Changeset 246

Timestamp:

Mar 13, 2007, 4:20:05 PM (17 years ago)

Author:

Johan Enell

Message:

RankProduct? calculates the rp correct

Location:

trunk/se/lu/onk/OneClass/src/oneclass/rankproduct

Files:

• RankProduct.java (modified) (2 diffs)
• Reporter.java (modified) (5 diffs)
• Spot.java (modified) (2 diffs)
• Start.java (modified) (5 diffs)

trunk/se/lu/onk/OneClass/src/oneclass/rankproduct/RankProduct.java

@@ -24 +24 @@
 package oneclass.rankproduct;
 
-import java.util.Arrays;
 import java.util.Comparator;
 
@@ -31 +30 @@
 public class RankProduct
 {
-  public void calculate(BASEFileSpotSection<Reporter, Spot> bfss)
+  public void calculate(BASEFileSpotSection<Reporter, Spot> bfss, boolean up)
   {
-    // Calucalte assay sizes
-    int[] assaySizes = new int[bfss.getWidth()];
-    Arrays.fill(assaySizes, bfss.getHeight());
-    for (int i = 0; i < bfss.getHeight(); ++i)
-    {
-      for (int j = 0; j < bfss.getWidth(); ++j)
-      {
-        if (Double.isNaN(bfss.getSpot(i + j).getM()))
-        {
-          --assaySizes[j];
-        }
-      }
-    }
-
     for (int i = 0; i < bfss.getWidth(); ++i)
     {
       // to be able use i in the comparator it has to be final
       final int finali = i;
+      final boolean finalup = up;
+      
       bfss.sortReporter(new Comparator<Reporter>()
       {
         public int compare(Reporter r1, Reporter r2)
         {
-          double s1 = r1.getSpots()[finali].getM();
-          double s2 = r2.getSpots()[finali].getM();
+          double s1 = r1.getSpot(finali).getM();
+          double s2 = r2.getSpot(finali).getM();
           
-          return Double.compare(s1, s2);
+          int ret = 0;
+          if (!Double.isNaN(s1) && !Double.isNaN(s2))
+          {
+            ret = Double.compare(s1, s2);
+            if (finalup)
+              ret *= -1;
+          }
+          else if (Double.isNaN(s1) && Double.isNaN(s2))
+            ret = 0;
+          else if (Double.isNaN(s1))
+            ret = 1;
+          else if (Double.isNaN(s2))
+            ret = -1;
+          return ret;
         }
       });
       
-      for (int j = 0; j < assaySizes[i]; ++j)
+      // set the rank
+      for (int j = 0; j < bfss.getHeight(); ++j)
       {
-        Reporter r = bfss.getReporter(j);
-        r.addRank((j+1.0) / assaySizes[i]);
-        if (r.getRankProduct() > 1)
+        Spot s = bfss.getReporter(j).getSpot(i);
+        if (!Double.isNaN(s.getM()))
         {
-          System.err.println(j + " " + assaySizes[i]);
-          System.exit(0);
+          s.setRank(j+1);
         }
       }
     }
-    
-    // Calculate M and "size" for each reporter
-    for (int i = 0; i < bfss.getHeight(); ++i)
-    {
-      Reporter r = bfss.getReporter(i);
-      double avg = 0;
-      int size = 0;
-      for (int j = 0; j < bfss.getWidth(); ++j)
-      {
-        if (!Double.isNaN(r.getSpots()[j].getM()))
-        {
-          avg = r.getSpots()[j].getM();
-          ++size;
-        }
-      }
-      r.setM(avg / size);
-      r.setSize(size);
-    }
   }
 }

trunk/se/lu/onk/OneClass/src/oneclass/rankproduct/Reporter.java

@@ -31 +31 @@
   private final int id;
   private final Spot[] spots;
-  private double rankProduct = 1;
   private double a;
-  private double m;
-  private int size;
+  private double m = 0;
+  private int size = 0;;
   
   public Reporter(int id, String reporter, String symbol, String locusLink, double a, Spot ... spots)
@@ -44 +43 @@
     this.a = a;
     this.spots = spots;
+    
+    for (Spot s : spots)
+    {
+      if (!Double.isNaN(s.getM()))
+      {
+        m += s.getM();
+        ++size;
+      }
+    }
+    m = m/size;
   }
 
@@ -68 +77 @@
   public final double getRankProduct()
   {
-    return rankProduct;
+    double rankProduct = 1;
+    
+    for (Spot s : spots)
+    {
+      if (!Double.isNaN(s.getM()))
+      {
+        rankProduct *= s.getRank();
+      }
+    }
+    
+    return Math.pow(rankProduct, 1.0/getSize());
   }
   
@@ -74 +93 @@
   {
     return reporter;
+  }
+
+  public final Spot getSpot(int i)
+  {
+    return spots[i];
   }
 
@@ -86 +110 @@
   }
 
-  public void setSize(int size)
-  {
-    this.size = size;
-  }
-
   public int getSize()
   {
     return size;
   }
-  
-  public final void setM(double m)
-  {
-    this.m = m;
-  }
-  
-  public void addRank(double rank)
-  {
-    rankProduct *= rank;
-  }
 }

trunk/se/lu/onk/OneClass/src/oneclass/rankproduct/Spot.java

@@ -28 +28 @@
   private double m;
   
