Changeset 217

Timestamp:

Dec 8, 2006, 5:20:24 PM (15 years ago)

Author:

Johan Enell

Message:

References #32. Needs a normsdist function and the HistogramDataset? must create new bins on the fly.

Location:

trunk/se/lu/onk/ZTest/src/ztest

Files:

• Plot.java (modified) (6 diffs)
• Start.java (modified) (6 diffs)
• ZTest.java (modified) (2 diffs)

trunk/se/lu/onk/ZTest/src/ztest/Plot.java

@@ -30 +30 @@
 import org.jfree.chart.plot.SeriesRenderingOrder;
 import org.jfree.chart.plot.XYPlot;
+import org.jfree.chart.renderer.xy.XYBarRenderer;
 import org.jfree.chart.renderer.xy.XYLineAndShapeRenderer;
 import org.jfree.data.RangeType;
+import org.jfree.data.statistics.SimpleHistogramDataset;
+import org.jfree.data.xy.IntervalXYDataset;
 import org.jfree.data.xy.XYSeries;
 import org.jfree.data.xy.XYSeriesCollection;
@@ -41 +44 @@
 public class Plot
 {
+  public static class HistogramDataset extends SimpleHistogramDataset
+  {
+
+    public HistogramDataset(Comparable key)
+    {
+      super(key);
+    }
+
+    @Override
+    public void addObservation(double value, boolean notify)
+    {
+      try
+      {
+        super.addObservation(value, notify);
+      }
+      catch (RuntimeException e)
+      {
+        //TODO create new bin
+        super.addObservation(value, notify);
+      }
+    }
+    
+    
+  }
+
   static void plotOE_FDR(XYSeries observed, XYSeries expected, XYSeries fdr)
     throws IOException
@@ -50 +78 @@
     rangeAxisFDR.setRangeType(RangeType.POSITIVE);
     rangeAxisFDR.setAutoRangeIncludesZero(true);
-    NumberAxis rangeAxisOE = new NumberAxis("Observed / Expected"); // y axis
-                                                                    // o/e
+    NumberAxis rangeAxisOE = new NumberAxis("Observed / Expected"); // y axis oe
     rangeAxisOE.setRangeType(RangeType.POSITIVE);
     rangeAxisOE.setAutoRangeIncludesZero(true);
@@ -82 +109 @@
     plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
 
-    JFreeChart chart;
-    chart = new JFreeChart(plot);
+    JFreeChart chart = new JFreeChart(plot);
     chart.setAntiAlias(false);
 
@@ -104 +130 @@
     plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
 
-    JFreeChart chart;
-    chart = new JFreeChart(plot);
+    JFreeChart chart = new JFreeChart(plot);
     chart.setAntiAlias(false);
     chart.removeLegend();
@@ -132 +157 @@
     plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
 
-    JFreeChart chart;
-    chart = new JFreeChart(plot);
+    JFreeChart chart = new JFreeChart(plot);
     chart.setAntiAlias(false);
 
     ChartUtilities.saveChartAsPNG(new File("oeplot.png"), chart, 800, 600);
   }
+
+  static void plotMHist(IntervalXYDataset m, double mean, double sd)
+    throws IOException
+  {
+    NumberAxis domainAxis = new NumberAxis("M, log2(int1/int2)");
+    NumberAxis rangeAxis = new NumberAxis("Frequence");
+    rangeAxis.setAutoRangeIncludesZero(true);
+
+    XYBarRenderer hRenderer = new XYBarRenderer();
+    XYLineAndShapeRenderer ndRenderer = new XYLineAndShapeRenderer(true, false);
+
+    XYPlot plot = new XYPlot();
+    plot.setDomainAxis(domainAxis);
+    plot.setRangeAxis(rangeAxis);
+    
+    plot.setDataset(0, m);
+    plot.setRenderer(0, hRenderer);
+    
+    plot.setDataset(1, null);
+    plot.setRenderer(1, ndRenderer);
+
+    JFreeChart chart = new JFreeChart(plot);
+    chart.setAntiAlias(false);
+
+    ChartUtilities.saveChartAsPNG(new File("mhist.png"), chart, 800, 600);
+  }
 }

trunk/se/lu/onk/ZTest/src/ztest/Start.java

@@ -40 +40 @@
 public class Start
 {
+  
+  private static ZTest ztest = new ZTest();
 
   /**
@@ -89 +91 @@
         data = bfr.readDataRow(dataLength);
       }
-      ZTest ztest = new ZTest();
       ztest.calculate(bfss);
 
@@ -131 +132 @@
       XYSeries eSeries = new XYSeries("Expected");
       XYSeries fdrSeries = new XYSeries("FDR");
-      
+      Plot.HistogramDataset mHist = new Plot.HistogramDataset("M");
+
       PrintWriter html = new PrintWriter(new File("index.html"));
       PrintWriter tab = new PrintWriter(new File("result.tsv"));
@@ -147 +149 @@
           "<th>P</th><th>Number of values</th><th>Rank</th><th>Expected</th><th>FDR</th></tr>");
       tab.println("Reporter\tGeneSymbol\tLocusLink\tAverageM\tP\tNumberOfValues\tRank\tExpected\tFDR");
-      
+
       for (int i = 0; i < bfss.getReporterSize(); i++)
       {
@@ -184 +186 @@
           eSeries.add(rank, expected);
           fdrSeries.add(rank, fdr);
+          mHist.addObservation(r.getM());
       }
       html.println("</table>");
@@ -194 +197 @@
       Plot.plotOE(oSeries, eSeries);
       Plot.plotOE_FDR(oSeries, eSeries, fdrSeries);
+      Plot.plotMHist(mHist, ztest.getTotalMean(), ztest.getTotalSD());
     }
     catch (IOException e)

trunk/se/lu/onk/ZTest/src/ztest/ZTest.java

@@ -34 +34 @@
 public class ZTest
 {
+  private HashMap<Integer, Double> means;
+  
+  private HashMap<Integer, Double> sds;
+  
   public void calculate(BASEFileSpotSection<Reporter, Spot> bfss)
   {
     List<Integer> assays = bfss.findFieldIntList("assays");
-    HashMap<Integer, Double> means = getAssayMeans(bfss, assays);
-    HashMap<Integer, Double> sds = getAssaySDS(bfss, assays, means);
+    means = getAssayMeans(bfss, assays);
+    sds = getAssaySDS(bfss, assays, means);
     
     for (int i = 0; i < bfss.getReporterSize(); i++)
@@ -72 +76 @@
       r.setSize(popSize);
     }
+  }
+  
+  public double getTotalSD()
+  {
+    double sd = 0;
+    for(Double d : sds.values())
+    {
+      sd += Math.pow(d, 2);
+    }
+    return Math.sqrt(sd) / sds.size();
+  }
+  
+  public double getTotalMean()
+  {
+    double mean = 0;
+    for(Double d : means.values())
+    {
+      mean += d;
+    }
+    return mean/means.size();
   }