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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml">
<head>
<meta http-equiv="content-type" content="text/html; charset=utf-8" />
<!--
<meta name="description" content="SourceForge presents the pygrace
project. pygrace is an open source application. SourceForge
provides the world's largest selection of Open Source
Software. A Python package for creating xmgrace files." />
<meta name="keywords" content="Open Source, Software, Development,
Developers, Projects, Downloads, OSTG, VA Software, SF.net,
SourceForge, GNU General Public License (GPL), End
Users/Desktop, Science/Research, Python, Project is a
graphics toolkit, Visualization, OS Independent (Written in
an interpreted language),pygrace" />
-->
<title>pygrace</title>
<link rel="stylesheet" href="pygrace.css" type="text/css" />
<script type="text/javascript">
function on_navigation_click(divtoshow) {
document.getElementById('about').style.display = 'none';
document.getElementById('installation').style.display = 'none';
document.getElementById('session').style.display = 'none';
document.getElementById('templates').style.display = 'none';
document.getElementById('publications').style.display = 'none';
document.getElementById(divtoshow).style.display = 'block';
document.getElementById('about'+'-nav').style.color = 'rgb(0,0,0)';
document.getElementById('installation'+'-nav').style.color = 'rgb(0,0,0)';
document.getElementById('session'+'-nav').style.color = 'rgb(0,0,0)';
document.getElementById('templates'+'-nav').style.color = 'rgb(0,0,0)';
document.getElementById('publications'+'-nav').style.color = 'rgb(0,0,0)';
document.getElementById(divtoshow+'-nav').style.color = 'rgb(255,75,0)';
};
</script>
</head>
<body>
<!-- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ HEADER -->
<div id="header">
<a href=""><img src="images/pygrace.png"/></a>
</div>
<div id="navigation">
<ul>
<li><a href="#" id="about-nav"
onclick="on_navigation_click('about');return
false;">About</a></li>
<li><a href="#" id="installation-nav"
onclick="on_navigation_click('installation');return
false;">Installation</a></li>
<!--
<li><a href="#" id="session-nav"
onclick="on_navigation_click('session');return
false;">Session</a></li>
-->
<li><a href="#" id="templates-nav"
onclick="on_navigation_click('templates');return
false;">Templates</a></li>
<li><a href="#" id="publications-nav"
onclick="on_navigation_click('publications');return
false;">Publications</a></li>
</ul>
</div>
<div id="main">
<!-- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ABOUT -->
<div id="about" class="content">
<!--<h2>About</h2>-->
<p>
The pygrace project is a set of tools designed to
act as an interface between
the <a href="http://www.python.org/">Python</a> programming
language and
the <a href="http://plasma-gate.weizmann.ac.il/Grace/">Grace</a>
plotting tool.
</p>
<p><b>pygrace</b> allows users to create complex Grace files
from within Python.</p><p>It is intended to:
<ul>
<li>assist in the automated creation of many figures for use
in large-scale, exploratory data analysis.</li>
<li>encourage code reuse, by offering an object-oriented
structure.</li>
<li> reduce the time required to create figures for
scientific journal articles.</li>
</ul>
</p>
<p>
<!--pygrace was originally created by <a href="http://datascopeanalytics.com/who-we-are/">Dean Malmgren</a>, <a href="http://datascopeanalytics.com/who-we-are/">Mike Stringer</a>, and-->
pygrace was originally created by Dean Malmgren, Mike Stringer, and
members of the <a href="http://www.amaral-lab.org/">Amaral Lab</a>. When they decided to let pygrace die a slow death, its maintainance was taken over by <a href="http://stoufferlab.org/people/stouffer/">Daniel Stouffer</a> and the <a href="http://stoufferlab.org">Stouffer Lab</a>.
</p>
<p>To get started with pygrace, see the <a href="#"
onclick="on_navigation_click('installation');return
false;">installation guide</a>.</p>
</div>
<!-- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
TUTORIAL -->
<div id="installation" class="content">
<!--
<h2>Tutorial</h2>
-->
<!--
<p>
<b>Important note: As of August 2009, the pygrace package is
in a time of transition. As such, the following tutorial
will be out of date very soon, but will be replaced by a
more comprehensive one. The following tutorial applies to
the pygrace/trunk version of the project.</b>
</p>
-->
<!--
<p>
Visualizing data may be an integral part of the data
analysis process, however, <em>pygrace is
explicity intended to <u>not</u> perform any type of data
analysis</em>, not even computing an average (and especially
not performing a linear regression). This principle
underlies much of the structure of pygrace, with
the purpose discouraging users to adopt a “black
box” approach to analysis. While visualizing data
should be as painless as possible, the pain required to
understand the analysis process is considered necessary, or
even desirable (if you're into that sort of thing).
