tnt.tree/src/layout.js

TnT tree display

// Based on the code by Ken-ichi Ueda in http://bl.ocks.org/kueda/1036776#d3.phylogram.js

var apijs = require("tnt.api");
var diagonal = require("./diagonal.js");
var tree = {};

tree.layout = function () {

    var l = function () {
    };

    var cluster = d3.layout.cluster()
	.sort(null)
	.value(function (d) {return d.length} )
	.separation(function () {return 1});
    
    var api = apijs (l)
	.getset ('scale', true)
	.getset ('max_leaf_label_width', 0)
	.method ("cluster", cluster)
	.method('yscale', function () {throw "yscale is not defined in the base object"})
	.method('adjust_cluster_size', function () {throw "adjust_cluster_size is not defined in the base object" })
	.method('width', function () {throw "width is not defined in the base object"})
	.method('height', function () {throw "height is not defined in the base object"});

    api.method('scale_branch_lengths', function (curr) {
	if (l.scale() === false) {
	    return
	}

	var nodes = curr.nodes;
	var tree = curr.tree;

	var root_dists = nodes.map (function (d) {
	    return d._root_dist;
	});

	var yscale = l.yscale(root_dists);
	tree.apply (function (node) {
	    node.property("y", yscale(node.root_dist()));
	});
    });

    return l;
};

tree.layout.vertical = function () {
    var layout = tree.layout();
    // Elements like 'labels' depend on the layout type. This exposes a way of identifying the layout type
    layout.type = "vertical";

    var api = apijs (layout)
	.getset ('width', 360)
	.get ('translate_vis', [20,20])
	.method ('diagonal', diagonal.vertical)
	.method ('transform_node', function (d) {
    	    return "translate(" + d.y + "," + d.x + ")";
	});

    api.method('height', function (params) {
    	return (params.n_leaves * params.label_height);
    }); 

    api.method('yscale', function (dists) {
    	return d3.scale.linear()
    	    .domain([0, d3.max(dists)])
    	    .range([0, layout.width() - 20 - layout.max_leaf_label_width()]);
    });

    api.method('adjust_cluster_size', function (params) {
    	var h = layout.height(params);
    	var w = layout.width() - layout.max_leaf_label_width() - layout.translate_vis()[0] - params.label_padding;
    	layout.cluster.size ([h,w]);
    	return layout;
    });

    return layout;
};

tree.layout.radial = function () {
    var layout = tree.layout();
    // Elements like 'labels' depend on the layout type. This exposes a way of identifying the layout type
    layout.type = 'radial';

    var default_width = 360;
    var r = default_width / 2;

    var conf = {
    	width : 360
    };

    var api = apijs (layout)
	.getset (conf)
	.getset ('translate_vis', [r, r]) // TODO: 1.3 should be replaced by a sensible value
	.method ('transform_node', function (d) {
	    return "rotate(" + (d.x - 90) + ")translate(" + d.y + ")";
	})
	.method ('diagonal', diagonal.radial)
	.method ('height', function () { return conf.width });

    // Changes in width affect changes in r
    layout.width.transform (function (val) {
    	r = val / 2;
    	layout.cluster.size([360, r])
    	layout.translate_vis([r, r]);
    	return val;
    });

    api.method ("yscale",  function (dists) {
	return d3.scale.linear()
	    .domain([0,d3.max(dists)])
	    .range([0, r]);
    });

    api.method ("adjust_cluster_size", function (params) {
	r = (layout.width()/2) - layout.max_leaf_label_width() - 20;
	layout.cluster.size([360, r]);
	return layout;
    });

    return layout;
};

module.exports = exports = tree.layout;