clustergrammer/src/dendrogram/binom_test.js

This is a clustergram implemented in D3.js. I started from the example http://bost.ocks.org/mike/miserables/ and added the following features

// Load the math.js core
// Create a new, empty math.js instance
// It will only contain methods `import` and `config`
// math.import(require('mathjs/lib/type/fraction'));
var p_dict = require('./binom_prop_pval_lookup');
var core = require('mathjs/core');
var math = core.create();

math.import(require('mathjs/lib/function/probability/factorial'));

module.exports = function binom_test(actual_k, n, p){

  var fact = math.factorial;
  var pval;

  function binom_dist(k, n, p){
    var bin_coeff = (fact(n))/( fact(k) * fact(n-k) );
    p = bin_coeff * (Math.pow(p, k) * Math.pow((1 - p), (n-k)) );
    return p;
  }

  function my_binom_test_2(actual_k, n, p){
    var cp = 0;
    var k;
    var dp;
    for (var inst_k=actual_k; inst_k < n+1; inst_k++ ){
      k = inst_k;
      dp = binom_dist(k, n, p);
      cp = cp + dp;
    }

    return cp;

  }

  // look up p-value from z-score using table
  function binom_prop_table(actual_k, n, p){

    // expected average number of successes
    var mu = n * p;

    // standard deviation
    var sigma = Math.sqrt(n * p * (1 - p));

    // how many standard deviations is the actual_k away
    // from the expected value
    var z = (actual_k - mu)/sigma;

    var z_vals = p_dict.z;
    var p_vals = p_dict.p;

    var found_index = -1;
    var found = false;

    for (var index=0; index < z_vals.length; index++){
      var inst_z = z_vals[index];

      // increasing inst_z until z is less than inst_z
      if (z < inst_z && found === false){
        found_index = index;
        found = true;
      }
    }

    // give it the smallest p-val if the z-score was larger than
    // any in the table
    if (found_index === -1){
      found_index = z_vals.length - 1;
    }
    pval = p_vals[found_index];

    return pval;

  }

  // calculate pval
  pval = my_binom_test_2(actual_k, n, p);
  if ( isNaN(pval) ){
    pval = binom_prop_table(actual_k, n, p);
  }

  return pval;

};