genome browser with numbering, color, reverse, and stagger

forked from grybnicky's block: genome browser with numbering, color, reverse, and stagger

forked from anonymous's block: genome browser with numbering, color, reverse, and stagger

forked from grybnicky's block: genome browser with numbering, color, reverse, and stagger

<!DOCTYPE html>
<head>
  <meta charset="utf-8">
  <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>

</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 rects = svg.selectAll(".genes")
  	  	.data(json)
    	  .enter()
      	.append("g");
			rects.append("rect")
  	    .attr("x", function (d) { return d.start/10; })
    	  .attr("y", function (d) { 
          if(d.direction === "forward" && d.name % 2 === 1) return 100  
          else if (d.direction === "forward" && d.name % 2 === 0) return 70
          else if (d.direction === "reverse" && d.name % 2 === 1) return 130
          else if (d.direction === "reverse" && d.name % 2 === 0) return 160;})
      	.attr("height", function(d) { return 0;})
      	.attr("width", function (d) { return (d.stop-d.start)/10; })
       	.style({"fill": function(d) { 
          if (d.direction === "reverse") 
            return "red"
          else if (d.direction === "forward") 
            return "green";},"stroke":"black", "stroke-width": "2px"})
   			.transition().delay(3000).duration(1000)
       	.attr("y", function (d) { 
          if(d.direction === "forward" && d.name % 2 === 1) return 70  
          else if (d.direction === "forward" && d.name % 2 === 0) return 40
          else if (d.direction === "reverse" && d.name % 2 === 1) return 130
          else if (d.direction === "reverse" && d.name % 2 === 0) return 160;})
        .attr("height", function (d) {return 30;});
      
      rects.append("text")
        .attr("text-anchor", "middle")
        .attr("x", function(d){return (d.start+((d.stop-d.start)/2))/10;})
        .attr("y", function (d) { 
          if(d.direction === "forward" && d.name % 2 === 1) return 90  
          else if (d.direction === "forward" && d.name % 2 === 0) return 60
          else if (d.direction === "reverse" && d.name % 2 === 1) return 150
          else if (d.direction === "reverse" && d.name % 2 === 0) return 180;})
        .text( function(d){return d.name})
        .attr("font-family", "arial")
        .attr("font-size", "20px")
        .attr("fill", function(d) { 
          if (d.direction === "reverse") 
            return "red"
          else if (d.direction === "forward") 
            return "green";})
        .transition().delay(3000).duration(1000)
     	  .attr("fill", "white")
      });
    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})
			.transition().duration(3000)
	    .attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
		group.append("text")
      .attr("y", 110)
      .attr("x", function(d){return (d/10)+3;})
      .text(function(d){return (d/1000)})
      .attr("font-family", "arial")
      .attr("font-size", "10px")
      .attr("fill", "lime");
    
    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