Merge pull request #181 from sumanthreddy542/Cluster-rows-in-HeatMap

Update heatmap clustering and dendrogram plot options.
urmi-21 · Sep 20, 2021 · 6ced6a4 · 6ced6a4
2 parents 68fd86d + 03cde67
commit 6ced6a4
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Showing 28 changed files with 862 additions and 123 deletions.
diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -1,5 +1,5 @@
 #CI to test MOG build
-#Contributor sumanthreddy542
+#Contributor Sumanth
 name: Maven CI
 
 on:
@@ -14,7 +14,6 @@ jobs:
     strategy:
       matrix:
         os: [macos-latest, windows-latest, ubuntu-latest]
-        #os: [windows-latest]
 
     steps:
     - uses: actions/checkout@v2
@@ -51,7 +50,18 @@ jobs:
     - name: Installing CustomBrowserLauncher dependency windows
       if: ${{ matrix.os == 'windows-latest'}}
       run: mvn install:install-file `-Dfile=src/lib/CustomBrowserLauncher.jar `-DgroupId=edu.iastate.metnet `-DartifactId=custombrowserlauncher `-Dversion=0.0.1 `-Dpackaging=jar `-DgeneratePom=true
-
+
+    - name: Downloading hierarchical-clustering zip file
+      run: curl -LJO https://github.com/lbehnke/hierarchical-clustering-java/releases/download/v1.2.0/hierarchical-clustering-1.2.0.jar
+
+    - name: Installing hierarchical-clustering dependency
+      if: ${{ matrix.os == 'ubuntu-latest' || matrix.os == 'macos-latest' }}
+      run: mvn install:install-file -Dfile=hierarchical-clustering-1.2.0.jar -DgroupId=com.apporiented -DartifactId=hierarchical-clustering -Dversion=1.2.0 -Dpackaging=jar -DgeneratePom=true
+
+    - name: Installing hierarchical-clustering dependency windows
+      if: ${{ matrix.os == 'windows-latest' }}
+      run: mvn install:install-file `-Dfile=hierarchical-clustering-1.2.0.jar `-DgroupId=com.apporiented `-DartifactId=hierarchical-clustering `-Dversion=1.2.0 `-Dpackaging=jar `-DgeneratePom=true
+
     - name: Build with Maven
       run: mvn -B package --file pom.xml
 

diff --git a/pom.xml b/pom.xml
@@ -229,6 +229,11 @@
 			<artifactId>tsne</artifactId>
 			<version>v2.6.3</version>
 		</dependency>
+		<dependency>
+			<groupId>com.apporiented</groupId>
+			<artifactId>hierarchical-clustering</artifactId>
+			<version>1.2.0</version>
+		</dependency>
 	</dependencies>
 
 </project>
diff --git a/src/edu/iastate/metnet/metaomgraph/ComputeTSNE.java b/src/edu/iastate/metnet/metaomgraph/ComputeTSNE.java
@@ -85,11 +85,11 @@ public double[][] projectData(){
 			if(error.contains("Perplexity too large")) {
 				String errorMessage = error;
 				errorMessage += "Please set it low, check the user guide for optimal values";
-				JOptionPane.showMessageDialog(MetaOmGraph.getMainWindow(), errorMessage, "Tsne error", JOptionPane.ERROR_MESSAGE);
+				JOptionPane.showMessageDialog(null, errorMessage, "Tsne error", JOptionPane.ERROR_MESSAGE);
 			}
 			else if(error.contains("theta")) {
 				String errorMessage = "Please set theta more than 0.0";
-				JOptionPane.showMessageDialog(MetaOmGraph.getMainWindow(), errorMessage, "Tsne error", JOptionPane.ERROR_MESSAGE);
+				JOptionPane.showMessageDialog(null, errorMessage, "Tsne error", JOptionPane.ERROR_MESSAGE);
 			}
 		}
 		catch(Exception e) {

diff --git a/src/edu/iastate/metnet/metaomgraph/CorrelationCalc.java b/src/edu/iastate/metnet/metaomgraph/CorrelationCalc.java
@@ -61,7 +61,7 @@ private void calcBaseValues() {
 		}*/
 	}
 
-	private double[] calcRank(double[] data) {
+	private static double[] calcRank(double[] data) {
 		SortableData[] myData = new SortableData[data.length];
 		for (int i = 0; i < myData.length; i++) {
 			myData[i] = new SortableData(data[i], i);
@@ -118,7 +118,8 @@ public double pearsonCorrelation(double[] b, boolean hasSkips, Double blankValue
 	public double pearsonCorrelationStandard(double[] b) {
 		return pearsonCorrelationStandard(a, b);
 	}
-	public double pearsonCorrelationStandard(double[] a,double[] b) {
+
+	public static double pearsonCorrelationStandard(double[] a,double[] b) {
 
 		if (b.length != a.length) {
 			JOptionPane.showMessageDialog(null, "Unequal lengths", "Error", JOptionPane.ERROR_MESSAGE);
@@ -162,8 +163,13 @@ public double pearsonCorrelationStandard(double[] a,double[] b) {
 		return corr;
 
