Support -log10(pval)*sign(NES) in legend

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/EnrichmentMap.java

@@ -694,6 +694,10 @@ public boolean hasNonGSEADataSet() {
 		return dataSets.values().stream().anyMatch(ds -> ds.getMethod() != Method.GSEA);
 	}
 
+	public boolean isSingleGSEA() {
+		return getDataSetCount() == 1 && getDataSetList().get(0).getMethod() == Method.GSEA;
+	}
+	
 	@Override
 	public String toString() {
 		return getName();

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

@@ -22,6 +22,9 @@ public String with(String prefix) {
 	}
 
 	public String with(String prefix, AbstractDataSet ds) {
+		if(prefix == null && ds == null)
+			return getBaseName();
+		
 		StringBuilder sb = new StringBuilder();
 		if(prefix != null)
 			sb.append(prefix);

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

@@ -36,6 +36,13 @@ public boolean isChartTypeSelectable() {
 		return this != NONE && this != DATA_SET && this != EXPRESSION_DATA;
 	}
 
+	/**
+	 * Returns true if the data range goes negative-zero-positive
+	 */
+	public boolean isDiverging() {
+		return this == NES_VALUE || this == NES_SIG || this == LOG10_PVAL_NES;
+	}
+	
 	@Override
 	public String toString() {
 		return label;

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

@@ -68,6 +68,18 @@ public List<Color> getColors() {
 		return Arrays.asList(colors);
 	}
 
+	public Color getPosColor() {
+		return colors[0];
+	}
+	
+	public Color getNegColor() {
+		return colors[colors.length-1];
+	}
+	
+	public Color getZeroColor() {
+		return colors[colors.length/2];
+	}
+	
 	/**
 	 * Can be used to create more complex gradients, with fixed range points,
 	 * such as the ones created by Continuous Mappings.

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

@@ -14,7 +14,6 @@
 import org.baderlab.csplugins.enrichmentmap.CytoscapeServiceModule.Discrete;
 import org.baderlab.csplugins.enrichmentmap.CytoscapeServiceModule.Passthrough;
 import org.baderlab.csplugins.enrichmentmap.model.EMDataSet;
-import org.baderlab.csplugins.enrichmentmap.model.EMDataSet.Method;
 import org.baderlab.csplugins.enrichmentmap.model.EMSignatureDataSet;
 import org.baderlab.csplugins.enrichmentmap.model.EnrichmentMap;
 import org.baderlab.csplugins.enrichmentmap.view.util.ChartUtil;
@@ -71,6 +70,8 @@ public class EMStyleBuilder {
 
 	private static final NodeShape SIGNATURE_NODE_SHAPE = DIAMOND;
 
+	public static final ColorScheme DEF_NODE_COLOR_SCHEME = ColorScheme.RD_BU_3;
+	
 	public static class Columns {
 		public static final String NAMESPACE = "EnrichmentMap";
 		public static final String NAMESPACE_PREFIX = NAMESPACE + "::"; // added in Cytoscape 3.7
@@ -152,14 +153,15 @@ public static class Colors {
 		public static final Color SIG_EDGE_COLOR = new Color(252, 141, 98);
 		public static final Color COMPOUND_EDGE_COLOR = new Color(102, 194, 165);
 
-		/* See http://colorbrewer2.org/#type=diverging&scheme=RdBu&n=9 */
-		public static final Color MAX_PHENOTYPE_1 = new Color(178, 24, 43);
-		public static final Color LIGHTER_PHENOTYPE_1 = new Color(214, 96, 77);
-		public static final Color LIGHTEST_PHENOTYPE_1 = new Color(244, 165, 130);
-		public static final Color OVER_COLOR = new Color(247, 247, 247);
-		public static final Color MAX_PHENOTYPE_2 = new Color(33, 102, 172);
-		public static final Color LIGHTER_PHENOTYPE_2 = new Color(67, 147, 195);
-		public static final Color LIGHTEST_PHENOTYPE_2 = new Color(146, 197, 222);
+//		/* See http://colorbrewer2.org/#type=diverging&scheme=RdBu&n=9 */
+		// These are deprecated, use ColorScheme.RD_BU_9 instead
+		@Deprecated public static final Color MAX_PHENOTYPE_1 = new Color(178, 24, 43);
+		@Deprecated public static final Color LIGHTER_PHENOTYPE_1 = new Color(214, 96, 77);
+		@Deprecated public static final Color LIGHTEST_PHENOTYPE_1 = new Color(244, 165, 130);
+		@Deprecated public static final Color OVER_COLOR = new Color(247, 247, 247);
+		@Deprecated public static final Color MAX_PHENOTYPE_2 = new Color(33, 102, 172);
+		@Deprecated public static final Color LIGHTER_PHENOTYPE_2 = new Color(67, 147, 195);
+		@Deprecated public static final Color LIGHTEST_PHENOTYPE_2 = new Color(146, 197, 222);
 
 		public static final Color LIGHT_GREY = new Color(190, 190, 190);
 		private static final Color BG_COLOR = Color.WHITE;
@@ -490,47 +492,57 @@ private void setNodeBorderColors(VisualStyle vs, EMStyleOptions options) {
 		vs.addVisualMappingFunction(dm);
 	}
 
