genome browser(testing3)

Genome browser for phamerator.org

forked from scresawn's block: genome browser(testing1)

forked from Darius9's block: genome browser(testing1)

<!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 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 rects = svg.selectAll(".genes")
    	.data(json)
      .enter()
    	.append("rect");
    
    
    
    var tickMarks = {thousand: [], fivehundred: [], onehundred: []};
    
    var genome_positions = [];
    	for  (var i = 1; i <= d.genomelength; i++) {genome_positions.push(i);}
    
    genome_positions.forEach(function(currentValue, index, myArray){
      if (currentValue % 1000 === 0) {tickMarks.thousand.push(currenValue);}
      else if (currentValue % 500 === 0) {tickMarks.fivehundred.push(currentValue);}
			else if (currentValue % 100 === 0) {tickMarks.onehundred.push(currentValue);}
    })
    var text= svg.selectAll (".text")
    	.data(json)
    	.enter()
    	.append("text");
      
    var textLabels= text
    	.attr("x", function (d) { return ((d.stop+d.start)/10)/2; })
			.attr("y", function (d) { return 90; })
			.attr("y", function (d) {
        if (d.direction==="forward"&& d.name%2!=0) { return 92;} 
				else if (d.direction==="forward" && d.name%2===0){return 62}
				else if (d.direction==="reverse"&& d.name%2 !=0){return 182;}
				else if (d.direction==="reverse"&&d.name%2 ===0){return 152}})
			.text(function (d){return d.name})
			.attr("font-family", "arial")
			.attr("font-size", "20px")
			.attr("text-anchor","middle")
			.attr("fill", "purple");
      
    var rectAttributes = rects
  	    .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({"fill": function (d) {
					if (d.direction ==="reverse") {return "silver"} 
					else if (d.direction === "forward"){ return"gold"}},
					"stroke":"black", "stroke-width": "2px"})
				.attr("y", function (d) {
					if (d.direction == "forward") {
					if (d.name % 2 === 0) {
					return 70;}
					else { return 40;}}
					else if (d.direction == "reverse") {
					if (d.name % 2 === 0) {
					return 160;}
					else { return 130; }}})
				.attr("x", function (d) {
					if (d.direction === "forward") {
					return (0 - ((d.stop-d.start)/10)) - 2;}
					else if (d.direction === "reverse") {
					return (d.genomelength/10) + 2;}})
				.transition().delay(3000).duration(1000)
				.attr("x", function (d) { return d.start/10; })
				.attr("y", function (d) {
					if (d.direction==="forward" && d.name%2 !=0) { return 70;}
					else if (d.direction==="forward" && d.name%2===0){return 40}
					else if (d.direction==="reverse"&&d.name%2 !=0){return 155;}
					else if (d.direction==="reverse"&&d.name%2 ===0){return 130}})
				.attr("height", function (d) {return 30;})
    
    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: 3, y: 113, width: "1px", height: 30})
    	.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; })
      .attr("font-family", "sans-serif")
      .attr("font-size", "15px")
      .attr("text-anchor","start")
      .attr("fill", "purple"); 
    
    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)"; });
    })})
    </script>
</body>

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