Author: ghannum
Date: 2010-07-30 11:00:57 -0700 (Fri, 30 Jul 2010)
New Revision: 21088
Added:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ComplexRegressionResult.java
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ComplexRegression.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/networks/linkedNetworks/TypedLinkNetwork.java
Log:
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ComplexRegression.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ComplexRegression.java
2010-07-30 17:48:23 UTC (rev 21087)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ComplexRegression.java
2010-07-30 18:00:57 UTC (rev 21088)
@@ -18,11 +18,11 @@
public class ComplexRegression
{
- public static SFNetwork complexRegress(SFNetwork net, List<SNodeModule>
complexList, boolean abs)
+ public static ComplexRegressionResult complexRegress(SFNetwork net,
List<SNodeModule> complexList, boolean abs)
{
int n = net.numEdges();
- double[][] x = new double[n][1];
+ double[][] x = new double[n][2];
double[] y = new double[n];
List<SEdge> edgeList = new ArrayList<SEdge>(n);
@@ -31,11 +31,16 @@
for (SFEdge e : net.edgeIterator())
{
x[i][0] = (abs) ? Math.abs(e.value()) : e.value();
+ x[i][1] = e.value();
+ y[i] = 0;
for (SNodeModule c : complexList)
- if (c.contains(e.getI1()) &&
c.contains(e.getI2())) y[i] = 1;
- else y[i] = 0;
-
+ if (c.contains(e.getI1()) &&
c.contains(e.getI2()))
+ {
+ y[i] = 1;
+ break;
+ }
+
edgeList.add(e);
i++;
@@ -69,6 +74,6 @@
out.add(edgeList.get(j).getI1(),edgeList.get(j).getI2(),(float)prob);
}
- return out;
+ return new ComplexRegressionResult(out,DoubleMatrix.getCol(x,
1),y,lm.coefficients().get(0),lm.coefficients().get(1));
}
}
Added:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ComplexRegressionResult.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ComplexRegressionResult.java
(rev 0)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/ComplexRegressionResult.java
2010-07-30 18:00:57 UTC (rev 21088)
@@ -0,0 +1,21 @@
+package org.idekerlab.PanGIAPlugin;
+
+import org.idekerlab.PanGIAPlugin.networks.*;
+
+public class ComplexRegressionResult
+{
+ public final SFNetwork net;
+ public final double[] x;
+ public final double[] y;
+ public final double coef;
+ public final double intercept;
+
+ public ComplexRegressionResult(SFNetwork net, double[] x, double[] y,
double coef, double intercept)
+ {
+ this.net = net;
+ this.x = x;
+ this.y = y;
+ this.coef = coef;
+ this.intercept = intercept;
+ }
+}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
2010-07-30 17:48:23 UTC (rev 21087)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/NestedNetworkCreator.java
2010-07-30 18:00:57 UTC (rev 21088)
@@ -1,7 +1,6 @@
package org.idekerlab.PanGIAPlugin;
-import java.net.URL;
import java.util.*;
import org.idekerlab.PanGIAPlugin.ModFinder.BFEdge;
@@ -163,8 +162,7 @@
int nodeIndex = 1;
double maxScore = Double.NEGATIVE_INFINITY;
maxSize = 0;
- for (final TypedLinkEdge<TypedLinkNodeModule<String, BFEdge>,
BFEdge> edge : networkOfModules
- .edges())
+ for (final TypedLinkEdge<TypedLinkNodeModule<String, BFEdge>,
BFEdge> edge : networkOfModules.edgeIterator())
{
final TypedLinkNodeModule<String, BFEdge> sourceModule
