Show size of maximum overlap in PA dialog.

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/postanalysis/PAMostSimilarTaskParallel.java

@@ -19,6 +19,9 @@
 import org.cytoscape.work.ObservableTask;
 import org.cytoscape.work.TaskMonitor;
 
+import com.google.common.collect.Sets;
+
+
 /**
  * Post Analysis.
  * Computes similarities between the signature gene sets that are being added and the 
@@ -66,6 +69,7 @@ public List<SigGeneSetDescriptor> compute(TaskMonitor tm, ExecutorService execut
 
 				boolean first = true;
 				double mostSimilar = Double.NaN;
+				int largestOverlap = 0;
 				boolean passes = false;
 
 				loop:
@@ -78,6 +82,9 @@ public List<SigGeneSetDescriptor> compute(TaskMonitor tm, ExecutorService execut
 						GeneSet enrGeneSet = dataSet.getGeneSetsOfInterest().getGeneSetByName(geneSetName);
 						if(enrGeneSet != null) {
 
+							int overlap = Sets.intersection(sigGeneSet.getGenes(), enrGeneSet.getGenes()).size();
+							largestOverlap = Math.max(largestOverlap, overlap);
+							
 							FilterMetric metric = metrics.get(dataSetName);
 							try {
 								double value = metric.computeValue(enrGeneSet.getGenes(), sigGeneSet.getGenes(), null);
@@ -98,7 +105,7 @@ public List<SigGeneSetDescriptor> compute(TaskMonitor tm, ExecutorService execut
 					}
 				}
 
-				results.add(new SigGeneSetDescriptor(sigGeneSet, mostSimilar, passes));
+				results.add(new SigGeneSetDescriptor(sigGeneSet, largestOverlap, mostSimilar, passes));
 				taskMonitor.inc();
 			});
 		}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/PADialogPage.java

@@ -360,14 +360,11 @@ public void runLoadFromUrlTasks(URL url, CardDialog webLoadDialog) {
 	private synchronized void updateTable(List<SigGeneSetDescriptor> filteredGenesets, PostAnalysisFilterType type, boolean preserveWidths) {
 		TableColumnModel columnModel = table.getColumnModel();
 
-		int[] widths = {60, 510, 80, 230};
+		int[] widths = {60, 480, 80, 140, 230};
 		if(preserveWidths) {
-			widths = new int[] {
-				columnModel.getColumn(0).getWidth(),
-				columnModel.getColumn(1).getWidth(),
-				columnModel.getColumn(2).getWidth(),
-				columnModel.getColumn(3).getWidth()
-			};
+			for(int i = 0; i < 5; i++) {
+				widths[i] = columnModel.getColumn(i).getWidth();
+			}
 		} 
 
 		tableModel = new SigGeneSetTableModel(filteredGenesets, type);
@@ -380,14 +377,13 @@ private synchronized void updateTable(List<SigGeneSetDescriptor> filteredGeneset
 			}
 		});
 
-		columnModel.getColumn(0).setPreferredWidth(widths[0]);
-		columnModel.getColumn(1).setPreferredWidth(widths[1]);
-		columnModel.getColumn(2).setPreferredWidth(widths[2]);
-		columnModel.getColumn(3).setPreferredWidth(widths[3]);
+		for(int i = 0; i < 5; i++) {
+			columnModel.getColumn(i).setPreferredWidth(widths[i]);
+		}
 
 		// Auto-sort
 		TableRowSorter<?> sorter = ((TableRowSorter<?>)table.getRowSorter());
-		RowSorter.SortKey sortKey = new RowSorter.SortKey(SigGeneSetTableModel.COL_OVERLAP, getSortOrder(type));
+		RowSorter.SortKey sortKey = new RowSorter.SortKey(SigGeneSetTableModel.COL_SIMILARITY, getSortOrder(type));
 		sorter.setSortKeys(Arrays.asList(sortKey));
 		sorter.sort();
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/SigGeneSetCellRenderer.java

