Author: scooter
Date: 2011-10-22 19:10:36 -0700 (Sat, 22 Oct 2011)
New Revision: 27275
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractClusterAlgorithm.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/AbstractAttributeClusterAlgorithm.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/AbstractAttributeClusterer.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/FeatureVector/FeatureVectorCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/Matrix.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/autosome/AutoSOMECluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/hierarchical/HierarchicalCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/kmeans/KMeansCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/kmedoid/KMedoidCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/AP/APCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/MCL/MCLCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/MCODE/MCODECluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/SCPS/SCPSCluster.java
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/glay/GLayCluster.java
Log:
Fixes for consistency in preparation for 1.10 release
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractClusterAlgorithm.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractClusterAlgorithm.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/AbstractClusterAlgorithm.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -93,9 +93,9 @@
clusterProperties.add(new Tunable("clusterAttrName", "Cluster
attribute",
Tunable.STRING,
clusterAttributeName));
clusterProperties.add(new Tunable("createGroups", "Create
metanodes with results",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(createGroups)));
clusterProperties.add(new Tunable("debug", "Enable debugging",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(debug)));
}
public void updateSettings(boolean force) {
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/AbstractAttributeClusterAlgorithm.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/AbstractAttributeClusterAlgorithm.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/AbstractAttributeClusterAlgorithm.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -76,7 +76,7 @@
protected boolean adjustDiagonals = false;
protected boolean debug = false;
protected boolean createGroups = false;
- protected boolean ignoreMissing = false;
+ protected boolean ignoreMissing = true;
protected boolean interimRun = false;
protected boolean selectedOnly = false;
protected boolean zeroMissing = false;
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/AbstractAttributeClusterer.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/AbstractAttributeClusterer.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/AbstractAttributeClusterer.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -58,8 +58,8 @@
protected String dataAttributes = null;
protected DistanceMetric distanceMetric = DistanceMetric.EUCLIDEAN;
protected boolean clusterAttributes = false;
- protected boolean createGroups = true;
- protected boolean ignoreMissing = false;
+ protected boolean createGroups = false;
+ protected boolean ignoreMissing = true;
protected boolean selectedOnly = false;
protected boolean adjustDiagonals = false;
protected boolean zeroMissing = false;
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/FeatureVector/FeatureVectorCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/FeatureVector/FeatureVectorCluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/FeatureVector/FeatureVectorCluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -48,9 +48,12 @@
import cytoscape.Cytoscape;
import cytoscape.data.CyAttributes;
import cytoscape.data.Semantics;
+import cytoscape.layout.CyLayoutAlgorithm;
+import cytoscape.layout.CyLayouts;
import cytoscape.layout.Tunable;
import cytoscape.layout.TunableListener;
import cytoscape.logger.CyLogger;
+import cytoscape.view.CyNetworkView;
import cytoscape.task.TaskMonitor;
import clusterMaker.algorithms.AbstractClusterAlgorithm;
@@ -64,8 +67,8 @@
public class FeatureVectorCluster extends AbstractAttributeClusterer
implements TunableListener {
- boolean createEdges = false;
- double edgeCutoff = 0.5;
+ boolean createNewNetwork = true;
+ double edgeCutoff = 0.001;
String dataAttributes = null;
String edgeAttribute = null;
final static String interaction = "distance";
@@ -77,7 +80,7 @@
}
public String getShortName() {return "featurevector";};
- public String getName() {return "Create Edges from Node Attributes";};
+ public String getName() {return "Create Correlation Network from Node
Attributes";};
public JPanel getSettingsPanel() {
// Everytime we ask for the panel, we want to update our
attributes
@@ -123,24 +126,25 @@
// Whether or not to only cluster selected nodes/edges
clusterProperties.add(new Tunable("selectedOnly",
"Only use selected
nodes/edges for cluster",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(selectedOnly)));
// For expression data, we might want to exclude missing data
clusterProperties.add(new Tunable("ignoreMissing",
"Ignore nodes/edges with no
data",
- Tunable.BOOLEAN, new
Boolean(true)));
+ Tunable.BOOLEAN, new
Boolean(ignoreMissing)));
// Whether to create a new network or add values to existing
network
- Tunable t = new Tunable("createEdges",
- "Create edges if they don't exist",
- Tunable.BOOLEAN, new Boolean(false));
+ Tunable t = new Tunable("createNewNetwork",
+ "Create a new network",
+ Tunable.BOOLEAN, new
Boolean(createNewNetwork));
t.addTunableValueListener(this);
clusterProperties.add(t);
// If we're creating edges, do we have a cut-off value?
