genome browser

Genome browser for phamerator.org

forked from scresawn'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>
	<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");

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") {
            return 70;
          }
        	else if (d.direction == "reverse") {
            return 130;
          }
      })
       	.attr("height", function (d) {return 30;});

genes.append("text")
      	.attr("x", function(d) { return ((d.start + d.stop)/2)/10;})
      	.attr("y", function (d) {
        if (d.direction == "forward") {
            return 90;
          }
        	else if (d.direction == "reverse") {
            return 150;
          }
      })
      	.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);
    });

//.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)"; });

</script>
</body>

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