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vsbuffalo/coal.js

Created April 21, 2015 03:25
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dancing genealogies
Raw
coal.js
function range(from, to, by) {
var by = typeof(by) === 'undefined' ? 1 : by;
var out = [];
for (var i = from; i <= to; i += by) out.push(i);
return out;
}
function sampleArrayWithoutReplacement(x, n) {
n = typeof x === 'undefined' ? 1 : n;
var sample = [];
if (n > x.length) throw new Error("n must be <= length of x");
while (n) {
sample.push(x.splice(Dist.dunif(0, x.length-1), 1)[0]);
n--;
}
return sample;
}
function CoalescentGenealogy(k) {
var geno = [], samples = range(0, k-1).map(function(o) {return {name: o};});
var coal, coal_time, total_time = 0, coal_times =
range(2, k).map(function(i) { return Dist.exp(i*(i-1)/2); });
// draw two lineages two coalesce, and pop up a coalescent time for them
while (coal_times.length) {
coal_time = coal_times.pop();
total_time += coal_time;
coal = {total_time: total_time,
coal_time: coal_time,
children: sampleArrayWithoutReplacement(samples, 2)};
samples.push(coal);
}
return samples[0];
}
/// Test
var margin = {top: 40, right: 10, bottom: 20, left: 10},
width = 800 - margin.right - margin.left,
height = 500 - margin.top - margin.bottom;
var tree_height = 0.9*height;
var svg = d3.select("body").append("svg")
.attr("width", width + margin.right + margin.left)
.attr("height", height + margin.top + margin.bottom);
// Test
function randomGenealogy() {
var coal = CoalescentGenealogy(9),
nodes = GenealogyTree(coal).nodes();
var tree = d3.layout.tree();
function xScale(x) {
return width*x;
}
function yScale(y) {
return tree_height*y;
}
svg.selectAll("*").remove();
svg.selectAll("circles")
.data(GenealogyTree(coal).nodes())
.enter().append("circle")
.attr("id", function(o) { return "ct" + o.coal_time; })
.attr("cx", function(o) { return xScale(o.x); })
.attr("cy", function(o) { return tree_height - yScale(o.y); })
.attr("r", 1)
.style("fill", "gray");
svg.selectAll("polyline")
.data(GenealogyTree(coal).links())
.enter().append("polyline")
.attr("points", function(n) {
var points = [[xScale(n.parent.x), tree_height-yScale(n.parent.y)],
[xScale(n.child.x), tree_height-yScale(n.parent.y)],
[xScale(n.child.x), tree_height-yScale(n.child.y)]];
return points.map(function(x) { return x.join(",") }).join(" ");
})
.style("fill", "none")
.style("stroke-width", 2)
.style("stroke", "gray");
svg.selectAll("text")
.data(GenealogyTree(coal).nodes())
.enter().append("text")
.filter(function(x) { return typeof x.children === 'undefined'; })
.attr("y", function(n) { return 16 + tree_height-yScale(n.y); })
.attr("x", function(n) { return -4 + xScale(n.x); })
.text(function(n) { return n.name; })
.style("fill", "gray");
}
randomGenealogy();
window.setInterval(randomGenealogy, 1000);
// svg.selectAll("lines")
// .data(GenealogyTree(coal).links())
// .enter().append("line")
// .attr({
// x1: function(n) { return xScale(n.parent.x); },
// x2: function(n) { return xScale(n.child.x); },
// y1: function(n) { return height - yScale(n.parent.y); },
// y2: function(n) { return height - yScale(n.child.y); }
// })
// .style("fill", "none")
// .style("stroke", "gray")
// .style("stroke-opacity", 0.4);
Raw
dist.js
var m = new MersenneTwister();
var Dist = (function(unif) {
// discrete uniform
function dunif(min, max) {
return Math.floor(m.random() * (max - min)) + min;