 	}
-
 
+
+	public static double spearmanCorrelation(double[] a, double[] b) {
+		double[] rankA = calcRank(a);
+		double[] rankB = calcRank(b);
+		return pearsonCorrelationStandard(rankA,rankB);
+	}
 
 	// using apache
 	public double newSpearmanCorrelation(double[] b) {
@@ -195,13 +201,6 @@ public double mySpearmanCorrelation(double[] b) {
 	}
 
 
-
-
-
-
-
-
-
 	public double euclideanDistance(Object[] b, boolean hasSkips, Double blankValue) {
 		if ((b == null) || (a == null))
 			return 0.0D;

diff --git a/src/edu/iastate/metnet/metaomgraph/FilterableTableModel.java b/src/edu/iastate/metnet/metaomgraph/FilterableTableModel.java
@@ -94,7 +94,7 @@ public void applyFilterold(String[] values) {
 	}
 
 	private TreeSet<Integer> applyAnyColFilter(String value, 
-			boolean isNotFlag, boolean doesNotFlag, boolean containsFlag){
+			boolean isNotFlag, boolean doesNotFlag, boolean isFlag){
 
 		TreeSet<Integer> hits = new TreeSet();
 		for (int row = 0; row < model.getRowCount(); row++) {
@@ -115,13 +115,13 @@ private TreeSet<Integer> applyAnyColFilter(String value,
 						break;
 					}
 				}
-				else if(containsFlag) {
-					if(thisValue.contains(value)) {
+				else if(isFlag) {
+					if (thisValue.contentEquals(value)) {
 						hits.add(Integer.valueOf(row));
 						break;
 					}
 				}
-				else if (thisValue.contentEquals(value)) {
+				else if(thisValue.contains(value)) {
 					hits.add(Integer.valueOf(row));
 					break;
 				}
@@ -131,7 +131,7 @@ else if (thisValue.contentEquals(value)) {
 	}
 
 	private TreeSet<Integer> applyAllColsFilter(String value, 
-			boolean isNotFlag, boolean doesNotFlag, boolean containsFlag){
+			boolean isNotFlag, boolean doesNotFlag, boolean isFlag){
 
 		TreeSet<Integer> hits = new TreeSet();
 		for (int row = 0; row < model.getRowCount(); row++) {
@@ -153,13 +153,13 @@ private TreeSet<Integer> applyAllColsFilter(String value,
 						break;
 					}
 				}
-				else if(containsFlag) {
-					if(!thisValue.contains(value)) {
-						allFields = false;
-						break;
+				else if(isFlag) {
+					if (!thisValue.contentEquals(value)) {
+							allFields = false;
+							break;
 					}
 				}
-				else if (!thisValue.contentEquals(value)) {
+				else if(!thisValue.contains(value)) {
 					allFields = false;
 					break;
 				}
@@ -188,29 +188,33 @@ public void applyFilter(String[] values) {
 			for (String findMe : values) {
 				boolean isNotFlag = false;
 				boolean doesNotFlag = false;
-				boolean containsFlag = false;
-				if(findMe.charAt(0) == '!') {
-					isNotFlag = true;
-					findMe = findMe.substring(1);
-				} else if(findMe.substring(0, 2).contentEquals("~!")) {
-					doesNotFlag = true;
-					findMe = findMe.substring(2);
-				} else if(findMe.charAt(0) == '~') {
-					containsFlag = true;
-					findMe = findMe.substring(1);
+				boolean isFlag = false;
+				if(findMe.length() > 1) {
+					if(findMe.substring(0, 2).contentEquals("!=")) {
+						isNotFlag = true;
+						findMe = findMe.substring(2);
+					} else if(findMe.charAt(0) == '!') {
+						doesNotFlag = true;
+						findMe = findMe.substring(1);
+					} else if(findMe.charAt(0) == '=') {
+						isFlag = true;
+						findMe = findMe.substring(1);
+					}
 				}
 				boolean colFlag = false;
 				int colInt = -1;
 				boolean allCols = false;
-				boolean anyCol = false;
+				boolean anyCol = true;
 				// delim should be present and should have values on both sides
 				if (findMe.indexOf(delim) > -1 && findMe.indexOf(delim) < findMe.length() - delim.length()) {
 					String col = findMe.split(delim)[1];
 					if(col.contentEquals("ALL")) {
 						allCols = true;
+						anyCol = false;
 						findMe = findMe.split(delim)[0];
 					} else if(col.contentEquals("ANY")) {
 						anyCol = true;
+						allCols = false;
 						findMe = findMe.split(delim)[0];
 					} else {
 						// check if col is a valid integer
@@ -258,12 +262,12 @@ public void applyFilter(String[] values) {
 							if(!thisValue.contains(findMe)) {
 								hits.add(Integer.valueOf(row));
 							}
-						} else if(containsFlag) {
-							if(thisValue.contains(findMe)) {
+						} else if(isFlag) {
+							if (thisValue.contentEquals(findMe)) {
 								hits.add(Integer.valueOf(row));
 							}
 						}
-						else if (thisValue.contentEquals(findMe)) {
+						else if(thisValue.contains(findMe)) {
 							hits.add(Integer.valueOf(row));
 						}
 					}
@@ -273,9 +277,9 @@ else if (thisValue.contentEquals(findMe)) {
 						findMe = findMe.split(caseFlag)[0];
 					}
 					if(anyCol) {
-						hits.addAll(applyAnyColFilter(findMe, isNotFlag, doesNotFlag, containsFlag));
+						hits.addAll(applyAnyColFilter(findMe, isNotFlag, doesNotFlag, isFlag));
 					} else if(allCols) {
-						hits.addAll(applyAllColsFilter(findMe, isNotFlag, doesNotFlag, containsFlag));
+						hits.addAll(applyAllColsFilter(findMe, isNotFlag, doesNotFlag, isFlag));
 					}
 				}
 			}

