wrigh3tl · April 26, 2017 22:22
diff --git a/.block b/.block
 license: mit
diff --git a/README.md b/README.md
diff --git a/index.html b/index.html
 <!DOCTYPE html>
 <html>
  <head>
    <meta charset="utf-8">
    <title>Sequences sunburst</title>
    <script src="//d3js.org/d3.v4.min.js"></script>
    <link rel="stylesheet" type="text/css"
      href="https://fonts.googleapis.com/css?family=Open+Sans:400,600">
    <link rel="stylesheet" type="text/css" href="sequences.css"/>
  </head>
  <body>
    <div id="main">
      <div id="sequence"></div>
      <div id="chart">
        <div id="explanation" style="visibility: hidden;">
          <span id="percentage"></span><br/>
          of Site 1 metagenome sampled on 9/11/15 
        </div>
      </div>
    </div>
    <div id="sidebar">
      <input type="checkbox" id="togglelegend"> Legend<br/>
      <div id="legend" style="visibility: hidden;"></div>
    </div>
    <script type="text/javascript" src="sequences.js"></script>
    <script type="text/javascript">
      // Hack to make this example display correctly in an iframe on bl.ocks.org
      d3.select(self.frameElement).style("height", "700px");
  </script> 
  </body>
 </html>
diff --git a/sequences.css b/sequences.css
 body {
  font-family: 'Open Sans', sans-serif;
  font-size: 12px;
  font-weight: 400;
  background-color: #fff;
  width: 960px;
  height: 700px;
  margin-top: 10px;
 }

 #main {
  float: left;
  width: 750px;
 }

 #sidebar {
  float: right;
  width: 100px;
 }

 #sequence {
  width: 600px;
  height: 70px;
 }

 #legend {
  padding: 10px 0 0 3px;
 }

 #sequence text, #legend text {
  font-weight: 600;
  fill: #fff;
 }

 #chart {
  position: relative;
 }

 #chart path {
  stroke: #fff;
 }

 #explanation {
  position: absolute;
  top: 260px;
  left: 305px;
  width: 140px;
  text-align: center;
  color: #666;
  z-index: -1;
 }

 #percentage {
  font-size: 2.5em;
 }
diff --git a/sequences.js b/sequences.js
 // Dimensions of sunburst.
 var width = 750;
 var height = 600;
 var radius = Math.min(width, height) / 2;

 // Breadcrumb dimensions: width, height, spacing, width of tip/tail.
 var b = {
  w: 75, h: 30, s: 3, t: 10
 };

 // Mapping of step names to colors.
 var colors = {
  "home": "#5687d1",
  "product": "#7b615c",
  "search": "#de783b",
  "account": "#6ab975",
  "other": "#a173d1",
  "end": "#bbbbbb"
 };

 // Total size of all segments; we set this later, after loading the data.
 var totalSize = 0; 

 var vis = d3.select("#chart").append("svg:svg")
    .attr("width", width)
    .attr("height", height)
    .append("svg:g")
    .attr("id", "container")
    .attr("transform", "translate(" + width / 2 + "," + height / 2 + ")");

 var partition = d3.partition()
    .size([2 * Math.PI, radius * radius]);

 var arc = d3.arc()
    .startAngle(function(d) { return d.x0; })
    .endAngle(function(d) { return d.x1; })
    .innerRadius(function(d) { return Math.sqrt(d.y0); })
    .outerRadius(function(d) { return Math.sqrt(d.y1); });

 // Use d3.text and d3.csvParseRows so that we do not need to have a header
 // row, and can receive the csv as an array of arrays.
 d3.text("visit-sequences.csv", function(text) {
  var csv = d3.csvParseRows(text);
  var json = buildHierarchy(csv);
  createVisualization(json);
 });

 // Main function to draw and set up the visualization, once we have the data.
 function createVisualization(json) {

  // Basic setup of page elements.
  initializeBreadcrumbTrail();
  drawLegend();
  d3.select("#togglelegend").on("click", toggleLegend);

  // Bounding circle underneath the sunburst, to make it easier to detect
  // when the mouse leaves the parent g.
  vis.append("svg:circle")
      .attr("r", radius)
      .style("opacity", 0);

  // Turn the data into a d3 hierarchy and calculate the sums.
  var root = d3.hierarchy(json)
      .sum(function(d) { return d.size; })
      .sort(function(a, b) { return b.value - a.value; });
  
