genome browser

Genome browser for phamerator.org

forked from scresawn's block: genome browser

forked from dunlapea's block: genome browser

forked from anonymous's block: genome browser

forked from dunlapea's block: genome browser

forked from anonymous's block: genome browser

forked from dunlapea's block: genome browser

forked from anonymous's block: genome browser

forked from dunlapea's block: genome browser

forked from anonymous's block: genome browser

forked from dunlapea's block: genome browser

<!DOCTYPE html>
<head>
  <meta charset="utf-8">
    
  <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.2.0/jquery.min.js"></script>
	<script src="https://cdnjs.cloudflare.com/ajax/libs/jqplot/1.0.8/jquery.jqplot.min.js"></script>
<script type="text/javascript">
function genome(sequence){
var i=1;
var geneBlockArray=[];
var twoGene=sequence[0];
this.getGeneBlocks= function(){
do{
	var gene = sequence.charAt(i);
	twoGene+=gene;
	if(twoGene.indexOf('C')>-1 || twoGene.indexOf('G')>-1){
		if(twoGene.indexOf('C')>-1 && twoGene.indexOf('G')>-1){
			geneBlockArray.push(100);
		}
		else if(twoGene=='CC' || twoGene=='GG'){
			geneBlockArray.push(100);
		}
		else{
			geneBlockArray.push(50);
		}
	}
	else{
		geneBlockArray.push(0);
	}
	twoGene=gene;
	i++;
}while(i<sequence.length);
	return geneBlockArray;
}
}
  
  </script>
	<link rel="stylesheet" type="text/css" href="https://cdnjs.cloudflare.com/ajax/libs/jqPlot/1.0.8/jquery.jqplot.min.css" />
  <script src="https://d3js.org/d3.v3.min.js">
  <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js"></script>
  <script src="https://d3js.org/d3-scale.v0.6.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>
    <section id='chartArea'>
     	<div id='chart1' class='chart'>
		</div>
		<div id='chart2' class='chart'>
		</div>
		<div id='chart3' class='chart'>
		</div>
		</section>
    <script type="text/javascript">
		$(document).ready(function(){
			var url='genes.json.txt';
    
			d3.json(url,function(error, json){console.log(json)
				var i=1;
				$.each(json,function(x,y){
					var g=[];
					$.each(y.genes, function(k, gene){
						x= new genome(gene.sequence);
						f=x.getGeneBlocks();
						g = g.concat(f);	
					})
					plotChart('chart'+i, g);
					i++;
				});	
			});
		});
		</script>
		<script type="text/javascript">
		function plotChart(chart,x){
			var plot1 = $.jqplot (chart, [x], {
				grid:{
					background:'#FFFFFF',	
				},
				seriesDefaults: {
					rendererOptions: {
						smooth: true
					}
				},
				axes: {
					xaxis: {
						min:0,
						max:180,
						tickOptions: {
							showGridline: false,
							showMark: false,
							fontFamily: 'DosisBold',
							textColor: '#ffffff',
							fontSize: 'larger',
              shadow: false
						},
					},
					yaxis: {
						tickOptions: {
							showGridline: false,
							showMark: true,
							showLabel: true,
							shadow: false,
						},
					},
				},
			});
		};
  </script>
    <script>
  	var svg = d3.select("#chartArea").attr("height", 1000);
 		d3.json("genes.json.txt", function(error, json) {
    if (error) return console.warn(error);
    //console.log(json);

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

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", "green")
      .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) { console.log(i, d); 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) {
     var C=0;
     var G=0;
     var min = 100;
     var max = 0;
     for(var i=0; i<=d.sequence.length;i++){
       if(d.sequence[i]==="C")
         {C++;}
       else if (d.sequence[i]==="G")
         {G++;}
     }
        var total=C+G;
        //var toPercent = d3.format("%");
        var grandtotal = (total / d.sequence.length)*255;
        if (grandtotal < min) {
          min = grandtotal;
        }
        if (grandtotal > max) {
          max = grandtotal;
        } 
        //grandtotalhex = (grandtotal*255).toString(16);
     		console.log(d3.rgb(0, grandtotal, 0));
       var Scale = d3.scale.linear()
                     .domain([80,180])
                     .range([0, 255]);
        console.log(Scale(grandtotal));
        return d3.rgb(0, Scale(grandtotal), 0);
        //if (grandtotal <=0.5 ) {
        //  return "rgb(0, " + (grandtotal) + ", 0)";
        //} 
        //else if (grandtotal >0.5) {
        //  return "rgb(0, " + (grandtotal) + ", 0)";
        //}
        //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": "white", "font-weight": "bold"})
      .attr("font-family", "sans-serif")
       
      .text(function(d){
     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++;}
     }
        var total=C+G;
        var toPercent = d3.format("%");
        var grandtotal = toPercent(total / d.sequence.length)
        { return (grandtotal) }
      }
         )
   
     
              
      .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", "font-weight": "bold"})
      .attr("font-family", "sans-serif")
      .text(function(d) {return d.pham})
      .attr("fill-opacity", 0)
      .transition().delay(3500).duration(1500)
      .attr("fill-opacity", 1);
      updatex();

});
  </script>
    <script>
function updatex(){    x=$('svg')[0];
y=$('svg')[1];
z=$('svg')[2];              
$('#chart1').append(x);
$('#chart2').append(y);       $('#chart3').append(z);
 $('#chart1 svg').css({position:'absolute',top:'280px'});
$('#chart1').css({width: '1000'});               
$('#chart2').css({width: '770', top:'220'});
$('#chart2 svg').css({position:'absolute',top:'100px'});
 $('#chart2').css('top',220);                  
 $('#chart3 svg').css({position:'absolute',top:'-130px',height:1500}); 
$('#chart3').css({width: '650', 'top':550});                   
}
  </script>
</body>

Updated missing url https://cdnjs.cloudflare.com/ajax/libs/jqPlot/1.0.8/jquery.jqplot.min.js to https://cdnjs.cloudflare.com/ajax/libs/jqplot/1.0.8/jquery.jqplot.min.js

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

https://ajax.googleapis.com/ajax/libs/jquery/2.2.0/jquery.min.js

https://cdnjs.cloudflare.com/ajax/libs/jqPlot/1.0.8/jquery.jqplot.min.js

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

https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.5/d3.min.js

https://d3js.org/d3-scale.v0.6.min.js