= edge.source().value();
CyNode sourceNode = moduleToCyNodeMap.get(sourceModule);
@@ -244,8 +242,7 @@
Integer.valueOf(sourceModule.size()));
edgeAttribs.setAttribute(newEdge.getIdentifier(),
"PanGIA.target size",
Integer.valueOf(targetModule.size()));
- final double density = edgeScore
- / (sourceModule.size() *
targetModule.size());
+ final double density = edgeScore / (sourceModule.size()
* targetModule.size());
edgeAttribs.setAttribute(newEdge.getIdentifier(),
"PanGIA.genetic interaction density", Double
.valueOf(density));
}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
2010-07-30 17:48:23 UTC (rev 21087)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/SearchTask.java
2010-07-30 18:00:57 UTC (rev 21088)
@@ -16,9 +16,8 @@
import org.idekerlab.PanGIAPlugin.ModFinder.SouravScore;
import org.idekerlab.PanGIAPlugin.ModFinder.BFEdge.InteractionType;
import org.idekerlab.PanGIAPlugin.data.*;
-import org.idekerlab.PanGIAPlugin.networks.SFNetwork;
-import org.idekerlab.PanGIAPlugin.networks.SNodeModule;
-import org.idekerlab.PanGIAPlugin.networks.hashNetworks.FloatHashNetwork;
+import org.idekerlab.PanGIAPlugin.networks.*;
+import org.idekerlab.PanGIAPlugin.networks.hashNetworks.*;
import org.idekerlab.PanGIAPlugin.networks.linkedNetworks.*;
import org.idekerlab.PanGIAPlugin.utilities.collections.HashMapUtil;
import org.idekerlab.PanGIAPlugin.utilities.collections.ListOps;
@@ -35,8 +34,6 @@
import org.idekerlab.PanGIAPlugin.util.Scaler;
import org.idekerlab.PanGIAPlugin.util.ScalerFactory;
-import java.io.*;
-
import javax.swing.*;
/**
@@ -66,12 +63,6 @@
if (needsToHalt) return;
- /***
- * TODO: Annotation
- * Use absolute value for training?
- */
-
-
final CyNetwork physicalInputNetwork =
parameters.getPhysicalNetwork();
SFNetwork physicalNetwork =
convertCyNetworkToSFNetwork(physicalInputNetwork,
@@ -107,10 +98,23 @@
if (needsToHalt) return;
//Perform training
- if (parameters.getComplexTrainingPhysical()) physicalNetwork =
ComplexRegression.complexRegress(physicalNetwork, trainingComplexes, true);
- if (parameters.getComplexTrainingGenetic()) geneticNetwork =
ComplexRegression.complexRegress(geneticNetwork, trainingComplexes, true);
+ ComplexRegressionResult physicalRegress=null;
+ ComplexRegressionResult geneticRegress=null;
+ if (parameters.getComplexTrainingPhysical())
+ {
+ physicalRegress =
ComplexRegression.complexRegress(physicalNetwork, trainingComplexes, true);
+ physicalNetwork = physicalRegress.net;
+ }
+ if (parameters.getComplexTrainingGenetic())
+ {
+ geneticRegress =
ComplexRegression.complexRegress(geneticNetwork, trainingComplexes, true);
+ geneticNetwork = geneticRegress.net;
+ }
+
+
+
if (needsToHalt) return;
//Apply the degree filter
@@ -121,9 +125,10 @@
int degreeFilter = parameters.getPhysicalNetworkFilterDegree();
if (degreeFilter!=-1)
{
+ System.out.println("Applying degree filter =
"+degreeFilter);
TypedLinkNetwork<String,Float> ptlnet =
physicalNetwork.asTypedLinkNetwork();
- Set<String> pnodes = physicalNetwork.getNodes();
- physicalNetwork = new
FloatHashNetwork(ptlnet.subNetwork(pnodes, degreeFilter));
+ Set<String> gnodes = geneticNetwork.getNodes();
+ physicalNetwork = new
