Changeset 2137

Timestamp:

Mar 31, 2006, 1:49:41 PM (18 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #124: Plot function for analysed data

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java (modified) (1 diff)
• src/clients/web/net/sf/basedb/clients/web/servlet/PlotServlet.java (modified) (11 diffs)
• src/core/net/sf/basedb/util/plot/HistogramPlot.java (modified) (24 diffs)
• src/core/net/sf/basedb/util/plot/PlotAnnotation.java (added)
• src/core/net/sf/basedb/util/plot/ScatterPlot.java (modified) (5 diffs)
• www/images/plot_generating.gif (modified) (previous)
• www/include/styles/tabcontrol.css (modified) (1 diff)
• www/views/experiments/plotter/index.jsp (modified) (12 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/DynamicUtil.java

@@ -70 +70 @@
     columns.add(new TableColumn(idPrefix + "column", propertyPrefix+"column", Type.INT, titlePrefix+"Column"));
     columns.add(new TableColumn(idPrefix + "x", propertyPrefix+"x", Type.INT, titlePrefix+"X"));
-    columns.add(new TableColumn(idPrefix + "x", propertyPrefix+"x", Type.INT, titlePrefix+"Y"));
+    columns.add(new TableColumn(idPrefix + "y", propertyPrefix+"y", Type.INT, titlePrefix+"Y"));
 
     List<RawDataProperty> rdpList = rawDataType.getProperties();

trunk/src/clients/web/net/sf/basedb/clients/web/servlet/PlotServlet.java

@@ -51 +51 @@
 import net.sf.basedb.util.jep.RawFunction;
 import net.sf.basedb.util.plot.HistogramPlot;
+import net.sf.basedb.util.plot.PlotAnnotation;
 import net.sf.basedb.util.plot.ScatterPlot;
 
@@ -69 +70 @@
 import java.io.IOException;
 import java.sql.SQLException;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
 import java.util.List;
 
@@ -139 +143 @@
     String yLabel = Values.getStringOrNull(request.getParameter("yLabel"));
     if (yLog && yLabel != null) yLabel = "log2("+yLabel+")";
+    final String annotation = Values.getStringOrNull(request.getParameter("annotation"));
+    final boolean hasAnnotation = annotation != null;
 
     // Scatter plot specified parameters
@@ -146 +152 @@
     final String yAggregate = Values.getString(request.getParameter("yAggregate"), "count");
     final boolean isCount = "count".equals(yAggregate);
+    if (!isCount && yLabel != null) yLabel = yLabel + " (" + yAggregate + ")";
+    final String hiloAggregate = isCount ? null : 
+      Values.getStringOrNull(request.getParameter("hiloAggregate"));
+    
     
     RenderedImage image = null;
@@ -171 +181 @@
         Expression[] x = xFormulas == null ? null : new Expression[xFormulas.length];
         Expression[] y = yFormulas == null ? null : new Expression[yFormulas.length];
+        
+        // If we should join the raw data table or not
+        boolean joinRaw = false;
         if (xFormulas != null)
         {
           for (int i = 0; i < xFormulas.length; ++i)
           {
+            joinRaw |= xFormulas[i].contains("raw(");
             x[i] = Jep.formulaToExpression(xFormulas[i], ch, raw);
             if (xLog) x[i] = Expressions.log2(x[i]);
@@ -183 +197 @@
           for (int i = 0; i < yFormulas.length; ++i)
           {
+            joinRaw |= yFormulas[i].contains("raw(");
             y[i] = Jep.formulaToExpression(yFormulas[i], ch, raw);
             if (yLog) y[i] = Expressions.log2(y[i]);
@@ -188 +203 @@
         }
   
