Genome Viewer(Original)

Genome browser for phamerator.org

forked from scresawn's block: genome browser

forked from nguyenbq's block: Genome Viewer

forked from cheneymb's block: Genome Viewer

<!DOCTYPE html>

body { 
        margin:45;
        position:fixed;
        top:0;
        right:0;
        bottom:0;
        left:0; 
    }
    /* Tip box */
    .d3-tip {
      line-height: 1;
  		font-weight: bold;
      padding: 11px;
      background: rgba(0, 0, 0, 0.8);
      color: #ff0505;
      border-radius: 2px;
    }
		/* This is for the little triangle for the tooltip */
    .d3-tip:after {
      box-sizing: border-box;
      display: inline;
      font-size: 10px;
      width: 100%;
      line-height: 1;
      color: rgba(0, 0, 0, 0.8);
      content: "\25BC";
      position: absolute;
      text-align: center;
    }
    /* Style northward tooltips differently */
    .d3-tip.n:after {
      margin: -1px 0 0 0;
      top: 100%;
      left: 0;
    }
    /* Lower tip box */
    .d3-hidden {
      line-height: 1;
  		font-weight: bold;
      padding: 11px;
      background: rgba(1, 34, 34, 0.8);
      color: #1fe429;
      border-radius: 2px;
    }
		/* This is for the little triangle for the tooltip */
    .d3-hidden:after {
      box-sizing: border-box;
      display: inline;
      font-size: 20px;
      width: 100%;
      line-height: 1;
      color: rgba(1, 0, 0, 0.8);
      content: "\25BC";
      position: absolute;
      text-align: center;
    }
    /* Style northward tooltips differently */
    .d3-hidden.n:after {
      margin: -60px 0 0 0;
      top: 100%;
      left: 0;
    }
  </style>
</head>

// Genome size
    var genomelength = 100000;
    
    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");
      
      //Hover box when you mouseover genes
      var tip = d3.tip()
      .attr('class', 'd3-tip')
      .offset(function (d) {
        if (d.direction == "forward") {
            return [-55, -48];
        }
        else if (d.direction == "reverse") {
            return [-55, -48];
        }
      })
      .html(function(d) {
        return "<b>Product:</b> <span style='color:white'>" 
          + d.product + "</span>";
      })
      //Clickable tip box attr
      var hidden = d3.tip()
        .attr('class', 'd3-hidden')
        .offset(function (d) {
        if (d.direction == "forward") {
            return [70, -48];
            }
        else if (d.direction == "reverse") {
            return [70, -48];
        }
      })
      .html(function(d) {
        return "<a style=color:white target=_blank href=https://blast.ncbi.nlm.nih.gov/Blast.cgi>BLAST:</a><span style='color:white'>" 
          + " " + d.translation + "</span>";
      })
      //call the "tool-tips"
      svg.call(tip);
      svg.call(hidden);
      	
		 //add in gene boxes with transistion
		 genes.append("rect")
       	.on('mouseover', tip.show).on('mouseout', tip.hide)
      	.on('click', hidden.show).on('dblclick', hidden.hide)
  	    .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) { 
          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 === "forward") {
            return "009900";
          }
          else if	(d.direction === "reverse"){
            return "FF6600";
          }
          else  {
            return "yellow";
          }
        })
      	.style({"stroke":"black", "stroke-width":"2px"})
   			.transition().delay(2000).duration(2000)
     		.attr("x", function (d) { 
          return d.start/10; 
        })
     	  .attr("y", function (d) { 
          if (d.direction == "forward" && d.name%2==0) {
          return 34; 
          }
          else if (d.direction == "forward" && d.name%2!==0) {
          	return 67; 
          }
          else if (d.direction == "reverse" && d.name%2==0) {
            return 133;
          }
          else if (d.direction == "reverse" && d.name%2!==0) {
            return 165;
          }
          else	{
            return 60;
          }
        })
       	.attr("height", function (d) {return 30;})
      	group.on("click", function() {
        	console.log("rect");
      	})
  		//text in gene boxes
      genes.append("text") 
        .attr("x", function (d) { return ((d.start+d.stop)/10)/2})
        .style("text-anchor","middle")
        .style({"font-family":"verdana","font-size":"18px","fill":"white"})
        .attr("y", function (d) { 
          if (d.direction === "forward" && d.name%2==0) {
            return 58;
          }
          else if (d.direction === "forward" && d.name%2!==0) {
            return 91;
          }
          else if (d.direction === "reverse" && d.name%2==0) {
            return 151;
          }
          else if (d.direction === "reverse" && d.name%2!==0) {
            return 185;
          }
          else {
            return 80;
        	}
      	})
        .text(function (d) {
        	return d.name;})
          //var c = 0;
          //var g = 0;
          //for (var i=0; i<=d.sequence.length; i++) {
           // if (d.sequence[i] === "C") {c++; }
           // else if (d.sequence[i] === "G") {g++;}
          //}
         // return (((c+g)/d.sequence.length)*100);})
        //.attr("fill-opacity",0)
        //.transition().duration(3000).delay(2000)
        //.attr("fill-opacity",1);

// text above or below boxes
      genes.append("text") 
        .attr("x", function(d) { return ((d.start + d.stop)/2)/10;})
        .attr("y", function (d) {
          if (d.direction == "forward") {
            if (d.name % 2 === 0) {
              return 28;
            }
            else { return 59;}
          }
          else if (d.direction == "reverse") {
            if (d.name % 2 === 0) {
              return 181;
            }
              else { return 213;}
          }
      	})
        .style({"text-anchor":"middle","fill":"black","font-weight":"bold"})
        .attr("font-family","sans-serif")
        .text(function(d) {return d.subnum})
        .attr("fill-opacity", 0)
        .transition().delay(4500).duration(1000)
        .attr("fill-opacity", 1);
    });
		//grouping the 3 tick groups and displaying them
    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)"; });
    //numbers @1000 ticks
    group.append("text")
   		.attr({y:110})
    	.attr("x", function(d) {
        return (d/10) + 1
      })
    	.style({"font-size":"20px","fill":"red"})
    	.transition().duration(2000).delay(1000)
    	.style({"font-family":"verdana","font-size":"10px","fill":"green"})
      .text(function(d) {return d/1000})
		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)"; 
    	});
  </script>
</body>

Modified http://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.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

https://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js