};
// Poisson rv
function pois(lambda) {
var n = 0,
limit = Math.exp(-lambda),
x = m.random();
while (x > limit) {
n++;
x *= m.random();
}
return n;
};
// Exponential rv
function exp(lambda) {
return -Math.log(m.random())/lambda;
};
function bern(p) {
return Number(m.random() < p);
};
// binomial rv
function binom(n, p) {
var x = 0;
for (var i = 0; i < n; i++) x += bern(p);
return x;
};
return {dunif: dunif,
pois: pois,
exp: exp,
bern: bern,
binom: binom};
})();
Raw
index.html
<!DOCTYPE html>
<html lang="en">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
<link rel="stylesheet" type="text/css" href="style.css"/>
<script language="JavaScript" src="http://d3js.org/d3.v3.min.js"></script>
<script language="JavaScript" src="mersenne-twister.js"></script>
<script language="JavaScript" src="dist.js"></script>
<script language="JavaScript" src="tree.js"></script>
<title>Tree Visualization</title>
</head>
<body>
<p> Below are random neutral coalescent genealogies for a sample of nine
individuals:</p>
<script language="JavaScript" src="coal.js"></script>
</body>
</html>
Raw
mersenne-twister.js
/*
I've wrapped Makoto Matsumoto and Takuji Nishimura's code in a namespace
so it's better encapsulated. Now you can have multiple random number generators
and they won't stomp all over eachother's state.
If you want to use this as a substitute for Math.random(), use the random()
method like so:
var m = new MersenneTwister();
var randomNumber = m.random();
You can also call the other genrand_{foo}() methods on the instance.
If you want to use a specific seed in order to get a repeatable random
sequence, pass an integer into the constructor:
var m = new MersenneTwister(123);
and that will always produce the same random sequence.
Sean McCullough ([email protected])
*/
/*
A C-program for MT19937, with initialization improved 2002/1/26.
Coded by Takuji Nishimura and Makoto Matsumoto.
Before using, initialize the state by using init_genrand(seed)
or init_by_array(init_key, key_length).
Copyright (C) 1997 - 2002, Makoto Matsumoto and Takuji Nishimura,
All rights reserved.
Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions
are met:
1. Redistributions of source code must retain the above copyright
notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright
notice, this list of conditions and the following disclaimer in the
documentation and/or other materials provided with the distribution.
3. The names of its contributors may not be used to endorse or promote
products derived from this software without specific prior written
permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Any feedback is very welcome.
http://www.math.sci.hiroshima-u.ac.jp/~m-mat/MT/emt.html
email: m-mat @ math.sci.hiroshima-u.ac.jp (remove space)
*/
var MersenneTwister = function(seed) {
if (seed == undefined) {
seed = new Date().getTime();
}
/* Period parameters */
this.N = 624;
this.M = 397;
this.MATRIX_A = 0x9908b0df; /* constant vector a */
this.UPPER_MASK = 0x80000000; /* most significant w-r bits */
this.LOWER_MASK = 0x7fffffff; /* least significant r bits */
this.mt = new Array(this.N); /* the array for the state vector */
this.mti=this.N+1; /* mti==N+1 means mt[N] is not initialized */
this.init_genrand(seed);
}
/* initializes mt[N] with a seed */
MersenneTwister.prototype.init_genrand = function(s) {
this.mt[0] = s >>> 0;
for (this.mti=1; this.mti<this.N; this.mti++) {