  // For efficiency, filter nodes to keep only those large enough to see.
  var nodes = partition(root).descendants()
      .filter(function(d) {
          return (d.x1 - d.x0 > 0.005); // 0.005 radians = 0.29 degrees
      });

  var path = vis.data([json]).selectAll("path")
      .data(nodes)
      .enter().append("svg:path")
      .attr("display", function(d) { return d.depth ? null : "none"; })
      .attr("d", arc)
      .attr("fill-rule", "evenodd")
      .style("fill", function(d) { return colors[d.data.name]; })
      .style("opacity", 1)
      .on("mouseover", mouseover);

  // Add the mouseleave handler to the bounding circle.
  d3.select("#container").on("mouseleave", mouseleave);

  // Get total size of the tree = value of root node from partition.
  totalSize = path.datum().value;
 };

 // Fade all but the current sequence, and show it in the breadcrumb trail.
 function mouseover(d) {

  var percentage = (100 * d.value / totalSize).toPrecision(3);
  var percentageString = percentage + "%";
  if (percentage < 0.1) {
    percentageString = "< 0.1%";
  }

  d3.select("#percentage")
      .text(percentageString);

  d3.select("#explanation")
      .style("visibility", "");

  var sequenceArray = d.ancestors().reverse();
  sequenceArray.shift(); // remove root node from the array
  updateBreadcrumbs(sequenceArray, percentageString);

  // Fade all the segments.
  d3.selectAll("path")
      .style("opacity", 0.3);

  // Then highlight only those that are an ancestor of the current segment.
  vis.selectAll("path")
      .filter(function(node) {
                return (sequenceArray.indexOf(node) >= 0);
              })
      .style("opacity", 1);
 }

 // Restore everything to full opacity when moving off the visualization.
 function mouseleave(d) {

  // Hide the breadcrumb trail
  d3.select("#trail")
      .style("visibility", "hidden");

  // Deactivate all segments during transition.
  d3.selectAll("path").on("mouseover", null);

  // Transition each segment to full opacity and then reactivate it.
  d3.selectAll("path")
      .transition()
      .duration(1000)
      .style("opacity", 1)
      .on("end", function() {
              d3.select(this).on("mouseover", mouseover);
            });

  d3.select("#explanation")
      .style("visibility", "hidden");
 }

 function initializeBreadcrumbTrail() {
  // Add the svg area.
  var trail = d3.select("#sequence").append("svg:svg")
      .attr("width", width)
      .attr("height", 50)
      .attr("id", "trail");
  // Add the label at the end, for the percentage.
  trail.append("svg:text")
    .attr("id", "endlabel")
    .style("fill", "#000");
 }

 // Generate a string that describes the points of a breadcrumb polygon.
 function breadcrumbPoints(d, i) {
  var points = [];
  points.push("0,0");
  points.push(b.w + ",0");
  points.push(b.w + b.t + "," + (b.h / 2));
  points.push(b.w + "," + b.h);
  points.push("0," + b.h);
  if (i > 0) { // Leftmost breadcrumb; don't include 6th vertex.
    points.push(b.t + "," + (b.h / 2));
  }
  return points.join(" ");
 }

 // Update the breadcrumb trail to show the current sequence and percentage.
 function updateBreadcrumbs(nodeArray, percentageString) {

  // Data join; key function combines name and depth (= position in sequence).
  var trail = d3.select("#trail")
      .selectAll("g")
      .data(nodeArray, function(d) { return d.data.name + d.depth; });

  // Remove exiting nodes.
  trail.exit().remove();

  // Add breadcrumb and label for entering nodes.
  var entering = trail.enter().append("svg:g");

  entering.append("svg:polygon")
      .attr("points", breadcrumbPoints)
      .style("fill", function(d) { return colors[d.data.name]; });

  entering.append("svg:text")
      .attr("x", (b.w + b.t) / 2)
      .attr("y", b.h / 2)
      .attr("dy", "0.35em")
      .attr("text-anchor", "middle")
      .text(function(d) { return d.data.name; });

  // Merge enter and update selections; set position for all nodes.
  entering.merge(trail).attr("transform", function(d, i) {
    return "translate(" + i * (b.w + b.s) + ", 0)";
  });

  // Now move and update the percentage at the end.
  d3.select("#trail").select("#endlabel")
      .attr("x", (nodeArray.length + 0.5) * (b.w + b.s))
      .attr("y", b.h / 2)
      .attr("dy", "0.35em")
      .attr("text-anchor", "middle")
      .text(percentageString);

  // Make the breadcrumb trail visible, if it's hidden.
  d3.select("#trail")
      .style("visibility", "");