+	public static ColumnDescriptor<Double> getDefaultMappingColumn(EMStyleOptions options) {
+		var isSingleGSEA = options.getEnrichmentMap().isSingleGSEA();
+		if(isSingleGSEA)
+			return Columns.NODE_LOG_PVALUE_NES;
+		else
+			return Columns.NODE_LOG_PVALUE_MAX;
+	}
 
-	private ContinuousMapping<Double,Paint> createLog10NodeColorMapping(EMStyleOptions options) {
+	public static String getDefaultMappingColumnName(EMStyleOptions options) {
 		var map = options.getEnrichmentMap();
 		var prefix = options.getAttributePrefix();
+		boolean isSingleGSEA = map.isSingleGSEA();
 
-		boolean isSingleGSEA = map.getDataSetCount() == 1 && map.getDataSetList().get(0).getMethod() == Method.GSEA;
-		
-		String logPValCol;
 		if(isSingleGSEA)
-			logPValCol = Columns.NODE_LOG_PVALUE_NES.with(prefix, map.getDataSetList().get(0));
+			return Columns.NODE_LOG_PVALUE_NES.with(prefix, map.getDataSetList().get(0));
 		else
-			logPValCol = Columns.NODE_LOG_PVALUE_MAX.with(prefix);
-		
+			return Columns.NODE_LOG_PVALUE_MAX.with(prefix);
+	}
+	
+	
+	private ContinuousMapping<Double,Paint> createLog10NodeColorMapping(EMStyleOptions options) {
+		var logPValCol = getDefaultMappingColumnName(options);
 
 		var mapping = (ContinuousMapping<Double,Paint>) cmFactory.createVisualMappingFunction(
 				logPValCol, Double.class, BasicVisualLexicon.NODE_FILL_COLOR);
 
-		if(mapping != null) { // can happen in tests
-			var network = options.getNetworkView().getModel();
-			var colList = List.of(columnIdFactory.createColumnIdentifier(logPValCol));
-			var range = ChartUtil.calculateGlobalRange(network, colList, true);
-			
-			var colors = ColorScheme.RD_BU_3.getColors();
-			var negColor  = colors.get(2);
-			var zeroColor = colors.get(1);
-			var posColor  = colors.get(0);
-			
-			var negPoint  = new BoundaryRangeValues<Paint>(negColor, negColor, negColor);
-			var zeroPoint = new BoundaryRangeValues<Paint>(zeroColor, zeroColor, zeroColor);
-			var posPoint  = new BoundaryRangeValues<Paint>(posColor, posColor, posColor);
-						
-			eventHelper.silenceEventSource(mapping);
-			try {
-				if(isSingleGSEA) {
-					mapping.addPoint(-range.max, negPoint);
-				}
-				mapping.addPoint(0.0, zeroPoint);
-				mapping.addPoint(range.max, posPoint);
-			} finally {
-				eventHelper.unsilenceEventSource(mapping);
+		if(mapping == null) // can happen in tests
+			return null;
+		
+		var network = options.getNetworkView().getModel();
+		var colList = List.of(columnIdFactory.createColumnIdentifier(logPValCol));
+		var range = ChartUtil.calculateGlobalRange(network, colList, true);
+		
+		var colors = DEF_NODE_COLOR_SCHEME.getColors();
+		var negColor  = colors.get(2);
+		var zeroColor = colors.get(1);
+		var posColor  = colors.get(0);
+		
+		var negPoint  = new BoundaryRangeValues<Paint>(negColor, negColor, negColor);
+		var zeroPoint = new BoundaryRangeValues<Paint>(zeroColor, zeroColor, zeroColor);
+		var posPoint  = new BoundaryRangeValues<Paint>(posColor, posColor, posColor);
+					
+		eventHelper.silenceEventSource(mapping);
+		try {
+			if(options.getEnrichmentMap().isSingleGSEA()) {
+				mapping.addPoint(-range.max, negPoint);
 			}
+			mapping.addPoint(0.0, zeroPoint);
+			mapping.addPoint(range.max, posPoint);
+		} finally {
+			eventHelper.unsilenceEventSource(mapping);
 		}
 
 		return mapping;

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

@@ -72,7 +72,7 @@ public class ColorLegendPanel extends JPanel {
 	private final boolean legacy;
 
 	public ColorLegendPanel(Color minColor, Color maxColor, String phenotype1, String phenotype2) {
-		this(minColor, maxColor, phenotype1, phenotype2, true);
+		this(minColor, maxColor, phenotype1, phenotype2, false);
 	}
 
 	public ColorLegendPanel(Color minColor, Color maxColor, String phenotype1, String phenotype2, boolean legacy) {

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

@@ -70,13 +70,14 @@ 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);
+//		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;
 	}
 
 	private static Image createNodeColor(PdfWriter writer, ColorLegendPanel colorPanel) throws DocumentException {

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

@@ -28,7 +28,9 @@ public interface LegendContent {
 
 	public Icon getSignatureNodeShape();
 
-	public ColorLegendPanel getNodeColorLegend();
+	public ColorLegendPanel getNodePosLegend();
+	
+	public ColorLegendPanel getNodeNegLegend();
 
 	public ColorLegendPanel getChartPosLegend();