+        // Get annotations
+        Collection<PlotAnnotation> annotations = null;
+        if (hasAnnotation)
+        {
+          annotations = new HashSet<PlotAnnotation>();
+          // TODO - implement other annotations than bioassay
+          for (BioAssay baa : bas.getBioAssays().list(dc))
+          {
+            annotations.add(new PlotAnnotation(baa.getName(), 
+              Collections.singleton(new Integer(baa.getDataCubeColumnNo()))));
+          }
+        }
+        
         // Get the query
         DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
@@ -197 +225 @@
           {
             query.reset();
-            query.joinRawData(JoinType.INNER); // TODO - only join if used in query
+            if (joinRaw) query.joinRawData(JoinType.INNER); 
+            if (hasAnnotation)
+            {
+              query.select(Dynamic.select(VirtualColumn.COLUMN));
+            }
             query.select(Selects.expression(x[i], "x"));
             query.select(Selects.expression(y[i], "y"));
-            plot.addData(query.iterate(dc), Integer.toString(i));
+            if (hasAnnotation)
+            {
+              plot.addData(query.iterate(dc), annotations);
+            }
+            else
+            {
+              plot.addData(query.iterate(dc), Integer.toString(i));
+            }
           }
           chart = plot.getChart();
@@ -211 +250 @@
           {
             query.reset();
-            query.joinRawData(JoinType.INNER); // TODO - only join if used in query
+            if (joinRaw) query.joinRawData(JoinType.INNER); 
+            if (hasAnnotation)
+            {
+              query.select(Dynamic.select(VirtualColumn.COLUMN));
+            }
             query.select(Selects.expression(x[i], "x"));
             if (!isCount) query.select(Selects.expression(y[i], "y"));
-            plot.addData(query.iterate(dc), Integer.toString(i), binSize, 
-              HistogramPlot.YAggregate.valueOf(yAggregate.toUpperCase()));
+            HistogramPlot.YAggregate ya = HistogramPlot.YAggregate.valueOf(yAggregate.toUpperCase());
+            HistogramPlot.YAggregate hilo = hiloAggregate == null ? null : 
+              HistogramPlot.YAggregate.valueOf(hiloAggregate.toUpperCase());
+            if (hasAnnotation)
+            {
+              plot.addData(query.iterate(dc), annotations, binSize, ya, hilo);
+            }
+            else
+            {
+              plot.addData(query.iterate(dc), Integer.toString(i), binSize, ya, hilo);
+            }
           }
           chart = plot.getChart();
@@ -222 +274 @@
       
       if (title != null) chart.setTitle(title);
-      chart.removeLegend();
+      if (!hasAnnotation) chart.removeLegend();
       image = chart.createBufferedImage(width, height);
       
@@ -260 +312 @@
           graphics.clearRect(0, 0, width, height);
           graphics.setColor(Color.RED);
-          graphics.drawString(t.getMessage(), 50, 50);
+          String message = t.getMessage();
+          graphics.drawString(message == null ? "null" : message, 50, 50);
           image = img;
           // TODO - write more of stack trace

trunk/src/core/net/sf/basedb/util/plot/HistogramPlot.java

@@ -25 +25 @@
 package net.sf.basedb.util.plot;
 
+import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.query.SqlResult;
 import net.sf.basedb.core.query.SqlResultIterator;
@@ -30 +31 @@
 import org.jfree.chart.JFreeChart;
 import org.jfree.chart.axis.NumberAxis;
+import org.jfree.chart.plot.DatasetRenderingOrder;
+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.XYStepRenderer;
+import org.jfree.chart.renderer.xy.YIntervalRenderer;
 import org.jfree.data.DomainOrder;
 import org.jfree.data.Range;
@@ -37 +42 @@
 import org.jfree.data.xy.IntervalXYDataset;
 
+import java.awt.geom.Rectangle2D;
 import java.sql.SQLException;
 import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
 import java.util.List;
+import java.util.Map;
 
 /**
@@ -53 +62 @@
   private XYPlot plot;
   private HistogramDataset histogram;
+  private HistogramDataset hilo;
   private JFreeChart chart;
 
@@ -59 +69 @@
     
     histogram = new HistogramDataset();
+    hilo = new HistogramDataset();
     NumberAxis domainAxis = new NumberAxis(nameX);
     domainAxis.setAutoRangeIncludesZero(false);
+    domainRange = new Range(0.0, 0.0);
+    rangeRange = new Range(0.0, 0.0);
     
