anchor.diff:  <%@ page import="org.mskcc.cbio.cgds.model.GeneticAlterationType" %>
   
   <script type="text/javascript" src="js/d3.v2.min.js"></script>
  -<link rel="stylesheet" type="text/css" href="css/bootstrap.min.css">
  +<!--link rel="stylesheet" type="text/css" href="css/bootstrap.min.css"-->
   
   <style type="text/css">
       .axis path,
  
positive.code:             }
          });
      }
      drawPlotType();
      drawScattersPlots();
  }
  
  var has_copy_no = false;
  var has_mrna = false;
  var has_dna_mythelation = false;
  var has_rppa = false;
  
  function drawDataType(inputStr, i) {
      if ((inputStr.indexOf("mRNA") != -1) || (inputStr.indexOf("microRNA") != -1)) {
          has_mrna = true;
          $('#data_type_mrna').append("<option value='" + genetic_profile_types[i] + "'>" + genetic_profile_types_description[i] + "</option>");
      } else if (inputStr.indexOf("copy-number") != -1) {
          has_copy_no = true;
          $('#data_type_copy_no').append("<option value='" + genetic_profile_types[i] + "'>" + genetic_profile_types_description[i] + "</option>");
      } else if (inputStr.indexOf("RPPA") != -1) {
          has_rppa = true;
      } else if (inputStr.indexOf("Methylation") != -1) {
          has_dna_mythelation = true;
      }
  }
  
  function drawPlotType() {
      if (has_copy_no == true && has_mrna == true) {
          $('#plot_type').append("<option value='mrna_vs_copy_no' selected='selected'>mRNA vs. Copy Number</option>");
      }
      if (has_dna_mythelation == true && has_mrna == true) {
          $('#plot_type').append("<option value='mrna_vs_dna_mythelation'>mRNA vs. DNA Methylation</option>");
      }
      if (has_rppa == true && has_mrna == true) {
          $('#plot_type').append("<option value='rppa_protein_level_vs_mrna'>RPPA Protein Level vs. mRNA</option>");
      }
  }
  
  function drawScattersPlots() {
  
      //Create Canvas
      $('#plots_tab').empty();
      var w = 800;
      var h = 800;
      var svg = d3.select("#plots_tab")
              .append("svg")
              .attr("width", w)
              .attr("height", h);
  
      //Prepare DataSet
      var mrna_type = document.getElementById('data_type_mrna').value;
      var copy_no_type = document.getElementById('data_type_copy_no').value;
      var tmp_mrna_index = findIndex(mrna_type, genetic_profile_types);
      var tmp_copy_no_index = findIndex(copy_no_type, genetic_profile_types);
      var tmp_rppa_index = findIndex("rppa_protein_level_index", result_set_index);
      var tmp_mythelation_index = findIndex("methylation_hm27_index", result_set_index);
      var tmp_mutation_index = findIndex("mutations_index", result_set_index);
  
      var xData = [];
      var yData = [];
      var zData = [];
      var dataset = [];
      var xLegend;
      var yLegend;
  
      var plot_type = document.getElementById('plot_type').value;
  
      if (plot_type == "mrna_vs_copy_no") {
          copyData(xData, result_set[tmp_copy_no_index]);
          copyData(yData, result_set[tmp_mrna_index]);
          copyData(zData, result_set[tmp_mutation_index]);
          var index = 0;
          for( var i = 0; i<case_set.length; i++) {
              //Skip NaN entries
              if ((xData[i] == "NaN") || (yData[i] == "NaN")) {
                  continue;
  
negative.code:     }
      var min_y = Math.min.apply(Math, tmp_yData);
      var max_y = Math.max.apply(Math, tmp_yData);
      var edge_y = (max_y - min_y) * 0.2;
      //-------------------tmp---------------------------
  
      //Define scale functions
      var padding = 200;
      var xScale = d3.scale.linear()
              .domain([min_x - edge_x, max_x + edge_x])
              .range([100, 600]);
      var yScale = d3.scale.linear()
              .domain([min_y - edge_y, max_y + edge_y])
              .range([520, 20]);
      //Define Axis
      var xAxis = d3.svg.axis()
              .scale(xScale)
  