Show in genemania/string, add option to select genes in expression file

Refs #438

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/GeneManiaTaskFactory.java

@@ -15,8 +15,8 @@
 import org.baderlab.csplugins.enrichmentmap.model.AssociatedApp;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
+import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListTunable;
 import org.baderlab.csplugins.enrichmentmap.util.TaskUtil;
-import org.baderlab.csplugins.enrichmentmap.view.heatmap.GSEALeadingEdgeRankingOption;
 import org.baderlab.csplugins.enrichmentmap.view.util.OpenBrowser;
 import org.cytoscape.command.AvailableCommands;
 import org.cytoscape.command.CommandExecutorTaskFactory;
@@ -47,7 +47,7 @@ public class GeneManiaTaskFactory {
 	@Inject private OpenBrowser openBrowser;
 
 
-	public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, List<String> selectedGenes, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {
+	public TaskIterator createTaskIterator(GeneListTunable geneListTaskParams) {
 		// Show message to user if genemania not installed
 		List<String> commands = availableCommands.getCommands(GENEMANIA_NAMESPACE);
 
@@ -67,7 +67,7 @@ public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, Li
 
 
 
-		QueryGeneManiaTask queryTask = queryGeneManiaTaskFactory.create(map, genes, selectedGenes, leadingEdgeRanks);
+		QueryGeneManiaTask queryTask = queryGeneManiaTaskFactory.create(geneListTaskParams);
 
 		// Get list of organisms from GeneMANIA
 		TaskIterator ti = commandExecutorTaskFactory.createTaskIterator(
@@ -95,7 +95,7 @@ public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, Li
 		ti.append(new AbstractTask() {
 			@Override
 			public void run(TaskMonitor taskMonitor) throws Exception {
-				onGeneManiaQueryFinished(queryTask.getResult(), map);
+				onGeneManiaQueryFinished(queryTask.getResult(), geneListTaskParams.getEnrichmentMap());
 			}
 		});
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/QueryGeneManiaNodeViewTaskFactory.java

@@ -5,6 +5,7 @@
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
 import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder.Columns;
+import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListTunable;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.GSEALeadingEdgeRankingOption;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.RankingOptionFactory;
 import org.cytoscape.model.CyNetwork;
@@ -34,7 +35,9 @@ public TaskIterator createTaskIterator(View<CyNode> nodeView, CyNetworkView netw
 
 		List<GSEALeadingEdgeRankingOption> rankOptions = rankingOptionFactory.getGSEADataSetSetRankOptions(map);
 
-		TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(map, genes, null, rankOptions);
+		
+		GeneListTunable geneListTunable = new GeneListTunable(map, genes, null, rankOptions);
+		TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(geneListTunable);
 		return tasks;
 	}
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/genemania/QueryGeneManiaTask.java

@@ -5,10 +5,8 @@
 import java.util.List;
 import java.util.Map;
 
-import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListTunable;
 import org.baderlab.csplugins.enrichmentmap.util.TaskUtil;
-import org.baderlab.csplugins.enrichmentmap.view.heatmap.GSEALeadingEdgeRankingOption;
 import org.cytoscape.command.CommandExecutorTaskFactory;
 import org.cytoscape.work.AbstractTask;
 import org.cytoscape.work.ProvidesTitle;
@@ -55,21 +53,12 @@ public class QueryGeneManiaTask extends AbstractTask {
 	@Inject private SynchronousTaskManager<?> syncTaskManager;
 
 	public static interface Factory {
-		QueryGeneManiaTask create(
-				EnrichmentMap map, 
-				@Assisted("geneList") List<String> geneList, 
-				@Assisted("selectedGenes") List<String> selectedGenes, 
-				List<GSEALeadingEdgeRankingOption> leadingEdgeRanks);
+		QueryGeneManiaTask create(GeneListTunable geneListTaskParams);
 	}
 
 	@AssistedInject
-	public QueryGeneManiaTask(
-			@Assisted EnrichmentMap map, 
-			@Assisted("geneList") List<String> geneList, 
-			@Assisted("selectedGenes") List<String> selectedGenes, 
-			@Assisted List<GSEALeadingEdgeRankingOption> leadingEdgeRanks)
-	{
-		this.geneList = new GeneListTunable(map, geneList, selectedGenes, leadingEdgeRanks);
+	public QueryGeneManiaTask(@Assisted GeneListTunable geneListTaskParams) {
+		this.geneList = geneListTaskParams;
 		this.organisms = new ListSingleSelection<>();
 		this.weightingMethods = new ListSingleSelection<>(GMWeightingMethod.values());
 		this.weightingMethods.setSelectedValue(weightingMethods.getPossibleValues().get(0));

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/string/QueryStringNodeViewTaskFactory.java

