danielecook/.block

## .block
license: gpl-3.0
height: 960

## README.md

      
    Raw
  

              README.md
            
          
    A re-implementation of Jason Davies’ Phylogenetic Tree of Life, with faded gray lines to connect the leaf nodes of the tree to their corresponding labels inspired by a figure from Nature.
This implementation modifies the depth of interior nodes in a cluster layout to show branch lengths. Toggle the checkbox in the top-left corner to show or hide branch lengths, and mouseover a label to highlight its path to the root.

  
## index.html
<!DOCTYPE html>
<meta charset="utf-8">
<style>

body {
  font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
  margin: 0;
}

#show-length {
  position: absolute;
  top: 10px;
  left: 10px;
}

.links {
  fill: none;
  stroke: #000;
}

.link-extensions {
  fill: none;
  stroke: #000;
  stroke-opacity: .25;
}

.labels {
  font: 10px sans-serif;
}

.link--active {
  stroke: #000 !important;
  stroke-width: 1.5px;
}

.link-extension--active {
  stroke-opacity: .6;
}

.label--active {
  font-weight: bold;
}

</style>
<label id="show-length">
  <input type="checkbox"> Show branch length
</label>

<!-- Copyright 2011 Jason Davies https://github.com/jasondavies/newick.js -->
<script>function parseNewick(a){for(var e=[],r={},s=a.split(/\s*(;|\(|\)|,|:)\s*/),t=0;t<s.length;t++){var n=s[t];switch(n){case"(":var c={};r.branchset=[c],e.push(r),r=c;break;case",":var c={};e[e.length-1].branchset.push(c),r=c;break;case")":r=e.pop();break;case":":break;default:var h=s[t-1];")"==h||"("==h||","==h?r.name=n:":"==h&&(r.length=parseFloat(n))}}return r}</script>

<!-- Copyright 2016 Mike Bostock https://d3js.org -->
<script src="https://d3js.org/d3.v4.min.js"></script>
<script>

var outerRadius = 960 / 2,
    innerRadius = outerRadius - 170;

var color = d3.scaleOrdinal()
    .domain(["Bacteria", "Eukaryota", "Archaea"])
    .range(d3.schemeCategory10);

var cluster = d3.cluster()
    .size([360, innerRadius])
    .separation(function(a, b) { return 1; });

var svg = d3.select("body").append("svg")
    .attr("width", outerRadius * 2)
    .attr("height", outerRadius * 2);

var legend = svg.append("g")
    .attr("class", "legend")
  .selectAll("g")
  .data(color.domain())
  .enter().append("g")
    .attr("transform", function(d, i) { return "translate(" + (outerRadius * 2 - 10) + "," + (i * 20 + 10) + ")"; });

legend.append("rect")
    .attr("x", -18)
    .attr("width", 18)
    .attr("height", 18)
    .attr("fill", color);

legend.append("text")
    .attr("x", -24)
    .attr("y", 9)
    .attr("dy", ".35em")
    .attr("text-anchor", "end")
    .text(function(d) { return d; });

var chart = svg.append("g")
    .attr("transform", "translate(" + outerRadius + "," + outerRadius + ")");

d3.text("life.txt", function(error, life) {
  if (error) throw error;

  var root = d3.hierarchy(parseNewick(life), function(d) { return d.branchset; })
      .sum(function(d) { return d.branchset ? 0 : 1; })
      .sort(function(a, b) { return (a.value - b.value) || d3.ascending(a.data.length, b.data.length); });

  cluster(root);

  var input = d3.select("#show-length input").on("change", changed),
      timeout = setTimeout(function() { input.property("checked", true).each(changed); }, 2000);

  setRadius(root, root.data.length = 0, innerRadius / maxLength(root));
  setColor(root);

  var linkExtension = chart.append("g")
      .attr("class", "link-extensions")
    .selectAll("path")
    .data(root.links().filter(function(d) { return !d.target.children; }))
    .enter().append("path")
      .each(function(d) { d.target.linkExtensionNode = this; })
      .attr("d", linkExtensionConstant);

  var link = chart.append("g")
      .attr("class", "links")
    .selectAll("path")
    .data(root.links())
    .enter().append("path")
      .each(function(d) { d.target.linkNode = this; })
      .attr("d", linkConstant)
      .attr("stroke", function(d) { return d.target.color; });

  chart.append("g")
      .attr("class", "labels")
    .selectAll("text")
    .data(root.leaves())
    .enter().append("text")
      .attr("dy", ".31em")
      .attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + (innerRadius + 4) + ",0)" + (d.x < 180 ? "" : "rotate(180)"); })
      .attr("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
      .text(function(d) { return d.data.name.replace(/_/g, " "); })
      .on("mouseover", mouseovered(true))
      .on("mouseout", mouseovered(false));

  function changed() {
    clearTimeout(timeout);
    var t = d3.transition().duration(750);
    linkExtension.transition(t).attr("d", this.checked ? linkExtensionVariable : linkExtensionConstant);
    link.transition(t).attr("d", this.checked ? linkVariable : linkConstant);
  }

  function mouseovered(active) {
    return function(d) {
      d3.select(this).classed("label--active", active);
      d3.select(d.linkExtensionNode).classed("link-extension--active", active).each(moveToFront);
      do d3.select(d.linkNode).classed("link--active", active).each(moveToFront); while (d = d.parent);
    };
  }

  function moveToFront() {
    this.parentNode.appendChild(this);
  }
});