</p>
-->
<p>
This tutorial is meant to help with installation of pygrace,
and give new users an idea of how pygrace is structured.
After reading this brief document, the next step for
learning to use pygrace is to go through the examples that
are located in the <span class="path"> pygrace
Examples</span> directory.
</p>
<h3>Installation</h3>
<p>
As pygrace is still young, the only method yet available to
install it is to check out the source code from the
git repository at
the <a href="http://github.com/pygrace/pygrace">Github
page</a>. The next section describes how to do so.
</p>
<h3>Installing a development version</h3>
<p>
To clone the pygrace repository, change to a directory where you
want to save the code and type:
</p>
<span class="command">
git clone https://github.com/pygrace/pygrace.git
</span>
<p>
To install pygrace, all you need to do is enter into the pygrace directory you just created and run setup.py:
</p>
<span class="command">
cd pygrace</br>
python setup.py install
</span>
<p>
By default, Python will attempt to install pygrace in the global Python site-packages directory. If you don't have permissions to do this (or prefer not to install pygrace globally), you can <a href="http://docs.python.org/2/install/index.html#alternate-installation-the-user-scheme">install it locally by adding the --user option</a>:
</p>
<span class="command">
python setup.py install --user
</span>
<p>
You can test that python can find the
pygrace package by opening an interactive python prompt and
typing:
</p>
<span class="command">
import PyGrace
</span>
<p>
If no error is raised, then installation was succesful!
</p>
<h3>Getting started</h3>
<p>
pygrace was designed so that, “anything you can do in
Grace, you can do in pygrace.” The best way to get
started is to go through the examples in the Examples
directory. Each example is fully commented. You may also
find the following three documents helpful:
</p>
<ul>
<li>
<a class="installationdiagram"
href="crow.pdf">
<img class="installationimage" src="images/crow.png"/>
<span class="title">
pygrace templates entity-relationship diagram
</span>
<span class="caption">
The inheritance structure of pygrace templates mirrors the file
structure of Grace. This diagram uses “crow's
foot” notation to indicate the relationship
between different entities. One thing to note is that
Drawing Objects can be associated with either a Grace or
a Graph. This is important in cases where one wants to,
e.g., create a custom data symbol and have the symbol
show up in the coordinate system of a graph.
</span>
</a>
</li>
<li>
<a class="installationlink"
href="cheatsheet.pdf">
<img class="installationimage" src="images/cheatsheet.png"/>
<span class="title">
pygrace templates Cheatsheet
</span>
<span class="caption">
This handy cheatsheet shows the all of the methods and
attributes of each pygrace templates class. It can be generated
for any custom template by calling the write_cheatsheet
method.
</span>
</a>
</li>
<li>
<a class="installationlink"
href="fulldiagram.pdf">
<img class="installationimage" src="images/fulldiagram.png"/>
<span class="title">
pygrace templates attribute diagram
</span>
<span class="caption">
This is a detailed diagram that shows all of the
attributes of the standard pygrace templates objects.
</span>
</a>
</li>
</ul>
By refering to these diagrams and going through the examples,
you can develop a sense of how to use pygrace. Please let us know what you think and
report bugs using <a href="http://github.com/pygrace/pygrace/issues">the GitHub page</a>.
</div>
<!-- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ SESSION -->
<div id="session" class="content">
<!--
<h2>Examples</h2>
-->
<p>
TBD.
</p>
</div>
<!-- +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ TEMPLATES -->
<div id="templates" class="content">
<!--
<h2>Examples</h2>
-->
<p>
Here are some examples of the types of figures that you can
create with pygrace templates. If you are interested in
contributing a screenshot of a figure made in pygrace templates,
<a href="mailto:pygrace@stoufferlab.org">contact us</a>.