t = new Tunable("edgeCutoff", "Only create edges if nodes are
closer than this",
- Tunable.DOUBLE, new Double(0.5));
- t.setImmutable(true);
+ Tunable.DOUBLE, new Double(edgeCutoff));
+ if (!createNewNetwork)
+ t.setImmutable(true);
clusterProperties.add(t);
clusterProperties.add(new Tunable("advancedParametersGroup",
@@ -157,7 +161,7 @@
// How to handle missing data
clusterProperties.add(new Tunable("zeroMissing",
"Set missing data to zero
(not common)",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(zeroMissing)));
clusterProperties.initializeProperties();
updateSettings(true);
@@ -168,10 +172,10 @@
}
public void tunableChanged(Tunable tunable) {
- if (tunable.getName().equals("createEdges")) {
- createEdges = ((Boolean)
tunable.getValue()).booleanValue();
+ if (tunable.getName().equals("createNewNetwork")) {
+ createNewNetwork = ((Boolean)
tunable.getValue()).booleanValue();
Tunable t = clusterProperties.get("edgeCutoff");
- if (createEdges)
+ if (createNewNetwork)
t.setImmutable(false);
else
t.setImmutable(true);
@@ -190,6 +194,10 @@
if ((t != null) && (t.valueChanged() || force))
selectedOnly = ((Boolean) t.getValue()).booleanValue();
+ t = clusterProperties.get("ignoreMissing");
+ if ((t != null) && (t.valueChanged() || force))
+ ignoreMissing = ((Boolean) t.getValue()).booleanValue();
+
t = clusterProperties.get("attributeList");
if ((t != null) && (t.valueChanged() || force)) {
dataAttributes = (String) t.getValue();
@@ -203,9 +211,9 @@
if ((t != null) && (t.valueChanged() || force))
edgeAttribute = (String) t.getValue();
- t = clusterProperties.get("createEdges");
+ t = clusterProperties.get("createNewNetwork");
if ((t != null) && (t.valueChanged() || force))
- createEdges = ((Boolean) t.getValue()).booleanValue();
+ createNewNetwork = ((Boolean)
t.getValue()).booleanValue();
t = clusterProperties.get("edgeCutoff");
if ((t != null) && (t.valueChanged() || force))
@@ -258,8 +266,8 @@
CyAttributes edgeAttributes = Cytoscape.getEdgeAttributes();
// For each node, get the distance to all other nodes
- double maxdistance = 0.0;
- double mindistance = 0.0;
+ double maxdistance = Double.MIN_VALUE;
+ double mindistance = Double.MAX_VALUE;
double distanceMatrix[][] = new double[nNodes][nNodes];
for (int i = 0; i < nNodes; i++) {
@@ -280,7 +288,7 @@
}
int[] nodeArray = new int[2];
- Map<CyEdge, Double> edgeList = new HashMap<CyEdge, Double>();
+ List<CyEdge> edgeList = new ArrayList<CyEdge>();
double scale = maxdistance - mindistance;
/* Performance tuning -- what's taking all the time!