@@ -22,7 +22,7 @@ public Component getTableCellRendererComponent(JTable table, Object value, boole
 		label.setOpaque(true); //MUST do this for background to show up.
 		SwingUtil.makeSmall(label);
 
-		if(col == SigGeneSetTableModel.COL_OVERLAP && value instanceof Number) {
+		if(col == SigGeneSetTableModel.COL_SIMILARITY && value instanceof Number) {
 			double val = ((Number)value).doubleValue();
 			label.setToolTipText(String.valueOf(val));
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/SigGeneSetDescriptor.java

@@ -7,13 +7,15 @@
 public class SigGeneSetDescriptor {
 
 	private final GeneSet geneSet;
+	private final int largestOverlap;
 	private final double mostSimilar;
 	private final boolean passes;
 
 	private boolean wanted = true;
 
-	public SigGeneSetDescriptor(GeneSet geneSet, double mostSimilar, boolean passes) {
+	public SigGeneSetDescriptor(GeneSet geneSet, int largestOverlap, double mostSimilar, boolean passes) {
 		this.geneSet = Objects.requireNonNull(geneSet);
+		this.largestOverlap = largestOverlap;
 		this.mostSimilar = mostSimilar;
 		this.passes = passes;
 	}
@@ -30,6 +32,10 @@ public String getName() {
 		return geneSet.getName();
 	}
 
+	public int getLargestOverlap() {
+		return largestOverlap;
+	}
+	
 	public int getGeneCount() {
 		return geneSet.getGenes().size();
 	}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/view/postanalysis/SigGeneSetTableModel.java

@@ -11,7 +11,7 @@
 @SuppressWarnings("serial")
 public class SigGeneSetTableModel extends AbstractTableModel {
 
-	public static final int COL_WANTED = 0, COL_NAME = 1, COL_GENES = 2, COL_OVERLAP = 3;
+	public static final int COL_WANTED = 0, COL_NAME = 1, COL_GENES = 2, COL_OVERLAP = 3, COL_SIMILARITY = 4;
 
 	private final List<SigGeneSetDescriptor> geneSets;
 	private final PostAnalysisFilterType filterType;
@@ -43,7 +43,7 @@ public int getRowCount() {
 
 	@Override
 	public int getColumnCount() {
-		return 4;
+		return 5;
 	}
 
 	public PostAnalysisFilterType getFilterType() {
@@ -63,10 +63,11 @@ public int getSelectedCount() {
 	public Object getValueAt(int row, int col) {
 		SigGeneSetDescriptor geneSet = geneSets.get(row);
 		switch(col) {
-			case COL_WANTED:  return geneSet.isWanted();
-			case COL_NAME:    return geneSet.getName();
-			case COL_GENES:   return geneSet.getGeneCount();
-			case COL_OVERLAP: return geneSet.getMostSimilar();
+			case COL_WANTED:     return geneSet.isWanted();
+			case COL_NAME:       return geneSet.getName();
+			case COL_GENES:      return geneSet.getGeneCount();
+			case COL_OVERLAP:    return geneSet.getLargestOverlap();
+			case COL_SIMILARITY: return geneSet.getMostSimilar();
 		}
 		return null;
 	}
@@ -77,7 +78,8 @@ public String getColumnName(int col) {
 			case COL_WANTED: return "Import";
 			case COL_NAME: return "Name";
 			case COL_GENES: return "Genes";
-			case COL_OVERLAP:
+			case COL_OVERLAP: return "Largest Overlap";
+			case COL_SIMILARITY:
 				switch(filterType) {
 					case HYPERGEOM: return "Hypergeometric";
 					case MANN_WHIT_GREATER: return "Mann-Whitney (Greater)";
@@ -98,7 +100,8 @@ public Class<?> getColumnClass(int col) {
 			case COL_WANTED:  return Boolean.class;
 			case COL_NAME:    return String.class;
 			case COL_GENES:   return Integer.class;
-			case COL_OVERLAP: return Double.class;
+			case COL_OVERLAP: return Integer.class;
+			case COL_SIMILARITY: return Double.class;
 		}
 		return null;
 	}