Conserved Domains

Genome browser for phamerator.org

forked from scresawn's block: genome browser

forked from smith13mr's block: genome browser for final group project

forked from scresawn's block: genome browser for final group project

forked from smith13mr's block: Two tooltips and fade out

forked from scresawn's block: Two tooltips and fade out

forked from scresawn's block: Conserved Domains

<!DOCTYPE html>
<head>
  <meta charset="utf-8">
	<link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto+Slab:400,100,300,700">
	<link rel="stylesheet" type="text/css" href="https://fonts.googleapis.com/css?family=Roboto:400,100,100italic,300,300italic,400italic,500,500italic,700,700italic,900,900italic">
  <link href='https://fonts.googleapis.com/css?family=Raleway' rel='stylesheet' type='text/css'>
    <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/materialize/0.97.6/css/materialize.min.css">
</head>

</script>

hsps
						.on("mousemove", function(){return tooltip.style("top", (event.pageY-10)+"px").style("left",(event.pageX+10)+"px");})
						.on("mouseout", function(){
         			d3.select(this).style("fill-opacity", 0.5);
		          d3.select(this).style("fill", "violet");
     			    return tooltip.style("visibility", "hidden");
       })

// Define the div for the tooltip
    var div = d3.select("body").append("div")
      .attr("class", "tooltip")
      .style("opacity", 0);

var phage = svg.selectAll(".genomes")
      .data(json)
      .enter()
      .append("g");

phage.attr("transform", function(d, i) { return "translate(0," + (100 + (i*225)) + ")"; });

phage.append("rect") // background for ruler
      .attr({x: 0, y: 0, width: function(d) { return d.genomelength/10; }, height: 30})
      .style({"stroke-width": "2px", "fill": "white", "stroke": "black"})
      .attr("stroke-opacity", 0)
      .transition().duration(1000)
      .attr("stroke-opacity", 1)
			;
      
    var group = phage.selectAll(".thousandticks")
      .data(function (d) {
          ticks = [];
          genome_positions = d3.range(d.genomelength);
          genome_positions.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: function (d) { return d/10; }, y: 0, width: "1px", height: 30})
      .attr({"fill-opacity": 0})
      .transition().duration(1500)
      .attr({"fill-opacity": 1});

group.append("text") // kbp label
      .attr("x", function(d) {return (d/10) + 3;})
      .attr("y", 12)
      .attr("font-family", "Roboto")
      .attr("font-size", "14px")
      .attr("fill", "black")
      .style("text-anchor", "start")
      .text(function(d) { return d/1000; })
      .attr({"fill-opacity": 0})
      .transition().duration(1500)
      .attr({"fill-opacity": 1});
    var group2 = phage.selectAll(".fivehundredticks")
      .data(function (d) {
        ticks = [];
        genome_positions = d3.range(d.genomelength);
        genome_positions.forEach(function (currentValue, index, myArray) {
          if (currentValue % 500 === 0 & currentValue % 1000 !== 0) {
            ticks.push(currentValue);
          }
        })
        return ticks;
      })
      .enter()
      .append("g");
    group2.append("rect")
      .style({"fill": "black"})
      .attr({x: function(d) {return d/10;}, y: 0, width: "1px", height: 15})
      .attr({"fill-opacity": 0})
      .transition().duration(1500)
      .attr({"fill-opacity": 1});
      
    var group3 = phage.selectAll(".onehundredticks")
      .data(function (d) {
        ticks = [];
        genome_positions = d3.range(d.genomelength);
        genome_positions.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: function (d) { return d/10; }, y: 15, width: "1px", height: 15})
      .attr("fill-opacity", 0)
      .transition().duration(1500)
      .attr("fill-opacity", 1);

gene = phage.selectAll(".genes")
      .data(function(d, i) { return d.genes;})
      .enter()
      .append("g").on("mouseover", function(d) {
	        nodedata = this.parentNode.__data__;
  	      div.transition()
    	      .duration(500)
      	    .style("opacity", .9);
        	div	.html(nodedata.phagename + " gp" + d.name)
        
