Author: mes
Date: 2011-01-03 11:40:56 -0800 (Mon, 03 Jan 2011)
New Revision: 23287
Modified:
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/VennAnalytic.java
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/display/VennDialog.java
Log:
added Lee's fix per paper reviewer and fixed a bug in network name mapping
Modified:
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/VennAnalytic.java
===================================================================
---
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/VennAnalytic.java
2011-01-03 14:57:46 UTC (rev 23286)
+++
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/VennAnalytic.java
2011-01-03 19:40:56 UTC (rev 23287)
@@ -40,12 +40,11 @@
private double maxArea;
private int totalCount;
- private CyLogger logger;
+ private static final CyLogger logger =
CyLogger.getLogger(VennAnalytic.class);
public VennAnalytic() {
stepsize = .01;
minStress = .000001;
- logger = CyLogger.getLogger(VennAnalytic.class);
}
public VennDiagram compute(VennData vd) {
@@ -89,51 +88,51 @@
}
double[] residuals = new double[nPolygons - 1];
String[] residualLabels = new String[nPolygons - 1];
- boolean[] warnings = new boolean[nPolygons -1];
- double[][] luneCenters = new double[nPolygons -1][2];
+ boolean[] warnings = new boolean[nPolygons -1];
+ double[][] luneCenters = new double[nPolygons -1][2];
double area = 0;
int nonZero = 0;
for (int i = 1; i < nPolygons; i++) {
residuals[i - 1] = polyAreas[i] - polyHats[i];
char[] c = encode(i);
String s = "";
- double numIntersecting = 0.0;
+ double numIntersecting = 0.0;
for (int j = 0; j < c.length; j++) {
if (c[j] == '1') {
s += (circleLabels[j] + "&");
- // record the centers of the circles
- luneCenters[i-1][0] += centers[j][0];
- luneCenters[i-1][1] += centers[j][1];
- numIntersecting += 1.0;
- }
+ // record the centers of the circles
+ luneCenters[i-1][0] += centers[j][0];
+ luneCenters[i-1][1] += centers[j][1];
+ numIntersecting += 1.0;
+ }
}
- // find the lune centers
- if ( numIntersecting > 0 ) {
- luneCenters[i-1][0] /= numIntersecting;
- luneCenters[i-1][1] /= numIntersecting;
- }
+ // find the lune centers
+ if ( numIntersecting > 0 ) {
+ luneCenters[i-1][0] /= numIntersecting;
+ luneCenters[i-1][1] /= numIntersecting;
+ }
area += polyAreas[i];
- if (residuals[i - 1] != 0)
- nonZero++;
- s = s.substring(0, s.length() - 1);
- residualLabels[i - 1] = s;
- logger.info("Set name: " + residualLabels[i - 1] + "
residual: " + residuals[i-1] + " set area: " + polyAreas[i] + " num members: "
+ polyData[i]);
+// if (residuals[i - 1] != 0)
+// nonZero++;
+// s = s.substring(0, s.length() - 1);
+// residualLabels[i - 1] = s;
+// logger.info("Set name: " + residualLabels[i - 1] + " residual:
" + residuals[i-1] + " set area: " + polyAreas[i] + " num members: " +
polyData[i]);
}
- double cut = area / nonZero;
- for (int i = 0; i < residuals.length; i++) {
- if (Math.abs(residuals[i]) > cut) {
- logger.warn("OUTLIER!! Set name: " +
residualLabels[i] + " residual: " + residuals[i]);
- warnings[i] = true;
- } else {
- warnings[i] = false;
- }
- }
+// double cut = area / nonZero;
+// for (int i = 0; i < residuals.length; i++) {
+// if (Math.abs(residuals[i]) > cut) {
+// logger.warn("OUTLIER!! Set name: " + residualLabels[i] + "
residual: " + residuals[i]);
+// warnings[i] = true;
+// } else {
+// warnings[i] = false;
+// }
+// }
logger.info("stress = " + stress + ", stress01 = " + stress01 + ",
stress05 = " + stress05);
return new VennDiagram(centers, diameters, polyAreas, residuals,
circleLabels, residualLabels, colors, polyData, warnings, luneCenters, stress,
stress01, stress05);
- }
+ }
private void processAreaData(String[][] data, double[] areas) {
HashMap<String,Double> sets = new HashMap<String,Double>();
@@ -181,7 +180,7 @@
}
private void processElementData(String[][] data) {
- @SuppressWarnings("unchecked")
+ @SuppressWarnings("unchecked")
HashMap<String,Double>[] categories = new HashMap[2];
categories[0] = new HashMap<String,Double>();
categories[1] = new HashMap<String,Double>();
@@ -338,8 +337,10 @@
}
for (int i = 0; i < nCircles; i++) {
- centers[i][0] = .5 + .25 * x[i][0] / (max[0] - min[0]);
- centers[i][1] = .5 + .25 * x[i][1] / (max[1] - min[1]);
+// centers[i][0] = .5 + .25 * x[i][0] / (max[0] - min[0]);
+// centers[i][1] = .5 + .25 * x[i][1] / (max[1] - min[1]);
+ centers[i][0] = .5 + .25 * x[i][0];
+ centers[i][1] = .5 + .25 * x[i][1];
}
}
@@ -366,18 +367,18 @@
continue;
s[j][k] += polyData[i];
s[k][j] = s[j][k];
+ nIntersections++;
}
}
}
- for (int j = 1; j < s.length; j++) {
+ for (int j = 0; j < nCircles; j++) {
+ s[j][j] = 0;
for (int k = 0; k < j; k++) {
- if (s[j][k] != 0)
- nIntersections++;
- s[j][k] = -s[j][k];
+ s[j][k] = 1 - s[j][k] / (circleData[j] + circleData[k]);
s[k][j] = s[j][k];
}
}
- if (nIntersections < nCircles)
+ if (nIntersections < 1)
s = null;
return s;
}
Modified:
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/display/VennDialog.java
===================================================================
---
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/display/VennDialog.java
2011-01-03 14:57:46 UTC (rev 23286)
+++
csplugins/trunk/ucsd/mes/VennDiagram/src/edu/uic/ncdm/venn/display/VennDialog.java
2011-01-03 19:40:56 UTC (rev 23287)
@@ -44,11 +44,17 @@
import java.util.Set;
import java.util.Arrays;
import java.util.Collections;
+import java.util.Map;
+import java.util.HashMap;
public class VennDialog extends JDialog implements ActionListener,
ItemListener {
private static final long serialVersionUID = 1554446356623443266L;
+
+ // So that we can display the title, but use the ID to lookup the
network.
+ private static Map<String,String> titleIdMap = new
HashMap<String,String>();
+
private String attrName;
private List<CyNetwork> networks;
private boolean printIntersection;
@@ -73,8 +79,10 @@
Set<CyNetwork> allNetworks = Cytoscape.getNetworkSet();
String[] allNames = new String[allNetworks.size()];
int i = 0;
- for ( CyNetwork n : allNetworks )
+ for ( CyNetwork n : allNetworks ) {
+ titleIdMap.put( n.getTitle(), n.getIdentifier() );
allNames[i++] = n.getTitle();
+ }
Arrays.sort(allNames);
@@ -192,7 +200,7 @@
if ("Select".equals(e.getActionCommand())) {
networks.clear();
for ( Object netName : netList.getSelectedValues() )
- networks.add( Cytoscape.getNetwork(
netName.toString() ) );
+ networks.add( Cytoscape.getNetwork(
titleIdMap.get( netName.toString() ) ) );
if ( networks.size() < 2 ) {
boolean isMac =
System.getProperty("os.name").startsWith("Mac");
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