// Compute the maximum cumulative length of any node in the tree.
function maxLength(d) {
  return d.data.length + (d.children ? d3.max(d.children, maxLength) : 0);
}

// Set the radius of each node by recursively summing and scaling the distance from the root.
function setRadius(d, y0, k) {
  d.radius = (y0 += d.data.length) * k;
  if (d.children) d.children.forEach(function(d) { setRadius(d, y0, k); });
}

// Set the color of each node by recursively inheriting.
function setColor(d) {
  var name = d.data.name;
  d.color = color.domain().indexOf(name) >= 0 ? color(name) : d.parent ? d.parent.color : null;
  if (d.children) d.children.forEach(setColor);
}

function linkVariable(d) {
  return linkStep(d.source.x, d.source.radius, d.target.x, d.target.radius);
}

function linkConstant(d) {
  return linkStep(d.source.x, d.source.y, d.target.x, d.target.y);
}

function linkExtensionVariable(d) {
  return linkStep(d.target.x, d.target.radius, d.target.x, innerRadius);
}

function linkExtensionConstant(d) {
  return linkStep(d.target.x, d.target.y, d.target.x, innerRadius);
}

// Like d3.svg.diagonal.radial, but with square corners.
function linkStep(startAngle, startRadius, endAngle, endRadius) {
  var c0 = Math.cos(startAngle = (startAngle - 90) / 180 * Math.PI),
      s0 = Math.sin(startAngle),
      c1 = Math.cos(endAngle = (endAngle - 90) / 180 * Math.PI),
      s1 = Math.sin(endAngle);
  return "M" + startRadius * c0 + "," + startRadius * s0
      + (endAngle === startAngle ? "" : "A" + startRadius + "," + startRadius + " 0 0 " + (endAngle > startAngle ? 1 : 0) + " " + startRadius * c1 + "," + startRadius * s1)
      + "L" + endRadius * c1 + "," + endRadius * s1;
}

</script>

## life.txt
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## thumbnail.png

      
    Raw
  

              thumbnail.png
	<!DOCTYPE html>
	<meta charset="utf-8">
	<style>

	body {
	font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
	margin: 0;
	}

	#show-length {
	position: absolute;
	top: 10px;
	left: 10px;
	}

	.links {
	fill: none;
	stroke: #000;
	}

	.link-extensions {
	fill: none;
	stroke: #000;
	stroke-opacity: .25;
	}

	.labels {
	font: 10px sans-serif;
	}

	.link--active {
	stroke: #000 !important;
	stroke-width: 1.5px;
	}

	.link-extension--active {
	stroke-opacity: .6;
	}

	.label--active {
	font-weight: bold;
	}

	</style>
	<label id="show-length">
	<input type="checkbox"> Show branch length
	</label>

	<!-- Copyright 2011 Jason Davies https://github.com/jasondavies/newick.js -->
	<script>function parseNewick(a){for(var e=[],r={},s=a.split(/\s(;\|\(\|\)\|,\|:)\s/),t=0;t<s.length;t++){var n=s[t];switch(n){case"(":var c={};r.branchset=[c],e.push(r),r=c;break;case",":var c={};e[e.length-1].branchset.push(c),r=c;break;case")":r=e.pop();break;case":":break;default:var h=s[t-1];")"==h\|\|"("==h\|\|","==h?r.name=n:":"==h&&(r.length=parseFloat(n))}}return r}</script>

	<!-- Copyright 2016 Mike Bostock https://d3js.org -->
	<script src="https://d3js.org/d3.v4.min.js"></script>
	<script>

	var outerRadius = 960 / 2,
	innerRadius = outerRadius - 170;

	var color = d3.scaleOrdinal()
	.domain(["Bacteria", "Eukaryota", "Archaea"])
	.range(d3.schemeCategory10);

	var cluster = d3.cluster()
	.size([360, innerRadius])
	.separation(function(a, b) { return 1; });

	var svg = d3.select("body").append("svg")
	.attr("width", outerRadius * 2)
	.attr("height", outerRadius * 2);

	var legend = svg.append("g")
	.attr("class", "legend")
	.selectAll("g")
	.data(color.domain())
	.enter().append("g")
	.attr("transform", function(d, i) { return "translate(" + (outerRadius * 2 - 10) + "," + (i * 20 + 10) + ")"; });

