D3 Examples - genome browser

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-<!DOCTYPE html>
<head>
  <meta charset="utf-8">
  <script type="text/javascript" src="https://d3js.org/d3.v2.min.js"></script>
<script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.8/jquery.min.js"></script>
 <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>
  <meta name="viewport" content="width=device-width, initial-scale=1">      
      <link rel="stylesheet" href="https://fonts.googleapis.com/icon?family=Material+Icons">
      <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/materialize/0.97.3/css/materialize.min.css">
 
  
  
  <script type="text/javascript" src="https://code.jquery.com/jquery-2.1.1.min.js"></script>           
      <script src="https://cdnjs.cloudflare.com/ajax/libs/materialize/0.97.3/js/materialize.min.js"></script> 
  <script src="jquery-1.11.2.js"></script> 
  
  
  
  
<style>query
​
​
  
    .d3-tip {
  line-height: 1;
  font-weight: bold;
  padding: 12px;
  background: rgba(0, 0, 0, 0.8);
  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;
}
  
  <script data-require="d3@3.5.3" data-semver="3.5.3" src="//cdnjs.cloudflare.com/ajax/libs/d3/3.5.3/d3.js"></script>
   <script type="text/javascript" src="https://d3js.org/d3.v2.min.js"></script>
        <script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.8/jquery.min.js"></script>
​
 
  
  
path.link {
                fill: none;
                stroke: #666;
                stroke-width: 1.5px;
            }
            
            path.link.licensing {
                stroke: green;
            }
            
            path.link.resolved {
                stroke-dasharray: 0,2 1;
            }
            
            marker#licensing {
                fill: green;
            }
            
            marker#suit,
            marker#resolved {
                fill: black;
            }
            
      
            text {
                font: 10px sans-serif;
                pointer-events: none;
            }
            
            text.shadow {
                stroke: #fff;
                stroke-width: 3px;
                stroke-opacity: .8;
            }
            
            body,
            .container {
                background-color: white;
                margin: 0px;
            }
            
            .graphContainer {
                text-shadow: -1px -1px 0 white, 1px -1px 0 white, -1px 1px 0 white, 1px 1px 0 white;
            }   
            #sidebar{
                position: absolute;
                z-index: 2;
                background-color: #FFF;
                padding: 10px;
                margin: 5px;
                border: 1px solid #6895b4;
                min-height: 3px;
                min-width: 8px;
            }
        
            .item-group {
                margin-bottom: 5px;
            }
            
            .item-group .item-label {
                width: 90px;
                text-align: right;
                font-family: Arial,sans-serif;
                font-size: 14px;
                font-weight: bold;
                position: relative;
                min-height: 1px;
                margin-top: 5px;
                display: inline;
                padding-right: 5px;
                font-size: .90em;
            }
    
            .checkbox-interaction-group {
                margin-left: 10px;
                margin-top: 5px;
                clear: both;
            }
            
            .checkbox-container {
                display: block;
                min-height: 22px;
                vertical-align: middle;
                margin-left: 10px;
            }
            
            .checkbox-container label{
                display:inline;
                margin-bottom: 0px;
            }           
  </style>
​
</head>
<body class="container">   
    
        
​
​
         
  
       
            <div id="sidebar" style="display: ">
     <div class="item-group">
     <label class="item-label">Pham Filter</label>  
    <div id="filterContainer" class="filterContainer checkbox-interaction-group"> </div>
              </div>
          </div>
       
        
            
​
       
         
    <input type="checkbox" class="pham" id="filled-in-box" checked="checked" />
      <label for="filled-in-box">Phamily 1</label>     
            
            
</html> 
<body>   
​
  
  <script type="text/javascript" src="https://code.jquery.com/jquery-2.1.1.min.js"></script>
  
  <script type="text/javascript" src="https://ajax.googleapis.com/ajax/libs/jquery/1.8/jquery.min.js"></script>
  
      <script type="text/javascript" src="js/materialize.min.js"></script>
  
 
  <script>
​
  
 var svg = d3.select("body").append("svg").attr("height", 1000);
 d3.json("genes.json.txt", function(error, json) {
    if (error) return console.warn(error);
    svg.attr("width", function (d) {
      return d3.max(json, function(d) {
        return d.genomelength/10;
      })
    });
​
   var tip = d3.tip()
   
  .attr('class', 'd3-tip')
  .offset([-10, 0])
  .html(function(d) {
    return d.sequence;
  })  
      svg.call(tip);
   
     
  
    
​
    
    var phage = svg.selectAll(".genomes")
      .data(json)
      .enter()
      .append("g");
    phage.attr("transform", function(d, i) { return "translate(0," + (100 + (i*225)) + ")"; });
​
    phage.append("rect")
      .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: function (d) { return d/10; }, y: 0, width: "1px", height: 30})
      .attr({"fill-opacity": 0})
      .transition().duration(1500)
      .attr({"fill-opacity": 1});
​
    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});
    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");
        
   
​
function createFilter()
   {d3.select(".filledContainer").selectAll("div")
   .data(json)
   .enter()
   .append("div")
        .attr("class","checkbox-container")
   .append("label")
   .each(function(d){
     d3.select(this).append("input")
     .attr("type","checkbox")
     .attr("id", function(d,i){return "chk_" + d.pham })
     .attr("checked", true)
     .on("click", function (d,i){
        var lVisibility = this.checked ? "visible" : "hidden";
       filterGraph(d.pham, lVisibility);
     })
     d3.select(this).append("span")
     .text(function(d){return d.pham;});
   })
    $("#sidebar").show(); }
            
    
   
   
   
   
  
 var phamcheckbox = d3.selectAll("pham")
    .attr('class','pham')
        .data (json)
    .enter()
            .append('div')
            .text(function(d,i){return d.pham + '';})
​
   
              
     //document.getElementsByClassName("pham")
 //  for (var i = 0; i < json.length; i++) 
  // {gene.append ("input")}
    
  
      
      
   //loop through checkboxes
  //.html("<input id= 'phamily 1' type='checkbox' class='pham'>");
   
   // .attr ("fill", function (d) {
    //  if (clicked == true) {
   //       return "red";
   //   }
    //  else {
   //     return "gray";
   //   } 
​
     //input id="Phamily 1" type="checkbox" class="pham" ><label for="Phamily 1">Phamily 1</label>
  
     // .getElementbyClass('pham')
   
   
      gene.append("rect")
         .on('mouseover', tip.show)
       .on('mouseout', tip.hide)
      .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 "purple";
        }
        else if (d.direction == "reverse") {
          return "blue";
        }
        else {
          return "black";
        }
      })
​
      .transition().delay(1000).duration(1500)
      .attr("x", function (d) { return d.start/10; });
​
   
   
   
    
 // var fillcolor = document.getElementsByClassName("pham")
    //console.log(fillcolor);
  
     //if (pham.clicked == true) {
     //  d.genes.style.fill ="red";
    // }
    // else {
   //   d.genes.style.fill ="gray";
   //  }
 //
  
   
   
   
   
   
   
  
   
      gene.append("text")
      .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 -50;
          }
          else { return -10;} 
        }
        else if (d.direction == "reverse") {
          if (d.name % 2 === 0) { 
            return 50;
          }
          else { return 80;} 
        }
      })
      .style({"text-anchor": "middle", "fill": "white"})
      .attr("font-family", "sans-serif")
      .text(function(d) {return d.name})
      .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);
   
   
   
});
 
​
    
    
  </script>
</body>
​
    