D3 Examples - genome browser

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<!DOCTYPE html>
<head>
  <meta charset="utf-8">
  
  <style>
​
body {
  font: 10px sans-serif;
}
​
.axis path,
.axis line {
  fill: none;
  stroke: #000;
  shape-rendering: crispEdges;
}
​
.x.axis path {
  display: none;
}
​
.line {
  fill: none;
  stroke: steelblue;
  stroke-width: 1.5px;
}
​
</style>
  
  <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.2.0/jquery.min.js"></script>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/jqplot/1.0.8/jquery.jqplot.min.js"></script>
    <script type="text/javascript">
    function genome(sequence){
    var i=1;
    var geneBlockArray=[];
    var twoGene=sequence[0];
    this.getGeneBlocks= function(){
    do{
        
        var gene = sequence.charAt(i);
        twoGene+=gene;
        if(twoGene.indexOf('C')>-1 || twoGene.indexOf('G')>-1){
            if(twoGene.indexOf('C')>-1 && twoGene.indexOf('G')>-1){
                geneBlockArray.push(100);
            }
            else if(twoGene=='CC' || twoGene=='GG'){
                geneBlockArray.push(100);
            }
            else{
​
                geneBlockArray.push(50);
            }
        }
        else{
            geneBlockArray.push(0);
        }
        twoGene=gene;
        i++;
    }while(i<sequence.length);
​
    return geneBlockArray;
}
}
  
  </script>
    <link rel="stylesheet" type="text/css" href="jquery.jqplot.min.css" />
    
​
  <script src="https://d3js.org/d3.v3.min.js">
  <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
    <link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto+Slab:400,100,300,700">
    <link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto:400,100,100italic,300,300italic,400italic,500,500italic,700,700italic,900,900italic">
</head>
​
<body>
    <div id="option">
    <input name="updateButton" 
           type="button" 
           value="Color by G/C content" 
           onclick="updateData()" />
</div>
   <section id='chartArea'>
        <div id='chart1' class='chart'>
        </div>
        <div id='chart2' class='chart'>
        </div>
        <div id='chart3' class='chart'>
        </div>
        </section>
        <script type="text/javascript">
        $(document).ready(function(){
            var url='genes.json.txt';
    
            d3.json(url,function(error, json){console.log(json)
                var i=1;
                $.each(json,function(x,y){
                    var g=[];
                    $.each(y.genes, function(k, gene){
                        x= new genome(gene.sequence);
                        f=x.getGeneBlocks();
                        g = g.concat(f);    
                    })
                    plotChart('chart'+i, g);
                    i++;
                }); 
            });
        });
        </script>
        <script type="text/javascript">
        function plotChart(chart,x){
            var plot1 = $.jqplot (chart, [x], {
                grid:{
                    background:'#FFFFFF',   
                },
                seriesDefaults: {
                    rendererOptions: {
                        smooth: true
                    }
                },
                axes: {
                    xaxis: {
                        min:0,
                        max:180,
                        tickOptions: {
                            showGridline: false,
                            showMark: false,
                            fontFamily: 'DosisBold',
                            textColor: '#ffffff',
                            fontSize: 'larger',
              shadow: false
                        },
                    },
                    yaxis: {
                        tickOptions: {
                            showGridline: false,
                            showMark: true,
                            showLabel: true,
                            shadow: false,
                        },
                    },
                },
            });
        };
  </script>
  <script>
  
