Fixes global chart range and Heat Strips colors.

Author: chrtannus

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/control/ControlPanelMediator.java

@@ -57,6 +57,7 @@
 import org.baderlab.csplugins.enrichmentmap.view.legend.LegendPanelMediator;
 import org.baderlab.csplugins.enrichmentmap.view.postanalysis.EdgeWidthDialog;
 import org.baderlab.csplugins.enrichmentmap.view.postanalysis.PostAnalysisPanelMediator;
+import org.baderlab.csplugins.enrichmentmap.view.util.ChartUtil;
 import org.baderlab.csplugins.enrichmentmap.view.util.SliderBarPanel;
 import org.cytoscape.application.CyApplicationManager;
 import org.cytoscape.application.events.SetCurrentNetworkViewEvent;
@@ -532,13 +533,25 @@ private CyCustomGraphics2<?> createChart(ChartData data, ChartType type, ColorSc
 				Map<String, Object> props = new HashMap<>(type.getProperties());
 				props.put("cy_dataColumns", columns);
 
-				if (type == ChartType.LINE) {
-					props.put("cy_colors", colorScheme.getColors(1));
-				} else if (colorScheme != null) {
-					if (colorScheme == ColorScheme.RANDOM)
-						props.put("cy_colors", colorScheme.getColors(columns.size()));
-					else
-						props.put("cy_colorScheme", colorScheme.getKey());
+				if (type != null && type != ChartType.PIE) {
+					List<Double> range = ChartUtil.calculateGlobalRange(options.getNetworkView().getModel(), columns);
+					
+					props.put("cy_range", range);
+					props.put("cy_globalRange", true);
+				}
+				
+				if (colorScheme == ColorScheme.CONTRASTING || colorScheme == ColorScheme.MODULATED
+						|| colorScheme == ColorScheme.RAINBOW) {
+					props.put("cy_colorScheme", colorScheme.getKey());
+				} else {
+					int nColors = columns.size(); 
+					
+					if (type == ChartType.LINE)
+						nColors = 1;
+					else if (type == ChartType.HEAT_STRIPS)
+						nColors = 3;
+					
+					props.put("cy_colors", colorScheme.getColors(nColors));
 				}
 
 				try {

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/util/ChartUtil.java

@@ -0,0 +1,88 @@
+package org.baderlab.csplugins.enrichmentmap.view.util;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+import java.util.stream.Collectors;
+
+import org.cytoscape.model.CyColumn;
+import org.cytoscape.model.CyNetwork;
+import org.cytoscape.model.CyNode;
+import org.cytoscape.model.CyRow;
+import org.cytoscape.view.presentation.property.values.CyColumnIdentifier;
+
+public final class ChartUtil {
+
+	private ChartUtil() {
+	}
+	
+	/**
+	 * @return List whose first item is the minimum value of the range, and whose second item is the maximum value.
+	 */
+	@SuppressWarnings("unchecked")
+	public static List<Double> calculateGlobalRange(CyNetwork network, List<CyColumnIdentifier> dataColumns) {
+		List<Double> range = new ArrayList<>(2);
+		List<CyNode> nodes = network.getNodeList();
+		
+		if (!nodes.isEmpty()) {
+			double min = Double.POSITIVE_INFINITY;
+			double max = Double.NEGATIVE_INFINITY;
+			
+			Collection<CyColumn> columns = network.getDefaultNodeTable().getColumns();
+			Map<String, CyColumn> columnMap = columns.stream().collect(Collectors.toMap(CyColumn::getName, c -> c));
+			
+			for (final CyColumnIdentifier colId : dataColumns) {
+				final CyColumn column = columnMap.get(colId);
+				
+				if (column == null)
+					continue;
+				
+				final Class<?> colType = column.getType();
+				final Class<?> colListType = column.getListElementType();
+				
+				if (Number.class.isAssignableFrom(colType) ||
+						(List.class.isAssignableFrom(colType) && Number.class.isAssignableFrom(colListType))) {
+					for (final CyNode n : nodes) {
+						List<? extends Number> values = null;
+						final CyRow row = network.getRow(n);
+						
+						if (List.class.isAssignableFrom(colType))
+							values = (List<? extends Number>) row.getList(column.getName(), colListType);
+						else if (row.isSet(column.getName()))
+							values = Collections.singletonList((Number)row.get(column.getName(), colType));
+						
+						double[] mm = minMax(min, max, values);
+						min = mm[0];
+						max = mm[1];
+					}
+				}
+			}
+			
+			if (min != Double.POSITIVE_INFINITY && max != Double.NEGATIVE_INFINITY) {
+				range.add(min);
+				range.add(max);
+			}
+		} else {
+			range.add(0d);
+			range.add(0d);
+		}
+		
+		return range;
+	}
+	
+	private static double[] minMax(double min, double max, final List<? extends Number> values) {
+		if (values != null) {
+			for (final Number v : values) {
+				if (v != null) {
+					final double dv = v.doubleValue();
+					min = Math.min(min, dv);
+					max = Math.max(max, dv);
+				}
+			}
+		}
+		
+		return new double[]{ min, max };
+	}
+}