@@ -5,6 +5,7 @@
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
 import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder.Columns;
+import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListTunable;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.GSEALeadingEdgeRankingOption;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.RankingOptionFactory;
 import org.cytoscape.model.CyNetwork;
@@ -34,7 +35,8 @@ public TaskIterator createTaskIterator(View<CyNode> nodeView, CyNetworkView netw
 
 		List<GSEALeadingEdgeRankingOption> rankOptions = rankingOptionFactory.getGSEADataSetSetRankOptions(map);
 
-		return stringAppFactory.createTaskIterator(map, genes, null, rankOptions);
+		GeneListTunable geneListTunable = new GeneListTunable(map, genes, null, rankOptions);
+		return stringAppFactory.createTaskIterator(geneListTunable);
 	}
 
 	@Override

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/string/QueryStringTask.java

@@ -4,10 +4,8 @@
 import java.util.List;
 import java.util.Map;
 
-import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListTunable;
 import org.baderlab.csplugins.enrichmentmap.util.TaskUtil;
-import org.baderlab.csplugins.enrichmentmap.view.heatmap.GSEALeadingEdgeRankingOption;
 import org.cytoscape.command.CommandExecutorTaskFactory;
 import org.cytoscape.model.CyNetwork;
 import org.cytoscape.work.AbstractTask;
@@ -51,21 +49,12 @@ public class QueryStringTask extends AbstractTask {
 	@Inject private CommandExecutorTaskFactory commandExecutorTaskFactory;
 
 	public static interface Factory {
-		QueryStringTask create(
-				EnrichmentMap map, 
-				@Assisted("geneList") List<String> geneList,
-				@Assisted("selectedGenes") List<String> selectedGenes,
-				List<GSEALeadingEdgeRankingOption> leadingEdgeRanks);
+		QueryStringTask create(GeneListTunable geneListTunable);
 	}
 
 	@AssistedInject
-	public QueryStringTask(
-			@Assisted EnrichmentMap map, 
-			@Assisted("geneList") List<String> geneList,
-			@Assisted("selectedGenes") List<String> selectedGenes,
-			@Assisted List<GSEALeadingEdgeRankingOption> leadingEdgeRanks)
-	{		
-		this.geneList = new GeneListTunable(map, geneList, selectedGenes, leadingEdgeRanks);
+	public QueryStringTask(@Assisted GeneListTunable geneListTunable) {		
+		this.geneList = geneListTunable;
 		this.organisms = new ListSingleSelection<>();
 	}
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/string/StringAppTaskFactory.java

@@ -15,8 +15,8 @@
 import org.baderlab.csplugins.enrichmentmap.model.AssociatedApp;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMapManager;
+import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListTunable;
 import org.baderlab.csplugins.enrichmentmap.util.TaskUtil;
-import org.baderlab.csplugins.enrichmentmap.view.heatmap.GSEALeadingEdgeRankingOption;
 import org.baderlab.csplugins.enrichmentmap.view.util.OpenBrowser;
 import org.cytoscape.command.AvailableCommands;
 import org.cytoscape.command.CommandExecutorTaskFactory;
@@ -44,7 +44,7 @@ public class StringAppTaskFactory {
 	@Inject private OpenBrowser openBrowser;
 
 
-	public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, List<String> selectedGenes, List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) {
+	public TaskIterator createTaskIterator(GeneListTunable geneListTunable) {
 		// Show message to user if STRING App not installed
 		List<String> commands = availableCommands.getCommands(STRING_NAMESPACE);
 
@@ -62,7 +62,7 @@ public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, Li
 			return null;
 		}
 
-		QueryStringTask queryTask = queryStringTaskFactory.create(map, genes, selectedGenes, leadingEdgeRanks);
+		QueryStringTask queryTask = queryStringTaskFactory.create(geneListTunable);
 
 		// Get list of organisms from STRING App
 		TaskIterator ti = commandExecutorTaskFactory.createTaskIterator(
@@ -89,7 +89,7 @@ public TaskIterator createTaskIterator(EnrichmentMap map, List<String> genes, Li
 		ti.append(new AbstractTask() {
 			@Override
 			public void run(TaskMonitor taskMonitor) throws Exception {
-				onStringQueryFinished(queryTask.getResult(), map);
+				onStringQueryFinished(queryTask.getResult(), geneListTunable.getEnrichmentMap());
 			}
 		});
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListGUITunableHandler.java

@@ -8,8 +8,6 @@
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 
-import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
-import org.baderlab.csplugins.enrichmentmap.view.heatmap.GSEALeadingEdgeRankingOption;
 import org.cytoscape.util.swing.LookAndFeelUtil;
 import org.cytoscape.work.Tunable;
 import org.cytoscape.work.swing.AbstractGUITunableHandler;
@@ -45,12 +43,7 @@ private JPanel createGeneListPanel() {
 		JLabel title = new JLabel(getDescription());
 