	legend.append("rect")
	.attr("x", -18)
	.attr("width", 18)
	.attr("height", 18)
	.attr("fill", color);

	legend.append("text")
	.attr("x", -24)
	.attr("y", 9)
	.attr("dy", ".35em")
	.attr("text-anchor", "end")
	.text(function(d) { return d; });

	var chart = svg.append("g")
	.attr("transform", "translate(" + outerRadius + "," + outerRadius + ")");

	d3.text("life.txt", function(error, life) {
	if (error) throw error;

	var root = d3.hierarchy(parseNewick(life), function(d) { return d.branchset; })
	.sum(function(d) { return d.branchset ? 0 : 1; })
	.sort(function(a, b) { return (a.value - b.value) \|\| d3.ascending(a.data.length, b.data.length); });

	cluster(root);

	var input = d3.select("#show-length input").on("change", changed),
	timeout = setTimeout(function() { input.property("checked", true).each(changed); }, 2000);

	setRadius(root, root.data.length = 0, innerRadius / maxLength(root));
	setColor(root);

	var linkExtension = chart.append("g")
	.attr("class", "link-extensions")
	.selectAll("path")
	.data(root.links().filter(function(d) { return !d.target.children; }))
	.enter().append("path")
	.each(function(d) { d.target.linkExtensionNode = this; })
	.attr("d", linkExtensionConstant);

	var link = chart.append("g")
	.attr("class", "links")
	.selectAll("path")
	.data(root.links())
	.enter().append("path")
	.each(function(d) { d.target.linkNode = this; })
	.attr("d", linkConstant)
	.attr("stroke", function(d) { return d.target.color; });

	chart.append("g")
	.attr("class", "labels")
	.selectAll("text")
	.data(root.leaves())
	.enter().append("text")
	.attr("dy", ".31em")
	.attr("transform", function(d) { return "rotate(" + (d.x - 90) + ")translate(" + (innerRadius + 4) + ",0)" + (d.x < 180 ? "" : "rotate(180)"); })
	.attr("text-anchor", function(d) { return d.x < 180 ? "start" : "end"; })
	.text(function(d) { return d.data.name.replace(/_/g, " "); })
	.on("mouseover", mouseovered(true))
	.on("mouseout", mouseovered(false));

	function changed() {
	clearTimeout(timeout);
	var t = d3.transition().duration(750);
	linkExtension.transition(t).attr("d", this.checked ? linkExtensionVariable : linkExtensionConstant);
	link.transition(t).attr("d", this.checked ? linkVariable : linkConstant);
	}

	function mouseovered(active) {
	return function(d) {
	d3.select(this).classed("label--active", active);
	d3.select(d.linkExtensionNode).classed("link-extension--active", active).each(moveToFront);
	do d3.select(d.linkNode).classed("link--active", active).each(moveToFront); while (d = d.parent);
	};
	}

	function moveToFront() {
	this.parentNode.appendChild(this);
	}
	});

	// Compute the maximum cumulative length of any node in the tree.
	function maxLength(d) {
	return d.data.length + (d.children ? d3.max(d.children, maxLength) : 0);
	}

	// Set the radius of each node by recursively summing and scaling the distance from the root.
	function setRadius(d, y0, k) {
	d.radius = (y0 += d.data.length) * k;
	if (d.children) d.children.forEach(function(d) { setRadius(d, y0, k); });
	}

	// Set the color of each node by recursively inheriting.
	function setColor(d) {
	var name = d.data.name;
	d.color = color.domain().indexOf(name) >= 0 ? color(name) : d.parent ? d.parent.color : null;
	if (d.children) d.children.forEach(setColor);
	}

	function linkVariable(d) {
	return linkStep(d.source.x, d.source.radius, d.target.x, d.target.radius);
	}

	function linkConstant(d) {
	return linkStep(d.source.x, d.source.y, d.target.x, d.target.y);
	}

	function linkExtensionVariable(d) {
	return linkStep(d.target.x, d.target.radius, d.target.x, innerRadius);
	}

	function linkExtensionConstant(d) {
	return linkStep(d.target.x, d.target.y, d.target.x, innerRadius);
	}

	// Like d3.svg.diagonal.radial, but with square corners.
	function linkStep(startAngle, startRadius, endAngle, endRadius) {
	var c0 = Math.cos(startAngle = (startAngle - 90) / 180 * Math.PI),
	s0 = Math.sin(startAngle),
	c1 = Math.cos(endAngle = (endAngle - 90) / 180 * Math.PI),
	s1 = Math.sin(endAngle);
	return "M" + startRadius * c0 + "," + startRadius * s0
	+ (endAngle === startAngle ? "" : "A" + startRadius + "," + startRadius + " 0 0 " + (endAngle > startAngle ? 1 : 0) + " " + startRadius * c1 + "," + startRadius * s1)
	+ "L" + endRadius * c1 + "," + endRadius * s1;
	}

	</script>
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