       NumberAxis rangeAxis = new NumberAxis(nameY);
@@ -66 +79 @@
 
       plot = new XYPlot(histogram, domainAxis, rangeAxis, new XYBarRenderer());
-    chart = new JFreeChart(plot);
+      plot.setDataset(1, hilo);
+      YIntervalRenderer yRenderer = new YIntervalRenderer();
+      yRenderer.setShape(new Rectangle2D.Float(-3, -1, 7, 2));
+      yRenderer.setSeriesVisibleInLegend(false, false);
+      plot.setRenderer(1, yRenderer, false);
+      
+      plot.setSeriesRenderingOrder(SeriesRenderingOrder.FORWARD);
+      plot.setDatasetRenderingOrder(DatasetRenderingOrder.FORWARD);
+      chart = new JFreeChart(plot);
     chart.setAntiAlias(false);
   }
 
-  public void addData(SqlResultIterator data, String name, float binSize, YAggregate yAggregate)
+  public void addData(SqlResultIterator data, String name, float binSize, YAggregate yAggregate, YAggregate hiloAggregate)
     throws SQLException
   {
@@ -84 +105 @@
       xValues[i++] = r.getFloat(1);
     }
-    histogram.addSeries(new HistogramSeries(name, xValues, yValues, binSize, yAggregate));
+    HistogramSeries main = new HistogramSeries(name, xValues, yValues, binSize, yAggregate, Float.NaN, Float.NaN);
+    histogram.addSeries(main);
+    if (hiloAggregate != null)
+    {
+      hilo.addSeries(new HistogramSeries(name, main, hiloAggregate));
+    }
+    adjustRanges();
+  }
+  
+  private void adjustRanges()
+  {
     domainRange = Range.combine(domainRange, plot.getRenderer().findDomainBounds(histogram));
-    rangeRange = Range.combine(rangeRange, plot.getRenderer().findRangeBounds(histogram));
+    if (hilo.getSeriesCount() > 0)
+    {
+      rangeRange = Range.combine(rangeRange, plot.getRenderer(1).findRangeBounds(hilo));
+    }
+    else
+    {
+      rangeRange = Range.combine(rangeRange, plot.getRenderer(0).findRangeBounds(histogram));
+    }
+    rangeRange = Range.expand(rangeRange, 0, 0.02);
     plot.getDomainAxis().setRange(domainRange);
-    plot.getRangeAxis().setRange(0, rangeRange.getUpperBound());
+    plot.getRangeAxis().setRange(rangeRange);
+  }
+  
+  public void addData(SqlResultIterator data, Collection<PlotAnnotation> annotations, float binSize, YAggregate yAggregate, YAggregate hiloAggregate)
+    throws SQLException
+  {
+    final boolean isCount = yAggregate == YAggregate.COUNT;
+    Map<Integer, TempSeries> series = new HashMap<Integer, TempSeries>(annotations.size());
+    List<TempSeries> tempSeries = new ArrayList<TempSeries>(annotations.size());
+    int meanCount = data.getTotalCount() / annotations.size();
+    for (PlotAnnotation pa : annotations)
+    {
+      TempSeries ts = new TempSeries(pa.getName(), meanCount, !isCount);
+      tempSeries.add(ts);
+      for (Integer column : pa.getColumns())
+      {
+        if (series.containsKey(column))
+        {
+          throw new BaseException("Column " + column + " has already been mapped to another series");
+        }
+        series.put(column, ts);
+      }
+    }
+    float maxX = Float.MIN_VALUE;
+    float minX = Float.MAX_VALUE;
+    while (data.hasNext())
+    {
+      SqlResult r = data.next();
+      TempSeries ts = series.get(r.getInt(1));
+      float x = r.getFloat(2);
+      if (maxX < x) maxX = x;
+      if (minX > x) minX = x;
+      ts.x.add(r.getFloat(2));
+      if (!isCount) ts.y.add(r.getFloat(3));
+    }
+    
+    for (TempSeries ts : tempSeries)
+    {
+      HistogramSeries main = new HistogramSeries(ts.name, ts.getX(), ts.getY(), binSize, yAggregate, minX, maxX);
+      histogram.addSeries(main);
+      if (hiloAggregate != null)
+      {
+        hilo.addSeries(new HistogramSeries(ts.name, main, hiloAggregate));
+      }
+    }
+    adjustRanges();
+    plot.setRenderer(new XYStepRenderer());
   }
   
