Fix for #540

Author: mikekucera

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

@@ -493,22 +493,19 @@ private void setNodeBorderColors(VisualStyle vs, EMStyleOptions options) {
 	}
 
 	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;
+		boolean isSingleGSEA = options.getEnrichmentMap().isSingleGSEA();
+		return isSingleGSEA
+			? Columns.NODE_LOG_PVALUE_NES
+			: Columns.NODE_LOG_PVALUE_MAX;
 	}
 
 	public static String getDefaultMappingColumnName(EMStyleOptions options) {
 		var map = options.getEnrichmentMap();
 		var prefix = options.getAttributePrefix();
 		boolean isSingleGSEA = map.isSingleGSEA();
-		
-		if(isSingleGSEA)
-			return Columns.NODE_LOG_PVALUE_NES.with(prefix, map.getDataSetList().get(0));
-		else
-			return Columns.NODE_LOG_PVALUE_MAX.with(prefix);
+		return isSingleGSEA
+			? Columns.NODE_LOG_PVALUE_NES.with(prefix, map.getDataSetList().get(0))
+			: Columns.NODE_LOG_PVALUE_MAX.with(prefix);
 	}
 
 
@@ -525,14 +522,14 @@ private ContinuousMapping<Double,Paint> createLog10NodeColorMapping(EMStyleOptio
 		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 colors = DEF_NODE_COLOR_SCHEME;
+		var negColor  = colors.getNegColor();
+		var zeroColor = colors.getZeroColor();
+		var posColor  = colors.getPosColor();
 
-		var negPoint  = new BoundaryRangeValues<Paint>(negColor, negColor, negColor);
+		var negPoint  = new BoundaryRangeValues<Paint>(negColor,  negColor,  negColor);
 		var zeroPoint = new BoundaryRangeValues<Paint>(zeroColor, zeroColor, zeroColor);
-		var posPoint  = new BoundaryRangeValues<Paint>(posColor, posColor, posColor);
+		var posPoint  = new BoundaryRangeValues<Paint>(posColor,  posColor,  posColor);
 
 		eventHelper.silenceEventSource(mapping);
 		try {

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

@@ -199,9 +199,9 @@ else if(result instanceof GenericResult)
 
 
 	private boolean needsInit = true;
-	private Double minPValueThatsNotZero = null;
+	private double minPValueThatsNotZero;
 
-	private Double getMinPValueThatsNotZero() {
+	private double getMinPValueThatsNotZero() {
 		if(needsInit) {
 			Double minPValue = null;
 
@@ -217,48 +217,45 @@ private Double getMinPValueThatsNotZero() {
 				}
 			}
 
-			minPValueThatsNotZero = minPValue; // could still possibly be null
+			if(minPValue == null) {
+				minPValueThatsNotZero = 1e-10; // bug #540
+			} else {
+				minPValueThatsNotZero = minPValue;
+			}
+			
 			needsInit = false;
 		}
 		return minPValueThatsNotZero;
 	}
 
 
-	private Double getNegLog10pval(EMDataSet dataset, EnrichmentResult result) {
+	private double getNegLog10pval(EMDataSet dataset, EnrichmentResult result) {
 		double pval = result.getPvalue();
 		if(pval > 0.0) {
 			return -Math.log10(pval);
-		} else if(pval == 0.0) {
-			Double minPval = getMinPValueThatsNotZero();
-			if(minPval != null) {
-				return -Math.log10(minPval);
-			}
+		} else {
+			double minPval = getMinPValueThatsNotZero();
+			return -Math.log10(minPval);
 		}
-		return null;
 	}
 
 
-	private Double getMaxNegLog10pval(String genesetName) {
-		boolean hasVal = false;
+	private double getMaxNegLog10pval(String genesetName) {
 		double maxVal = Double.MIN_VALUE;
 
 		for(EMDataSet ds : map.getDataSetList()) {
 			var result = ds.getEnrichment(genesetName);
 			if(result != null) {
 				double pval = result.getPvalue();
 				if(pval > 0.0) {
-					hasVal = true;
 					maxVal = Math.max(maxVal, -Math.log10(pval));
 				} else {
-					Double minPval = getMinPValueThatsNotZero();
-					if(minPval != null) {
-						hasVal = true;
-						maxVal = Math.max(maxVal, -Math.log10(minPval));
-					}
+					double minPval = getMinPValueThatsNotZero();
+					maxVal = Math.max(maxVal, -Math.log10(minPval));
 				}
 			}
 		}
-		return hasVal ? maxVal : null; // leave the cell blank
+		return maxVal; // leave the cell blank
 	}