Old school D3 from simpler times

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mcgovemc

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genome browser

Genome browser for phamerator.org

forked from scresawn's block: genome browser

forked from Wanagram's block: genome browser

<!DOCTYPE html>
<had>
  <meta charset="utf-8">
  <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
	<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.12.0/jquery.min.js"></script>

</head>

<body>
  <script>
//jQuery		
var maxLength= 0;

window.addEventListener('load', function () {
    $.getJSON("genes.json.txt", function(data){
       for(i=0; i < data.length; i++){
      	if(data[i].stop > maxLength){
      		maxLength = data[i].stop;
        }
         
      }
    genomelength = maxLength + maxLength/50;

//Tick mark object
    var tickMarks = {thousand: [], fivehundred: [], onehundred: []};
    
//Array with numbers from 1->genomelength
		var genome_positions = [];
		for (var i = 1; i <= genomelength; i++) {
    	genome_positions.push(i);
		}
    
//Creates 1000, 500 and 100 bp ticks
    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("g")
   		.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 jsonData = svg.selectAll(".genes")
  	 // 	.data(json)
     //	  .enter();
      
			var rects = svg.selectAll(".genes")
  	  	.data(json)
    	  .enter()
      	.append("rect");

var rectAttributes = rects
  	    .attr("x", function (d) { return d.start/10; })
      	.attr("width", function (d) { return (d.stop-d.start)/10; })
      	.style({"stroke":"black", "stroke-width": "2px", "fill-opacity":0.5})
     	  .attr("y", function (d) { 
          if(d.direction == "reverse" && d.name%2==0){
            return 130
          }
          else if(d.direction == "reverse" && d.name%2!=0){
            return 160
          }
          else if(d.direction == "forward" && d.name%2!=0){
            return 70
          }
          else{
            return 40
          }; 
        })
       	.attr("height", function (d) {return 30;})
      	.style({"fill": function(d) {if(d.direction == "forward"){
          return "green"}
        else if(d.direction == "reverse"){
          return "red"
        }
        	}})
      
      var text = svg.selectAll(".genes")
  	  	.data(json)
    	  .enter()
      	.append("text");
       
      var texts = text
      	.text(function(d){return d.name})
      	.attr("y", function(d){
          if(d.direction == "reverse" && d.name%2==0){
            return 150
          }
          else if(d.direction == "reverse" && d.name%2!=0){
            return 180
          }
           else if(d.direction == "forward" && d.name%2!=0){
            return 90
          }
          else{
            return 60
          }
        })
      	.attr("x", function(d) {return ((d.start+(d.stop-d.start)/2)/10)})
      	.attr("font-size", "20px")
			   	
      });
    
    
    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})
	    .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",110)
		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})
      .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})
      .attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });

}
    )

}, false);

</script>
</body>

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

https://ajax.googleapis.com/ajax/libs/jquery/1.12.0/jquery.min.js