diff --git a/src/edu/iastate/metnet/metaomgraph/IconTheme.java b/src/edu/iastate/metnet/metaomgraph/IconTheme.java
@@ -52,6 +52,8 @@ public interface IconTheme {
     ImageIcon getExternalSource();
 
     ImageIcon getSort();
+
+    ImageIcon getClusterIcon();
 
     ImageIcon getExcel();
 

diff --git a/src/edu/iastate/metnet/metaomgraph/JavaIconTheme.java b/src/edu/iastate/metnet/metaomgraph/JavaIconTheme.java
@@ -27,6 +27,7 @@ public class JavaIconTheme implements IconTheme {
 	private ImageIcon zoomIn;
 	private ImageIcon zoomOut;
 	private ImageIcon sort;
+	private ImageIcon cluster;
 	private ImageIcon excel;
 	private ImageIcon report;
 	private ImageIcon groupBy;
@@ -95,6 +96,8 @@ public JavaIconTheme() {
 	private String rIconPath =  "/resource/customicon/r_logoIcon16.png";
 
 	private String selectIconPath = "/resource/customicon/select16.png";
+
+	private final String clusterIconPath = "/resource/customicon/cluster16.png";
 
 	@Override
 	public ImageIcon getProperties() {
@@ -295,6 +298,14 @@ public ImageIcon getSort() {
 		}
 		return sort;
 	}
+
+	@Override
+	public ImageIcon getClusterIcon() {
+		if (cluster == null) {
+			cluster = new ImageIcon(getClass().getResource(clusterIconPath));
+		}
+		return cluster;
+	}
 
 	@Override
 	public ImageIcon getExcel() {

diff --git a/src/edu/iastate/metnet/metaomgraph/MetaOmGraph.java b/src/edu/iastate/metnet/metaomgraph/MetaOmGraph.java
@@ -4113,6 +4113,8 @@ private static String downloadProjSelectionPanel(File projDirectory, DownloadSam
         	destPath += File.separator + "MOG_Athaliana_Metabolomics";
         	if(Utils.downloadFile(projURL, destPath + ".zip")) {
         		Utils.unZipFile(destPath + ".zip", destPath);
+        	} else {
+        		destPath = "";
         	}
         } else if (project == DownloadSampleProject.MicroArray) {
         	try {
@@ -4124,6 +4126,8 @@ private static String downloadProjSelectionPanel(File projDirectory, DownloadSam
         	destPath += File.separator + "MOG_Athaliana_MicroArray";
         	if(Utils.downloadFile(projURL, destPath + ".zip")) {
         		Utils.unZipFile(destPath + ".zip", destPath);
+        	} else {
+        		destPath = "";
         	}
         } else {
         	try {
@@ -4135,14 +4139,16 @@ private static String downloadProjSelectionPanel(File projDirectory, DownloadSam
         	destPath += File.separator + "MOG_HumanCancerRNASeq";
         	if(Utils.downloadFile(projURL, destPath + ".zip")) {
         		Utils.unZipFile(destPath + ".zip", destPath);
+        	} else {
+        		destPath = "";
         	}
         }
         return destPath;
 	}
 
