genome browser w/ alignments

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

<!DOCTYPE html>
<head>
  <meta charset="utf-8">
  <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
	<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">
</head>

<body>    
  <script>
    
    
 var svg = d3.select("body").append("svg").attr("height", 1000);
 //new gene comparison
 			d3.json("test.json", function(error, json) {
        //console.log(json);
   			//	if (error) return console.warn(error);         
        //console.log(hsps);
      var data = function(hsps) {
        //console.log(Array.isArray(hsps));
        var paths = Array();
        
        hsps.forEach(function(value, index, myArray) {
          //console.log(value);
          var dataset = Array();
	        dataset.push({x: value.query_from/10, y: 130});
          dataset.push({x: value.query_to/10, y: 130});
          dataset.push({x: value.hit_to/10, y: 325});
          dataset.push({x: value.hit_from/10, y: 325});
          paths.push(dataset);
        });
        //console.log(dataset);
        return paths;
      }
      var hsps = json.BlastOutput2[0].report.results.bl2seq[0].hits[0].hsps;
      //console.log(hsps);
      /*var hsps = svg.selectAll(".hsps")
      	.data(json.BlastOutput2[0].report.results.bl2seq[0].hits[0].hsps);*/

pathset = data(hsps);
      var hsps = svg.selectAll(".hsps")
      	.data(pathset);
      var d3line2 = d3.svg.line()
                        .x(function(d) { return d.x; })
                        .y(function(d) { return d.y; })
									      .interpolate("linear-closed");
      hsps.enter()
          .append("svg:path")
        	.style("fill-opacity", 0)
		      .style("stroke-width", 0)
          .attr("d", function(d) { console.log(d); return d3line2(d);})
          .transition()
          .duration(3000)
      		.delay(4000)
          .style("stroke-width", 1)
          .style("stroke", "black")
          .style("fill", "violet")
        	.style("fill-opacity", 0.5);
        
 });
    d3.json("genes.json.txt", function(error, json) {
    if (error) return console.warn(error);
    
   //console.log(json);
    svg.attr("width", function (d) {
      return d3.max(json, function(d) {
        return d.genomelength/10;
      })
    });

// 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);

//.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
    group.append("text") // kbp label
      .attr("x", function(d) {return (d/10) + 3;})
      .attr("y", 12)
      .attr("font-family", "sans-serif")
      .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});
    //.attr("transform", function (d) { return "translate(" + d/10 + ",0)"; });
    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");
      gene.append("rect")
      .attr("y", function (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;}
        }
      })
      .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;
        }
      })
      .attr("height", function (d) {return 30;})
      .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 "aquamarine";
        }
        else if (d.direction == "reverse") {
          return "pink";
        }
        else {
          return "black";
        }
      })
      .on("mouseover", function(d) {
        //console.log(d);
        div.transition()
          .duration(500)
          .style("opacity", .9);
        div	.html("The direction of gene " + d.name + " is " + d.direction)// 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);
      })
      .transition().delay(1000).duration(1500)
      .attr("x", function (d) { return d.start/10; });

gene.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) { // forward and even
            return -50;
          }
          else { return -10;} // forward and odd
        }
        else if (d.direction == "reverse") {
          if (d.name % 2 === 0) { // reverse and even
            return 50;
          }
          else { return 80;} //reverse and odd
        }
      })
      .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);

gene.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 -80;
          }
          else { return -40;}
        }
        else if (d.direction == "reverse") {
          if (d.name % 2 === 0) {
            return 80;
          }
          else { return 110;}
        }
      })

.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);
  
   
  });
  </script>
  <script>
    
  </script>
</body>

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