@@ -296,7 +304,7 @@
for (int i = 0; i < nNodes; i++) {
for (int j = i+1; j < nNodes; j++) {
// time = System.currentTimeMillis();
- double distance = distanceMatrix[i][j]/scale;
+ double distance =
(distanceMatrix[i][j]-mindistance)/scale;
CyNode source =
Cytoscape.getCyNode(matrix.getRowLabel(i));
CyNode target =
Cytoscape.getCyNode(matrix.getRowLabel(j));
nodeArray[0] = source.getRootGraphIndex();
@@ -304,34 +312,25 @@
// nodeFetchTime +=
System.currentTimeMillis()-time;
- if (createEdges == true && distance >
edgeCutoff)
+ if (createNewNetwork == true && distance >
edgeCutoff)
continue;
// time = System.currentTimeMillis();
-
CyEdge edge;
- int[] edgeArray =
network.getConnectingEdgeIndicesArray(nodeArray);
- // edgeFetchTime +=
System.currentTimeMillis()-time;
- // time = System.currentTimeMillis();
-
- if ((edgeArray == null || edgeArray.length ==
0) && createEdges == true) {
+ if (createNewNetwork == true) {
edge = myCreateEdge(source, target,
edgeAttributes);
-
- // edgeCreateTime +=
System.currentTimeMillis()-time;
- // System.out.println("Creating edge
between "+source+" and "+target);
- if (edge != null) {
- // System.out.println("Adding
edge "+edge.getIdentifier()+" to network");
- // time =
System.currentTimeMillis();
- network.addEdge(edge);
- // networkAddTime +=
System.currentTimeMillis()-time;
- }
- } else if (edgeArray == null ||
edgeArray.length == 0) {
- continue;
+ edgeList.add(edge);
} else {
- edge =
(CyEdge)network.getEdge(edgeArray[0]);
+ int[] edgeArray =
network.getConnectingEdgeIndicesArray(nodeArray);
// edgeFetchTime +=
System.currentTimeMillis()-time;
+ // time = System.currentTimeMillis();
+ if (edgeArray == null ||
edgeArray.length == 0) {
+ continue;
+ } else {
+ edge =
(CyEdge)network.getEdge(edgeArray[0]);
+ // edgeFetchTime +=
System.currentTimeMillis()-time;
+ }
}
-
if (edge == null) continue;
// time = System.currentTimeMillis();
edgeAttributes.setAttribute(edge.getIdentifier(), edgeAttribute, distance);
@@ -343,6 +342,18 @@
}
}
+ // If we're supposed to, create the new network
+ if (createNewNetwork) {
+ List nodeList = network.nodesList();
+ CyNetwork net = Cytoscape.createNetwork(nodeList,
edgeList, network.getTitle()+"--clustered",network,false);
+ // Create the network view
+ CyNetworkView view = Cytoscape.createNetworkView(net);
+ // If available, do a force-directed layout
+ CyLayoutAlgorithm alg =
CyLayouts.getLayout("force-directed");
+ if (alg != null)
+ view.applyLayout(alg);
+ }
+
/*
System.out.println("Created "+newEdges+" edges");
System.out.println("Edge creation time: "+edgeCreateTime+"ms");
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/Matrix.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/Matrix.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/Matrix.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -32,12 +32,13 @@
*/
package clusterMaker.algorithms.attributeClusterers;
-import java.util.List;
-import java.util.HashMap;
import java.util.ArrayList;
-import java.util.Set;
import java.util.Arrays;
import java.util.Comparator;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
import java.lang.Exception;
import cytoscape.CyNode;
@@ -478,7 +479,7 @@
nodeList = sortNodeList(nodeList);
// Make a map of the conditions, indexed by CyNode
- HashMap<CyNode,HashMap<String,Double>>nodeCondMap = new
HashMap<CyNode,HashMap<String,Double>>();
+ Map<CyNode,Map<String,Double>>nodeCondMap = new
HashMap<CyNode,Map<String,Double>>();
// Make a map of the conditions, by name
List<String>condList = Arrays.asList(weightAttributes);
@@ -489,7 +490,7 @@
// Iterate over all of our nodes, getting the conditions
attributes
for (CyNode node: nodeList) {
// Create the map for this node
- HashMap<String,Double>thisCondMap = new
HashMap<String,Double>();
+ Map<String,Double>thisCondMap = new
HashMap<String,Double>();
for (int attrIndex = 0; attrIndex <
weightAttributes.length; attrIndex++) {
String attr = weightAttributes[attrIndex];
@@ -505,6 +506,7 @@
continue; // At some point, handle
lists?
