Alex Reynolds alexpreynolds

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Pug caregiver, curler, cyclist, gardener, beginning French scholar

alexpreynolds / plotEulergrid.R

Last active December 17, 2015 01:49

plotEulergrid.R

	plotEulergrid <- function (plotTitle, offCellColor, onCellColor, setNames, setCardinalities, setTotal, setTotalWithout, outputFilename, showWholeSets, ctsCardinalities)
	{
	library(grDevices)
	library(gplots)

	showWholeSets <- as.numeric(showWholeSets)
	if (showWholeSets == 1) wholeColors <- c("red", "green", "blue", "darkgoldenrod2", "purple", "grey50", "gold3")

	setTotal <- as.numeric(setTotal)
	unadjSetTotal <- setTotal

alexpreynolds / eulergrid.pl

Last active December 17, 2015 02:29

eulergrid.pl is a wrapper script to call plotEulergrid.R

	#!/usr/bin/env perl

	use warnings;
	use strict;
	use Getopt::Long;

	# -------------------------------------------------------------------------------------------
	# options

	my ($plotTitle, $offCellColor, $onCellColor, $setNames, $setCardinalities, $setTotal, $setTotalWithout, $outputFilename, $showWholeSets, $rGraphScript, $ctsCounts);

alexpreynolds / hg19.gaps.bed

Created July 31, 2013 22:58

Unmappable hg19 regions via UCSC browser search

alexpreynolds / hg19.extents.bed

Created July 31, 2013 23:01

Sorted chromosome extents for hg19 via UCSC genome browser search

alexpreynolds / first_fit.py

Last active December 20, 2015 11:59

First-fit bin packing for gapped genomic data

	#!/usr/bin/env python

	''' Using first-fit bin packing algorithm implementation from: https://bitbucket.org/kent37/python-tutor-samples/src/f657aeba5328/BinPacking.py '''

	class Bin(object):
	def __init__(self):
	self.elements = []
	self.size = 0
	self.index = 0

alexpreynolds / hg19.gapped_extents.bed

Created July 31, 2013 23:06

Chromosome extents for hg19 with unmappable regions removed via BEDOPS partition and difference operations

alexpreynolds / index.html

Created October 29, 2013 20:51

Effect of adding tickSize() to d3 axis

	<!DOCTYPE html>
	<html lang="en">
	<head>
	<meta charset="utf-8">
	<title>D3 Demo: Axes</title>
	<script type="text/javascript" src="http://d3js.org/d3.v3.min.js"></script>
	<style type="text/css">

	.axis path,
	.axis line {

alexpreynolds / consolidate.py

Last active August 29, 2015 13:56

Consolidating genomic elements by ID relationship

alexpreynolds / seqIdTest.mtx

Last active August 29, 2015 13:57

Example sequence identifier adjacency matrix

alexpreynolds / minSeqIdLister.py

Last active August 29, 2015 13:57

Output the minimum value in an adjacency matrix, along with a list of row and column IDs for that minimum value