@@ -94 +179 @@
   {
     return chart;
+  }
+  
+  private static class TempSeries
+  {
+    final String name;
+    final List<Float> x;
+    final List<Float> y;
+    
+    TempSeries(String name, int size, boolean hasY)
+    {
+      this.name = name;
+      this.x = new ArrayList<Float>(size);
+      this.y = hasY ? new ArrayList<Float>(size) : null;
+    }
+    
+    public float[] getX()
+    {
+      if (x == null) return null;
+      float[] xf = new float[x.size()];
+      int i = 0;
+      for (Float f : x)
+      {
+        xf[i++] = f.floatValue();
+      }
+      return xf;
+    }
+    
+    public float[] getY()
+    {
+      if (y == null) return null;
+      float[] yf = new float[y.size()];
+      int i = 0;
+      for (Float f : y)
+      {
+        yf[i++] = f.floatValue();
+      }
+      return yf;
+    }
+    
   }
   
@@ -141 +265 @@
     public double getXValue(int series, int item)
     {
-      return all.get(series).getBin(item).getStartX();
+      HistogramBin bin = all.get(series).getBin(item);
+      return (bin.getStartX() + bin.getEndX()) / 2;
     }
 
@@ -150 +275 @@
     public double getYValue(int series, int item)
     {
-      return all.get(series).getY(item);
+      return all.get(series).getMaxY(item);
     }
     // -------------------------------------------
@@ -187 +312 @@
     public double getStartYValue(int series, int item)
     {
-      return 0;
+      return all.get(series).getMinY(item);
     }
     // -------------------------------------------
     
-    
     public void addSeries(HistogramSeries s)
     {
@@ -197 +321 @@
     }
   }
-  
+
   
   private static class HistogramSeries
@@ -205 +329 @@
     private final YAggregate yAggregate;
     
-    private HistogramSeries(String name, float[] xValues, float[] yValues, float binSize, YAggregate yAggregate)
+    private HistogramSeries(String name, float[] xValues, float[] yValues, float binSize, YAggregate yAggregate, float xMin, float xMax)
     {
       this.name = name;
@@ -211 +335 @@
       
       // Find max and min --> number of bins
-      float xMin = Float.MAX_VALUE;
-      float xMax = Float.MIN_VALUE;
-      for (float x : xValues)
-      {
-        if (xMax < x) xMax = x;
-        if (xMin > x) xMin = x;
+      if (Float.isNaN(xMin) || Float.isNaN(xMax))
+      {
+        xMin = Float.MAX_VALUE;
+        xMax = Float.MIN_VALUE;
+        for (float x : xValues)
+        {
+          if (xMax < x) xMax = x;
+          if (xMin > x) xMin = x;
+        }
       }
       int numBins = 1 + (int)((xMax - xMin) / binSize);
@@ -243 +370 @@
     }
     
+    private HistogramSeries(String name, HistogramSeries other, YAggregate yAggregate)
+    {
+      this.name = name;
+      this.bins = other.bins;
+      this.yAggregate = yAggregate;
+    }
+    
     public String getName()
     {
@@ -258 +392 @@
     }
     
-    public float getY(int index)
-    {
-      return yAggregate.getY(bins[index]);
+    public float getMaxY(int index)
+    {
+      return yAggregate.getMaxY(bins[index]);
+    }
+    public float getMinY(int index)
+    {
+      return yAggregate.getMinY(bins[index]);
     }
   }
@@ -271 +409 @@
     private int count = 0;
     private float sum = 0.0f;
+    private float squaredSum = 0.0f;
     private float min = Float.MAX_VALUE;
     private float max = Float.MIN_VALUE;
@@ -299 +438 @@
       count++;
       sum += y;
+      squaredSum += y * y;
       if (y < min) min = y;
       if (y > max) max = y;
@@ -326 +466 @@
       return max;
     }
+    public float getStdev()
+    {
+      return (float)Math.sqrt((squaredSum - sum * sum / count) / (count - 1));
+    }
   }
   