}
if (!ignoreMissing || value != null) {
+ // System.out.println("Node =
"+node.getIdentifier()+", attribute = "+attr+", ignoreMissing =
"+ignoreMissing+" value = "+value);
// Set it
thisCondMap.put(attr, value);
}
@@ -530,7 +532,7 @@
if (!nodeCondMap.containsKey(node))
continue;
- HashMap<String,Double>thisCondMap =
nodeCondMap.get(node);
+ Map<String,Double>thisCondMap =
nodeCondMap.get(node);
this.columnLabels[column] =
node.getIdentifier();
this.columnNodes[column] = node;
for (int row=0; row < this.nRows; row++) {
@@ -558,7 +560,7 @@
continue;
this.rowLabels[row] = node.getIdentifier();
this.rowNodes[row] = node;
- HashMap<String,Double>thisCondMap =
nodeCondMap.get(node);
+ Map<String,Double>thisCondMap =
nodeCondMap.get(node);
for (int column=0; column < this.nColumns;
column++) {
String columnLabel =
this.columnLabels[column];
if
(thisCondMap.containsKey(columnLabel)) {
@@ -588,7 +590,7 @@
// sortNodeList does an alphabetical sort on the names of the nodes.
private List<CyNode>sortNodeList(List<CyNode>nodeList) {
- HashMap<String,CyNode>nodeMap = new HashMap<String, CyNode>();
+ Map<String,CyNode>nodeMap = new HashMap<String, CyNode>();
// First build a string array
String nodeNames[] = new String[nodeList.size()];
int index = 0;
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/autosome/AutoSOMECluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/autosome/AutoSOMECluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/autosome/AutoSOMECluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -137,6 +137,15 @@
logger = CyLogger.getLogger(AutoSOMECluster.class);
this.heatmap = heatmap;
if (heatmap) cluster_output = 1;
+
+ // Initialize our settings
+ settings.ensemble_runs = 50;
+ settings.mst_pval = 0.05;
+ settings.threads = Runtime.getRuntime().availableProcessors();
+ settings.logNorm = false;
+ settings.unitVar = false;
+ settings.distMatrix = false;
+
initializeProperties();
}
@@ -178,7 +187,7 @@
(Object)attributeArray,
(Object)null, Tunable.MULTISELECT));
clusterProperties.add(new Tunable("selectedOnly", "Only use
selected nodes for clustering",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(selectedNodes)));
Tunable ign = new Tunable("ignoreMissing", "Ignore nodes/edges
with no data",
Tunable.BOOLEAN, ignoreMissing);
@@ -198,20 +207,20 @@
// Clustering Threshold
ensembleRuns = new Tunable("ensembleRuns",
"Number of Ensemble Runs",
- Tunable.INTEGER, new
Integer(50),
+ Tunable.INTEGER, new
Integer(settings.ensemble_runs),
new Integer(1), (Object)null,
0);
clusterProperties.add(ensembleRuns);
// Number of iterations
clusterProperties.add(new Tunable("pvalueThresh",
"P-Value Threshold",
- Tunable.DOUBLE, new
Double(0.05),
+ Tunable.DOUBLE, new
Double(settings.mst_pval),
new Double(0), new Double(1),
0));
// Number of iterations
clusterProperties.add(new Tunable("numThreads",
"Number of Threads (No.
