Building a hierarchy from a flat table

A test block to experiment with building hierarchies from flat files. Pretty messy at the moment.

The flatToHierarchy() function transforms a flat and wide table into a hierarchy based on a sequence of field names. Adapted from this Stack Overflow answer.

<!DOCTYPE html>
<head>
  <meta charset="utf-8">
  <script src="https://d3js.org/d3.v4.min.js"></script>
  <style>
    body { margin:0;position:fixed;top:0;right:0;bottom:0;left:0; }
  </style>
</head>
<meta charset="utf-8">
<style>
	body {text-align:center}
	svg { font-family: Courier;}
</style>
<body>
<svg width="960" height="620">
    <text class="title" x=10 y=30>a little tree</text>
</svg>
  
  	
<script src="https://d3js.org/d3.v4.min.js"></script>
  
<script>
const svg   = d3.select("svg"),
  		width = +svg.attr("width"),
  		height= +svg.attr("height"),
      margin= 20

// Set up a size scale
const radius = d3.scaleLinear()
			.range( [1, 14])
			.domain([1,1000])
			.clamp(true)

// Declare a D3 layout
const tree = d3.tree()
			.size([height * 0.85, width * 0.8])

// Load our external data
d3.csv("data.csv", function(data) {
  
  data.sort(function(x, y){
     return d3.descending(+x.described, +y.described);
  })

// Build our hierarchy from a series of levels
  // change/reorder the level elements for a different tree
  const levels = ["kingdom", "phylum_latin", "notes"],
        hierarchy = flatToHierarchy(data, levels, 'taxon', 'described'),
      	nodes = hierarchy.descendants(),
      	leaves=hierarchy.leaves(),
      	links = tree(hierarchy).links()
  
  // Draw on screen
  svg.selectAll('path')
    	.data(links)
    .enter().append('path')
    		.attr('d', d3.linkHorizontal()
        .x(function(d) { return d.y; })
        .y(function(d) { return d.x; }))
  			.style('fill', 'none')
  			.style('stroke', '#aaa')
  			.style('stroke-width',1)
  
  svg.selectAll('circle')
    	.data(nodes)
    .enter().append('circle')
    	.style('r', (d) => radius(d.value))
  		.style('fill', 'white')
  		.style('stroke', '#444')
  		.style('stroke-width',1)
  		// TODO - make clearer
  		.attr('transform', function (d) {
    		return 'translate(' + d.y + ',' + d.x + ')'
  		})
})

// Helper function for converting flat data to a hierarchy
// with a name and count field on each node.
// TODO - probably shouldn't name the value field "count"

function flatToHierarchy(flatData, levels, nameField, countField) {
  // Adapted from https://stackoverflow.com/a/19317823
  var nestedData = { name :"root", children : [] }
  
  // For each data row, loop through the expected levels traversing the output tree
  flatData.forEach(function(d){
      // Keep this as a reference to the current level
      var depthCursor = nestedData.children;
      // Go down one level at a time
      levels.forEach(function( property, depth ){

// See if a branch has already been created
          var index;
          depthCursor.forEach(function(child,i){
              if ( d[property] == child.name ) index = i;
          });
          // Add a branch if it isn't there
          if ( isNaN(index) ) {
              depthCursor.push({ name : d[property], children : []});
              index = depthCursor.length - 1;
          }
          // Reference the new child array as we go deeper into the tree
          depthCursor = depthCursor[index].children;
          // This is a leaf, so add last element to specified branch
          if ( depth === levels.length - 1 ) {
            depthCursor.push({
              'name':d[nameField],
              'count':+d[countField]
            });
          } 
      })
  })
  
  // sum up the leaves / branches and return the hierarchy
  return d3.hierarchy(nestedData).sum(function(d){ return d.count; })
  
}
  
</script>
</body>
</html>

https://d3js.org/d3.v4.min.js