@@ -333 +477 @@
     COUNT
     {
-      public float getY(HistogramBin bin)
+      public float getMaxY(HistogramBin bin)
       {
         return bin.getCount();
@@ -340 +484 @@
     SUM
     {
-      public float getY(HistogramBin bin)
+      public float getMaxY(HistogramBin bin)
       {
         return bin.getSum();
@@ -347 +491 @@
     MEAN
     {
-      public float getY(HistogramBin bin)
+      public float getMaxY(HistogramBin bin)
       {
         return bin.getMean();
@@ -354 +498 @@
     MAX
     {
-      public float getY(HistogramBin bin)
+      public float getMaxY(HistogramBin bin)
       {
         return bin.getMax();
@@ -361 +505 @@
     MIN
     {
-      public float getY(HistogramBin bin)
+      public float getMaxY(HistogramBin bin)
       {
         return bin.getMin();
       }
-    };
-    
-    public abstract float getY(HistogramBin bin);
+    },
+    STDEV
+    {
+      public float getMaxY(HistogramBin bin)
+      {
+        return bin.getStdev();
+      }
+      public float getMinY(HistogramBin bin)
+      {
+        return bin.getMean() - bin.getStdev();
+      }
+    },
+    HILOSTDEV
+    {
+      public float getMaxY(HistogramBin bin)
+      {
+        return bin.getMean() + bin.getStdev();
+      }
+      public float getMinY(HistogramBin bin)
+      {
+        return bin.getMean() - bin.getStdev();
+      }
+      
+    },
+    HILOMAXMIN
+    {
+      public float getMaxY(HistogramBin bin)
+      {
+        return bin.getMax();
+      }
+      public float getMinY(HistogramBin bin)
+      {
+        return bin.getMin();
+      }
+    }
+    ;
+    
+    public abstract float getMaxY(HistogramBin bin);
+    public float getMinY(HistogramBin bin)
+    {
+      return 0;
+    }
     
   }

trunk/src/core/net/sf/basedb/util/plot/ScatterPlot.java

@@ -25 +25 @@
 package net.sf.basedb.util.plot;
 
+import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.query.SqlResult;
 import net.sf.basedb.core.query.SqlResultIterator;
@@ -37 +38 @@
 
 import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
 
 
@@ -66 +72 @@
     chart.setAntiAlias(false);
   }
-
+  
   public void addData(SqlResultIterator data, String... names)
     throws SQLException
@@ -73 +79 @@
     for (int i = 0; i < names.length; ++i)
     {
-      series[i] = new XYSeries(names[i]);
+      XYSeries s = new XYSeries(names[i]);
+      s.setNotify(false);
+      series[i] = s;
     }
     while (data.hasNext())
@@ -90 +98 @@
   }
   
+  public void addData(SqlResultIterator data, Collection<PlotAnnotation> annotations)
+    throws SQLException
+  {
+    Map<Integer, XYSeries> series = new HashMap<Integer, XYSeries>(annotations.size());
+    List<XYSeries> newSeries = new ArrayList<XYSeries>(annotations.size());
+    for (PlotAnnotation pa : annotations)
+    {
+      XYSeries s = new XYSeries(pa.getName());
+      s.setNotify(false);
+      newSeries.add(s);
+      for (Integer column : pa.getColumns())
+      {
+        if (series.containsKey(column))
+        {
+          throw new BaseException("Column " + column + " has already been mapped to another series");
+        }
+        series.put(column, s);
+      }
+    }
+    while (data.hasNext())
+    {
+      SqlResult r = data.next();
+      XYSeries s = series.get(r.getInt(1));
+      s.add(r.getFloat(2), r.getFloat(3));
+    }
+    for (XYSeries s : newSeries)
+    {
+      allSeries.addSeries(s);
+    }
+  }
+  
   public JFreeChart getChart()
   {

