Jverma/README.md

## README.md

      
    Raw
  

              README.md
            
          
    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.

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

    <title>Tree Example</title>

    <style>

	.node {
		cursor: pointer;
	}

	.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>

<script src="http://d3js.org/d3.v3.min.js"></script>

<script>


// ************** 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>

## parentChild.csv

          
            name
            parent
            start
            end
            type

            
              chromosomeI
              null
              1
              50000
              chromosome

            
              cassava4.1_012921m.g
              chromosomeI
              8260
              15046
              gene

            
              cassava4.1_012921m
              cassava4.1_012921m.g
              8260
              15046
              transcript

            
              PAC:17967856.CDS.1
              cassava4.1_012921m
              9850
              10232
              CDS

            
              PAC:17967856.CDS.2
              cassava4.1_012921m
              14217
              14721
              CDS

            
              cassava4.1_032021m.g
              chromosomeI
              17167
              18209
              gene

            
              cassava4.1_032021m
              cassava4.1_032021m.g
              17167
              18209
              transcript

            
              PAC:17967858.CDS.1
              cassava4.1_032021m
              17167
              17314
              CDS

            
              PAC:17967858.CDS.2
              cassava4.1_032021m
              17404
              17484
              CDS

            
              PAC:17967858.CDS.3
              cassava4.1_032021m
              17607
              17881
              CDS

            
              PAC:17967858.CDS.4
              cassava4.1_032021m
              18009
              18209
              CDS

            
              cassava4.1_018871m.g
              chromosomeI
              39560
              40433
              gene

            
              cassava4.1_018871m
              cassava4.1_018871m.g
              39560
              40433
              transcript

            
              PAC:17967850.CDS.1
              cassava4.1_018871m
              39623
              39765
              CDS

            
              PAC:17967850.CDS.2
              cassava4.1_018871m
              39877
              40144
              CDS

            
              cassava4.1_007010m.g
              chromosomeI
              42479
              46245
              gene

            
              cassava4.1_007010m
              cassava4.1_007010m.g
              42479
              46245
              transcript

            
              PAC:17967843.CDS.1
              cassava4.1_007010m
              44750
              45416
              CDS

            
              PAC:17967843.CDS.2
              cassava4.1_007010m
              44420
              44641
              CDS

            
              PAC:17967843.CDS.3
              cassava4.1_007010m
              43532
              43779
              CDS

            
              PAC:17967843.CDS.4
              cassava4.1_007010m
              43159
              43298
              CDS

            
              PAC:17967843.CDS.5
              cassava4.1_007010m
              42809
              42935
              CDS
	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="utf-8">

	<title>Tree Example</title>

	<style>

	.node {
	cursor: pointer;
	}

	.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>

	<script src="http://d3js.org/d3.v3.min.js"></script>

	<script>



	// ************ 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>
name	parent	start	end	type
chromosomeI	null	1	50000	chromosome
cassava4.1_012921m.g	chromosomeI	8260	15046	gene
cassava4.1_012921m	cassava4.1_012921m.g	8260	15046	transcript
PAC:17967856.CDS.1	cassava4.1_012921m	9850	10232	CDS
PAC:17967856.CDS.2	cassava4.1_012921m	14217	14721	CDS
cassava4.1_032021m.g	chromosomeI	17167	18209	gene
cassava4.1_032021m	cassava4.1_032021m.g	17167	18209	transcript
PAC:17967858.CDS.1	cassava4.1_032021m	17167	17314	CDS
PAC:17967858.CDS.2	cassava4.1_032021m	17404	17484	CDS
PAC:17967858.CDS.3	cassava4.1_032021m	17607	17881	CDS
PAC:17967858.CDS.4	cassava4.1_032021m	18009	18209	CDS
cassava4.1_018871m.g	chromosomeI	39560	40433	gene
cassava4.1_018871m	cassava4.1_018871m.g	39560	40433	transcript
PAC:17967850.CDS.1	cassava4.1_018871m	39623	39765	CDS
PAC:17967850.CDS.2	cassava4.1_018871m	39877	40144	CDS
cassava4.1_007010m.g	chromosomeI	42479	46245	gene
cassava4.1_007010m	cassava4.1_007010m.g	42479	46245	transcript
PAC:17967843.CDS.1	cassava4.1_007010m	44750	45416	CDS
PAC:17967843.CDS.2	cassava4.1_007010m	44420	44641	CDS
PAC:17967843.CDS.3	cassava4.1_007010m	43532	43779	CDS
PAC:17967843.CDS.4	cassava4.1_007010m	43159	43298	CDS
PAC:17967843.CDS.5	cassava4.1_007010m	42809	42935	CDS