FloatHashNetwork(ptlnet.subNetwork(gnodes, degreeFilter));
}
int pnetNodes2 = physicalNetwork.numNodes();
@@ -219,6 +224,8 @@
Map<TypedLinkNodeModule<String, BFEdge>,String> module_name =
null;
System.out.println("PARAM:
"+parameters.getComplexTrainingPhysical()+",
"+parameters.getComplexTrainingPhysical()+",
"+parameters.getComplexAnnotation()+", "+parameters.getAnnotationThreshold());
+ int annotMatches = -1;
+
if (parameters.getComplexAnnotation())
{
module_name = new HashMap<TypedLinkNodeModule<String,
BFEdge>,String>(results.numNodes(),1);
@@ -240,7 +247,8 @@
if (bestNode!=null &&
bestScore>=parameters.getAnnotationThreshold()) module_name.put(bestNode,
complex.getID());
}
- System.out.println("Number of module annotation
matches: "+module_name.size());
+ annotMatches = module_name.size();
+ System.out.println("Number of module annotation
matches: "+annotMatches);
}
if (needsToHalt) return;
@@ -260,6 +268,7 @@
setPercentCompleted(100);
+ /*
// Create an edge attribute "overlapScore", which is defined as
NumberOfSharedNodes/min(two network sizes)
CyAttributes cyEdgeAttrs = Cytoscape.getEdgeAttributes();
int[] edgeIndexArray =
nnCreator.getOverviewNetwork().getEdgeIndicesArray();
@@ -274,12 +283,13 @@
double overlapScore =
(double)NumberOfSharedNodes/minNodeCount;
cyEdgeAttrs.setAttribute(aEdge.getIdentifier(),
"overlapScore", overlapScore);
- }
+ }*/
//Generate report
- if (!parameters.getReportPath().equals(""))
generateReport(parameters.getReportPath(), networkName, pnetNodes1, pnetNodes2,
pnetEdges1, pnetEdges2, geneticNetwork.numNodes(), geneticNetwork.numEdges(),
trainingComplexes);
+ if (!parameters.getReportPath().equals(""))
generateReport(parameters.getReportPath(), networkName, pnetNodes1, pnetNodes2,
pnetEdges1, pnetEdges2, geneticNetwork.numNodes(), geneticNetwork.numEdges(),
trainingComplexes, physicalRegress, geneticRegress, annotMatches, results);
}
+ /*
private static int getNumberOfSharedNodes(CyNetwork networkA, CyNetwork
networkB){
int[] nodeIndicesA = networkA.getNodeIndicesArray();
@@ -299,7 +309,7 @@
}
return sharedNodeCount;
- }
+ }*/
public void halt() {
@@ -516,7 +526,7 @@
return scaledEdgeAttribValues;
}
- private void generateReport(String path, String networkName, int
pnetNodes1, int pnetNodes2, int pnetEdges1, int pnetEdges2, int gnetNodes, int
gnetEdges, List<SNodeModule> trainingComplexes)
+ private void generateReport(String path, String networkName, int
pnetNodes1, int pnetNodes2, int pnetEdges1, int pnetEdges2, int gnetNodes, int
gnetEdges, List<SNodeModule> trainingComplexes, ComplexRegressionResult
physicalRegress, ComplexRegressionResult geneticRegress, int annotMatches,
TypedLinkNetwork<TypedLinkNodeModule<String, BFEdge>, BFEdge> results)
{
HTMLPage report = new HTMLPage();
report.setTitle("PanGIA report: "+networkName);
@@ -550,30 +560,134 @@
b.add("Annotation:
"+parameters.getAnnotationAttrName()+" ("+trainingComplexes.size()+"
entries)");
b.add("");
+ double background =
(parameters.getComplexTrainingPhysical() ||
parameters.getComplexTrainingGenetic()) ? getBackground(trainingComplexes) :
Double.NaN;
+
if (parameters.getComplexTrainingPhysical())
{
b.add("Physical interaction annotation
