Fix wrong values in legend, refs #418

Author: mikekucera

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

@@ -188,7 +188,7 @@ public CyCustomGraphics2<?> createChart() {
 					List<CyColumnIdentifier> columns = ChartUtil.getSortedColumnIdentifiers(prefix,
 							dataSets, columnDescriptor, columnIdFactory);
 
-					List<Color> colors = ChartUtil.getChartColors(chartOptions);
+					List<Color> colors = ChartUtil.getChartColors(chartOptions, true);
 					List<Double> range = ChartUtil.calculateGlobalRange(options.getNetworkView().getModel(), columns);
 
 					props.put("cy_dataColumns", columns);

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/legend/LegendPanel.java

@@ -319,7 +319,7 @@ private void updateNodeChartColorPanel(Collection<EMDataSet> dataSets) {
 			List<CyColumnIdentifier> columns = ChartUtil.getSortedColumnIdentifiers(options.getAttributePrefix(),
 					dataSets, columnDescriptor, columnIdFactory);
 
-			List<Color> colors = ChartUtil.getChartColors(chartOptions);
+			List<Color> colors = ChartUtil.getChartColors(chartOptions, false);
 			List<Double> range = ChartUtil.calculateGlobalRange(options.getNetworkView().getModel(), columns);
 			double min = range.get(0) ;
 			double max = range.get(1);

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

@@ -135,18 +135,21 @@ else if (row.isSet(column.getName()))
 		return range;
 	}
 
-	public static List<Color> getChartColors(ChartOptions options) {
+	public static List<Color> getChartColors(ChartOptions options, boolean forStyle) {
 		ColorScheme colorScheme = options != null ? options.getColorScheme() : null;
 		List<Color> colors = colorScheme != null ? colorScheme.getColors() : null;
 		ChartData data = options != null ? options.getData() : null;
 
-		// Swap UP and ZERO colors if q or p-value (it should not have negative values!)
-		if ((data == ChartData.FDR_VALUE || data == ChartData.P_VALUE) && colors.size() == 3)
-			colors = Arrays.asList(new Color[] { colors.get(1), colors.get(0), colors.get(1) });
-		
 		if (colors == null || colors.size() < 3) // UP, ZERO, DOWN:
 			colors = Arrays.asList(new Color[] { Color.LIGHT_GRAY, Color.WHITE, Color.DARK_GRAY });
 
+		if(forStyle) {
+			// The 3-color schemes need to be swapped when the chart only includes positive numbers.
+			// Swap UP and ZERO colors if q or p-value (it should not have negative values!)
+			if ((data == ChartData.FDR_VALUE || data == ChartData.P_VALUE) && colors.size() == 3)
+				colors = Arrays.asList(new Color[] { colors.get(1), colors.get(0), colors.get(1) });
+		}
+				
 		return colors;
 	}