The genome browser

Genome browser for phamerator.org

forked from scresawn's block: genome browser

forked from AdamBlaine1's block: The genome browser

<!DOCTYPE html>
<head>
  <meta charset="utf-8">

.axis path,
.axis line {
  fill: none;
  stroke: #000;
  shape-rendering: crispEdges;
}

.bar {
  fill: orange;
}

.bar:hover {
  fill: orangered ;
}

.x.axis path {
  display: none;
}

.d3-tip {
  line-height: 1;
  font-weight: bold;
  padding: 12px;
  background: rgba(0, 0, 0, 0.8);
  color: #fff;
  border-radius: 2px;
}

/* Creates a small triangle extender 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;
  }
    
  </style>

</head>

<body>
  <script src="https://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js"></script>    
  <script>
    // Feel free to change or delete any of the code you see!
    var genomelength = 7800;

}
      else if (currentValue % 100 === 0) {
        tickMarks.onehundred.push(currentValue);
      }
    });  
    
    var tip = d3.tip()
 		 .attr('class', 'd3-tip')
 		 .offset([-10, 0])
 		 .html(function(d) {
    return "<strong>Name:</strong> <span style='color:red'>" + d.name + "</span>";
  })
    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"})
    	.attr("stroke-opacity", 0)
    	.transition().duration(1000)
    	.attr("stroke-opacity", 1);
    
    svg.call(tip);

d3.json("genes.json.txt", function(error, json) {
		  if (error) return console.warn(error);
			var genes = svg.selectAll(".genes")
  	  	.data(json)
    	  .enter()
      	.append("g");

genes.append("rect")
     	  .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 (genomelength/10) + 2;
          }
      })
       	.attr("height", function (d) {return 30;})
      	.on('mouseover', tip.show)
      	.on('mouseout', tip.hide)
        .attr("width", function (d) { return (d.stop-d.start)/10; })
       	.style({"stroke":"black", "stroke-width": "2px"})
      	.attr("fill", function (d) {
        	if (d.direction == "forward") {
            return "green";
          }
        	else if (d.direction == "reverse") {
            return "red";
          }
        	else {
            return "black";
          }
      	})
   			.transition().delay(1000).duration(1500).attr("x", function (d) { return d.start/10; });
      
    genes.append("text") // gene name
    	.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 90;
        }
        else { return 60;}
      }
			else if (d.direction == "reverse") {
      	if (d.name % 2 === 0) {
        	return 180;
        }
        	else { return 150;}
      }
    })
    .style({"text-anchor": "middle", "fill": "black"})
    .attr("font-family", "sans-serif")
    .text(function(d) {return d.name})
    .attr("fill-opacity", 0)
    .transition().delay(2000).duration(1500)
		.attr("fill-opacity", 1);

genes.append("text") // pham name
    	.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 60;
        }
        else { return 30;}
      }
			else if (d.direction == "reverse") {
      	if (d.name % 2 === 0) {
        	return 210;
        }
        	else { return 180;}
      }
    })
    
    .style({"text-anchor": "middle", "fill": "black"})
    .attr("font-family", "sans-serif")
    .text(function(d) {
      return d.pham
    })
    .attr("fill-opacity", 0)
    .transition().delay(3500).duration(1500)
		.attr("fill-opacity", 1);
    });

//.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
  	group.append("text") //green letters in boxes
	    .attr("x", function(d) {return (d/10) + 3;})
  	  .attr("y", (90) + 22)
	    .attr("font-family", "sans-serif")
	    .attr("font-size", "14px")
	    .attr("fill", "green")
	    .style("text-anchor", "start")
	    .text(function(d) { return d/1000; })
    	.attr({"fill-opacity": 0})
			.transition().duration(1500)
    	.attr({"fill-opacity": 1});
		var group2 = svg.selectAll(".fivehundredticks")
      .data(tickMarks.fivehundred)
      .enter()
	    .append("g");
    group2.append("rect")
     	.style({"fill": "black"})
		  .attr({x: function(d) {return d/10;}, y: 100, width: "1px", height: 15})
      .attr({"fill-opacity": 0})
     	.transition().duration(1500)
    	.attr({"fill-opacity": 1});
      //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
		var group3 = svg.selectAll(".onehundredticks")
      .data(tickMarks.onehundred)
      .enter()
	    .append("g");
    group3.append("rect")
     	.style({"fill": "black"})
      .attr({x: function (d) { return d/10; }, y: 115, width: "1px", height: 15})
    	.attr("fill-opacity", 0)
    	.transition().duration(1500)
    	.attr("fill-opacity", 1);
      //.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://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js