var s = this.mt[this.mti-1] ^ (this.mt[this.mti-1] >>> 30);
this.mt[this.mti] = (((((s & 0xffff0000) >>> 16) * 1812433253) << 16) + (s & 0x0000ffff) * 1812433253)
+ this.mti;
/* See Knuth TAOCP Vol2. 3rd Ed. P.106 for multiplier. */
/* In the previous versions, MSBs of the seed affect */
/* only MSBs of the array mt[]. */
/* 2002/01/09 modified by Makoto Matsumoto */
this.mt[this.mti] >>>= 0;
/* for >32 bit machines */
}
}
/* initialize by an array with array-length */
/* init_key is the array for initializing keys */
/* key_length is its length */
/* slight change for C++, 2004/2/26 */
MersenneTwister.prototype.init_by_array = function(init_key, key_length) {
var i, j, k;
this.init_genrand(19650218);
i=1; j=0;
k = (this.N>key_length ? this.N : key_length);
for (; k; k--) {
var s = this.mt[i-1] ^ (this.mt[i-1] >>> 30)
this.mt[i] = (this.mt[i] ^ (((((s & 0xffff0000) >>> 16) * 1664525) << 16) + ((s & 0x0000ffff) * 1664525)))
+ init_key[j] + j; /* non linear */
this.mt[i] >>>= 0; /* for WORDSIZE > 32 machines */
i++; j++;
if (i>=this.N) { this.mt[0] = this.mt[this.N-1]; i=1; }
if (j>=key_length) j=0;
}
for (k=this.N-1; k; k--) {
var s = this.mt[i-1] ^ (this.mt[i-1] >>> 30);
this.mt[i] = (this.mt[i] ^ (((((s & 0xffff0000) >>> 16) * 1566083941) << 16) + (s & 0x0000ffff) * 1566083941))
- i; /* non linear */
this.mt[i] >>>= 0; /* for WORDSIZE > 32 machines */
i++;
if (i>=this.N) { this.mt[0] = this.mt[this.N-1]; i=1; }
}
this.mt[0] = 0x80000000; /* MSB is 1; assuring non-zero initial array */
}
/* generates a random number on [0,0xffffffff]-interval */
MersenneTwister.prototype.genrand_int32 = function() {
var y;
var mag01 = new Array(0x0, this.MATRIX_A);
/* mag01[x] = x * MATRIX_A for x=0,1 */
if (this.mti >= this.N) { /* generate N words at one time */
var kk;
if (this.mti == this.N+1) /* if init_genrand() has not been called, */
this.init_genrand(5489); /* a default initial seed is used */
for (kk=0;kk<this.N-this.M;kk++) {
y = (this.mt[kk]&this.UPPER_MASK)|(this.mt[kk+1]&this.LOWER_MASK);
this.mt[kk] = this.mt[kk+this.M] ^ (y >>> 1) ^ mag01[y & 0x1];
}
for (;kk<this.N-1;kk++) {
y = (this.mt[kk]&this.UPPER_MASK)|(this.mt[kk+1]&this.LOWER_MASK);
this.mt[kk] = this.mt[kk+(this.M-this.N)] ^ (y >>> 1) ^ mag01[y & 0x1];
}
y = (this.mt[this.N-1]&this.UPPER_MASK)|(this.mt[0]&this.LOWER_MASK);
this.mt[this.N-1] = this.mt[this.M-1] ^ (y >>> 1) ^ mag01[y & 0x1];
this.mti = 0;
}
y = this.mt[this.mti++];
/* Tempering */
y ^= (y >>> 11);
y ^= (y << 7) & 0x9d2c5680;
y ^= (y << 15) & 0xefc60000;
y ^= (y >>> 18);
return y >>> 0;
}
/* generates a random number on [0,0x7fffffff]-interval */
MersenneTwister.prototype.genrand_int31 = function() {
return (this.genrand_int32()>>>1);
}
/* generates a random number on [0,1]-real-interval */
MersenneTwister.prototype.genrand_real1 = function() {
return this.genrand_int32()*(1.0/4294967295.0);
/* divided by 2^32-1 */
}
/* generates a random number on [0,1)-real-interval */
MersenneTwister.prototype.random = function() {
return this.genrand_int32()*(1.0/4294967296.0);
/* divided by 2^32 */
}
/* generates a random number on (0,1)-real-interval */
MersenneTwister.prototype.genrand_real3 = function() {
return (this.genrand_int32() + 0.5)*(1.0/4294967296.0);
/* divided by 2^32 */
}
/* generates a random number on [0,1) with 53-bit resolution*/
MersenneTwister.prototype.genrand_res53 = function() {