 }

 function drawLegend() {

  // Dimensions of legend item: width, height, spacing, radius of rounded rect.
  var li = {
    w: 75, h: 30, s: 3, r: 3
  };

  var legend = d3.select("#legend").append("svg:svg")
      .attr("width", li.w)
      .attr("height", d3.keys(colors).length * (li.h + li.s));

  var g = legend.selectAll("g")
      .data(d3.entries(colors))
      .enter().append("svg:g")
      .attr("transform", function(d, i) {
              return "translate(0," + i * (li.h + li.s) + ")";
           });

  g.append("svg:rect")
      .attr("rx", li.r)
      .attr("ry", li.r)
      .attr("width", li.w)
      .attr("height", li.h)
      .style("fill", function(d) { return d.value; });

  g.append("svg:text")
      .attr("x", li.w / 2)
      .attr("y", li.h / 2)
      .attr("dy", "0.35em")
      .attr("text-anchor", "middle")
      .text(function(d) { return d.key; });
 }

 function toggleLegend() {
  var legend = d3.select("#legend");
  if (legend.style("visibility") == "hidden") {
    legend.style("visibility", "");
  } else {
    legend.style("visibility", "hidden");
  }
 }

 // Take a 2-column CSV and transform it into a hierarchical structure suitable
 // for a partition layout. The first column is a sequence of step names, from
 // root to leaf, separated by hyphens. The second column is a count of how 
 // often that sequence occurred.
 function buildHierarchy(csv) {
  var root = {"name": "root", "children": []};
  for (var i = 0; i < csv.length; i++) {
    var sequence = csv[i][0];
    var size = +csv[i][1];
    if (isNaN(size)) { // e.g. if this is a header row
      continue;
    }
    var parts = sequence.split("-");
    var currentNode = root;
    for (var j = 0; j < parts.length; j++) {
      var children = currentNode["children"];
      var nodeName = parts[j];
      var childNode;
      if (j + 1 < parts.length) {
   // Not yet at the end of the sequence; move down the tree.
 	var foundChild = false;
 	for (var k = 0; k < children.length; k++) {
 	  if (children[k]["name"] == nodeName) {
 	    childNode = children[k];
 	    foundChild = true;
 	    break;
 	  }
 	}
  // If we don't already have a child node for this branch, create it.
 	if (!foundChild) {
 	  childNode = {"name": nodeName, "children": []};
 	  children.push(childNode);
 	}
 	currentNode = childNode;
      } else {
 	// Reached the end of the sequence; create a leaf node.
 	childNode = {"name": nodeName, "size": size};
 	children.push(childNode);
      }
    }
  }
  return root;
 };
diff --git a/visit-sequences.csv b/visit-sequences.csv
	<!DOCTYPE html>
	<html>
	<head>
	<meta charset="utf-8">
	<title>Sequences sunburst</title>
	<script src="//d3js.org/d3.v4.min.js"></script>
	<link rel="stylesheet" type="text/css"
	href="https://fonts.googleapis.com/css?family=Open+Sans:400,600">
	<link rel="stylesheet" type="text/css" href="sequences.css"/>
	</head>
	<body>
	<div id="main">
	<div id="sequence"></div>
	<div id="chart">
	<div id="explanation" style="visibility: hidden;">
	<span id="percentage"></span><br/>
	of Site 1 metagenome sampled on 9/11/15
	</div>
	</div>
	</div>
	<div id="sidebar">
	<input type="checkbox" id="togglelegend"> Legend<br/>
	<div id="legend" style="visibility: hidden;"></div>
	</div>
	<script type="text/javascript" src="sequences.js"></script>
	<script type="text/javascript">
	// Hack to make this example display correctly in an iframe on bl.ocks.org
	d3.select(self.frameElement).style("height", "700px");
	</script>
	</body>
	</html>
	body {
	font-family: 'Open Sans', sans-serif;
	font-size: 12px;
	font-weight: 400;
	background-color: #fff;
	width: 960px;
	height: 700px;
	margin-top: 10px;
	}

	#main {
	float: left;
	width: 750px;
	}

	#sidebar {
	float: right;
	width: 100px;
	}

	#sequence {
	width: 600px;
	height: 70px;
	}

	#legend {
	padding: 10px 0 0 3px;
	}

	#sequence text, #legend text {
	font-weight: 600;
	fill: #fff;
	}

	#chart {
	position: relative;
	}

	#chart path {
	stroke: #fff;
	}

	#explanation {
	position: absolute;
	top: 260px;
	left: 305px;
	width: 140px;
	text-align: center;
	color: #666;
	z-index: -1;
	}

	#percentage {
	font-size: 2.5em;
	}
	// Dimensions of sunburst.
	var width = 750;
	var height = 600;
	var radius = Math.min(width, height) / 2;

