Changeset 5149

Timestamp:

Oct 20, 2009, 2:49:09 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1386: Plot function in the bioassay table in experiment explorer

It is now possible to use a bar or line plot.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/servlet/ExperimentExplorerPlotServlet.java (modified) (6 diffs)
• www/views/experiments/explorer/view/plotter.jsp (modified) (10 diffs)
• www/views/experiments/explorer/view/view.jsp (modified) (3 diffs)

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

@@ -29 +29 @@
 import java.awt.font.FontRenderContext;
 import java.awt.geom.Rectangle2D;
+import java.awt.geom.RectangularShape;
 import java.awt.image.BufferedImage;
 import java.io.IOException;
@@ -58 +59 @@
 import org.jfree.chart.plot.CategoryPlot;
 import org.jfree.chart.plot.Plot;
+import org.jfree.chart.renderer.category.BarPainter;
+import org.jfree.chart.renderer.category.BarRenderer;
+import org.jfree.chart.renderer.category.BarRenderer3D;
 import org.jfree.chart.renderer.category.BoxAndWhiskerRenderer;
+import org.jfree.chart.renderer.category.CategoryItemRenderer;
 import org.jfree.chart.renderer.category.LineAndShapeRenderer;
+import org.jfree.chart.renderer.category.StandardBarPainter;
 import org.jfree.chart.title.TextTitle;
 import org.jfree.data.category.DefaultCategoryDataset;
 import org.jfree.data.statistics.BoxAndWhiskerItem;
 import org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset;
+import org.jfree.ui.RectangleEdge;
 
 import net.sf.basedb.clients.web.ExperimentExplorer;
@@ -134 +141 @@
     final int reporterIndex = Values.getInt(request.getParameter("reporterIndex"));
     final int positionIndex = Values.getInt(request.getParameter("positionIndex"));
-    final String plotType = Values.getString(request.getParameter("type"), "line");
+    final String plotType = Values.getString(request.getParameter("type"), "assay");
+    final String subType = Values.getString(request.getParameter("subtype"), "line");
     
     // Where to deliver the image
@@ -207 +215 @@
           
         JFreeChart chart = null;
-        if ("box".equals(plotType))
+        if ("annotation".equals(plotType))
         {
           // Collect all spot data values in one list per annotation group
@@ -255 +263 @@
           chart = new JFreeChart(plot);
         }
-        else if ("line".equals(plotType))
+        else if ("assay".equals(plotType))
         {
           // Load annotation summaries
@@ -307 +315 @@
           // Create the plot and chart objects
             categoryAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_90);
-          Plot plot = new CategoryPlot(dataset, categoryAxis, valueAxis, new LineAndShapeRenderer());
+            CategoryItemRenderer renderer = null;
+            if ("line".equals(subType))
+            {
+              renderer = new LineAndShapeRenderer();
+            }
+            else
+            {
+              BarRenderer br = new BarRenderer();
+              renderer = br;
+              br.setShadowVisible(false);
+              br.setBarPainter(new StandardBarPainter());
+              br.setDrawBarOutline(true);
+            }
+          Plot plot = new CategoryPlot(dataset, categoryAxis, valueAxis, renderer);
           chart = new JFreeChart(plot);
         }

trunk/www/views/experiments/explorer/view/plotter.jsp

@@ -75 +75 @@
   final int reporterIndex = Values.getInt(request.getParameter("reporterIndex"));
   final int positionIndex = Values.getInt(request.getParameter("positionIndex"));
-  final String plotType = Values.getString(request.getParameter("type"), "line");
+  final String plotType = Values.getString(request.getParameter("type"), "assay");
   final int annotationTypeId = Values.getInt(request.getParameter("annotationTypeId"));
   final boolean needAverageMethod = positionIndex == ExperimentExplorer.SPOT_AVG;
@@ -137 +137 @@
   {
     var plotType = getPlotType();
-    if (plotType == 'line')
-    {
-      return validateLinePlot();
-    }
-    else if (plotType == 'box')
-    {
-      return validateBoxPlot();
+    if (plotType == 'assay')
+    {
+      return validateAssayPlot();
+    }
+    else if (plotType == 'annotation')
+    {
+      return validateAnnotationPlot();
     }
     return false;
   }
   
-  function validateLinePlot()
-  {
-    var frm = document.forms['line'];
+  function validateAssayPlot()
+  {
+    var frm = document.forms['assay'];
     if (Main.trimString(frm.yFormula.value) == '')
     {
@@ -160 +160 @@
   }
   
