Visualizing a genome annotation file (gff)

D3 JavaScript interactive visualization of a genome feature file(GFF). More information on how to parse the gff file and create the parent-child CSV file is on the GitHub Repository.

<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">

<title>Tree Example</title>

.node circle {
	  fill: #fff;
	  stroke: steelblue;
	  stroke-width: 3px;
	}

.node text {
	  font: 12px sans-serif;
	}

.link {
	  fill: none;
	  stroke: #ccc;
	  stroke-width: 2px;
	}

.tooltip{
		position: absolute;
		width: 200px;
		height: 28px;
		pointer-events: none;
	}
	
    </style>

</head>

<body>

// ************** Generate the tree diagram	 *****************
var margin = {top: 20, right: 120, bottom: 20, left: 120},
	width = 2000 - margin.right - margin.left,
	height = 1000 - margin.top - margin.bottom;
	
var i = 0,
	duration = 750,
	root;

var tree = d3.layout.tree()
	.size([height, width]);

var diagonal = d3.svg.diagonal()
	.projection(function(d) { return [d.y, d.x]; });

var svg = d3.select("body").append("svg")
	.attr("width", width + margin.right + margin.left)
	.attr("height", height + margin.top + margin.bottom)
  .append("g")
	.attr("transform", "translate(" + margin.left + "," + margin.top + ")");

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

d3.csv("parentChild.csv", function(error, data) {
// create a name: node map
var dataMap = data.reduce(function(map, node) {
	map[node.name] = node;
	return map;
}, {});

// create the tree array
var treeData = [];
data.forEach(function(node) {
	// add to parent
	var parent = dataMap[node.parent];
	var start = dataMap[node.start];
	if (parent) {
		// create child array if it doesn't exist
		(parent.children || (parent.children = []))
			// add node to child array
			.push(node);
	} else {
		// parent is null or missing
		treeData.push(node);
	}
});

root = treeData[0];
  update(root);
});

function update(source) {

// Compute the new tree layout.
  var nodes = tree.nodes(root).reverse(),
	  links = tree.links(nodes);

// Normalize for fixed-depth.
  nodes.forEach(function(d) { d.y = d.depth * 180; });

// Update the nodes…
  var node = svg.selectAll("g.node")
	  .data(nodes, function(d) { return d.id || (d.id = ++i); });

// Enter any new nodes at the parent's previous position.
  var nodeEnter = node.enter().append("g")
	  .attr("class", "node")
	  .attr("transform", function(d) { return "translate(" + source.y0 + "," + source.x0 + ")"; })
	  .on("click", click);

nodeEnter.append("circle")
	  .attr("r", 1e-6)
	  .style("fill", function(d) { return d._children ? "lightsteelblue" : "#fff"; });

nodeEnter.append("text")
	  .attr("x", function(d) { return d.children || d._children ? -13 : 13; })
	  .attr("dy", ".35em")
	  .attr("text-anchor", function(d) { return d.children || d._children ? "end" : "start"; })
	  .text(function(d) { return d.name; })
	  .style("fill-opacity", 1e-6)
	  .on("mouseover", function(d){
	  	tooltip.transition()
	  		.duration(200)
	  		.style("opacity", .9);
	  	tooltip.html(d.type + "<br/>" + "(" + d.start + "," + d.end + ")" )
	  		.style("left", (d3.event.pageX) + 5 + "px")
	  		.style("top", (d3.event.pageY) - 50 + "px" );
	  })
	  .on("mouseout", function(d){
	  	tooltip.transition()
	  		.duration(500)
	  		.style("opacity", 0);
	  });

// Transition nodes to their new position.
  var nodeUpdate = node.transition()
	  .duration(duration)
	  .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; });

nodeUpdate.select("circle")
	  .attr("r", 10)
	  .style("fill", function(d) { return d._children ? "lightsteelblue" : "#fff"; });

nodeUpdate.select("text")
	  .style("fill-opacity", 1);

// Transition exiting nodes to the parent's new position.
  var nodeExit = node.exit().transition()
	  .duration(duration)
	  .attr("transform", function(d) { return "translate(" + source.y + "," + source.x + ")"; })
	  .remove();

nodeExit.select("circle")
	  .attr("r", 1e-6);

nodeExit.select("text")
	  .style("fill-opacity", 1e-6);

// Update the links…
  var link = svg.selectAll("path.link")
	  .data(links, function(d) { return d.target.id; });

// Enter any new links at the parent's previous position.
  link.enter().insert("path", "g")
	  .attr("class", "link")
	  .attr("d", function(d) {
		var o = {x: source.x0, y: source.y0};
		return diagonal({source: o, target: o});
	  });

// Transition links to their new position.
  link.transition()
	  .duration(duration)
	  .attr("d", diagonal);

// Transition exiting nodes to the parent's new position.
  link.exit().transition()
	  .duration(duration)
	  .attr("d", function(d) {
		var o = {x: source.x, y: source.y};
		return diagonal({source: o, target: o});
	  })
	  .remove();

// Stash the old positions for transition.
  nodes.forEach(function(d) {
	d.x0 = d.x;
	d.y0 = d.y;
  });
}

// Toggle children on click.
function click(d) {
  if (d.children) {
	d._children = d.children;
	d.children = null;
  } else {
	d.children = d._children;
	d._children = null;
  }
  update(d);
}

</script>
	
  </body>
</html>

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

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