trunk/www/include/styles/tabcontrol.css

@@ -31 +31 @@
 .tabcontrol, .tabcontrol_bottom {
   border-left: 1px solid #999999;
-  margin-bottom: 4px;
+  margin-bottom: 0px;
 }
 

trunk/www/views/experiments/plotter/index.jsp

@@ -82 +82 @@
     addFormulaOption(formulaOptions, f.getFormula(0), f.getName(), f.getDescription());
   }
+  addFormulaOption(formulaOptions, "raw('block')", "[Raw] Block", "Block number");
+  addFormulaOption(formulaOptions, "raw('metaGridX')", "[Raw] Meta grid X", "Meta grid X coordinate");
+  addFormulaOption(formulaOptions, "raw('metaGridY')", "[Raw] Meta grid Y", "Meta grid Y coordinate");
+  addFormulaOption(formulaOptions, "raw('row')", "[Raw] Row", "Row number");
+  addFormulaOption(formulaOptions, "raw('column')", "[Raw] Column", "Column number");
+  addFormulaOption(formulaOptions, "raw('x')", "[Raw] X", "X coordinate");
+  addFormulaOption(formulaOptions, "raw('y')", "[Raw] Y", "Y coordinate");
   for (RawDataProperty property : rdt.getProperties())
   {
@@ -91 +98 @@
   }
   
+  // TODO - add extra columns to list of options
   
   String title = HTML.encodeTags("Plot " + (ba == null ? bas.getName() : ba.getName()));
@@ -151 +159 @@
     var index = list.selectedIndex;
     formula.value = list[index].value;
-    label.value = list[index].text;
+    if (list[index].value != '') label.value = list[index].text;
   }
   
@@ -162 +170 @@
     frm.yPresets.disabled = isCount;
     frm.yLog.disabled = isCount;
+    for (var i = 0; i < frm.hiloAggregate.length; i++)
+    {
+      frm.hiloAggregate[i].disabled = isCount;
+    }
     if (isCount)
     {
       Main.removeClass(frm.yFormula, 'required');
+      frm.yLabel.value = 'Count';
     }
     else
     {
       Main.addClass(frm.yFormula, 'required');
+      var yPreset = frm.yPresets[frm.yPresets.selectedIndex];
+      if (yPreset.value != '') frm.yLabel.value = yPreset.text;
     }
   }
@@ -196 +211 @@
         url += '&yLog='+(frm.yLog.checked ? 1 : 0);
         url += '&yLabel='+Main.encodeURI(frm.yLabel.value);
+        if (frm.annotation)
+        {
+          url += '&annotation='+frm.annotation[frm.annotation.selectedIndex].value;
+        }
       }
       else
@@ -211 +230 @@
           url += '&y='+Main.encodeURI(frm.yFormula.value);
           url += '&yLog='+(frm.yLog.checked ? 1 : 0);
+          url += '&hiloAggregate='+Forms.getCheckedRadio(frm.hiloAggregate).value
         }
         url += '&yLabel='+Main.encodeURI(frm.yLabel.value);
+        if (frm.annotation)
+        {
+          url += '&annotation='+frm.annotation[frm.annotation.selectedIndex].value;
+        }
       }
       return url;
@@ -288 +312 @@
   <div class="boxed">
 
-  <table class="form">
-  <tr valign="top">
+  <table class="form" border="0" cellspacing="0" cellpadding="2">
+  <tr valign="bottom">
     <td width="50%">
     
@@ -297 +321 @@
       <td class="prompt">Plot title</td>
       <td colspan="2"><input type="text" class="text" size="30" maxlength="255" name="title" 
-        value="<%=HTML.encodeTags(ba.getName())%>"></td>
+        value="<%=HTML.encodeTags(ba == null ? bas.getName() : ba.getName())%>"></td>
     </tr>
     <tr>
@@ -315 +339 @@
     <p>
 
