Command for setting dataset colors. Refs #455

Author: mikekucera

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

@@ -2,6 +2,7 @@
 
 import org.baderlab.csplugins.enrichmentmap.actions.OpenEnrichmentMapAction;
 import org.baderlab.csplugins.enrichmentmap.commands.ChartCommandTask;
+import org.baderlab.csplugins.enrichmentmap.commands.DatasetColorCommandTask;
 import org.baderlab.csplugins.enrichmentmap.commands.DatasetShowCommandTask;
 import org.baderlab.csplugins.enrichmentmap.commands.EMBuildCommandTask;
 import org.baderlab.csplugins.enrichmentmap.commands.EMGseaCommandTask;
@@ -90,6 +91,12 @@ public CommandTaskFactory provideDatasetHide(DatasetShowCommandTask.Factory task
 		return CommandTaskFactory.create("dataset hide", desc, longDesc, () -> taskFactory.create(false));
 	}
 
+	@ProvidesIntoSet
+	public CommandTaskFactory provideDatasetColor(Provider<DatasetColorCommandTask> taskProvider) {
+		String desc = "Allows to change the colors assigned to data sets.";
+		return CommandTaskFactory.create("dataset color", desc, null, taskProvider);
+	}
+	
 	@ProvidesIntoSet
 	public CommandTaskFactory provideChart(Provider<ChartCommandTask> taskFactory) {
 		String desc = "Sets the chart options for an EnrichmentMap network.";

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/ChartCommandTask.java

@@ -10,7 +10,6 @@
 import org.baderlab.csplugins.enrichmentmap.style.ChartType;
 import org.baderlab.csplugins.enrichmentmap.style.ColorScheme;
 import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder.StyleUpdateScope;
-import org.baderlab.csplugins.enrichmentmap.task.ApplyEMStyleTask;
 import org.baderlab.csplugins.enrichmentmap.view.control.ControlPanelMediator;
 import org.baderlab.csplugins.enrichmentmap.view.control.io.ViewParams;
 import org.cytoscape.view.model.CyNetworkView;
@@ -23,7 +22,6 @@
 public class ChartCommandTask extends AbstractTask {
 
 	@Inject private ControlPanelMediator controlPanelMediator;
-	@Inject private ApplyEMStyleTask.Factory applyStyleTaskFactory;
 
 	@ContainsTunables @Inject
 	public NetworkTunable networkTunable;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/DatasetColorCommandTask.java

@@ -0,0 +1,81 @@
+package org.baderlab.csplugins.enrichmentmap.commands;
+
+import java.awt.Color;
+import java.util.List;
+import java.util.Map;
+
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.DatasetColorTunable;
+import org.baderlab.csplugins.enrichmentmap.commands.tunables.NetworkTunable;
+import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
+import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
+import org.baderlab.csplugins.enrichmentmap.style.EMStyleBuilder.StyleUpdateScope;
+import org.baderlab.csplugins.enrichmentmap.style.EMStyleOptions;
+import org.baderlab.csplugins.enrichmentmap.view.control.ControlPanelMediator;
+import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapMediator;
+import org.cytoscape.view.model.CyNetworkView;
+import org.cytoscape.work.AbstractTask;
+import org.cytoscape.work.ContainsTunables;
+import org.cytoscape.work.TaskMonitor;
+
+import com.google.inject.Inject;
+import com.google.inject.Provider;
+
+public class DatasetColorCommandTask extends AbstractTask {
+
+	@Inject private Provider<HeatMapMediator> heatMapMediatorProvider;
+	@Inject private ControlPanelMediator controlPanelMediator;
+	
+	@ContainsTunables @Inject
+	public NetworkTunable networkTunable;
+	
+	@ContainsTunables @Inject
+	public DatasetColorTunable datasetColorTunable;
+	
+	@Override
+	public void run(TaskMonitor tm) throws Exception {
+		tm.setTitle("Change Data Set Colors");
+		tm.setProgress(0.1);
+		
+		CyNetworkView netView = networkTunable.getNetworkView();
+		EnrichmentMap map = networkTunable.getEnrichmentMap();
+		if(netView == null || map == null)
+			throw new IllegalArgumentException("network is not an EnrichmentMap network");
+		
+		Map<String,Color> colors = datasetColorTunable.getColors();
+		if(colors.isEmpty())
+			throw new IllegalArgumentException("no colors specified");
+		
+		List<EMDataSet> datasetList = map.getDataSetList();
+		
+		for(var entry : colors.entrySet()) {
+			String dsName = entry.getKey();
+			Color color = entry.getValue();
+			
+			EMDataSet ds = map.getDataSet(dsName);
+			if(ds != null) {
+				ds.setColor(color);
+				tm.setStatusMessage("Color changed for dataset: '" + dsName + "'");
+			} else {
+				try {
+					int index = Integer.parseInt(dsName);
+					ds = datasetList.get(index);
+					ds.setColor(color);
+					tm.setStatusMessage("Color changed for dataset: '" + dsName + "'");
+				} catch(NumberFormatException | IndexOutOfBoundsException e) {
+					tm.setStatusMessage("Dataset not found: '" + dsName + "'");
+				}
+			}
+		};
+		
+		// update panels
+		controlPanelMediator.updateDataSetList(networkTunable.getNetworkView());
+		heatMapMediatorProvider.get().reset();
+
+		// update visual style
+		EMStyleOptions styleOptions = controlPanelMediator.createStyleOptions(netView);
+		controlPanelMediator.applyVisualStyle(styleOptions, StyleUpdateScope.ONLY_DATASETS);
+		heatMapMediatorProvider.get().reset();
+		
+		tm.setProgress(1.0);
+	}
+}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/tunables/DatasetColorTunable.java

@@ -0,0 +1,45 @@
+package org.baderlab.csplugins.enrichmentmap.commands.tunables;
+
+import java.awt.Color;
+import java.util.Collections;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.stream.Collectors;
+
+import org.cytoscape.work.Tunable;
+
+import com.google.common.base.Splitter;
+import com.google.common.base.Strings;
+
+public class DatasetColorTunable {
+	
+	@Tunable(description="Comma separated list of key=value pairs where the key is the "
+			+ "name or index of a data set, and the value is an HTML hex color code. "
+			+ "Example: \"DataSet1=#224433,DataSet2=#887766\"")
+	public String colors = null;
+	
+	
+	public Map<String,Color> getColors() {
+		if(Strings.isNullOrEmpty(colors))
+			return Collections.emptyMap();
+
+		return 
+			Splitter.on(',')
+			.omitEmptyStrings()
+			.withKeyValueSeparator(
+				Splitter.on('=')
+				.limit(2)
+				.trimResults()
+			)  
+			.split(colors)
+			.entrySet()
+			.stream()
+			.collect(
+				Collectors.toMap(
+					Entry::getKey, 
+					v -> Color.decode(v.getValue())
+				)
+			);
+	}
+
+}