genome browser 2 with numbers

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>

</head>

<body>
  <script>
    var genomelength = 9000;
    
    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; })
      	.attr("style", function (d) { return (d.dirction)})
      	.style ("fill", function (d) {
            if (d.direction === "forward") { 
              return "cyan";
            }
            else if (d.direction === "reverse") { 
              return "pink";
            }
        		else {
              return "black";
            }
        })
 
      	.attr("y", function (d) {
        if (d.direction === "forward") {
          if (d.name%2 === 0)
          	return 70;
          else {
            return 40;
          }
        }
        else {
          if (d.name%2 === 0)
          	return 130;
          else {
            return 170;
          }
        }
      })
				.attr("x", function (d) {
        	if (d.direction === "forward") {
            return (0 - ((d.stop-d.start)/10)) - 2;
          }
        	else if (d.direction === "reverse") {
            return (genomelength/10) + 2;
          }
      })
      	.style ({"stroke-width": "2px", "stroke": "black"})
   			.transition().delay(3000).duration(1000)
       	.attr("height", function (d) {
        		return 30;
        })
      	.attr("x", function (d) { 
        		return d.start/10; 
      });
      
      genes.append("text") // gene name
      	.attr("x", function (d) { 
        		return ((d.stop+d.start)/2)/10; 
        })
    	  .attr("y", function (d) { 
        if (d.direction === "forward") {
          if (d.name%2 === 0)
            return 90;
        	else {
          	return 60;
        }
        }
        else {
          if (d.name%2 === 0)
            return 150;
          else {
            return 190;
          }
        }
      })
        .transition().delay(4000).duration(1000)
      	.text ( function (d) { return d.name; })
     		.style({"text-anchor": "middle", "font-family": "ariel", "font-weight": "bold"})
        .style ("fill", function(d) {
        if (d.direction === "forward") {
          return "black";
        }
        else {
          return "black";
        }
      });
      	
    		
    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)"; });
		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")
    	.text(function (d,i) {
            return i+1;
    })
      .attr({y: 115, width: "1px", height: 15})
    	.attr("x", function(d) {return (d/10)+2;})
    	.attr({"font-size": "10px", "fill":"grey"});
    });

</script>
</body>

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