NES column in build-table command. Refs #421

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/tunables/TableTunables.java

@@ -27,6 +27,9 @@ public class TableTunables {
 	@Tunable(description="Name of column that contains q values. At least one of 'pvalueColumn' or 'qvalueColumn' must be provided.")
 	public String qvalueColumn;
 
+	@Tunable(description="Name of column that contains NES values (optional).")
+	public String nesColumn;
+	
 	@Tunable(description="Name of column that contains the gene set description (optional).")
 	public String descriptionColumn;
 
@@ -79,8 +82,9 @@ public TableParameters getTableParameters() throws IllegalArgumentException {
 		validateColumn(table, "descriptionColumn", descriptionColumn, false, String.class, false);
 		validateColumn(table, "pvalueColumn", pvalueColumn, false, Double.class, false);
 		validateColumn(table, "qvalueColumn", qvalueColumn, false, Double.class, false);
+		validateColumn(table, "nesColumn", nesColumn, false, Double.class, false);
 
-		return new TableParameters(table, nameColumn, genesColumn, pvalueColumn, qvalueColumn, descriptionColumn, null);
+		return new TableParameters(table, nameColumn, genesColumn, pvalueColumn, qvalueColumn, nesColumn, descriptionColumn, null);
 	}
 
 

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

@@ -15,6 +15,7 @@ public class TableParameters {
 	private final String genesColumn;
 	private final String pvalueColumn;
 	private final String qvalueColumn;
+	private final String nesColumn;
 	private final String descriptionColumn;
 
 	private final @Nullable Predicate<CyRow> filter;
@@ -26,6 +27,7 @@ public TableParameters(
 			String genesColumn, 
 			String pvalueColumn, 
 			String qvalueColumn,
+			String nesColumn,
 			String descriptionColumn, 
 			Predicate<CyRow> filter
 	) {
@@ -34,6 +36,7 @@ public TableParameters(
 		this.genesColumn = Objects.requireNonNull(genesColumn);
 		this.pvalueColumn = pvalueColumn;
 		this.qvalueColumn = qvalueColumn;
+		this.nesColumn = nesColumn;
 		this.descriptionColumn = descriptionColumn;
 		this.filter = filter;
 	}
@@ -57,6 +60,10 @@ public String getPvalueColumn() {
 	public String getQvalueColumn() {
 		return qvalueColumn;
 	}
+	
+	public String getNesColumn() {
+		return nesColumn;
+	}
 
 	public String getDescriptionColumn() {
 		return descriptionColumn;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/parsers/LoadEnrichmentsFromTableTask.java

@@ -61,6 +61,13 @@ public void run(TaskMonitor taskMonitor) {
 				if(qvalue == null)
 					qvalue = 1.0;
 
+				Double nes = null;
+				if(tableParams.getNesColumn() != null)
+					nes = row.get(tableParams.getNesColumn(), Double.class);
+				if(nes == null)
+					nes = 1.0;
+				
+				
 				// Skip row if data is invalid in any way
 				if(!(genes == null || genes.isEmpty() || name == null || name.isEmpty())) {
 					String description = null;
@@ -81,7 +88,7 @@ public void run(TaskMonitor taskMonitor) {
 					int gsSize = gs.getGenes().size();
 					genesets.put(name, gs);
 
-					GenericResult result = new GenericResult(name, description, pvalue, gsSize, qvalue);
+					GenericResult result = new GenericResult(name, description, pvalue, gsSize, qvalue, nes);
 					enrichments.getEnrichments().put(name, result);
 				}
 			}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/creation/genemania/StringDialogPage.java

@@ -58,7 +58,7 @@ public DataSetParameters getDataSetParameters() {
 		CyTable table = getStringTable(tableManager);
 
 		TableParameters tableParams = 
-				new TableParameters(table, NAME_COLUMN, GENES_COLUMN, null, FDR_COLUMN, DESC_COLUMN, filter);
+				new TableParameters(table, NAME_COLUMN, GENES_COLUMN, null, FDR_COLUMN, null, DESC_COLUMN, filter);
 
 		return new DataSetParameters(dataSetName, tableParams, null);
 	}