Changeset 214

Timestamp:

Dec 7, 2006, 3:15:33 PM (15 years ago)

Author:

Johan Enell

Message:

Fixes #29 #30

File:

• trunk/se/lu/onk/ZTest/src/ztest/Start.java (modified) (6 diffs)

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

@@ -24 +24 @@
 package ztest;
 
+import org.jfree.chart.ChartFactory;
 import org.jfree.chart.ChartUtilities;
 import org.jfree.chart.JFreeChart;
 import org.jfree.chart.axis.LogarithmicAxis;
 import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.plot.CombinedDomainXYPlot;
 import org.jfree.chart.plot.SeriesRenderingOrder;
 import org.jfree.chart.plot.XYPlot;
@@ -35 +37 @@
 import org.jfree.data.xy.XYSeriesCollection;
 
+import java.awt.Color;
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -139 +142 @@
       XYSeries oSeries = new XYSeries("Observed");
       XYSeries eSeries = new XYSeries("Expected");
+      XYSeries fdrSeries = new XYSeries("FDR");
       
       PrintWriter html = new PrintWriter(new File("index.html"));
@@ -189 +193 @@
           fdr);
         
-          oSeries.add(rank, rank, true);
-          eSeries.add(rank, expected, true);
+          oSeries.add(rank, rank);
+          eSeries.add(rank, expected);
+          fdrSeries.add(rank, fdr);
       }
       html.println("</table>");
@@ -198 +203 @@
       tab.close();
       
-      
-      XYSeriesCollection allSeries = new XYSeriesCollection();
-      allSeries.addSeries(oSeries);
-      allSeries.addSeries(eSeries);
-      
-      NumberAxis domainAxis = new LogarithmicAxis(""); //x axis
-      domainAxis.setAutoRangeIncludesZero(false);
-      domainAxis.setRangeType(RangeType.POSITIVE);
-      NumberAxis rangeAxis = new NumberAxis(); //y axis
-      rangeAxis.setRangeType(RangeType.POSITIVE);
-      rangeAxis.setAutoRangeIncludesZero(true);
-      XYPlot oePlot = new XYPlot(allSeries, domainAxis, rangeAxis, new XYLineAndShapeRenderer(true, false));
-      oePlot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
-
-      JFreeChart oeChart;
-      oeChart = new JFreeChart(oePlot);
-      oeChart.setAntiAlias(false);
-      
-      ChartUtilities.saveChartAsPNG(new File("oeplot.png"), oeChart, 800, 600);
+      plotFDR(fdrSeries);
+      plotOE(oSeries, eSeries);
+      plotOE_FDR(oSeries, eSeries, fdrSeries);
     }
     catch (IOException e)
@@ -222 +211 @@
       e.printStackTrace();
     }
-
+  }
+
+  private static void plotOE_FDR(XYSeries observed, XYSeries expected, XYSeries fdr)
+    throws IOException
+  {
+    NumberAxis domainAxis = new LogarithmicAxis("Rank"); //x axis
+    domainAxis.setAutoRangeIncludesZero(false);
+    domainAxis.setRangeType(RangeType.POSITIVE);
+    NumberAxis rangeAxisFDR = new NumberAxis("FDR"); //y axis fdr
+    rangeAxisFDR.setRangeType(RangeType.POSITIVE);
+    rangeAxisFDR.setAutoRangeIncludesZero(true);
+    NumberAxis rangeAxisOE = new NumberAxis("Observed / Expected"); //y axis o/e
+    rangeAxisOE.setRangeType(RangeType.POSITIVE);
+    rangeAxisOE.setAutoRangeIncludesZero(true);
+    
+    XYSeriesCollection datasetOE = new XYSeriesCollection();
+    datasetOE.addSeries(observed);
+    datasetOE.addSeries(expected);
+    XYSeriesCollection datasetFDR = new XYSeriesCollection();
+    datasetFDR.addSeries(fdr);
+
+    XYLineAndShapeRenderer oeRenderer = new XYLineAndShapeRenderer(true, false);
+    oeRenderer.setSeriesPaint(0, Color.RED);
+    oeRenderer.setSeriesPaint(1, Color.BLUE);
+    XYLineAndShapeRenderer fdrRenderer = new XYLineAndShapeRenderer(true, false);
+    fdrRenderer.setSeriesPaint(0, Color.BLACK);
+    
+    XYPlot plot = new XYPlot();
+    plot.setDomainAxis(domainAxis);
+    
+    plot.setDataset(0, datasetOE);
+    plot.setRangeAxis(0, rangeAxisOE);
+    plot.mapDatasetToRangeAxis(0, 0);
+    plot.setRenderer(0, oeRenderer);
+    
+    plot.setDataset(1, datasetFDR);
+    plot.setRangeAxis(1, rangeAxisFDR);
+    plot.mapDatasetToRangeAxis(1, 1);
+    plot.setRenderer(1, fdrRenderer);
+    
+    plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
+    
+    JFreeChart chart;
+    chart = new JFreeChart(plot);
+    chart.setAntiAlias(false);
+    
+    ChartUtilities.saveChartAsPNG(new File("oe_fdrplot.png"), chart, 800, 600);
+  }
+  
+  private static void plotFDR(XYSeries fdr) throws IOException
+  {
+    XYLineAndShapeRenderer fdrRenderer = new XYLineAndShapeRenderer(true, false);
+    fdrRenderer.setSeriesPaint(0, Color.BLACK);
+    
+    NumberAxis domainAxis = new LogarithmicAxis("Rank"); //x axis
+    domainAxis.setAutoRangeIncludesZero(false);
+    domainAxis.setRangeType(RangeType.POSITIVE);
+    NumberAxis rangeAxis = new NumberAxis("FDR"); //y axis
+    rangeAxis.setRangeType(RangeType.POSITIVE);
+    rangeAxis.setAutoRangeIncludesZero(true);
+    XYPlot plot = new XYPlot(new XYSeriesCollection(fdr), domainAxis, rangeAxis, fdrRenderer);
+    plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
+
+    JFreeChart chart;
+    chart = new JFreeChart(plot);
+    chart.setAntiAlias(false);
+    chart.removeLegend();
+    
+    ChartUtilities.saveChartAsPNG(new File("fdrplot.png"), chart, 800, 600);
+  }
+  
+  private static void plotOE(XYSeries observed, XYSeries expected) throws IOException
+  {
+    XYSeriesCollection allSeries = new XYSeriesCollection();
+    allSeries.addSeries(observed);
+    allSeries.addSeries(expected);
+    
+    XYLineAndShapeRenderer oeRenderer = new XYLineAndShapeRenderer(true, false);
+    oeRenderer.setSeriesPaint(0, Color.RED);
+    oeRenderer.setSeriesPaint(1, Color.BLUE);
+    
+    NumberAxis domainAxis = new LogarithmicAxis("Rank"); //x axis
+    domainAxis.setAutoRangeIncludesZero(false);
+    domainAxis.setRangeType(RangeType.POSITIVE);
+    NumberAxis rangeAxis = new NumberAxis(); //y axis
+    rangeAxis.setRangeType(RangeType.POSITIVE);
+    rangeAxis.setAutoRangeIncludesZero(true);
+    XYPlot plot = new XYPlot(allSeries, domainAxis, rangeAxis, oeRenderer);
+    plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
+
+    JFreeChart chart;
+    chart = new JFreeChart(plot);
+    chart.setAntiAlias(false);
+    
+    ChartUtilities.saveChartAsPNG(new File("oeplot.png"), chart, 800, 600);
   }