Use FDR q-value for STRING import.

Author: mikekucera

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

@@ -58,7 +58,7 @@ public TableParameters getTableParameters() throws IllegalArgumentException {
 		validateColumn(table, pvalueColumn, false, Double.class, true);
 		validateColumn(table, descriptionColumn, false, String.class, false);
 
-		return new TableParameters(table, nameColumn, genesColumn, pvalueColumn, descriptionColumn, null);
+		return new TableParameters(table, nameColumn, genesColumn, pvalueColumn, null, descriptionColumn, null);
 	}
 
 

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

@@ -15,16 +15,26 @@ public class TableParameters {
 	private final String nameColumn;
 	private final String genesColumn;
 	private final String pvalueColumn;
+	private final String qvalueColumn;
 	private final Optional<String> descriptionColumn;
 
 	private final @Nullable Predicate<CyRow> filter;
 
 
-	public TableParameters(CyTable table, String nameColumn, String genesColumn, String pvalueColumn, String descriptionColumn, Predicate<CyRow> filter) {
+	public TableParameters(
+			CyTable table, 
+			String nameColumn, 
+			String genesColumn, 
+			String pvalueColumn, 
+			String qvalueColumn,
+			String descriptionColumn, 
+			Predicate<CyRow> filter
+	) {
 		this.table = Objects.requireNonNull(table);
 		this.nameColumn = Objects.requireNonNull(nameColumn);
 		this.genesColumn = Objects.requireNonNull(genesColumn);
-		this.pvalueColumn = Objects.requireNonNull(pvalueColumn);
+		this.pvalueColumn = pvalueColumn;
+		this.qvalueColumn = qvalueColumn;
 		this.descriptionColumn = Optional.ofNullable(descriptionColumn);
 		this.filter = filter;
 	}
@@ -44,6 +54,10 @@ public String getGenesColumn() {
 	public String getPvalueColumn() {
 		return pvalueColumn;
 	}
+	
+	public String getQvalueColumn() {
+		return qvalueColumn;
+	}
 
 	public Optional<String> getDescriptionColumn() {
 		return descriptionColumn;

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

@@ -48,10 +48,21 @@ public void run(TaskMonitor taskMonitor) {
 			if(filter == null || filter.test(row)) {
 				List<String> genes = row.getList(tableParams.getGenesColumn(), String.class);
 				String name = row.get(tableParams.getNameColumn(), String.class);
-				Double pvalue = row.get(tableParams.getPvalueColumn(), Double.class);
+				
+				Double pvalue = null;
+				if(tableParams.getPvalueColumn() != null)
+					pvalue = row.get(tableParams.getPvalueColumn(), Double.class);
+				if(pvalue == null)
+					pvalue = 1.0;
+				
+				Double qvalue = null;
+				if(tableParams.getQvalueColumn() != null)
+					qvalue = row.get(tableParams.getQvalueColumn(), Double.class);
+				if(qvalue == null)
+					qvalue = 1.0;
 
 				// Skip row if data is invalid in any way
-				if(genes == null || genes.isEmpty() || name == null || name.isEmpty() || pvalue == null)
+				if(genes == null || genes.isEmpty() || name == null || name.isEmpty())
 					continue;
 
 				String description = null;
@@ -72,12 +83,14 @@ public void run(TaskMonitor taskMonitor) {
 				int gsSize = gs.getGenes().size();
 				genesets.put(name, gs);
 
-				GenericResult result = new GenericResult(name, description, pvalue, gsSize);
+				GenericResult result = new GenericResult(name, description, pvalue, gsSize, qvalue);
 				enrichments.getEnrichments().put(name, result);
 			}
 			tm.inc();
 		}
 
+		map.getParams().setFDR(tableParams.getQvalueColumn() != null);
+		
 		// TODO if we add support for fdr q-value column then make sure to set the following...
 		// dataset.getMap().getParams().setFDR(FDR);
 	}

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, FDR_COLUMN, DESC_COLUMN, filter);
+				new TableParameters(table, NAME_COLUMN, GENES_COLUMN, null, FDR_COLUMN, DESC_COLUMN, filter);
 
 		return new DataSetParameters(dataSetName, tableParams);
 	}