var a=this.genrand_int32()>>>5, b=this.genrand_int32()>>>6;
return(a*67108864.0+b)*(1.0/9007199254740992.0);
}
/* These real versions are due to Isaku Wada, 2002/01/09 added */
Raw
style.css
body {
font-family: "Helvetica Neue", Helvetica, sans-serif;
margin: 1em auto 4em auto;
color: #333;
width: 960px;
}
h1 {
font-weight: 400;
}
h2 {
font-weight: 400;
}
h3 {
font-weight: 400;
padding-bottom: 0em;
margin-bottom: 0em;
}
.button {
font-weight: 200;
padding: .5em 1em;
color: #444;
color: rgba(0,0,0,.8);
border: 1px solid #999;
border: 0 rgba(0,0,0,0);
background-color: #E6E6E6;
text-decoration: none;
border-radius: 2px;
}
.button:hover {
background-color: #ddd;
}
body > p {
width: 720px;
}
Raw
tree.js
function range(from, to, by) {
var by = typeof(by) === 'undefined' ? 1 : by;
var out = [];
for (var i = from; i <= to; i += by) out.push(i);
return out;
}
function countLeaves(tree) {
var count = 0;
function leafCounter(subtree) {
if (typeof subtree.children === 'undefined') {
count++;
return;
}
subtree.children.forEach(function(l) {
leafCounter(l);
});
}
leafCounter(tree);
return count;
}
function depth(depth) {
var tmp = function(x) { return x.depth == depth; };
return tmp;
}
function GenealogyTree(tree, options) {
if (typeof options === 'undefined')
options = {stem:0.1}; // TODO
// functions for recursing through a tree (nested object) and grabbing all
// edges and nodes.
// Coal time parameters
var t_time = tree.total_time;
var max_depth = 0, depth = 0, left_depth, right_depth;
function maxDepth(node) {
if (node.children) {
node.children[0].depth = node.depth + 1;
node.children[1].depth = node.depth + 1;
left_depth = maxDepth(node.children[0]);
right_depth = maxDepth(node.children[1]);
if (left_depth > right_depth)
return left_depth + 1;
else
return right_depth + 1;
} else {
return 0;
}
};
tree.depth = 1;
max_depth = maxDepth(tree); // get total time by recursing tree
function nodes() {
// Get all nodes in a nice array. This has side effects: it will append
// slots.
var _nodes = [], depth = 0, center = 0.5/max_depth,
ymax = t_time/(1-options.stem);
var get_nodes = function(node, slots, is_left) {
node.is_left = is_left;
node.slots = slots.slice(0);
node.y = typeof node.coal_time==='undefined' ? 0 : node.total_time/ymax;
_nodes.push(node);
if (node.children) {
if (node.children.length != 2)
throw new Error("length children != 2");
// get the nodes for left and right children
var left = node.children[0];
var right = node.children[1];
var left_slots = slots.splice(0, countLeaves(left));
var right_slots = slots.splice(0, countLeaves(right));
left.x = node.x - center/node.depth;
right.x = node.x + center/node.depth;
get_nodes(left, left_slots, true);
get_nodes(right, right_slots, false);
}
//console.log(center);
};
tree.x = 0.5;
get_nodes(tree, range(0, countLeaves(tree)-1), null);
return _nodes;
};
function links() {
// get all edges as a link (parent |---| child) for all nodes, return in
// arary
var _edges = [];
var get_edges = function(node, depth) {
var depth = typeof depth == 'undefined' ? 0 : depth + 1;
if (typeof node.children != 'undefined') {
node.children.forEach(function(b) {
var edge = {
parent: node,
child: b,
depth: depth
};
_edges.push(edge);
get_edges(b, depth);
});
}
};
get_edges(tree);
return _edges;
};
return {max_depth: max_depth, total_time: t_time, tree: tree, nodes: nodes, links: links};
}
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