	// Breadcrumb dimensions: width, height, spacing, width of tip/tail.
	var b = {
	w: 75, h: 30, s: 3, t: 10
	};

	// Mapping of step names to colors.
	var colors = {
	"home": "#5687d1",
	"product": "#7b615c",
	"search": "#de783b",
	"account": "#6ab975",
	"other": "#a173d1",
	"end": "#bbbbbb"
	};

	// Total size of all segments; we set this later, after loading the data.
	var totalSize = 0;

	var vis = d3.select("#chart").append("svg:svg")
	.attr("width", width)
	.attr("height", height)
	.append("svg:g")
	.attr("id", "container")
	.attr("transform", "translate(" + width / 2 + "," + height / 2 + ")");

	var partition = d3.partition()
	.size([2 * Math.PI, radius * radius]);

	var arc = d3.arc()
	.startAngle(function(d) { return d.x0; })
	.endAngle(function(d) { return d.x1; })
	.innerRadius(function(d) { return Math.sqrt(d.y0); })
	.outerRadius(function(d) { return Math.sqrt(d.y1); });

	// Use d3.text and d3.csvParseRows so that we do not need to have a header
	// row, and can receive the csv as an array of arrays.
	d3.text("visit-sequences.csv", function(text) {
	var csv = d3.csvParseRows(text);
	var json = buildHierarchy(csv);
	createVisualization(json);
	});

	// Main function to draw and set up the visualization, once we have the data.
	function createVisualization(json) {

	// Basic setup of page elements.
	initializeBreadcrumbTrail();
	drawLegend();
	d3.select("#togglelegend").on("click", toggleLegend);

	// Bounding circle underneath the sunburst, to make it easier to detect
	// when the mouse leaves the parent g.
	vis.append("svg:circle")
	.attr("r", radius)
	.style("opacity", 0);

	// Turn the data into a d3 hierarchy and calculate the sums.
	var root = d3.hierarchy(json)
	.sum(function(d) { return d.size; })
	.sort(function(a, b) { return b.value - a.value; });

	// For efficiency, filter nodes to keep only those large enough to see.
	var nodes = partition(root).descendants()
	.filter(function(d) {
	return (d.x1 - d.x0 > 0.005); // 0.005 radians = 0.29 degrees
	});

	var path = vis.data([json]).selectAll("path")
	.data(nodes)
	.enter().append("svg:path")
	.attr("display", function(d) { return d.depth ? null : "none"; })
	.attr("d", arc)
	.attr("fill-rule", "evenodd")
	.style("fill", function(d) { return colors[d.data.name]; })
	.style("opacity", 1)
	.on("mouseover", mouseover);

	// Add the mouseleave handler to the bounding circle.
	d3.select("#container").on("mouseleave", mouseleave);

	// Get total size of the tree = value of root node from partition.
	totalSize = path.datum().value;
	};

	// Fade all but the current sequence, and show it in the breadcrumb trail.
	function mouseover(d) {

	var percentage = (100 * d.value / totalSize).toPrecision(3);
	var percentageString = percentage + "%";
	if (percentage < 0.1) {
	percentageString = "< 0.1%";
	}

	d3.select("#percentage")
	.text(percentageString);

	d3.select("#explanation")
	.style("visibility", "");

	var sequenceArray = d.ancestors().reverse();
	sequenceArray.shift(); // remove root node from the array
	updateBreadcrumbs(sequenceArray, percentageString);

	// Fade all the segments.
	d3.selectAll("path")
	.style("opacity", 0.3);

	// Then highlight only those that are an ancestor of the current segment.
	vis.selectAll("path")
	.filter(function(node) {
	return (sequenceArray.indexOf(node) >= 0);
	})
	.style("opacity", 1);
	}

	// Restore everything to full opacity when moving off the visualization.
	function mouseleave(d) {

	// Hide the breadcrumb trail
	d3.select("#trail")
	.style("visibility", "hidden");

	// Deactivate all segments during transition.
	d3.selectAll("path").on("mouseover", null);

	// Transition each segment to full opacity and then reactivate it.
	d3.selectAll("path")
	.transition()
	.duration(1000)
	.style("opacity", 1)
	.on("end", function() {
	d3.select(this).on("mouseover", mouseover);
	});

	d3.select("#explanation")
	.style("visibility", "hidden");
	}

	function initializeBreadcrumbTrail() {
	// Add the svg area.
	var trail = d3.select("#sequence").append("svg:svg")
	.attr("width", width)
	.attr("height", 50)
	.attr("id", "trail");
	// Add the label at the end, for the percentage.
	trail.append("svg:text")
	.attr("id", "endlabel")
	.style("fill", "#000");
	}