 	private static void downloadAndOpenProject(DownloadSampleProject project) {
 		File currDir = Utils.getLastDir();
-		File projSelDir = CustomFileSaveDialog.showDirectoryDialog(currDir);
+		File projSelDir = CustomFileSaveDialog.showDirectoryDialog(currDir, "Save sample project to");
 		if(projSelDir == null) {
 			return;
 		}

diff --git a/src/edu/iastate/metnet/metaomgraph/MetaOmTips.java b/src/edu/iastate/metnet/metaomgraph/MetaOmTips.java
@@ -42,7 +42,7 @@ public MetaOmTips() {
         tips = new ArrayList();
         addTip(
                 "Welcome to MetaOmGraph!",
-                "<html><p style=\"color:9ACD32\">You can press F1 at any time to get help with whatever you're working on.\n\nOn some laptops (especially Mac laptops), you may need to press Fn-F1.</p></html>");
+                "<html><p style=\"color:3335FF\">You can press F1 at any time to get help with whatever you're working on.\n\nOn some laptops (especially Mac laptops), you may need to press Fn-F1.</p></html>");
 
         tipPane = new JTextPane();
         tipPane.setEditable(false);
@@ -62,7 +62,7 @@ public MetaOmTips() {
         addTip("Properties", 
         		"<html><p style=\"color:FF00FF\">Plot defaults (axis titles, background gradient), as well as row and column names, can be edited by selecting Project->Properties from the menu bar.</p></html>");
         addTip("Saving Metadata sorts", 
-        		"<html><p style=\"color:7FFF00\">To quickly re-order any plot to the result of a metadata sort, save the result as a custom sort.  Run the metadata sort, then select the custom sort option, then click the Save button.</p></html>");
+        		"<html><p style=\"color:FF4C33\">To quickly re-order any plot to the result of a metadata sort, save the result as a custom sort.  Run the metadata sort, then select the custom sort option, then click the Save button.</p></html>");
 
 
         createTipPanel();

diff --git a/src/edu/iastate/metnet/metaomgraph/SilkIconTheme.java b/src/edu/iastate/metnet/metaomgraph/SilkIconTheme.java
@@ -33,6 +33,7 @@ public class SilkIconTheme implements IconTheme {
     private ImageIcon groupBy;
     private ImageIcon rIcon;
     private ImageIcon selectIcon;
+    private ImageIcon clusterIcon;
 
     private String defaultZoomPath = "/resource/silkicon/zoom.png";
 
@@ -94,6 +95,8 @@ public SilkIconTheme() {
     private String rIconPath =  "/resource/customicon/r_logoIcon16.png";
 
     private String selectIconPath = "/resource/customicon/select16.png";
+
+    private final String clusterIconPath = "/resource/customicon/cluster16.png";
 
     @Override
 	public ImageIcon getProperties() {
@@ -363,4 +366,11 @@ public ImageIcon getSelectIcon() {
 		}
 		return selectIcon;
 	}
+
+	public ImageIcon getClusterIcon() {
+		if(clusterIcon == null) {
+			clusterIcon = new ImageIcon(getClass().getResource(clusterIconPath));
+		}
+		return clusterIcon;
+	}
 }
diff --git a/src/edu/iastate/metnet/metaomgraph/TangoIconTheme.java b/src/edu/iastate/metnet/metaomgraph/TangoIconTheme.java
@@ -36,6 +36,7 @@ public class TangoIconTheme implements IconTheme {
     private ImageIcon groupBy;
     private ImageIcon rIcon;
     private ImageIcon selectIcon;
+    private ImageIcon clusterIcon;
 
     private String dir = "/resource/tango/16x16/";
 
@@ -103,6 +104,8 @@ public class TangoIconTheme implements IconTheme {
 
     private String selectIconPath = "/resource/customicon/select16.png";
 
+    private final String clusterIconPath = "/resource/customicon/cluster16.png";
+
     public TangoIconTheme() {
     }
 
@@ -373,6 +376,13 @@ public ImageIcon getSelectIcon() {
 		return selectIcon;
 	}
 
+	public ImageIcon getClusterIcon() {
+		if(clusterIcon == null) {
+			clusterIcon = new ImageIcon(getClass().getResource(clusterIconPath));
+		}
+		return clusterIcon;
+	}
+
     public static void main(String[] args) {
         java.lang.reflect.Method[] methods = SilkIconTheme.class.getDeclaredMethods();
         IconTheme theme = new SilkIconTheme();