CPUs)",
- Tunable.INTEGER, new
Integer(Runtime.getRuntime().availableProcessors()),
+ Tunable.INTEGER, new
Integer(settings.threads),
new Integer(1), (Object)null,
0));
@@ -230,12 +239,12 @@
logscaling = new Tunable("logScaling",
"Log2 Scaling",
- Tunable.BOOLEAN, new
Boolean(false));
+ Tunable.BOOLEAN, new
Boolean(settings.logNorm));
clusterProperties.add(logscaling);
unitVar = new Tunable("unitVariance",
"Unit Variance",
- Tunable.BOOLEAN, new
Boolean(false));
+ Tunable.BOOLEAN, new
Boolean(settings.unitVar));
clusterProperties.add(unitVar);
medCent = new Tunable("medCenter",
@@ -263,7 +272,7 @@
new Boolean(true), null,
Tunable.COLLAPSABLE));
Tunable fcn = new Tunable("enableFCN", "Perform Fuzzy
Clustering",
- Tunable.BOOLEAN, new
Boolean(false));
+ Tunable.BOOLEAN, new
Boolean(settings.distMatrix));
fcn.addTunableValueListener(this);
clusterProperties.add(fcn);
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/hierarchical/HierarchicalCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/hierarchical/HierarchicalCluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/hierarchical/HierarchicalCluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -130,17 +130,17 @@
// Whether or not to only cluster selected nodes/edges
clusterProperties.add(new Tunable("selectedOnly",
"Only use selected
nodes/edges for cluster",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(selectedOnly)));
// Whether or not to cluster attributes as well as nodes
clusterProperties.add(new Tunable("clusterAttributes",
"Cluster attributes as well
as nodes",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(clusterAttributes)));
// For expression data, we might want to exclude missing data
clusterProperties.add(new Tunable("ignoreMissing",
"Ignore nodes/edges with no
data",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(ignoreMissing)));
clusterProperties.add(new Tunable("advancedParametersGroup",
"Advanced Parameters",
@@ -151,17 +151,17 @@
// How to handle missing data
clusterProperties.add(new Tunable("zeroMissing",
"Set missing data to zero
(not common)",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(zeroMissing)));
// Adjust loops
clusterProperties.add(new Tunable("adjustDiagonals",
"Adjust loops (not common)",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(adjustDiagonals)));
// Whether or not to create groups
clusterProperties.add(new Tunable("createGroups",
"Create groups from
clusters",
- Tunable.BOOLEAN, new
Boolean(true)));
+ Tunable.BOOLEAN, new
Boolean(createGroups)));
clusterProperties.initializeProperties();
updateSettings(true);
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/kmeans/KMeansCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/kmeans/KMeansCluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/kmeans/KMeansCluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -56,7 +56,7 @@
// clusterMaker imports
public class KMeansCluster extends AbstractAttributeClusterer {
- int rNumber = 0;
+ int rNumber = 50;
KnnView knnView = null;
public KMeansCluster() {
@@ -100,7 +100,7 @@
// Number of iterations
clusterProperties.add(new Tunable("iterations",
"Number of iterations",
- Tunable.INTEGER, new
Integer(50),
+ Tunable.INTEGER, new
Integer(rNumber),
(Object)new Integer(rNumber),
(Object)null, 0));
// The distance metric to use
@@ -123,12 +123,12 @@
// Whether or not to only cluster selected nodes/edges
clusterProperties.add(new Tunable("selectedOnly",
"Only use selected
nodes/edges for cluster",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(selectedOnly)));
// Whether or not to cluster attributes as well as nodes
clusterProperties.add(new Tunable("clusterAttributes",
"Cluster attributes as well