-    <t:tabcontrol id="plotType" contentstyle="<%="height: "+(int)(scale*260)+"px;"%>">
+    <t:tabcontrol id="plotType" contentstyle="<%="height: "+(int)(scale*340)+"px;"%>">
     <t:tab id="scatter" title="Scatter plot">
       <form name="scatter">
@@ -371 +395 @@
         <td><input type="checkbox" name="xLog" value="1"></td>
       </tr>
+      <%
+      if (ba == null)
+      {
+        %>
+        <tr>
+          <td class="prompt">Annotation</td>
+          <td>
+          <select name="annotation">
+            <option value="">- none -
+            <option value="bioassay">Bioassay
+          </select>
+          </td>
+        </tr>
+        <%
+      }
+      %>
       </table>
       </form>
@@ -383 +423 @@
           <input type="radio" name="yAggregate" value="count" checked onchange="aggregateOnChange()"> Count
           <input type="radio" name="yAggregate" value="mean" onchange="aggregateOnChange()"> Mean
-          <input type="radio" name="yAggregate" value="max" onchange="aggregateOnChange()"> Max
-          <input type="radio" name="yAggregate" value="min" onchange="aggregateOnChange()"> Min
+        </td>
+      </tr>
+      <tr>
+        <td>&nbsp;Hi-lo</td>
+        <td>
+          <input type="radio" name="hiloAggregate" value="" checked> None
+          <input type="radio" name="hiloAggregate" value="hilomaxmin"> Min/Max
+          <input type="radio" name="hiloAggregate" value="hilostdev"> Stdev
         </td>
       </tr>
@@ -444 +490 @@
         <td><input type="text" class="text" name="binSize" value="1"></td>
       </tr>
+      <%
+      if (ba == null)
+      {
+        %>
+        <tr>
+          <td class="prompt">Annotation</td>
+          <td>
+          <select name="annotation">
+            <option value="">- none -
+            <option value="bioassay">Bioassay
+          </select>
+          </td>
+        </tr>
+        <%
+      }
+      %>
       </table>
       </form>
-    
     </t:tab>
     </t:tabcontrol>
-  
-    <base:buttongroup>
-      <base:button title="Preview" onclick="previewPlot()" tooltip="Generate a preview of the plot" />
-      <base:button title="View&hellip;" onclick="viewPlot()" tooltip="View a fullsized version of the plot (in a popup)" />
-      <base:button title="Download&hellip;" onclick="downloadPlot()" tooltip="Downlad a fullsized version of the plot to you computer" />
-      <base:button title="Save as&hellip;" onclick="savePlotAs()" tooltip="Save a fullsized version of the plot on the BASE server" />
-    </base:buttongroup>
-    
     </td>
     <td width="50%">
       <div style="position: relative; top: 0px; left: 0px; border: 10px solid #00000;">
       <img src="../../../images/plot_empty.png" id="background" 
-        style="position: absolute; top: 0px; left: 0px; z-index: 1;">
+        style="position: absolute; top: 0px; left: 0px; z-index: 1; border: 1px solid #999999;">
       <img src="../../../images/plot_select.gif" id="preview" 
-        style="position: relative; top: 0px; left: 0px; z-index: 2;">
+        style="position: relative; top: 0px; left: 0px; z-index: 2; border: 1px solid #999999;">
       </div>
     </td>
   </tr>
   </table>
-
   </div>
-
-    <table align="center">
-    <tr>
-      <td><base:button onclick="window.close()" title="Close" /></td>
-    </tr>
-    </table>
+    <p>
+    <div align="center">
+    <base:buttongroup>
+      <base:button title="Preview" onclick="previewPlot()" 
+        tooltip="Generate a preview of the plot" />
+      <base:button title="View&hellip;" onclick="viewPlot()" 
+        tooltip="View a fullsized version of the plot (in a popup)" />
+      <base:button title="Download&hellip;" onclick="downloadPlot()" 
+        tooltip="Downlad a fullsized version of the plot to you computer" />
+      <base:button title="Save as&hellip;" onclick="savePlotAs()" 
+        tooltip="Save a fullsized version of the plot on the BASE server" />
+      <base:button onclick="window.close()" title="Close" />
+    </base:buttongroup>
+    </div>
   
   </base:body>