enrichment");
- float[] x = new
FloatVector(DoubleVector.getScale(0,100,2).getData()).getData();
- float[] y = new
FloatVector(DoubleVector.times(DoubleVector.rUnif(51),100)).getData();
+ double[][] curve =
getCurve(physicalRegress.x,physicalRegress.y,40,background);
- b.add("<IMG
src=\"http://chart.apis.google.com/chart?cht=lxy&chs=500x300&chd=t:"+ListOps.collectionToString(x,",")+"|"+ListOps.collectionToString(y,",")+"&chxr=0,-25,10,5&chxt=x,x,y,y&chxl=1:|Interaction_Score|2:|10^-2|10^-1|10^0|10^1|10^2|10^3|3:|Enrichment&chxp=1,60|3,50&chco=0000FF&chxs=0,000000,12,0,lt|1,000000,12,1,lt|2,000000,12,2,lt|3,000000,12,3,lt&chg=0,100,3,3,0,40\">");
+ double xmin = DoubleVector.min(curve[0]);
+ double xmax = DoubleVector.max(curve[0]);
+
+ double ymin = -2;
+ double ymax = 3;
+
+ float[] x = new
FloatVector(DoubleVector.divideBy(DoubleVector.subtract(curve[0],xmin),(xmax-xmin)/100)).getData();
+ float[] y = new
FloatVector(DoubleVector.divideBy(DoubleVector.subtract(curve[1],ymin),(ymax-ymin)/100)).getData();
+
+ b.add("<IMG
src=\"http://chart.apis.google.com/chart?cht=lxy&chs=500x300&chd=t:"+ListOps.collectionToString(x,",")+"|"+ListOps.collectionToString(y,",")+"&chxr=0,"+xmin+","+xmax+"&chxt=x,x,y,y&chxl=1:|Interaction_Score|2:|10^-2|10^-1|10^0|10^1|10^2|10^3|3:|Enrichment&chxp=1,60|3,50&chco=0000FF&chxs=0,000000,12,0,lt|1,000000,12,1,lt|2,000000,12,2,lt|3,000000,12,3,lt&chg=0,100,3,3,0,40\">");
b.add("");
+ b.add("Logistic regression:
beta="+physicalRegress.coef+", intercept="+physicalRegress.intercept);
+ b.add("");
}
+ if (parameters.getComplexTrainingGenetic())
+ {
+ b.add("Genetic interaction annotation
enrichment");
+ double[][] curve =
getCurve(geneticRegress.x,geneticRegress.y,40,background);
+
+ double xmin = DoubleVector.min(curve[0]);
+ double xmax = DoubleVector.max(curve[0]);
+
+ double ymin = -2;
+ double ymax = 3;
+
+ float[] x = new
FloatVector(DoubleVector.divideBy(DoubleVector.subtract(curve[0],xmin),(xmax-xmin)/100)).getData();
+ float[] y = new
FloatVector(DoubleVector.divideBy(DoubleVector.subtract(curve[1],ymin),(ymax-ymin)/100)).getData();
+
+ b.add("<IMG
src=\"http://chart.apis.google.com/chart?cht=lxy&chs=500x300&chd=t:"+ListOps.collectionToString(x,",")+"|"+ListOps.collectionToString(y,",")+"&chxr=0,"+xmin+","+xmax+"&chxt=x,x,y,y&chxl=1:|Interaction_Score|2:|10^-2|10^-1|10^0|10^1|10^2|10^3|3:|Enrichment&chxp=1,60|3,50&chco=0000FF&chxs=0,000000,12,0,lt|1,000000,12,1,lt|2,000000,12,2,lt|3,000000,12,3,lt&chg=0,100,3,3,0,40\">");
+ b.add("");
+ b.add("Logistic regression:
beta="+geneticRegress.coef+", intercept="+geneticRegress.intercept);
+ b.add("");
+ }
+ if (annotMatches!=-1)
+ {
+ b.add("Annotation labeling:");
+
b.add("Threshold="+parameters.getAnnotationThreshold());
+ b.add("Modules annotated: "+annotMatches+" /
"+results.numNodes());
+ b.add("");
+ }
}
b.add("Search parameters: alpha="+parameters.getAlpha()+",
alphaMultiplier="+parameters.getAlphaMultiplier());
b.add("Edge filtering:
pval="+parameters.getPValueThreshold()+",
samples="+parameters.getNumberOfSamples());
+ b.add("");
+ b.add("PanGIA overview network: (Nodes: "+results.numNodes()+",
Edges: "+results.numEdges()+")");
- //What else to report?