as nodes",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(clusterAttributes)));
/*
// For expression data, we might want to exclude missing data
@@ -140,7 +140,7 @@
// Whether or not to create groups
clusterProperties.add(new Tunable("createGroups",
"Create groups from
clusters",
- Tunable.BOOLEAN, new
Boolean(true)));
+ Tunable.BOOLEAN, new
Boolean(createGroups)));
clusterProperties.initializeProperties();
updateSettings(true);
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/kmedoid/KMedoidCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/kmedoid/KMedoidCluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/attributeClusterers/kmedoid/KMedoidCluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -57,7 +57,7 @@
// clusterMaker imports
public class KMedoidCluster extends AbstractAttributeClusterer {
- int rNumber = 0;
+ int rNumber = 10;
KnnView knnView = null;
public KMedoidCluster() {
@@ -101,7 +101,7 @@
// Number of iterations
clusterProperties.add(new Tunable("iterations",
"Number of iterations",
- Tunable.INTEGER, new
Integer(10),
+ Tunable.INTEGER, new
Integer(rNumber),
(Object)rNumber,
(Object)null, 0));
// The distance metric to use
@@ -124,12 +124,12 @@
// Whether or not to only cluster selected nodes/edges
clusterProperties.add(new Tunable("selectedOnly",
"Only use selected
nodes/edges for cluster",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(selectedOnly)));
// Whether or not to cluster attributes as well as nodes
clusterProperties.add(new Tunable("clusterAttributes",
"Cluster attributes as well
as nodes",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(clusterAttributes)));
/*
// For expression data, we might want to exclude missing data
@@ -141,7 +141,7 @@
// Whether or not to create groups
clusterProperties.add(new Tunable("createGroups",
"Create groups from
clusters",
- Tunable.BOOLEAN, new
Boolean(true)));
+ Tunable.BOOLEAN, new
Boolean(createGroups)));
clusterProperties.initializeProperties();
updateSettings(true);
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/AP/APCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/AP/APCluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/AP/APCluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -106,18 +106,18 @@
// Lambda Parameter
clusterProperties.add(new Tunable("lambda",
"Lambda Parameter",
- Tunable.DOUBLE, new
Double(.5),
+ Tunable.DOUBLE, new
Double(lambda),
(Object)null, (Object)null,
0));
// Clustering Threshold
clusterProperties.add(new Tunable("preference",
"Preference Parameter (Set to
Avg Edge Weight if < 0)",
- Tunable.DOUBLE, new
Double(-1),
+ Tunable.DOUBLE, new
Double(preference),
(Object)null, (Object)null,
0));
// Number of iterations
clusterProperties.add(new Tunable("iterations",
"Number of iterations",
- Tunable.INTEGER, new
Integer(10),
+ Tunable.INTEGER, new
Integer(rNumber),
(Object)null, (Object)null,
0));
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/MCL/MCLCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/MCL/MCLCluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/MCL/MCLCluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -68,7 +68,7 @@
public class MCLCluster extends AbstractNetworkClusterer {
double inflation_parameter = 2.0;
- int rNumber = 8;
+ int rNumber = 16;
double clusteringThresh = 1e-15;
double maxResidual = 0.001;
int maxThreads = 0;
@@ -108,7 +108,7 @@
// Inflation Parameter
clusterProperties.add(new Tunable("inflation_parameter",
"Granularity parameter
(inflation value)",
- Tunable.DOUBLE, new
Double(2.0),
+ Tunable.DOUBLE, new
Double(inflation_parameter),
(Object)null, (Object)null,
0));
// Use the standard edge attribute handling stuff....
