Fix color gradient for log transform. Refs #290

Author: mikekucera

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

@@ -178,7 +178,9 @@ private float mean() {
 	private float std(final float mean) {
 		float sum = 0;
 		for(float exp : expression) {
-			sum += (float)Math.pow(Math.abs(exp - mean), 2);
+			if(Float.isFinite(exp)) {
+				sum += (float)Math.pow(Math.abs(exp - mean), 2);
+			}
 		}
 		return (float) Math.sqrt(sum) / expression.length;
 	}

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

@@ -54,9 +54,6 @@
  * Class representing a set of genes/proteins expresion profile
  */
 public class GeneExpressionMatrix {
-
-	
-	
 
 	//name of columns - specified by first or second row in the expression matrix
 	private String[] columnNames;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/table/DataSetColorRange.java

@@ -21,6 +21,7 @@ private DataSetColorRange(ColorGradientTheme theme, ColorGradientRange range) {
 	 * Reset color gradients based on a change in the data transformation.
 	 */
 	public static Optional<DataSetColorRange> create(GeneExpressionMatrix expression, Transform transform) {
+		System.out.println("DataSetColorRange.create()");
 		float[] minMax = expression.getMinMax(transform);
 		if(minMax == null || minMax.length < 2)
 			return Optional.empty();
@@ -37,6 +38,11 @@ public static Optional<DataSetColorRange> create(GeneExpressionMatrix expression
 			ColorGradientRange range = ColorGradientRange.getInstance(0, median, median, max, 0, median, median, max);
 			ColorGradientTheme theme = ColorGradientTheme.GREEN_ONECOLOR_GRADIENT_THEME;
 			return Optional.of(new DataSetColorRange(theme, range));
+		} else if(Math.abs(min) > max) {
+			min = Math.abs(min);
+			ColorGradientRange range = ColorGradientRange.getInstance(-min, 0, 0, min, -min, 0, 0, min);
+			ColorGradientTheme theme = ColorGradientTheme.PR_GN_GRADIENT_THEME;
+			return Optional.of(new DataSetColorRange(theme, range));
 		} else {
 			ColorGradientRange range = ColorGradientRange.getInstance(-max, 0, 0, max, -max, 0, 0, max);
 			ColorGradientTheme theme = ColorGradientTheme.PR_GN_GRADIENT_THEME;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/heatmap/table/HeatMapCellRenderer.java

@@ -91,9 +91,9 @@ public static Color getColor(Double measurement, DataSetColorRange range) {
 	}
 
 	public static Color getColor(Double measurement, ColorGradientTheme theme, ColorGradientRange range) {
-		if (theme == null || range == null || measurement == null)
+		if (theme == null)
 			return Color.GRAY;
-		if(!Double.isFinite(measurement)) // missing data can result in NaN, log transformed value of -1 can result in -Infinity
+		if(range == null || measurement == null || !Double.isFinite(measurement)) // missing data can result in NaN, log transformed value of -1 can result in -Infinity
 			return theme.getNoDataColor();
 
 		float rLow = (float)theme.getMinColor().getRed()   / 255f;

EnrichmentMapPlugin/src/test/java/org/baderlab/csplugins/enrichmentmap/model/ExpressionOpsTest.java

@@ -9,7 +9,6 @@
 
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.HeatMapParams.Transform;
 import org.baderlab.csplugins.enrichmentmap.view.heatmap.table.DataSetColorRange;
-import org.junit.Ignore;
 import org.junit.Test;
 
 public class ExpressionOpsTest {
@@ -111,7 +110,7 @@ public void testExpressionMatrixOpsZeros() {
 		assertEquals(0f, matrix.getClosestToZero(), 0.0f);
 	}
 
-	@Ignore
+	@Test
 	public void testDataSetColorRangeNaN() {
 		Map<Integer,GeneExpression> map = new HashMap<>();
 		map.put(1, new GeneExpression("ge1", "", new float[] {Float.NaN, Float.NaN, 1.0f, Float.NaN, Float.NaN}));