genome browser 4 with numbers and tooltip

Genome browser for phamerator.org

forked from scresawn's block: genome browser

forked from smith13mr's block: genome browser 2 with numbers

forked from smith13mr's block: genome browser 4 with numbers

<!DOCTYPE html>
<head>
  <meta charset="utf-8">
  <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
  <script src="https://d3js.org/d3.v3.min.js"></script>
<body>
  <style>
    
 /* set the CSS */
div.tooltip {	
    position: absolute;			
    text-align: center;			
    width: 60px;					
    height: 28px;					
    padding: 2px;				
    font: 12px ariel;		
    background: aquamarine;	
    border: 0px;		
    border-radius: 8px;			
    pointer-events: none;			
}
  </style>
  
  <script>
    var svg = d3.select("body").append("svg");
    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;
        })
      })
      .attr("height", 2000);
      
      // Define the div for the tooltip
var div = d3.select("body").append("div")	
    .attr("class", "tooltip")				
    .style("opacity", 0);
      
			var genomes = svg.selectAll(".genomes")
  	  	.data(json)
    	  .enter()
      	.append ("g");
    genomes.attr("transform", function(d, i){ return "translate(0," + ( (i*225)) + ")"});
      
    genomes.append("rect") //background for ruler
      .attr({x: 0, y: 100, width: function (d) {return d.genomelength/10}, height: 30})
    	.style({"stroke-width": "2px", "fill": "white", "stroke": "black"});
      
      var genes = genomes.selectAll(".genes")
  	  	.data(function(d) { return d.genes; })
    	  .enter()
      	.append ("g");
      
      genes.append("rect") // gene boxes
  	    .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; })
      	.attr("style", function (d) { return (d.dirction)})
      .on("mouseover", function(d) {		
            div.transition()		
                .duration(200)		
                .style("opacity", .9);		
            div	.html(d.direction)
                .style("left", (d3.event.pageX) + "px")		
                .style("top", (d3.event.pageY - 28) + "px");	
            })					
        .on("mouseout", function(d) {		
            div.transition()		
                .duration(500)		
                .style("opacity", 0);	
        })
      	.style ("fill", function (d) {
            if (d.direction === "forward") { 
              return "turquoise";
            }
            else if (d.direction === "reverse") { 
              return "lightpink";
            }
        		else {
              return "black";
            }
        })

.attr("y", function (d) {
        if (d.direction === "forward") {
          if (d.name%2 === 0)
          	return 60;
          else {
            return 40;
          }
        }
        else {
          if (d.name%2 === 0)
          	return 140;
          else {
            return 170;
          }
        }
      })
				.attr("x", function (d) {
        	if (d.direction === "forward") {
            return (0 - ((d.stop-d.start)/10)) - 2;
          }
        	else if (d.direction === "reverse") {
            w = d3.select("svg").style("width");
            return w;
          }
      })
      .style ("stroke", function (d) {
            if (d.direction === "forward") { 
              return "lightseagreen";
            }
            else if (d.direction === "reverse") { 
              return "hotpink";
            }
        		else {
              return "black";
            }
        })
      	.style ({"stroke-width": "2px"})
   			.transition().delay(3000).duration(1000)
       	.attr("height", function (d) {
        		return 30;
        })
      	.attr("x", function (d) { 
        		return d.start/10; 
      });

genes.append("text") // gene name
      	.attr("x", function (d) { 
        		return ((d.stop+d.start)/2)/10; 
        })
    	  .attr("y", function (d) { 
        if (d.direction === "forward") {
          if (d.name%2 === 0)
            return 80;
        	else {
          	return 60;
        }
        }
        else {
          if (d.name%2 === 0)
            return 160;
          else {
            return 190;
          }
        }
      })
        .transition().delay(4000).duration(1000)
      	.text ( function (d) { return d.name; })
     		.style({"text-anchor": "middle", "font-family": "ariel", "font-weight": "bold"})
        .style ("fill", function(d) {
        if (d.direction === "forward") {
          return "black";
        }
        else {
          return "black";
        }
      });
      
      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 50;
        }
        else { 
          return 30;
        }
      }
			else if (d.direction == "reverse") {
      	if (d.name % 2 === 0) {
        	return 190;
        }
        	else { 
            return 220;}
      }
    })
    .style({"text-anchor": "middle", "fill": "black", "font-family": "ariel", "font-weight": "bold"})
    .text(function(d) {
      return d.pham
    })
    .attr("fill-opacity", 0)
    .transition().delay(3500).duration(1500)
		.attr("fill-opacity", 1);
    
    		
    var group = genomes.selectAll(".a") // tickmarks
      .data(function (d) {
        ticks = [];
        genome_position = d3.range(d.genomelength);
        genome_position.forEach(function (currentValue, index, myArray) {
          if(currentValue % 1000 === 0) {
            ticks.push(currentValue);
          }
        });
        return ticks;
      })
      .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)"; });
		var group2 = genomes.selectAll(".b")
      .data(function (d) {
        ticks = [];
        genome_position = d3.range(d.genomelength);
        genome_position.forEach(function (currentValue, index, myArray) {
          if(currentValue % 500 === 0) {
            ticks.push(currentValue);
          }
        });
        return ticks;
      })
      .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 = genomes.selectAll(".c")
      .data(function (d) {
        ticks = [];
        genome_position = d3.range(d.genomelength);
        genome_position.forEach(function (currentValue, index, myArray) {
          if(currentValue % 100 === 0 & currentValue % 1000 !== 0 & currentValue % 500 !== 0) {
            ticks.push(currentValue);
          }
        });
        return ticks;
      })
      .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)"; })
    group.append("text")
    	.text(function (d,i) {
            return i;
    })
      .attr({y: 115, width: "1px", height: 15})
    	.attr("x", function(d) {return (d/10)+2;})
    	.attr({"font-size": "10px", "fill":"grey"});
    });
    
  </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