@@ -120,25 +120,25 @@
// Clustering Threshold
clusterProperties.add(new Tunable("clusteringThresh",
"Weak edge weight pruning
threshold",
- Tunable.DOUBLE, new
Double(1e-15),
+ Tunable.DOUBLE, new
Double(clusteringThresh),
(Object)null, (Object)null,
0));
// Number of iterations
clusterProperties.add(new Tunable("iterations",
"Number of iterations",
- Tunable.INTEGER, new
Integer(16),
+ Tunable.INTEGER, new
Integer(rNumber),
(Object)null, (Object)null,
0));
// Number of iterations
clusterProperties.add(new Tunable("maxResidual",
"Maximum residual value",
- Tunable.DOUBLE, new
Double(.0001),
+ Tunable.DOUBLE, new
Double(maxResidual),
(Object)null, (Object)null,
0));
// Maximum number of CPU's to use
clusterProperties.add(new Tunable("maxThreads",
"Maximum number of threads",
- Tunable.INTEGER, new
Integer(0),
+ Tunable.INTEGER, new
Integer(maxThreads),
(Object)null, (Object)null,
0));
super.advancedProperties();
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/MCODE/MCODECluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/MCODE/MCODECluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/MCODE/MCODECluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -74,6 +74,16 @@
final static int INTERRUPTION = 3;
int analyze = FIRST_TIME;
+ boolean includeLoops = false;
+ boolean haircut = true;
+ boolean fluff = false;
+ double scoreCutoff = 0.2;
+ boolean selectedOnly = false;
+ int degreeCutoff = 2;
+ int kCore = 2;
+ int maxDepth = 100;
+
+
MCODEParameterSet currentParamsCopy;
RunMCODE runMCODE;
@@ -110,7 +120,7 @@
{
clusterProperties.add(new Tunable("selectedOnly",
"Cluster only
selected nodes",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(selectedOnly)));
clusterProperties.add(new Tunable("advanced_panel",
"Advanced Tuning
Options",
@@ -126,11 +136,11 @@
{
clusterProperties.add(new
Tunable("includeLoops",
"Include loops",
-
Tunable.BOOLEAN, new Boolean(false)));
+
Tunable.BOOLEAN, new Boolean(includeLoops)));
clusterProperties.add(new
Tunable("degreeCutoff",
"Degree Cutoff",
-
Tunable.INTEGER, new Integer(2)));
+
Tunable.INTEGER, new Integer(degreeCutoff)));
}
clusterProperties.add(new
Tunable("cluster_panel",
@@ -141,23 +151,23 @@
{
clusterProperties.add(new
Tunable("haircut",
"Haircut",
-
Tunable.BOOLEAN, new Boolean(true)));
+
Tunable.BOOLEAN, new Boolean(haircut)));
clusterProperties.add(new
Tunable("fluff",
"Fluff",
-
Tunable.BOOLEAN, new Boolean(false)));
+
Tunable.BOOLEAN, new Boolean(fluff)));
clusterProperties.add(new
Tunable("scoreCutoff",
"Node
Score Cutoff",
-
Tunable.DOUBLE, new Double(0.2)));
+
Tunable.DOUBLE, new Double(scoreCutoff)));
clusterProperties.add(new
Tunable("kCore",
"K-Core",
-
Tunable.INTEGER, new Integer(2)));
+
Tunable.INTEGER, new Integer(kCore)));
clusterProperties.add(new
Tunable("maxDepth",
"Max
Depth",
-
Tunable.INTEGER, new Integer(100)));
+
Tunable.INTEGER, new Integer(maxDepth)));
}
}
@@ -178,7 +188,7 @@
Tunable t = clusterProperties.get("selectedOnly");
if ((t != null) && (t.valueChanged() || force)) {
- boolean selectedOnly = ((Boolean)
t.getValue()).booleanValue();
+ selectedOnly = ((Boolean) t.getValue()).booleanValue();
if (selectedOnly)
currentParamsCopy.setScope(MCODEParameterSet.SELECTION);
else
@@ -187,43 +197,43 @@
t = clusterProperties.get("includeLoops");
if ((t != null) && (t.valueChanged() || force)) {
- boolean includeLoops = ((Boolean)
t.getValue()).booleanValue();
+ includeLoops = ((Boolean) t.getValue()).booleanValue();
