Support -log10(pval)*sign(NES) in PDF export

Author: mikekucera

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

@@ -70,14 +70,19 @@ public void run(TaskMonitor taskMonitor) throws IOException, DocumentException {
 
 
 	private List<Element> createNodeColorSection(PdfWriter writer) throws DocumentException {
-//		ColorLegendPanel colorPanel = content.getNodeColorLegend();
-//		if(colorPanel == null)
-//			return null;
-//		Paragraph title = new Paragraph(new Chunk(LegendContent.NODE_COLOR_HEADER));
-//		Paragraph body = new Paragraph();
-//		body.add(createNodeColor(writer, colorPanel));
-//		return Arrays.asList(title, body);
-		return null;
+		ColorLegendPanel posColorPanel = content.getNodePosLegend();
+		ColorLegendPanel negColorPanel = content.getNodeNegLegend();
+		if(posColorPanel == null)
+			return null;
+		
+		String colName = content.getNodeColorMappingColName();
+		Paragraph title = new Paragraph(new Chunk(LegendContent.NODE_COLOR_HEADER + ": " + colName));
+		Paragraph body = new Paragraph();
+		body.add(createNodeColor(writer, posColorPanel));
+		if(negColorPanel != null)
+			body.add(createNodeColor(writer, negColorPanel));
+		
+		return Arrays.asList(title, body);
 	}
 
 	private static Image createNodeColor(PdfWriter writer, ColorLegendPanel colorPanel) throws DocumentException {

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

@@ -10,7 +10,7 @@
 
 public interface LegendContent {
 
-	public static final String NODE_COLOR_HEADER = "Node Fill Color: Phenotype * (1-P_value)";
+	public static final String NODE_COLOR_HEADER = "Node Fill Color";
 	public static final String NODE_CHART_HEADER = "Node Charts";
 	public static final String NODE_SHAPE_HEADER = "Node Shape";
 	public static final String NODE_CHART_COLOR_HEADER = "Node Chart Colors";
@@ -20,25 +20,27 @@ public interface LegendContent {
 	public static final int LEGEND_ICON_SIZE = 18;
 
 
-	public JFreeChart getChart();
+	JFreeChart getChart();
 
-	public String getChartLabel();
+	String getChartLabel();
 
-	public Icon getGeneSetNodeShape();
+	Icon getGeneSetNodeShape();
 
-	public Icon getSignatureNodeShape();
+	Icon getSignatureNodeShape();
 
-	public ColorLegendPanel getNodePosLegend();
+	ColorLegendPanel getNodePosLegend();
 
-	public ColorLegendPanel getNodeNegLegend();
+	ColorLegendPanel getNodeNegLegend();
 
-	public ColorLegendPanel getChartPosLegend();
+	String getNodeColorMappingColName();
 
-	public ColorLegendPanel getChartNegLegend();
+	ColorLegendPanel getChartPosLegend();
 
-	public Map<Object,Paint> getEdgeColors();
+	ColorLegendPanel getChartNegLegend();
 
-	public Map<Object,Paint> getDataSetColors();
+	Map<Object,Paint> getEdgeColors();
 
-	public EMStyleOptions getOptions();
+	Map<Object,Paint> getDataSetColors();
+	
+	EMStyleOptions getOptions();
 }

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

@@ -188,6 +188,11 @@ public ColorLegendPanel getNodeNegLegend() {
 		return nodeNegLegend;
 	}
 
+	@Override
+	public String getNodeColorMappingColName() {
+		return EMStyleBuilder.getDefaultMappingColumn(options).getBaseName(); 
+	}
+	
 	@Override
 	public JFreeChart getChart() {
 		return chart;