Fix p-value colors going in wrong direction.

Refs #452

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/style/EMStyleBuilder.java

@@ -198,7 +198,6 @@ public static NodeShape getDefaultNodeShape(ChartType chartType) {
 
 
 	public void updateStyle(VisualStyle vs, EMStyleOptions options, CyCustomGraphics2<?> chart, StyleUpdateScope scope) {
-		System.out.println("EMStyleBuilder.updateStyle(): " + scope);
 		String chartName = chart != null ? chart.getDisplayName() : null;
 		ChartType chartType = ChartType.toChartType(chartName);
 

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

@@ -261,16 +261,13 @@ public CyCustomGraphics2<?> createChart() {
 
 					ColorScheme colorScheme = chartOptions != null ? chartOptions.getColorScheme() : null;
 
-					if (colorScheme != null && colorScheme.getPoints() != null) {
-						List<Double> points = colorScheme.getPoints();
-						
-						if (!points.isEmpty())
-							props.put(AbstractChart.COLOR_POINTS, points);
-					}
+					if (colorScheme != null && !colorScheme.getPoints().isEmpty()) {
+						props.put(AbstractChart.COLOR_POINTS, colorScheme.getPoints());
+					} 
 				}
+				
 				try {
 					CyCustomGraphics2Factory<?> factory = chartFactoryManager.getChartFactory(type.getId());
-					
 					if (factory != null)
 						chart = factory.getInstance(props);
 				} catch (Exception e) {

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

@@ -325,8 +325,16 @@ private void updateNodeChartColorPanel(Collection<EMDataSet> dataSets) {
 			double max = range.get(1);
 
 			String posMaxLabel = max > 0 ? String.format("%.2f", max) : "N/A";
-			Color posMaxColor = colors.get(0);
-			Color posMinColor = colors.get(colors.size()/2);
+			Color posMaxColor;
+			Color posMinColor;
+			if(data == ChartData.NES_VALUE) {
+				posMaxColor = colors.get(0);
+				posMinColor = colors.get(colors.size()/2);
+			} else {
+				posMaxColor = colors.get(colors.size()/2);
+				posMinColor = colors.get(0);
+			}
+			
 			chartPosLegend = new ColorLegendPanel(posMaxColor, posMinColor, posMaxLabel, "0", false);
 			JLabel posLabel = new JLabel("Positive");
 			SwingUtil.makeSmall(posLabel);

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

@@ -147,7 +147,7 @@ public static List<Color> getChartColors(ChartOptions options, boolean 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(colors.get(1), colors.get(0), colors.get(1));
+				colors = Arrays.asList(colors.get(0), colors.get(1));
 		}
 
 		return colors;