currentParamsCopy.setIncludeLoops(includeLoops);
}
t = clusterProperties.get("degreeCutoff");
if ((t != null) && (t.valueChanged() || force)) {
- int degreeCutoff = ((Integer) t.getValue()).intValue();
+ degreeCutoff = ((Integer) t.getValue()).intValue();
currentParamsCopy.setDegreeCutoff(degreeCutoff);
}
t = clusterProperties.get("haircut");
if ((t != null) && (t.valueChanged() || force)) {
- boolean haircut = ((Boolean)
t.getValue()).booleanValue();
+ haircut = ((Boolean) t.getValue()).booleanValue();
currentParamsCopy.setHaircut(haircut);
}
t = clusterProperties.get("fluff");
if ((t != null) && (t.valueChanged() || force)) {
- boolean fluff = ((Boolean) t.getValue()).booleanValue();
+ fluff = ((Boolean) t.getValue()).booleanValue();
currentParamsCopy.setFluff(fluff);
}
t = clusterProperties.get("scoreCutoff");
if ((t != null) && (t.valueChanged() || force)) {
- double scoreCutoff = ((Double)
t.getValue()).doubleValue();
+ scoreCutoff = ((Double) t.getValue()).doubleValue();
currentParamsCopy.setNodeScoreCutoff(scoreCutoff);
}
t = clusterProperties.get("kCore");
if ((t != null) && (t.valueChanged() || force)) {
- int kCore = ((Integer) t.getValue()).intValue();
+ kCore = ((Integer) t.getValue()).intValue();
currentParamsCopy.setKCore(kCore);
}
t = clusterProperties.get("maxDepth");
if ((t != null) && (t.valueChanged() || force)) {
- int maxDepth = ((Integer) t.getValue()).intValue();
+ maxDepth = ((Integer) t.getValue()).intValue();
currentParamsCopy.setMaxDepthFromStart(maxDepth);
}
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/SCPS/SCPSCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/SCPS/SCPSCluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/SCPS/SCPSCluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -106,21 +106,21 @@
// Lambda Parameter
clusterProperties.add(new Tunable("epsilon",
"epsilon Parameter",
- Tunable.DOUBLE, new
Double(1.02),
+ Tunable.DOUBLE, new
Double(epsilon),
(Object)null, (Object)null,
0));
// Number of iterations
clusterProperties.add(new Tunable("iterations",
"Number of iterations",
- Tunable.INTEGER, new
Integer(50),
+ Tunable.INTEGER, new
Integer(rNumber),
(Object)null, (Object)null,
0));
// K. Trumps epsilon if set to greater then zero
clusterProperties.add(new Tunable("knumber",
"Number of clusters",
- Tunable.INTEGER, new
Integer(-1),
+ Tunable.INTEGER, new
Integer(knumber),
(Object)null, (Object)null,
0));
Modified:
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/glay/GLayCluster.java
===================================================================
---
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/glay/GLayCluster.java
2011-10-22 18:46:42 UTC (rev 27274)
+++
csplugins/trunk/ucsf/scooter/clusterMaker/src/clusterMaker/algorithms/networkClusterers/glay/GLayCluster.java
2011-10-23 02:10:36 UTC (rev 27275)
@@ -98,11 +98,11 @@
// Whether or not to create a new network from the results
clusterProperties.add(new Tunable("selectedOnly","Cluster only
selected nodes",
- Tunable.BOOLEAN, new
Boolean(false)));
+ Tunable.BOOLEAN, new
Boolean(selectedOnly)));
//Whether or not to assume the edges are undirected
clusterProperties.add(new Tunable("undirectedEdges","Assume
edges are undirected",
- Tunable.BOOLEAN, new
Boolean(true)));
+ Tunable.BOOLEAN, new
Boolean(undirectedEdges)));
clusterProperties.add(new Tunable("results_panel",
"Results",
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