Genome Ruler

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>
	<script type="text/javascript" src="https://d3js.org/d3.v3.min.js"></script>

</head>

<body>
  <style>
  div.tooltip {
  position: absolute;	
  text-align: center;	
  width: 60px;	
  height: 28px;		
  padding: 2px;	
  font: 12px sans-serif;	
  background: lightsteelblue;	
  border: 0px;					
  border-radius: 8px;
 /*  pointer-events: none;	This line needs to be removed */
	
}
  </style>
  
  <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("g")
      .append("rect")
      .attr({x: 0, y: 100, width: genomelength/10, height: 30})
    	.style({"stroke-width": "2px", "fill": "white", "stroke": "black"});
    
 // Define 'div' for tooltips
var div = d3.select("body")
	.append("div")  // declare the tooltip div 
	.attr("class", "tooltip")              // apply the 'tooltip' class
	.style("opacity", 0);                  // set the opacity to nil

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) { 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":"green","stroke":"black", "stroke-width": "2px"})
   			//.transition().delay(3000).duration(1000)
   .on("mouseover", function(d) {		
            div.transition()		
                .duration(200)		
                .style("opacity", .9);		
            div	.html(d.name)
                .style("left", (d3.event.pageX) + "px")		
                .style("top", (d3.event.pageY - 28) + "px");	
            })					
        
      
      
     
     	  .attr("y", function (d) {
          if(d.direction=="forward" && d.name%2==0){
            return 70;
          }
          else if (d.direction=="forward"&& d.name%2!=0){
            return 30
          }
          else if(d.direction=="reverse" && d.name%2==0){
            return 130}
          else if(d.direction=="reverse" && d.name%2!==0){
            return 160
          }
            
          })

.attr("height", function (d) {return 30;})
      	.style({"fill":function(d){if(d.direction=="forward"){return "green"}else if (d.direction=="reverse"){return "red"}} 
      });  
    });

d3.json("genes.json.txt", function(error, json) {
		  if (error) return console.warn(error);
			var text = svg.selectAll(".genes")
  	  	.data(json)
    	  .enter()
      	.append("text");
    	var texts = text
      	.text(function(d)  
              {
          			var percent = 0;
          			var GC = 0;
            		for (var i=0;i<d.sequence.length;i++){
      						// calculate % of G and C
                  if (d.sequence[i] === "G" || d.sequence[i] === "C") {
                    GC++;
                    // this symbol: || means "or"
                  }
    						}  
          		percent = (GC/d.sequence.length) * 100;
          		return percent;
              })
      
      		.attr("y", function(d){
          if(d.direction=="forward" && d.name%2==0){
            return 90;
          }
          else if (d.direction=="forward"&& d.name%2!=0){
            return 50
          }
          else if(d.direction=="reverse" && d.name%2==0){
            return 150}
          else if(d.direction=="reverse" && d.name%2!==0){
            return 180
          }})
      .attr("x",function(d){return ((d.start+(d.stop - d.start)/2)/10)})
      
      })

</script>
</body>

Modified http://d3js.org/d3.v3.min.js to a secure url

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

https://d3js.org/d3.v3.min.js