	// Generate a string that describes the points of a breadcrumb polygon.
	function breadcrumbPoints(d, i) {
	var points = [];
	points.push("0,0");
	points.push(b.w + ",0");
	points.push(b.w + b.t + "," + (b.h / 2));
	points.push(b.w + "," + b.h);
	points.push("0," + b.h);
	if (i > 0) { // Leftmost breadcrumb; don't include 6th vertex.
	points.push(b.t + "," + (b.h / 2));
	}
	return points.join(" ");
	}

	// Update the breadcrumb trail to show the current sequence and percentage.
	function updateBreadcrumbs(nodeArray, percentageString) {

	// Data join; key function combines name and depth (= position in sequence).
	var trail = d3.select("#trail")
	.selectAll("g")
	.data(nodeArray, function(d) { return d.data.name + d.depth; });

	// Remove exiting nodes.
	trail.exit().remove();

	// Add breadcrumb and label for entering nodes.
	var entering = trail.enter().append("svg:g");

	entering.append("svg:polygon")
	.attr("points", breadcrumbPoints)
	.style("fill", function(d) { return colors[d.data.name]; });

	entering.append("svg:text")
	.attr("x", (b.w + b.t) / 2)
	.attr("y", b.h / 2)
	.attr("dy", "0.35em")
	.attr("text-anchor", "middle")
	.text(function(d) { return d.data.name; });

	// Merge enter and update selections; set position for all nodes.
	entering.merge(trail).attr("transform", function(d, i) {
	return "translate(" + i * (b.w + b.s) + ", 0)";
	});

	// Now move and update the percentage at the end.
	d3.select("#trail").select("#endlabel")
	.attr("x", (nodeArray.length + 0.5) * (b.w + b.s))
	.attr("y", b.h / 2)
	.attr("dy", "0.35em")
	.attr("text-anchor", "middle")
	.text(percentageString);

	// Make the breadcrumb trail visible, if it's hidden.
	d3.select("#trail")
	.style("visibility", "");

	}

	function drawLegend() {

	// Dimensions of legend item: width, height, spacing, radius of rounded rect.
	var li = {
	w: 75, h: 30, s: 3, r: 3
	};

	var legend = d3.select("#legend").append("svg:svg")
	.attr("width", li.w)
	.attr("height", d3.keys(colors).length * (li.h + li.s));

	var g = legend.selectAll("g")
	.data(d3.entries(colors))
	.enter().append("svg:g")
	.attr("transform", function(d, i) {
	return "translate(0," + i * (li.h + li.s) + ")";
	});

	g.append("svg:rect")
	.attr("rx", li.r)
	.attr("ry", li.r)
	.attr("width", li.w)
	.attr("height", li.h)
	.style("fill", function(d) { return d.value; });

	g.append("svg:text")
	.attr("x", li.w / 2)
	.attr("y", li.h / 2)
	.attr("dy", "0.35em")
	.attr("text-anchor", "middle")
	.text(function(d) { return d.key; });
	}

	function toggleLegend() {
	var legend = d3.select("#legend");
	if (legend.style("visibility") == "hidden") {
	legend.style("visibility", "");
	} else {
	legend.style("visibility", "hidden");
	}
	}

	// Take a 2-column CSV and transform it into a hierarchical structure suitable
	// for a partition layout. The first column is a sequence of step names, from
	// root to leaf, separated by hyphens. The second column is a count of how
	// often that sequence occurred.
	function buildHierarchy(csv) {
	var root = {"name": "root", "children": []};
	for (var i = 0; i < csv.length; i++) {
	var sequence = csv[i][0];
	var size = +csv[i][1];
	if (isNaN(size)) { // e.g. if this is a header row
	continue;
	}
	var parts = sequence.split("-");
	var currentNode = root;
	for (var j = 0; j < parts.length; j++) {
	var children = currentNode["children"];
	var nodeName = parts[j];
	var childNode;
	if (j + 1 < parts.length) {
	// Not yet at the end of the sequence; move down the tree.
	var foundChild = false;
	for (var k = 0; k < children.length; k++) {
	if (children[k]["name"] == nodeName) {
	childNode = children[k];
	foundChild = true;
	break;
	}
	}
	// If we don't already have a child node for this branch, create it.
	if (!foundChild) {
	childNode = {"name": nodeName, "children": []};
	children.push(childNode);
	}
	currentNode = childNode;
	} else {
	// Reached the end of the sequence; create a leaf node.
	childNode = {"name": nodeName, "size": size};
	children.push(childNode);
	}
	}
	}
	return root;
	};