 		GeneListTunable geneListTunable = getGeneListTunable();
-		EnrichmentMap map = geneListTunable.getEnrichmentMap();
-		List<String> genes = geneListTunable.getGenes();
-		List<String> selectedGenes = geneListTunable.getSelectedGenes();
-		List<GSEALeadingEdgeRankingOption> leadingEdgeRanks = geneListTunable.getLeadingEdgeRanks();
-		
-		checkboxPanel = new GeneListPanel(map, genes, selectedGenes, leadingEdgeRanks);
+		checkboxPanel = new GeneListPanel(geneListTunable);
 
 		JPanel panel = new JPanel();
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListPanel.java

@@ -7,7 +7,6 @@
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
@@ -44,17 +43,14 @@ public class GeneListPanel extends JPanel {
 	private JButton selectAllButton;
 	private JButton selectNoneButton;
 	private JButton selectEdgeButton;
+	private JButton selectExprButton;
 
-	public GeneListPanel(
-			EnrichmentMap map, 
-			List<String> genes, 
-			List<String> selectedGenes, 
-			List<GSEALeadingEdgeRankingOption> leadingEdgeRanks) 
-	{
-		this.map = map;
-		
-		
-		Set<String> selected = selectedGenes == null ? Collections.emptySet() : new HashSet<>(selectedGenes);
+	public GeneListPanel(GeneListTunable geneListTunable) {
+		this.map = geneListTunable.getEnrichmentMap();
+		List<String> genes = geneListTunable.getGenes();
+		List<String> selected = geneListTunable.getSelectedGenes();
+		List<String> expressionGenes = geneListTunable.getExpressionGenes();
+		List<GSEALeadingEdgeRankingOption> leadingEdgeRanks = geneListTunable.getLeadingEdgeRanks();
 
 		checkboxListModel = new CheckboxListModel<>();
 		genes.stream().sorted().forEach(gene -> {
@@ -70,15 +66,18 @@ public GeneListPanel(
 		selectAllButton  = new JButton("Select All");
 		selectNoneButton = new JButton("Select None");
 		selectEdgeButton = new JButton("Select Leading Edge");
+		selectExprButton = new JButton("Select Genes With Expressions");
 
 		selectAllButton .addActionListener(selectionListener(cb -> cb.setSelected(true)));
 		selectNoneButton.addActionListener(selectionListener(cb -> cb.setSelected(false)));
 		selectEdgeButton.addActionListener(e -> selectLeadingEdge(genes, leadingEdgeRanks));
+		selectExprButton.addActionListener(e -> selectGenesWithExpressions(expressionGenes));
 
 		selectAllButton.setEnabled(false);
 		selectNoneButton.setEnabled(false);
 		selectEdgeButton.setEnabled(true);
 		selectEdgeButton.setVisible(!leadingEdgeRanks.isEmpty());
+		selectExprButton.setVisible(!expressionGenes.isEmpty());
 
 		checkboxListModel.addListDataListener(new ListDataListener() {
 			@Override
@@ -102,8 +101,8 @@ public void contentsChanged(ListDataEvent e) {
 			}
 		});
 
-		SwingUtil.makeSmall(selectAllButton, selectEdgeButton, selectNoneButton);		
-		LookAndFeelUtil.equalizeSize(selectAllButton, selectNoneButton, selectEdgeButton);
+		SwingUtil.makeSmall(selectAllButton, selectEdgeButton, selectNoneButton, selectExprButton);		
+		LookAndFeelUtil.equalizeSize(selectAllButton, selectNoneButton, selectEdgeButton, selectExprButton);
 
 		final GroupLayout layout = new GroupLayout(this);
 		setLayout(layout);
@@ -116,6 +115,7 @@ public void contentsChanged(ListDataEvent e) {
 						.addComponent(selectAllButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)
 						.addComponent(selectNoneButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)
 						.addComponent(selectEdgeButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)
+						.addComponent(selectExprButton, PREFERRED_SIZE, DEFAULT_SIZE, PREFERRED_SIZE)
    				)
    		);
    		layout.setVerticalGroup(layout.createParallelGroup()
@@ -125,6 +125,7 @@ public void contentsChanged(ListDataEvent e) {
 						.addComponent(selectNoneButton)
 						.addGap(20)
 						.addComponent(selectEdgeButton)
+						.addComponent(selectExprButton)
    				)
    		);
 
@@ -155,7 +156,6 @@ public void actionPerformed(ActionEvent e) {
 		}
 	}
 
-	
 	private void selectLeadingEdge(List<String> genes, GSEALeadingEdgeRankingOption ranks) {
 		List<CheckboxData<String>> oldValue = getSelectedData();
 		List<Integer> geneKeys = genes.stream().map(map::getHashFromGene).collect(Collectors.toList());
@@ -172,7 +172,19 @@ private void selectLeadingEdge(List<String> genes, GSEALeadingEdgeRankingOption
 		fireCheckboxListUpdated(oldValue);
 	}
 
