Use 1 as CorrelationValue for same pair instead of 0

urmi-21 · Jul 30, 2021 · c369cf9 · c369cf9
1 parent 1e322b8
commit c369cf9
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Showing 6 changed files with 32 additions and 3 deletions.
diff --git a/src/edu/iastate/metnet/metaomgraph/chart/HeatMapChart.java b/src/edu/iastate/metnet/metaomgraph/chart/HeatMapChart.java
@@ -397,6 +397,9 @@ public Object construct() {
 						double[][] pairWiseEuclidianDistance = Utils.computePairWiseEuclidianDistances(heatMapData);
 						HierarchicalClusterData clusteredData = new HierarchicalClusterData(rowNames, pairWiseEuclidianDistance);
 						List<String> clusteredOrderedData = clusteredData.getClusteredOrderedData();
+						if(clusteredOrderedData == null || clusteredOrderedData.isEmpty()) {
+							return null;
+						}
 						String[] clusterOrderedRowNames = clusteredOrderedData.stream().toArray(String[]::new);
 						heatMapData = rearrangeHeatMapDataBasedOnClusters(clusterOrderedRowNames);
 						if(splitIndex != null) {
@@ -429,6 +432,9 @@ public Object construct() {
 						double[][] pairWisePearsonCorrelation = Utils.computePairWisePearsonCorrelations(heatMapData);
 						HierarchicalClusterData clusteredData = new HierarchicalClusterData(rowNames, pairWisePearsonCorrelation);
 						List<String> clusteredOrderedData = clusteredData.getClusteredOrderedData();
+						if(clusteredOrderedData == null || clusteredOrderedData.isEmpty()) {
+							return null;
+						}
 						String[] clusterOrderedRowNames = clusteredOrderedData.stream().toArray(String[]::new);
 						heatMapData = rearrangeHeatMapDataBasedOnClusters(clusterOrderedRowNames);
 						if(splitIndex != null) {
@@ -461,6 +467,9 @@ public Object construct() {
 						double[][] pairWiseSpearmanCorrelation = Utils.computePairWiseSpearmanCorrelations(heatMapData);
 						HierarchicalClusterData clusteredData = new HierarchicalClusterData(rowNames, pairWiseSpearmanCorrelation);
 						List<String> clusteredOrderedData = clusteredData.getClusteredOrderedData();
+						if(clusteredOrderedData == null || clusteredOrderedData.isEmpty()) {
+							return null;
+						}
 						String[] clusterOrderedRowNames = clusteredOrderedData.stream().toArray(String[]::new);
 						heatMapData = rearrangeHeatMapDataBasedOnClusters(clusterOrderedRowNames);
 						if(splitIndex != null) {

diff --git a/src/edu/iastate/metnet/metaomgraph/ui/DiffCorrResultsTable.java b/src/edu/iastate/metnet/metaomgraph/ui/DiffCorrResultsTable.java
@@ -1099,6 +1099,7 @@ public void keyPressed(KeyEvent e) {
 				}
 			});
 			filterField.getDocument().addDocumentListener(new FilterFieldListener());
+			filterField.setToolTipText("Prefix search text with '~' for \"contains\", '!' for \"is not\", and '~!' for \"does not contain\".");
 			filterField.setDefaultText("Use semicolon (;) for multiple filters");
 			filterField.setColumns(30);
 			searchPanel.add(filterField, "Center");

diff --git a/src/edu/iastate/metnet/metaomgraph/ui/MetaOmTablePanel.java b/src/edu/iastate/metnet/metaomgraph/ui/MetaOmTablePanel.java
@@ -714,6 +714,7 @@ public void keyPressed(KeyEvent e) {
 			}
 		});
 		filterField.getDocument().addDocumentListener(new FilterFieldListener());
+		filterField.setToolTipText("Prefix search text with '~' for \"contains\", '!' for \"is not\", and '~!' for \"does not contain\".");
 		filterField.setDefaultText("Use semicolon (;) for multiple filters");
 		filterField.setColumns(20);
 		searchPanel.add(filterField, "Center");

diff --git a/src/edu/iastate/metnet/metaomgraph/ui/logFCResultsFrame.java b/src/edu/iastate/metnet/metaomgraph/ui/logFCResultsFrame.java
@@ -1253,6 +1253,7 @@ public void keyPressed(KeyEvent e) {
 			}
 		});
 		filterField.getDocument().addDocumentListener(new FilterFieldListener());
+		filterField.setToolTipText("Prefix search text with '~' for \"contains\", '!' for \"is not\", and '~!' for \"does not contain\".");
 		filterField.setDefaultText("Use semicolon (;) for multiple filters");
 		filterField.setColumns(30);
 		searchPanel.add(filterField, "Center");

diff --git a/src/edu/iastate/metnet/metaomgraph/utils/HierarchicalClusterData.java b/src/edu/iastate/metnet/metaomgraph/utils/HierarchicalClusterData.java
@@ -6,6 +6,8 @@
 import java.util.ArrayList;
 import java.util.List;
 
+import javax.swing.JOptionPane;
+
 import com.apporiented.algorithm.clustering.AverageLinkageStrategy;
 import com.apporiented.algorithm.clustering.Cluster;
 import com.apporiented.algorithm.clustering.ClusteringAlgorithm;
@@ -30,9 +32,14 @@ public HierarchicalClusterData(String[] names, double[][] data) {
 
 	// do the heirarchical clustering
 	private void doClustering(double[][] data, String[] names) {
-		ClusteringAlgorithm algorithm = new DefaultClusteringAlgorithm();
-		Cluster cluster = algorithm.performClustering(data, names, new AverageLinkageStrategy());
-		fillClusteredOrderedDataFromChildren(cluster);
+		try {
+			ClusteringAlgorithm algorithm = new DefaultClusteringAlgorithm();
+			Cluster cluster = algorithm.performClustering(data, names, new AverageLinkageStrategy());
+			fillClusteredOrderedDataFromChildren(cluster);
+		}catch(Exception e){
+			JOptionPane.showMessageDialog(null, "Duplicate identifiers found, the feature names should be unique", "Clustering error", JOptionPane.ERROR_MESSAGE);
+			return;
+		}
 	}
 
 	// Fill clustered data recursively

diff --git a/src/edu/iastate/metnet/metaomgraph/utils/Utils.java b/src/edu/iastate/metnet/metaomgraph/utils/Utils.java
@@ -1594,6 +1594,11 @@ public static double[][] computePairWisePearsonCorrelations(double[][] data){
 			}
 		}
 
+		// fill the diagonals with 1
+		for(int i = 0; i < data.length; i++) {
+			pairWisePearsonCorrelation[i][i] = 1;
+		}
+
 		// Now, use the lower triangular part to fill the upper triangular part
 		for(int i = 0; i < data.length; i++) {
 			for(int j = i + 1; j < data.length; j++) {
@@ -1619,6 +1624,11 @@ public static double[][] computePairWiseSpearmanCorrelations(double[][] data){
 			}
 		}
 
+		// fill the diagonals with 1
+		for(int i = 0; i < data.length; i++) {
+			pairWiseSpearmanCorrelation[i][i] = 1;
+		}
+
 		// Now, use the lower triangular part to fill the upper triangular part
 		for(int i = 0; i < data.length; i++) {
 			for(int j = i + 1; j < data.length; j++) {