D3 Examples - acriths genome browser

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<!DOCTYPE html>
<head>
  <meta charset="utf-8">
  <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
  <script src="https://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js"></script>
   <style>
​
    body { 
        margin:45;
        position:fixed;
        top:0;
        right:0;
        bottom:0;
        left:0; 
    }
​
div.tooltip {   
  position: absolute;           
  text-align: center;           
  width: 60px;                  
  height: 28px;                 
  padding: 2px;             
  font: 12px sans-serif;        
  background: lightsteelblue;   
  border: 0px;      
  border-radius: 8px;           
  pointer-events: none;         
}
  .d3-tip {
  line-height: 1;
  font-weight: bold;
  padding: 12px;
  background: lightsteelblue;
  color: #fff;
  border-radius: 2px;
}
.d3-tip:after {
  box-sizing: border-box;
  display: inline;
  font-size: 10px;
  width: 100%;
  line-height: 1;
  color: rgba(0, 0, 0, 0.8);
  content: "\25BC";
  position: absolute;
  text-align: center;
}
.d3-tip.n:after {
  margin: -1px 0 0 0;
  top: 100%;
  left: 0;
}
</style>
    <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>    
  <script>
    // Feel free to change or delete any of the code you see!
    var genomelength = 7800;
    
    var tickMarks = {thousand: [], fivehundred: [], onehundred: []};
    
        var genome_positions = [];
        for (var i = 1; i <= genomelength; i++) {
        genome_positions.push(i);
        }
    
    genome_positions.forEach(function(currentValue, index, myArray){
      if (currentValue % 1000 === 0) {
        tickMarks.thousand.push(currentValue);
      }
      else if (currentValue % 500 === 0) {
        tickMarks.fivehundred.push(currentValue);
​
      }
      else if (currentValue % 100 === 0) {
        tickMarks.onehundred.push(currentValue);
      }
    });    
    var svg = d3.select("body").append("svg").attr({height: 500,width: genomelength/10});
    svg.append("rect")
      .attr({x: 0, y: 100, width: genomelength/10, height: 30})
        .style({"stroke-width": "2px", "fill": "white", "stroke": "black"});
    
    d3.json("genes.json.txt", function(error, json) {
          if (error) return console.warn(error);
            var genes = svg.selectAll(".genes")
        .data(json)
          .enter()
        .append("g");
        var tip = d3.tip()
      .attr('class', 'd3-tip')
      .offset(function (d) {
        if (d.direction == "forward") {
            return [-55, -48];
        }
        else if (d.direction == "reverse") {
            return [-55, -48];
        }
      })
      .html(function(d) {
        return "<span style='color:green'><b>Pham:</b>"+"</span>" 
          + d.pham + "       "+"<span style='color:red'>"+"GC content:</span>"+((((d.sequence.match(/G/gi).length)+(d.sequence.match(/C/gi).length))/(d.sequence.length))*100).toPrecision(3)+"%" ;
      })
      //Clickable tip box attr
      var hidden = d3.tip()
        .attr('class', 'd3-hidden')
        .offset(function (d) {
        if (d.direction == "forward") {
            return [70, -48];
            }
        else if (d.direction == "reverse") {
            return [70, -48];
        }
      })
      //possible incert g/c content calculator
      .html(function(d) {
        return "<a style=color:white target=_blank href=https://blast.ncbi.nlm.nih.gov/Blast.cgi>BLAST:</a><span style='color:white'>" 
          + " " + d.translation + "</span>";
      })
      //call the "tool-tips"
      svg.call(tip);
      svg.call(hidden);
    
  var rectAttributes = genes
        .on('mouseover', tip.show)
        .on('mouseout', tip.hide)
        .on('click', hidden.show)
        .on('dblclick', hidden.hide)
​
            genes.append("rect")
        
        .attr("x", function (d) { return d.start/10; })
          .attr("y", function (d) { return 100; })
        .attr("height", function(d) { return 0;})
        .attr("width", function (d) { return (d.stop-d.start)/10; })
        .style({"stroke":"black", "stroke-width": "2px"})
            .transition().delay(3000).duration(1500)
        .attr("fill", function (d) {
            if (d.direction == "forward") {
            return "green";
          }
            else if (d.direction == "reverse") {
            return "red";
          }
            else {
            return "black";
          }
        })
          .attr("y", function (d) {
        if (d.direction == "forward" && d.name % 2 === 0 ) 
            return 70
        else if (d.direction == "forward" && d.name % 2 === 1) 
            return 30
        else if (d.direction == "reverse" && d.name % 2 === 0) 
            return 130
        else if (d.direction == "reverse" && d.name % 2 === 1)
          return 170
      })
        .attr("height", function (d) {return 30;});
      
      genes.append("text") // GC
        .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 65;
        }
        else { return 25;}
      }
            else if (d.direction == "reverse") {
        if (d.name % 2 === 0) {
            return 180;
        }
            else { return 215;}
      }
    })
    .style({"text-anchor": "middle", "fill": "black"})
    .attr("font-family", "sans-serif")
    .text(function(d) {
      return ((((d.sequence.match(/G/gi).length)+(d.sequence.match(/C/gi).length))/(d.sequence.length))*100).toPrecision(3)+"%";
    })
    .attr("fill-opacity", 0)
    .transition().delay(2000).duration(1500)
        .attr("fill-opacity", 1);
​
​
      genes.append("text")
        .attr("x", function(d) { return ((d.start + d.stop)/2)/10;})
        .attr("y", function (d) {
        if (d.direction == "forward" && d.name % 2 === 0) 
            return 90;
          else if (d.direction == "forward" && d.name % 2 === 1)
            return 50
            else if (d.direction == "reverse" && d.name % 2 === 0) 
            return 150
          else if (d.direction == "reverse" && d.name % 2 === 1)
            return 190
          
      })
        .style({"text-anchor": "middle", "fill": "black"})
        .text(function(d) {return d.name})
        .attr("fill-opacity", 0)
        .transition().delay(4500).duration(1000)
                .attr("fill-opacity", 1);
    });
​
    var group = svg.selectAll(".a")
      .data(tickMarks.thousand)
      .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: 100, width: "1px", height: 30})
        .attr({"fill-opacity": 0})
            .transition().duration(3000)
        .attr({"fill-opacity": 1});
​
        //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
        var group2 = svg.selectAll(".b")
      .data(tickMarks.fivehundred)
      .enter()
        .append("g");
    group2.append("rect")
        .style({"fill": "black"})
      .attr({x: 0, y: 100, width: "1px", height: 15})
        .transition().duration(2000)
      .attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
        var group3 = svg.selectAll(".c")
      .data(tickMarks.onehundred)
      .enter()
        .append("g");
    group3.append("rect")
        .style({"fill": "black"})
      .attr({x: 0, y: 115, width: "1px", height: 15})
        .transition().duration(1000)
      .attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
        group.append("text")
        .attr("x", function(d) {return (d/10) + 3;})
      .attr("y", (90) + 22)
        .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});
​
​
  </script>
</body>
​
    