-	
+	private void selectGenesWithExpressions(List<String> expressionGenes) {
+		Set<String> exgSet = new HashSet<>(expressionGenes);
+		List<CheckboxData<String>> oldValue = getSelectedData();
+		
+		checkboxListModel.forEach(checkBox -> {
+			String geneName = checkBox.getData();
+			boolean selected = exgSet.contains(geneName);
+			checkBox.setSelected(selected);
+		});
+		
+		fireCheckboxListUpdated(oldValue);
+	}
+
 	private ActionListener selectionListener(Consumer<CheckboxData<String>> action) {
 		return e -> {
 			List<CheckboxData<String>> oldValue = getSelectedData();

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/tunables/GeneListTunable.java

@@ -3,7 +3,9 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Objects;
+import java.util.stream.Collectors;
 
+import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.GSEALeadingEdgeRankingOption;
 
@@ -14,6 +16,8 @@ public class GeneListTunable {
 	private List<String> selectedGenes;
 	private List<GSEALeadingEdgeRankingOption> leadingEdgeRanks;
 
+	private List<String> expressionGenes;
+	
 
 	public GeneListTunable(
 			EnrichmentMap map, 
@@ -47,4 +51,20 @@ public EnrichmentMap getEnrichmentMap() {
 		return map;
 	}
 
+	public List<String> getExpressionGenes() {
+		if(expressionGenes == null) {
+			expressionGenes = genes.stream().filter(gene -> hasExpressions(map, gene)).collect(Collectors.toList());
+		}
+		return expressionGenes;
+	}
+	
+	private static boolean hasExpressions(EnrichmentMap map, String gene) {
+		int geneId = map.getHashFromGene(gene);
+		for(EMDataSet ds : map.getDataSetList()) {
+			if(ds.getExpressionGenes().contains(geneId)) {
+				return true;
+			}
+		}
+		return false;
+	}
 }

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

@@ -31,6 +31,7 @@
 import org.baderlab.csplugins.enrichmentmap.task.ApplyEMStyleTask;
 import org.baderlab.csplugins.enrichmentmap.task.genemania.GeneManiaTaskFactory;
 import org.baderlab.csplugins.enrichmentmap.task.string.StringAppTaskFactory;
+import org.baderlab.csplugins.enrichmentmap.task.tunables.GeneListTunable;
 import org.baderlab.csplugins.enrichmentmap.util.CoalesceTimer;
 import org.baderlab.csplugins.enrichmentmap.util.NetworkUtil;
 import org.baderlab.csplugins.enrichmentmap.view.control.ControlPanelMediator;
@@ -543,26 +544,26 @@ public static Collection<Integer> getGenes(EnrichmentMap map, Map<String,Set<Int
 		}
 	}
 
-	
-	private void runGeneMANIA() {
+	private GeneListTunable createGeneListTaskParams() {
 		EnrichmentMap map = getContentPanel().getEnrichmentMap();
 		List<String> genes = getContentPanel().getGenes();
 		List<String> selectedGenes = getContentPanel().getSelectedGenes();
 		List<GSEALeadingEdgeRankingOption> gseaOptions = rankingOptionFactory.getGSEADataSetSetRankOptions(map);
-		TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(map, genes, selectedGenes, gseaOptions);
+		return new GeneListTunable(map, genes, selectedGenes, gseaOptions);
+	}
+	
+	private void runGeneMANIA() {
+		GeneListTunable geneListTaskParams = createGeneListTaskParams();
+		TaskIterator tasks = geneManiaTaskFactory.createTaskIterator(geneListTaskParams);
 		taskManager.execute(tasks);
 	}
 
 	private void runString() {
-		EnrichmentMap map = getContentPanel().getEnrichmentMap();
-		List<String> genes = getContentPanel().getGenes();
-		List<String> selectedGenes = getContentPanel().getSelectedGenes();
-		List<GSEALeadingEdgeRankingOption> gseaOptions = rankingOptionFactory.getGSEADataSetSetRankOptions(map);
-		TaskIterator tasks = stringAppTaskFactoy.createTaskIterator(map, genes, selectedGenes, gseaOptions);
+		GeneListTunable geneListTaskParams = createGeneListTaskParams();
+		TaskIterator tasks = stringAppTaskFactoy.createTaskIterator(geneListTaskParams);
 		taskManager.execute(tasks);
 	}
 
-	
 	private void runPathwayCommons() {
 		long uuid = getEnrichmentMap().getNetworkID();
 		CyNetwork network = networkManager.getNetwork(uuid);