        // the text of the tooltip ...
          .style("left", (d3.event.pageX) + "px")
          .style("top", (d3.event.pageY - 28) + "px");
      })
      .on("mouseout", function(d) {
        div.transition()
          .duration(500)
          .style("opacity", 0);
      });
    gene_group_x = function(d) {
    	return (d.start)/10;
    };
    gene_group_y = function(d) {
      console.log(d);
      if (d.direction == "forward") {
          if (d.name % 2 === 0) {
            return  -70;
          }
          else { return -30;}
        }
        else if (d.direction == "reverse") {
          if (d.name % 2 === 0) {
            return 30;
          }
          else { return 60;}
        }
    };
    
    gene
      .attr("transform", function (d) { return "translate(" + gene_group_x(d) + "," + gene_group_y(d) + ")"});
      gene.append("rect")
      .attr("height", function (d) {return 30;})
      .style({"stroke":"black", "stroke-width": "2px"})
      .attr("fill", function (d) {
        if (d.direction == "forward") {
          return "aquamarine";
        }
        else if (d.direction == "reverse") {
          return "lightskyblue";
        }
        else {
          return "black";
        }
      })
      .attr("width", 0)
      .transition()
      .duration(1600)
      .attr("width", function (d) { return (d.stop-d.start)/10; })
      
        ;

domain = gene.selectAll(".domains")
      .data(function(d, i) { return d.domains;})
      .enter()
      .append("g")
      .on('click', function(d,i){
    		d3.select('#domain_header').text(d.description)
        d3.select('#domain_body').text(d.description + " description could go here")

$('#modal1').openModal();
			})
;
  domain.append("rect")
  		.attr("fill-opacity", 0)
      .attr("height", function (d) {return 28;})
      .attr("width", function (d) { return ((d.stop*3)-(d.start*3))/10; })
  		.attr("x", function(d) {return (d.start*3)/10; })
      .attr("y", function (d) {
    		g = this.parentNode.parentNode.__data__;
        if (g.direction == "forward") {
          if (g.name % 2 === 0) {
            return -78;
          }
          else { return -38;}
        }
        else if (g.direction == "reverse") {
          if (g.name % 2 === 0) {
            return 1;
          }
          else { return 1;}
        }
      })
  		.attr("fill", "orange")
  		.transition()
  		.duration(750)
  		.delay(3000)
  		.attr("fill-opacity", 0.9);

gene.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) { // forward and even
            return 20;
          }
          else { return 20;} // forward and odd
        }
        else if (d.direction == "reverse") {
          if (d.name % 2 === 0) { // reverse and even
            return 20;
          }
          else { return 20;} //reverse and odd
        }
      })
      .style({"text-anchor": "middle", "fill": "black"})
      .attr("font-family", "ariel")
      .text(function(d) {return d.name})
      .attr("fill-opacity", 0)
      .transition().delay(2000).duration(1500)
      .attr("fill-opacity", 1)
      ;

gene.append("text") // pham 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) { // forward and even
            return -10;
          }
          else { return -10;} // forward and odd
        }
        else if (d.direction == "reverse") {
          if (d.name % 2 === 0) { // reverse and even
            return 50;
          }
          else { return 50;} //reverse and odd
        }
      })

.style({"text-anchor": "middle", "fill": "black"})
      .attr("font-family", "ariel")
      .text(function(d) {return d.pham})
      .attr("fill-opacity", 0)
      .transition().delay(3500).duration(1500)
      .attr("fill-opacity", 1);

});

</script>

</body>

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

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

https://code.jquery.com/jquery-2.2.3.min.js

https://cdnjs.cloudflare.com/ajax/libs/materialize/0.97.6/js/materialize.min.js