes")
 	public static List<Property<?>> getAllProperties() {
 		List<Property<?>> properties = new ArrayList<>();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/AbstractDataSet.java

@@ -1,10 +1,14 @@
 package org.baderlab.csplugins.enrichmentmap.model;
 
 import java.text.Collator;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
 import java.util.Set;
 
+import org.cytoscape.model.CyEdge;
+import org.cytoscape.model.CyNode;
+
 public abstract class AbstractDataSet implements Comparable<AbstractDataSet> {
 
 	private final String name;
@@ -42,6 +46,24 @@ public EnrichmentMap getMap() {
 		return map;
 	}
 
+	public boolean containsAnyNode(Collection<CyNode> nodes) {
+		for(CyNode node : nodes) {
+			if(nodeSuids.contains(node.getSUID())) {
+				return true;
+			}
+		}
+		return false;
+	}
+	
+	public boolean containsAnyEdge(Collection<CyEdge> edges) {
+		for(CyEdge edge : edges) {
+			if(edgeSuids.contains(edge.getSUID())) {
+				return true;
+			}
+		}
+		return false;
+	}
+	
 	public Set<Long> getNodeSuids() {
 		synchronized (lock) {
 			return Collections.unmodifiableSet(nodeSuids);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/HeatMapMediator.java

@@ -7,6 +7,7 @@
 import java.util.Collection;
 import java.util.Collections;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
@@ -104,6 +105,7 @@ public class HeatMapMediator implements RowsSetListener, SetCurrentNetworkViewLi
 	@AfterInjection
 	public void setPropertyListeners() {
 		propertyManager.addListener(PropertyManager.HEATMAP_DATASET_SYNC, (prop, value) -> reset());
+		propertyManager.addListener(PropertyManager.HEATMAP_SELECT_SYNC,  (prop, value) -> reset());
 	}
 
 
@@ -235,21 +237,38 @@ private void heatMapParamsChanged(HeatMapParams params) {
 		}
 	}
 
-	private Collection<EMDataSet> getEnabledDataSets(CyNetworkView networkView, EnrichmentMap map) {
-		if(Boolean.TRUE.equals(propertyManager.getValue(PropertyManager.HEATMAP_DATASET_SYNC))) {
-			// sync with the data set list on the control panel
+	
+	private Collection<EMDataSet> getEnabledDataSets(
+			CyNetworkView networkView, EnrichmentMap map, 
+			List<CyNode> selectedNodes, List<CyEdge> selectedEdges
+	) {
+		// must maintain the order returned by map.getDataSetList() (issue #390)
+		List<EMDataSet> dataSets = new ArrayList<>(map.getDataSetList());
+		
+		// Remove Data Sets that are not selected in the control panel
+		if(propertyManager.isTrue(PropertyManager.HEATMAP_DATASET_SYNC)) {
 			ViewParams params = controlPanelMediatorProvider.get().getAllViewParams().get(networkView.getSUID());
 			if(params != null) {
-				// important to maintain the order returned by map.getDataSetList() (issue #390)
-				List<EMDataSet> dataSets = new ArrayList<>(map.getDataSetList());
 				Set<String> filter = params.getFilteredOutDataSets();
 				dataSets.removeIf(ds -> filter.contains(ds.getName()));
-				return dataSets;
 			}
 		}
-		return map.getDataSetList();
+		
+		// Remove Data Sets that are not part of the selected nodes/edges
+		if(propertyManager.isTrue(PropertyManager.HEATMAP_SELECT_SYNC)) {
+			Iterator<EMDataSet> iter = dataSets.iterator();
+			while(iter.hasNext()) {
+				EMDataSet ds = iter.next();
+				if(!ds.containsAnyNode(selectedNodes) && !ds.containsAnyEdge(selectedEdges)) {
+					iter.remove();
+				}
+			}
+		}
+		
+		return dataSets;
 	}
 
+	
 	private void updateHeatMap(CyNetworkView networkView) {
 		if (!isHeatMapPanelRegistered())
 			return;
@@ -271,7 +290,7 @@ private void updateHeatMap(CyNetworkView networkView) {
 		if (emManager.isEnrichmentMap(networkView)) {
 			String prefix = map.getParams().getAttributePrefix();
 
-			dataSets = getEnabledDataSets(networkView, map);
+			dataSets = getEnabledDataSets(networkView, map, selectedNodes, selectedEdges);
 			Map<String,Set<Integer>> geneSetToGenes = map.unionGeneSetsOfInterest(dataSets);
 
 			union = unionGenesets(geneSetToGenes, map, network, selectedNodes, selectedEdges, prefix);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/OptionsPopup.java

@@ -95,12 +95,18 @@ private void createContents() {
 			propertyManager.setValue(PropertyManager.HEATMAP_AUTOFOCUS, autofocusCheckbox.isSelected());
 		});
 
-		JCheckBoxMenuItem syncCheckbox = new JCheckBoxMenuItem("Sync with Control Panel");
+		JCheckBoxMenuItem syncCheckbox = new JCheckBoxMenuItem("Sync Data Sets with Control Panel");
 		syncCheckbox.setSelected(propertyManager.getValue(PropertyManager.HEATMAP_DATASET_SYNC));
 		syncCheckbox.addActionListener(e -> {
 			propertyManager.setValue(PropertyManager.HEATMAP_DATASET_SYNC, syncCheckbox.isSelected());
 		});
 
+		JCheckBoxMenuItem selectedCheckbox = new JCheckBoxMenuItem("Display only selected Data Sets");
+		selectedCheckbox.setSelected(propertyManager.getValue(PropertyManager.HEATMAP_SELECT_SYNC));
+		selectedCheckbox.addActionListener(e -> {
+			propertyManager.setValue(PropertyManager.HEATMAP_SELECT_SYNC, selectedCheckbox.isSelected());
+		});
+		
 		JCheckBoxMenuItem autoSortCheckbox = new JCheckBoxMenuItem("Auto sort leading edge");
 		autoSortCheckbox.setSelected(propertyManager.getValue(PropertyManager.HEATMAP_AUTO_SORT));
 		autoSortCheckbox.addActionListener(e -> {
@@ -118,6 +124,7 @@ private void createContents() {
 		add(distanceMenu);
 		add(autofocusCheckbox);
 		add(syncCheckbox);
+		add(selectedCheckbox);
 		add(autoSortCheckbox);
 	}