Changeset 227

Timestamp:

Jan 17, 2007, 4:48:19 PM (16 years ago)

Author:

Johan Enell

Message:

Fixes #37 Added boxplot

Location:

trunk/se/lu/onk/Smooth/src/smooth

Files:

• Smooth.java (modified) (4 diffs)
• SmoothMain.java (modified) (5 diffs)

trunk/se/lu/onk/Smooth/src/smooth/Smooth.java

@@ -117 +117 @@
           if (stop < reporters.size())
           {
+            winSizes.add(reporters.get(stop).getChrPosition() - reporters.get(start).getChrPosition());
             if (!window.isEmpty())
             {
@@ -128 +129 @@
             }
           }
-          winSizes.add(reporters.get(stop).getChrPosition() - reporters.get(start).getChrPosition());
         }
         else if (winType.equals("bp"))
@@ -134 +134 @@
           if (stop < reporters.size())
           {
+            winSizes.add(stop - start);
             while (!window.isEmpty() && r.getChrPosition() - reporters.get(start).getChrPosition() > winSize / 2)
             {
@@ -145 +146 @@
             }
           }
-          winSizes.add(stop - start);
         }
         float mean = Float.NaN;

trunk/se/lu/onk/Smooth/src/smooth/SmoothMain.java

@@ -27 +27 @@
 import org.jfree.chart.JFreeChart;
 import org.jfree.chart.axis.CategoryAxis;
-import org.jfree.chart.axis.LogarithmicAxis;
 import org.jfree.chart.axis.NumberAxis;
-import org.jfree.chart.axis.ValueAxis;
 import org.jfree.chart.plot.CategoryPlot;
+import org.jfree.chart.plot.PlotRenderingInfo;
 import org.jfree.chart.renderer.category.BoxAndWhiskerRenderer;
-import org.jfree.data.RangeType;
+import org.jfree.chart.renderer.category.CategoryItemRendererState;
 import org.jfree.data.statistics.BoxAndWhiskerItem;
 import org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset;
@@ -41 +40 @@
 import basefile.BASEFileSpotSection;
 
+import java.awt.Graphics2D;
+import java.awt.geom.Rectangle2D;
 import java.io.File;
 import java.io.IOException;
@@ -55 +56 @@
 public class SmoothMain
 {
+
+  private static String wType = "";
 
   /**
@@ -80 +83 @@
       }
 
-      String wType = bfs.findStringOpt("w_type");
+      wType = bfs.findStringOpt("w_type");
       String average = bfs.findStringOpt("average");
       int wSize = bfs.findIntOpt("w_size");
@@ -173 +176 @@
     {
       BoxAndWhiskerItem bw = smooth.getBoxAndWhiskerItem(assayId);
-      data.add(bw, "Windows distibution", assays.get(assayId));
-    }
-    
-    CategoryAxis domainAxis = new CategoryAxis("Sample"); // x axis
-    NumberAxis rangeAxis = new NumberAxis("Window size"); // y axis fdr
-    rangeAxis.setAutoRangeIncludesZero(true);
-    
-    BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer();
-    CategoryPlot plot = new CategoryPlot(data, domainAxis, rangeAxis, renderer);
+      data.add(bw, "Window distibution", assays.get(assayId));
+    }
+    
+    CategoryAxis xAxis = new CategoryAxis("Sample");
+    NumberAxis yAxis = new NumberAxis("Window size (" + (wType.equals("cl") ? "bp" : "clones") + ")");
+    yAxis.setAutoRangeIncludesZero(false);
+    
+    BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer() 
+    {
+      @Override
+      public CategoryItemRendererState initialise(Graphics2D g2, Rectangle2D dataArea, CategoryPlot plot, int rendererIndex, PlotRenderingInfo info)
+      {
+        CategoryItemRendererState state = super.initialise(g2, dataArea, plot, rendererIndex, info);
+        state.setBarWidth(20);
+        return state;
+      }
+    };
+    CategoryPlot plot = new CategoryPlot(data, xAxis, yAxis, renderer);
+    
     
     JFreeChart chart = new JFreeChart(plot);
+    chart.removeLegend();
     chart.setAntiAlias(false);
 
-    ChartUtilities.saveChartAsPNG(new File("windowsize.png"), chart, 800, 600);
+    int w = 150 + 40 * assays.size();
+    ChartUtilities.saveChartAsPNG(new File("windowsize.png"), chart, w, 600);
   }