-
+ double sum = 0;
+ for (TypedLinkEdge<TypedLinkNodeModule<String, BFEdge>, BFEdge>
edge : results.edgeIterator())
+ sum += edge.value().link();
+ sum /= results.numEdges();
+ b.add("Average edge score: "+sum);
report.addToBody(b);
report.write(path);
}
+
+ private static double getBackground(List<SNodeModule> annots)
+ {
+ Set<String> nodes = new HashSet<String>(20000);
+ for (SNodeModule m : annots)
+ nodes.addAll(m.getMemberData());
+
+ int possible = nodes.size()*(nodes.size()-1)/2;
+
+ Set<UndirectedSEdge> net = new
HashSet<UndirectedSEdge>(possible/100);
+ for (SNodeModule m : annots)
+ for (String g1 : m)
+ for (String g2 : m)
+ if (!g1.equals(g2)) net.add(new
UndirectedSEdge(g1, g2));
+
+ return net.size() / (double) possible;
+ }
+
+ private static double[][] getCurve(double[] x, double[] y, int n,
double background)
+ {
+ int[] order = DoubleVector.sort_I(x);
+ x = DoubleVector.get(x, order);
+ y = DoubleVector.get(y, order);
+
+ int stepSize = x.length/(n-1);
+
+ double[][] out = new double[2][n];
+
+ for (int i=0;i<n-1;i++)
+ {
+ out[0][i] = getX(x,i*stepSize,(i+1)*stepSize);
+ out[1][i] =
getY(x,y,i*stepSize,(i+1)*stepSize,background);
+ }
+
+ out[0][n-1] = getX(x,x.length-stepSize,x.length);
+ out[1][n-1] = getY(x,y,x.length-stepSize,x.length,background);
+
+ int[] ok = new
BooleanVector(DoubleVector.isNaN(out[1])).not().asIndexes().getData();
+ out[0] = DoubleVector.get(out[0], ok);
+ out[1] = DoubleVector.get(out[1], ok);
+
+ return out;
+ }
+
+ private static double getX(double[] x, int i1, int i2)
+ {
+ double sum = 0;
+ for (int i=i1;i<i2;i++)
+ sum += x[i];
+
+ return sum/(i2-i1);
+ }
+
+ private static double getY(double[] x, double[] y, int i1, int i2,
double background)
+ {
+ int hits = 0;
+ for (int i=i1;i<i2;i++)
+ hits += (int)Math.round(y[i]);
+
+ return (hits==0) ? Double.NaN : Math.log10(
(hits/(double)(i2-i1)) / background );
+ }
}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
2010-07-30 17:48:23 UTC (rev 21087)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/VisualStyleObserver.java
2010-07-30 18:00:57 UTC (rev 21088)
@@ -7,6 +7,7 @@
import java.util.Map;
import cytoscape.Cytoscape;
+import cytoscape.layout.CyLayoutAlgorithm;
import cytoscape.view.CyNetworkView;
import cytoscape.view.CytoscapeDesktop;
import cytoscape.visual.VisualStyle;
@@ -79,10 +80,23 @@
if(style == null)
return;
- view.setVisualStyle(style.getName());
-
if(Cytoscape.getVisualMappingManager().getVisualStyle().equals(style) == false)
-
Cytoscape.getVisualMappingManager().setVisualStyle(style);
- view.redrawGraph(false, true);
+ if (style.getName().equals(VS_MODULE_NAME))
+ {
+ view.setVisualStyle(style.getName());
+
if(Cytoscape.getVisualMappingManager().getVisualStyle().equals(style) == false)
+
Cytoscape.getVisualMappingManager().setVisualStyle(style);
+
+ CyLayoutAlgorithm alg =
cytoscape.layout.CyLayouts.getLayout("force-directed");
+ view.applyLayout(alg);
+
+ view.redrawGraph(true, true);
+ }else
+ {
+ view.setVisualStyle(style.getName());
+
if(Cytoscape.getVisualMappingManager().getVisualStyle().equals(style) == false)
+
Cytoscape.getVisualMappingManager().setVisualStyle(style);
+ view.redrawGraph(false, true);
+ }
}
}
}
Modified:
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/networks/linkedNetworks/TypedLinkNetwork.java
===================================================================
---
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/networks/linkedNetworks/TypedLinkNetwork.java
2010-07-30 17:48:23 UTC (rev 21087)
+++
csplugins/trunk/ucsd/ruschein/PanGIA/src/org/idekerlab/PanGIAPlugin/networks/linkedNetworks/TypedLinkNetwork.java
2010-07-30 18:00:57 UTC (rev 21088)
@@ -267,7 +267,10 @@
{
Set<NT> toadd = new HashSet<NT>(100);
for (NT node : nodes)
-
toadd.addAll(this.getNode(node).neighbors(degree).getMemberValues());
+ {
+ TypedLinkNode<NT,ET> n = this.getNode(node);
+ if (n!=null)
toadd.addAll(n.neighbors(degree).getMemberValues());
+ }
allNodes.addAll(toadd);
}
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