+  private int rank = -1;
+  
   public Spot(Double m)
   {
@@ -38 +40 @@
   }
   
+  public final int getRank()
+  {
+    return rank;
+  }
+  
+  public final void setRank(int rank)
+  {
+    this.rank = rank;
+  }
+  
   @Override
   public String toString()

trunk/se/lu/onk/OneClass/src/oneclass/rankproduct/Start.java

@@ -103 +103 @@
         data = bfr.readDataRow(dataLength);
       }
-      rankproduct.calculate(bfss);
-      bfss.sortReporter(new Comparator<Reporter>()
-        {
-
-          public int compare(Reporter r1, Reporter r2)
-          {
-            if (r1.getRankProduct() < r2.getRankProduct()) return -1;
-            else if (r1.getRankProduct() == r2.getRankProduct()) return 0;
-            else return 1;
-          }
-        });
-      print(bfss);
-    }
-    catch (FileNotFoundException e)
-    {
-      System.err.println("Can't find the file " + (args.length == 1 ? args[0] : "stdin.txt"));
-    }
-    catch (BadFormatException e)
-    {
-      System.err.println((args.length == 1 ? args[0] : "stdin.txt") + " is not a basefile");
-    }
-    catch (IOException e)
-    {
-      System.err.println("An error when reading file " + (args.length == 1 ? args[0] : "stdin.txt"));
-      e.printStackTrace();
-    }
-    catch (BASEFileException e)
-    {
-      e.printStackTrace();
-    }
-  }
-
-  private static void print(BASEFileSpotSection<Reporter, Spot> bfss)
-  {
-
-    try
-    {
-      XYSeries oSeries = new XYSeries("Observed");
-      XYSeries eSeries = new XYSeries("Expected");
-      XYSeries fdrSeries = new XYSeries("FDR");
-      HistogramDataset mHist = new HistogramDataset("M", 0.1);
-
-      PrintWriter html = new PrintWriter(new File("index.html"));
-      PrintWriter tab = new PrintWriter(new File("result.tsv"));
-      int maxRank = bfss.getHeight();
-      
-      Object[] tableRow = {"Reporter","GeneSymbol","LocusLink","AverageM","up/down","Rank","Rank product","NumberOfValues"};
-
+      
       System.out.println("BASEfile");
       System.out.println("section\tassays");
@@ -157 +110 @@
       System.out.println("count\t1");
       System.out.println("%");
-      System.out.println("1\tztest\t"+bfss.findStringOpt("assays").replaceAll("\t", "/"));
+      System.out.println("1\tRankProduct down\t"+bfss.findStringOpt("assays").replaceAll("\t", "/"));
+      System.out.println("2\tRankProduct up\t"+bfss.findStringOpt("assays").replaceAll("\t", "/"));
       System.out.println();
+      
+      rankproduct.calculate(bfss, false);
+
       System.out.println("section\tspots");
       System.out.println("channels\t2");
@@ -167 +124 @@
       System.out.println("count\t"+bfss.getReporterSize());
       System.out.println("%");
+      
+      print(bfss, "down");
+
+      rankproduct.calculate(bfss, true);
+
+      System.out.println("section\tspots");
+      System.out.println("channels\t2");
+      System.out.println("setExtraFloats\tJE_nbrOfElements\tJE_rank\tJE_rankProduct");
+      System.out.println("assayFields\tl2ratio1_2\tl10intgmean1_2\tJJE_nbrOfElements\tJE_rank\tE_rankProduct");
+      System.out.println("columns\tposition\treporter\tassayData");
+      System.out.println("assays\t2");
+      System.out.println("count\t"+bfss.getReporterSize());
+      System.out.println("%");
+      
+      print(bfss, "up");
+      
+    }
+    catch (FileNotFoundException e)
+    {
+      System.err.println("Can't find the file " + (args.length == 1 ? args[0] : "stdin.txt"));
+    }
+    catch (BadFormatException e)
+    {
+      System.err.println((args.length == 1 ? args[0] : "stdin.txt") + " is not a basefile");
+    }
+    catch (IOException e)
+    {
+      System.err.println("An error when reading file " + (args.length == 1 ? args[0] : "stdin.txt"));
+      e.printStackTrace();
+    }
+    catch (BASEFileException e)
+    {
+      e.printStackTrace();
+    }
+  }
+
+  private static void print(BASEFileSpotSection<Reporter, Spot> bfss, String prefix)
+  {
+    try
+    {
+      bfss.sortReporter(new Comparator<Reporter>()
+        {
+          public int compare(Reporter r1, Reporter r2)
+          {
+            return Double.compare(r1.getRankProduct(), r2.getRankProduct());
+          }
+        });
+      XYSeries oSeries = new XYSeries("Observed");
+      XYSeries eSeries = new XYSeries("Expected");
+      XYSeries fdrSeries = new XYSeries("FDR");
+      HistogramDataset mHist = new HistogramDataset("M", 0.1);
+
+      PrintWriter html = new PrintWriter(new File(prefix+"index.html"));
+      PrintWriter tab = new PrintWriter(new File(prefix+"result.tsv"));
+      
+      Object[] tableRow = {"Reporter","GeneSymbol","LocusLink","AverageM","up/down","Rank","Rank product","NumberOfValues"};
+
       
       html.println("<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Frameset//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd\">");
@@ -184 +198 @@
         int rank = i + 1;
         Reporter r = bfss.getReporter(i);
-        double rankProduct = r.getRankProduct() * maxRank;
+        double rankProduct = r.getRankProduct();
         
         System.out.printf("%d\t%d\t", (-1*rank), r.getId());
@@ -221 +235 @@
       tab.close();
       
-      Plot.plotFDR(fdrSeries);
-      Plot.plotOE(oSeries, eSeries);
-      Plot.plotOE_FDR(oSeries, eSeries, fdrSeries);
+//      Plot.plotFDR(fdrSeries);
+//      Plot.plotOE(oSeries, eSeries);
+//      Plot.plotOE_FDR(oSeries, eSeries, fdrSeries);
 //      Plot.plotMHist(mHist, ztest.getTotalMean(), ztest.getTotalSD());
     }