-  function validateBoxPlot()
-  {
-    var frm = document.forms['box'];
+  function validateAnnotationPlot()
+  {
+    var frm = document.forms['annotation'];
     if (Main.trimString(frm.yFormula.value) == '')
     {
@@ -180 +180 @@
   function switchTab(tabControlId, tabId)
   {
-    if (tabId == 'line' || tabId == 'box')
+    if (tabId == 'assay' || tabId == 'annotation')
     {
       plotType = tabId;
@@ -217 +217 @@
       }
       var plotType = getPlotType();
-      if (plotType == 'line')
-      {
-        var frm = document.forms['line'];
-        url += '&type=line';
+      if (plotType == 'assay')
+      {
+        var frm = document.forms['assay'];
+        url += '&type=assay';
+        url += '&subtype=' + frm.subtype[frm.subtype.selectedIndex].value;
         url += '&y='+Main.encodeURI(frm.yFormula.value);
         url += '&yLog='+(frm.yLog.checked ? 1 : 0);
@@ -230 +231 @@
         }
       }
-      else if (plotType == 'box')
-      {
-        var frm = document.forms['box'];
-        url += '&type=box';
+      else if (plotType == 'annotation')
+      {
+        var frm = document.forms['annotation'];
+        url += '&type=annotation';
         url += '&y='+Main.encodeURI(frm.yFormula.value);
         url += '&yLog='+(frm.yLog.checked ? 1 : 0);
@@ -359 +360 @@
       active="<%=plotType%>" remember="false"
       switch="switchTab">
-    <t:tab id="line" title="Line plot" helpid="explorer.lineplot"
-      tooltip="Create a line plot with bioassays along the x axis">
-      <form name="line">
+    <t:tab id="assay" title="By bioassay" helpid="explorer.assayplot"
+      tooltip="Create a line/bar plot with bioassays along the x axis">
+      <form name="assay">
       <table border="0" cellspacing="0" cellpadding="2" class="form">
+      <tr>
+        <td class="prompt">Plot type</td>
+        <td colspan="2">
+          <select name="subtype">
+          <option value="line">Line plot</option>
+          <option value="bar">Bar plot</option>
+          </select>
+      </tr>
       <tr>
         <td class="prompt" colspan="3">Y-axis</td>
@@ -385 +394 @@
             image="expression_builder.gif"
             tooltip="Use the Expression builder"
-            onclick="openExpressionBuilder('Y-axis expression', 'line', 'yFormula', 'COLUMN_EXPRESSION')"
+            onclick="openExpressionBuilder('Y-axis expression', 'assay', 'yFormula', 'COLUMN_EXPRESSION')"
           />
         </td>
@@ -431 +440 @@
       </form>
     </t:tab>
-    <t:tab id="box" title="Box plot" helpid="explorer.boxplot"
+    <t:tab id="annotation" title="By annotation" helpid="explorer.annotationplot"
       tooltip="Create a box plot with annotation values along the x axis">
-      <form name="box">
+      <form name="annotation">
       <table border="0" cellspacing="0" cellpadding="2" class="form">
       <tr>
@@ -457 +466 @@
             image="expression_builder.gif"
             tooltip="Use the Expression builder"
-            onclick="openExpressionBuilder('Y-axis expression', 'box', 'yFormula', 'COLUMN_EXPRESSION')"
+            onclick="openExpressionBuilder('Y-axis expression', 'annotation', 'yFormula', 'COLUMN_EXPRESSION')"
           />
         </td>

trunk/www/views/experiments/explorer/view/view.jsp

@@ -254 +254 @@
       }
     }
-    function plotSpotData()
-    {
-      var url = 'plotter.jsp?ID=<%=ID%>&type=line';
+    function assayPlot()
+    {
+      var url = 'plotter.jsp?ID=<%=ID%>&type=assay';
       url += '&bioAssaySetId=<%=bioAssaySetId%>';
       url += '&reporterIndex=<%=reporterIndex%>';
       url += '&positionIndex=<%=positionIndex%>';
-      Main.openPopup(url, 'SpotPlot', 1100, 700);
-    }
-    function boxPlot(annotationType)
-    {
-      var url = 'plotter.jsp?ID=<%=ID%>&type=box';
+      Main.openPopup(url, 'AssayPlot', 1100, 700);
+    }
+    function annotationPlot(annotationType)
+    {
+      var url = 'plotter.jsp?ID=<%=ID%>&type=annotation';
       url += '&bioAssaySetId=<%=bioAssaySetId%>';
       url += '&reporterIndex=<%=reporterIndex%>';
       url += '&positionIndex=<%=positionIndex%>';
       url += '&annotationTypeId=' + annotationType;
-      Main.openPopup(url, 'BoxPlot', 1100, 700);
+      Main.openPopup(url, 'AnnotationPlot', 1100, 700);
     }
   </script>
@@ -469 +469 @@
               <td class="summaryheader"><base:icon
                 image="plotter.gif"
-                onclick="<%="boxPlot(" + at.getId() + ")"%>"
+                onclick="<%="annotationPlot(" + at.getId() + ")"%>"
                 tooltip="Box plot for selected spot data per annotation group"
               /></td>
@@ -736 +736 @@
         <tbl:button 
           image="plotter.gif"
-          onclick="plotSpotData()"
+          onclick="assayPlot()"
           title="Plot&hellip;"
           tooltip="Plot selected data from this table"