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Jalil F. jfarid27

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jfarid27 / tsvdatagen.py
Last active December 20, 2015 18:49
fake data generator in tsv format for heatmap testing.
"""
Random Number generator for tsv format data.
Calling method: 'python tsvdatagen.py <rows> <columns> <outputfilename.ext>'
Arguments:
"""
@jfarid27
jfarid27 / Heatmap.js
Last active December 22, 2015 22:39 — forked from correiak/Heatmap.js
D3 code for visualizing microarray clustering data.
var newdata;
var scope = new Object();
scope.marginleft = 400;
scope.marginright = 80;
scope.margintop = 300;
scope.marginbottom = 80;
scope.width = 1200;
scope.height = 1100;
scope.showlabels = true;
@jfarid27
jfarid27 / d3.layout.min.js
Last active December 27, 2015 02:29
Jason Davies style radial phylogenetic tree. source: http://www.jasondavies.com/tree-of-life/
(function(){function a(a){var b=a.source,d=a.target,e=c(b,d),f=[b];while(b!==e)b=b.parent,f.push(b);var g=f.length;while(d!==e)f.splice(g,0,d),d=d.parent;return f}function b(a){var b=[],c=a.parent;while(c!=null)b.push(a),a=c,c=c.parent;return b.push(a),b}function c(a,c){if(a===c)return a;var d=b(a),e=b(c),f=d.pop(),g=e.pop(),h=null;while(f===g)h=f,f=d.pop(),g=e.pop();return h}function g(a){a.fixed|=2}function h(a){a!==f&&(a.fixed&=1)}function i(){j(),f.fixed&=1,e=f=null}function j(){f.px=d3.event.x,f.py=d3.event.y,e.resume()}function k(a,b,c){var d=0,e=0;a.charge=0;if(!a.leaf){var f=a.nodes,g=f.length,h=-1,i;while(++h<g){i=f[h];if(i==null)continue;k(i,b,c),a.charge+=i.charge,d+=i.charge*i.cx,e+=i.charge*i.cy}}if(a.point){a.leaf||(a.point.x+=Math.random()-.5,a.point.y+=Math.random()-.5);var j=b*c[a.point.index];a.charge+=a.pointCharge=j,d+=j*a.point.x,e+=j*a.point.y}a.cx=d/a.charge,a.cy=e/a.charge}function l(a){return 20}function m(a){return 1}function o(a){return a.x}function p(a){return a.y}function q(a,b,c)
@jfarid27
jfarid27 / unpack.sh
Last active December 29, 2015 12:09
sudo apt-get update
sudo apt-get upgrade
#Version Control
sudo apt-get install -y git gitk xxdiff
#Python Stuff
sudo apt-get install -y python ipython-notebook ipython python-numpy python-scipy python-matplotlib python-dev python-sphinx python-setuptools nose
sudo apt-get install -y gfortran openmpi-bin liblapack-dev
sudo apt-get install -y xxdiff
@jfarid27
jfarid27 / block_matching.m
Created May 26, 2014 15:17
Some imaging files written for matlab.
function [ tlc , error ] = block_matching(target, reference, error_func)
dims = size(reference);
target_size = size(target);
range = [dims(1)-target_size(1), dims(2)-target_size(1) ];
zeroes = zeros(range);
for i=1:range(1)
@jfarid27
jfarid27 / bufferDataEmitter.js
Last active August 29, 2015 14:08
Observable Buffer?
var events = require('events'),
util = require('util');
var bufferDataEmitter = function(stream){
var self = this;
events.EventEmitter.call(self)
var buffer = [];
stream.on('data', function(chunk){
@jfarid27
jfarid27 / readableStreamAccumulator.js
Created October 31, 2014 18:16
Node.js readableStreamAccumulator
var events = require('events'),
util = require('util')
var readableStreamAccumulator = function (readableStream){
var self = this
events.EventEmitter.call(self)
self.cache = []
@jfarid27
jfarid27 / histogram.js
Created November 27, 2014 05:07
a d3 histogram prototype
d3.custom = {}
d3.custom.histogram = function module() {
var width = 600,
height = 600,
margin = {
top: 10,
bottom: 10,
left: 10,
right: 10,
@jfarid27
jfarid27 / gulpfile.js
Created January 14, 2015 23:13
prototype gulpfile.js
var gulp = require('gulp'),
gutil = require('gulp-util'),
gbower = require('gulp-bower'),
bower = require('bower'),
fs = require('fs'),
del = require('del');
gulp.task('default', ['test'], function(){
return
})
@jfarid27
jfarid27 / gulp_chunk.js
Last active August 29, 2015 14:13
gulputil vinyl file pipe to destination
var configString = head + body + footer
var buffer = new Buffer(configString)
var file = new gutil.File({contents:buffer, path:'karma.config.js'})
function readableWrapper(params, options){
Readable.call(this, options)
this._params = params