genome browser

Genome browser for phamerator.org

forked from scresawn's block: genome browser

forked from BDAguila's block: genome browser

forked from ericamartel's block: genome browser

forked from anonymous's block: genome browser

-<!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>
	<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">
<style>

.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;
}
  </style>

</head>

<body>    
  <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);

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");
      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; });

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 + " ("+ d.pham_abundance +")"})
   
      .attr("fill-opacity", 0)
      .transition().delay(3500).duration(1500)
      .attr("fill-opacity", 1);

});
    
    
  </script>
</body>

Modified http://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js to a secure url

https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js

https://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js