  
 var svg1 = d3.selectAll("#chartArea").attr('height','1000');
​
 d3.json("genes.json.txt", function(error, json) {
    if (error) return console.warn(error);
   // console.log(json);
   svg1.attr("class", 'genechart');
​
    // Define the div for the tooltip
    var div = d3.select("body").append("div")
      .attr("class", "tooltip")
      .style("opacity", 0);
​
    var phage = svg1.selectAll("genechart")
      .data(json)
      .enter().append('svg').attr("width", function (d) {
      return d3.max(json, function(d) {
        return d.genomelength/10;
      })
    })
   .attr('height','500')
      .append("g");
    phage.attr("transform", function(d, i) { return "translate(0," + (100 + (i*225)) + ")"; });
​
    phage.append("rect") // background for ruler
      .attr({x: 0, y: 0, width: function(d) { return d.genomelength/10; }, height: 30})
      .style({"stroke-width": "2px", "fill": "white", "stroke": "black"})
      .attr("stroke-opacity", 0)
      .transition().duration(1000)
      .attr("stroke-opacity", 1);
​
    var group = phage.selectAll(".thousandticks")
      .data(function (d) {
          ticks = [];
          genome_positions = d3.range(d.genomelength);
          genome_positions.forEach(function (currentValue, index, myArray) {
            if (currentValue % 1000 === 0) {
              ticks.push(currentValue);
            }
          });
          return ticks;
        }
      )
      .enter()
      .append("g");
    group.append("rect")
      .style({"fill": "black"})
      //.attr({x: 0, y: 100, width: "1px", height: 30})
      .attr({x: function (d) { return d/10; }, y: 0, width: "1px", height: 30})
      .attr({"fill-opacity": 0})
      .transition().duration(1500)
      .attr({"fill-opacity": 1});
​
    //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
    group.append("text") // kbp label
      .attr("x", function(d) {return (d/10) + 3;})
      .attr("y", 12)
      .attr("font-family", "sans-serif")
      .attr("font-size", "14px")
      .attr("fill", "green")
      .style("text-anchor", "start")
      .text(function(d) { return d/1000; })
      .attr({"fill-opacity": 0})
      .transition().duration(1500)
      .attr({"fill-opacity": 1});
    var group2 = phage.selectAll(".fivehundredticks")
      .data(function (d) {
        ticks = [];
        genome_positions = d3.range(d.genomelength);
        genome_positions.forEach(function (currentValue, index, myArray) {
          if (currentValue % 500 === 0 & currentValue % 1000 !== 0) {
            ticks.push(currentValue);
          }
        })
        return ticks;
      })
      .enter()
      .append("g");
    group2.append("rect")
      .style({"fill": "black"})
      .attr({x: function(d) {return d/10;}, y: 0, width: "1px", height: 15})
      .attr({"fill-opacity": 0})
      .transition().duration(1500)
      .attr({"fill-opacity": 1});
    //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
    var group3 = phage.selectAll(".onehundredticks")
      .data(function (d) {
        ticks = [];
        genome_positions = d3.range(d.genomelength);
        genome_positions.forEach(function (currentValue, index, myArray) {
          if (currentValue % 100 === 0 & currentValue % 1000 !== 0 & currentValue % 500 !== 0) {
            ticks.push(currentValue);
          }
        })
        return ticks;
      })
      .enter()
      .append("g");
    group3.append("rect")
      .style({"fill": "black"})
      .attr({x: function (d) { return d/10; }, y: 15, width: "1px", height: 15})
      .attr("fill-opacity", 0)
      .transition().duration(1500)
      .attr("fill-opacity", 1);
​
    gene = phage.selectAll(".genes")
      .data(function(d, i) { //console.log(i, d); 
      return d.genes;})
      .enter()
      .append("g");
      gene.append("rect")
      .attr("y", function (d) {
        if (d.direction == "forward") {
          if (d.name % 2 === 0) {
            return  -70;
          }
          else { return -30;}
        }
        else if (d.direction == "reverse") {
          if (d.name % 2 === 0) {
            return 30;
          }
          else { return 60;}
        }
      })
      .attr("x", function (d) {
        if (d.direction === "forward") {
          return (0 - ((d.stop-d.start)/10)) - 2;
        }
        else if (d.direction === "reverse") {
          w = d3.select("svg").style("width");
          return w;
        }
      })
      .attr("height", function (d) {return 30;})
      .attr("width", function (d) { return (d.stop-d.start)/10; })
      .style({"stroke":"black", "stroke-width": "2px"})
      .attr("fill", function (d) {
        if (d.direction == "forward") {
          return "green";
        }
        else if (d.direction == "reverse") {
          return "red";
        }
        else {
          return "black";
        }
      })
      .on("mouseover", function(d) {
       // console.log(d);
        div.transition()
          .duration(500)
          .style("opacity", .9);
        div .html("The direction of gene " + d.name + " is " + d.direction)// the text of the tooltip ...
          .style("left", (d3.event.pageX) + "px")
          .style("top", (d3.event.pageY - 28) + "px");
      })
      .on("mouseout", function(d) {
        div.transition()
          .duration(500)
          .style("opacity", 0);
      })
      .transition().delay(1000).duration(1500)
      .attr("x", function (d) { return d.start/10; });
​
      gene.append("text") // gene name
      .attr("x", function(d) { return ((d.start + d.stop)/2)/10;})
      .attr("y", function (d) {
        if (d.direction == "forward") {
          if (d.name % 2 === 0) { // forward and even
            return -50;
          }
          else { return -10;} // forward and odd
        }
        else if (d.direction == "reverse") {
          if (d.name % 2 === 0) { // reverse and even
            return 50;
          }
          else { return 80;} //reverse and odd
        }
      })
      .style({"text-anchor": "middle", "fill": "black"})
      .attr("font-family", "sans-serif")
       
      .text(function(d){
     var C=0;
     var G=0;
     for(var i=0; i<=d.sequence.length;i++){
       if(d.sequence[i]==="C")
         {C++;}
       else if (d.sequence[i]==="G")
         {G++;}
     }
        var total=C+G;
        var toPercent = d3.format("%");
        var grandtotal = toPercent(total / d.sequence.length)
        { return (grandtotal) }
      }
         )
   
     
              
      .attr("fill-opacity", 0)
      .transition().delay(2000).duration(1500)
      .attr("fill-opacity", 1);
​
​
    gene.append("text") // pham name
      .attr("x", function(d) { return ((d.start + d.stop)/2)/10;})
      .attr("y", function (d) {
        if (d.direction == "forward") {
          if (d.name % 2 === 0) {
            return -80;
          }
          else { return -40;}
        }
        else if (d.direction == "reverse") {
          if (d.name % 2 === 0) {
            return 80;
          }
          else { return 110;}
        }
      })
​
      .style({"text-anchor": "middle", "fill": "blue"})
      .attr("font-family", "sans-serif")
      .text(function(d) {return d.pham})
      .attr("fill-opacity", 0)
      .transition().delay(3500).duration(1500)
      .attr("fill-opacity", 1);
   updatex();
​
  });
  </script>
  <script>
function updatex(){    x=$('svg')[0];
y=$('svg')[1];
z=$('svg')[2];              
$('#chart1').append(x);
$('#chart2').append(y);       $('#chart3').append(z);
 $('#chart1 svg').css({position:'absolute',top:'280px'});
$('#chart2').css({width: '770', top:'220'});
$('#chart2 svg').css({position:'absolute',top:'150px'});
 $('#chart2').css('top',220);                  
 $('#chart3 svg').css({position:'absolute',top:'-100px',height:1500}); 
$('#chart3').css('top',550);                   
}
  </script>
</body>
​
    