Genome Thing

Genome browser for phamerator.org

forked from scresawn's block: genome browser

forked from zaccagbj's block: Genome Thing

forked from anonymous's block: Genome Thing

<!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("rect");
			
      var rectAttributes = rects
  	    .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;}
                })
    	  .attr("y", function (d) {if (d.direction == "forward" && d.name%2!=0)
                {return 30}
                 else if (d.direction == "forward" && d.name%2==0)
                   {return 70}
                 else if (d.direction =="reverse" && d.name%2!=0)
                 {return 130} 
                 else if (d.direction =="reverse" && d.name%2==0)
                   {return 170}
                 else {return 0}})
      	.attr("height", function(d) { return 30;})
      	.attr("width", function (d) { return (d.stop-d.start)/10; })
       	.style({"fill":function(d)
                {if (d.direction == "forward")
                {return "blue"} 
                 else if (d.direction =="reverse")
                 {return"darkOrange"} 
                 else {return "black"}},"stroke":"black", "stroke-width": "2px"})
   			.transition().delay(3000).duration(1000)
     		.attr("x", function (d) { return d.start/10; });
      
     		
      var name = svg.selectAll(".name")
      	.data(json)
      	.enter()
      	.append("text");
      
      var nameAttributes = name
      	.attr("x", function (d) { return ((d.stop+d.start)/2)/10})
      	.attr("y", function (d) {if (d.direction == "forward" && d.name%2!=0)
                {return 50}
                 else if (d.direction == "forward" && d.name%2==0)
                   {return 90}
                 else if (d.direction =="reverse" && d.name%2!=0)
                 {return 150} 
                 else if (d.direction =="reverse" && d.name%2==0)
                   {return 190}
                 else {return 0}})
      	.text(function (d) {return d.name})
      	.attr("text-anchor", "middle")
        .attr("font-family", "sans-serif")
        .attr("font-size", "20px")
        .attr("fill", "white")
      	.attr("stroke", "white")
      	.attr("stroke-width",".5px");

})
    
    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")
    	.text(function (d) {return d/1000})
    	.attr("x", function(d){return d/10 })
      .attr({y: 112, width: "1px", height: 30})
			.attr("text-anchor", "end")
    	.attr("font-size", "13px")

</script>
</body>

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