not sure what happened, but genes

Genome browser for phamerator.org

forked from scresawn's block: genome browser

forked from cheneymb's block: genome browser blocks

forked from anonymous's block: genome browser named

forked from cheneymb's block: genome browser 3/15

<!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="//d3js.org/d3.v3.min.js" language="JavaScript"></script>
  <script src="https://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js"></script>
</head>

<body>
  <script>
    var genomelength = 9500;
    
    var tickMarks = {thousand: [], fivehundred: [], onehundred: []};
    
		var genome_positions = [];
		for (var i = 1; i <= genomelength; i++) {
    	genome_positions.push(i);
		}
    
    genome_positions.forEach(function(currentValue, index, myArray){
      if (currentValue % 1000 === 0) {
        tickMarks.thousand.push(currentValue);
      }
      else if (currentValue % 500 === 0) {
        tickMarks.fivehundred.push(currentValue);

}
      else if (currentValue % 100 === 0) {
        tickMarks.onehundred.push(currentValue);
      }
    }); 
    var rulerNumber = [];
    
    //setting the ruler and scaling it
    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"});
    
    //calling the data to the ruler 
    d3.json("genes.json.txt", function(error, json) {
		  if (error) return console.warn(error);
			var rects = svg.selectAll(".genes")
  	  	.data(json)
    	  .enter()
      	.append("rect")
      	;
     
     //Defining hoverboxes when you mouseover genes
      var hover = d3.tip()
      .attr('class','d3-hover')
      .offset(function(d) {
        if (d.direction == "forward") {
          return [-29, -1];
        }
        if (d.direction == "reverse") {
          return [-40, -1];
        }
      })
      .html(function(d) {
        return "<b>Product:</b> <span style='color:white'>" 
          + d.product + "</span>";
      })
      
      //Defining boxes linked to blast when you click on genes 
      var click = d3.tip()
      .attr('class', 'd3-click')
      .offset(function(d){
        if (d.direction == "forward") {
          return [100, -1];
        }
        if (d.direction == "reverse")	{
          return [90, -1];
        }
      })
      .html(function(d) {
        return "<a style=color:white target=_blank href=https://blast.ncbi.nlm.nih.gov/Blast.cgi>BLAST:</a><span style='color:white'>" 
          + " " + d.translation + "</span>";
      })
      
      //calling the hover and click boxes
      svg.call(hover);
      svg.call(click);
      
     	//calling labels for genes
      var rectLabels = svg.selectAll(".name")
      .data(json)
      .enter()
      .append("text");
      
      //setting the style and position of the gene name 
      var geneNames = rectLabels
      .attr("x", function (d) { return ((d.start+d.stop)/10)/2})
      .style("text-anchor","middle")
      .style({
        "font-family":"Arial",
      	"font-size":"18px",
      	"fill":"#f9fffe"
      	})
    	
      //setting the genes position depending on name and direction
      .attr("y", function (d) { 
      	if (d.direction === "forward" && d.name%2==0)
        {return 58;}
        if (d.direction === "forward" && d.name%2!==0)
        {return 91;}
      	else if (d.direction === "reverse" && d.name%2==0) 
        {return 151;}
      	else if (d.direction === "reverse" && d.name%2!==0) 
        {return 185;}
        else {
        return 80;
      }})
      
      //setting the text to the gene name from the data 
      .text(function (d) {
        return d.name;});
        //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++;}
        
       // return (((c+g)/d.sequence.length)*100);})
      //.attr("fill-opacity",0)
      //.transition().duration(3000).delay(2000)
      //.attr("fill-opacity",1);

//setting style and position of rectangle depending on direction
      var rectAttributes = rects
      	.on('mouseover', hover.show).on('mouseout', hover.hide)
      	.on('click', click.show).on('dblclick', click.hide)
    	  .attr("y", function (d) { 
          if (d.direction == "forward") {return 100; }
        	else if (d.direction == "reverse")	{return 130;}
        	else {return 200}})
      	.attr("x", function (d) {
          if (d.direction == "forward") {return 0 - ((d.stop-d.start)) - 3;}
          else if (d.direction == "reverse") {return (genomelength/10) + 2;}})
      	.attr("height", function(d) { return 0;})
      	.attr("width", function(d) { return (d.stop-d.start)/10; })
      	.transition().duration(2000).delay(1000)
        .attr("x", function (d) { return d.start/10; })
      	.style("fill", function(d) {            
            if (d.direction === "forward") {return "#659EC7"}  
            else	{return "#837E7C"}})	
   			.style({"stroke":"black", "stroke-width":"2px"})
     	  .attr("y", function (d) {
      			if (d.direction == "forward" && d.name%2==0) {return 37;}
          	else if (d.direction == "forward" && d.name%2!==0) {return 70;}
          	else if (d.direction == "reverse" && d.name%2==0) {return 130;}
          	else if (d.direction == "reverse" && d.name%2!==0) {return 163;}
        		else {return 70} 
          })
      	.attr("height", function (d) {return 30;})
    
     var famLabels = svg.selectAll(".famname")
      .data(json)
      .enter()
      .append("text");
    	
    	var famtext = famLabels	
        .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 28;
            }
            else { return 59;}
          }
          else if (d.direction == "reverse") {
            if (d.name % 2 === 0) {
              return 181;
            }
              else { return 213;}
          }
      	})
        .style({"text-anchor":"middle","fill":"black","font-weight":"bold"})
        .attr("font-family","sans-serif")
        .text(function(d) {return d.famname})
        .attr("fill-opacity", 0)
        .transition().delay(4500).duration(1000)
        .attr("fill-opacity", 1);
    });

//setting tick marks and labeling the thousand marks with numbers on ruler
    var group = svg.selectAll(".a")
      .data(tickMarks.thousand)
      .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)"; })
    group.append("text")
    	.style({
      "font-family":"Arial",
      "font-size":"14px",
      "fill":"#C36241"})
    	.attr({y:112})
    	.attr("x", function(d) { 
     			 return d/10 - 8})
    	.transition().duration(3000).delay(3000)
    	.text(function (d) {return d/1000});
    
		var group2 = svg.selectAll(".b")
      .data(tickMarks.fivehundred)
      .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 = svg.selectAll(".c")
      .data(tickMarks.onehundred)
      .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)"; });

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

https://labratrevenge.com/d3-tip/javascripts/d3.tip.v0.6.3.js