</p>
<div class="screenshot">
<a href="images/block_network-math.png"><img src="images/block_network-math_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed by <a href="http://amaral.chem-eng.northwestern.edu/people/guimera/">Roger Guimera</a>
</div>
-->
</div>
<div class="screenshot">
<a href="images/time_series_diagram.png"><img src="images/time_series_diagram_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://amaral.chem-eng.northwestern.edu/people/stringer/">Mike Stringer</a>
</div>
-->
</div>
<div class="screenshot">
<a href="images/sweetdash.png"><img src="images/sweetdash_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://amaral.chem-eng.northwestern.edu/people/malmgren/">Dean Malmgren</a>
</div>
-->
</div>
<div class="bottom"></div>
<div class="screenshot">
<a href="images/bayes.png"><img src="images/bayes_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://amaral.chem-eng.northwestern.edu/people/stringer/">Mike Stringer</a>
</div>
-->
</div>
<div class="screenshot">
<a href="images/bootstrap.png"><img src="images/bootstrap_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://amaral.chem-eng.northwestern.edu/people/malmgren/">Dean Malmgren</a>
</div>
-->
</div>
<div class="screenshot">
<a href="images/transfernet.png"><img src="images/transfernet_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://amaral.chem-eng.northwestern.edu/people/sirer/">Irmak Sirer</a>
</div>
-->
</div>
<div class="bottom"></div>
<div class="screenshot">
<a href="images/mutualinfo.png"><img src="images/mutualinfo_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://amaral.chem-eng.northwestern.edu/people/sirer/">Irmak Sirer</a>
</div>
-->
</div>
<div class="screenshot">
<a href="images/crosscorrelation.png"><img src="images/crosscorrelation_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://amaral.chem-eng.northwestern.edu/people/campanharo/">Andriana Campanharo</a>
</div>
-->
</div>
<div class="screenshot">
<a href="images/density.png"><img src="images/density_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://amaral.chem-eng.northwestern.edu/people/stringer/">Mike Stringer</a>
</div>
-->
</div>
<div class="bottom"></div>
<div class="screenshot">
<a href="images/08_latexlabels.png"><img src="images/08_latexlabels_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://pygrace.svn.sourceforge.net/viewvc/pygrace/trunk/Examples/08_latexlabels.py?view=markup">pygrace</a>
</div>
-->
</div>
<div class="screenshot">
<a href="images/quintiles.png"><img src="images/quintiles_small.png" alt=""/></a>
<!--
<div class="contributor">
Contributed
by <a href="http://amaral.chem-eng.northwestern.edu/people/stringer/">Mike Stringer</a>
</div>
-->
</div>
<div class="bottom"></div>
</div>
<!-- ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ PUBLICATIONS -->
<div id="publications" class="content">
<!--<h2>Publications</h2>-->
<p>If you use pygrace in a scientific publication, please let
us know and we will add a link to your publication on this
page (where <em>everybody</em> will see it).</p>
<ul>
<li>
<a class="publink"
href="http://dx.doi.org/10.1126/science.1216556">
<img class="pubimage" src="images/daniel-science.gif"/>
<span class="title">
Evolutionary conservation of species' roles in food webs
</span>
<span class="authors">
Stouffer DB, Sales-Pardo M, Sirer MI, Bascompte J
</span>
<span class="journal">
Science
</span>
<span class="volumepage">
335(6075): 1489-1492
</span>
<span class="year">
2012
</span>
</a>
</li>
<li>
<a class="publink"
href="http://dx.doi.org/10.1038/nature10433">
<img class="pubimage" src="images/saavedra-nature.jpg"/>
<span class="title">
Strong contributors to network persistence are the most vulnerable to extinction
</span>
<span class="authors">
Saavedra S, Stouffer DB, Uzzi B, Bascompte J
</span>
<span class="journal">
Nature
</span>
<span class="volumepage">
478(7368): 233-235
</span>
<span class="year">
2011
</span>
</a>
</li>
<li>
<a class="publink"
href="http://dx.doi.org/10.1371/journal.pone.0023378">
<img class="pubimage" src="images/journal.pone.0023378.g009.png"/>
<span class="title">
Duality between time series and networks
</span>
<span class="authors">
Campanharo ASLO, Sirer MI, Malmgren RD, Ramos FM, Amaral LAN
</span>
<span class="journal">
PLoS One
</span>
<span class="volumepage">
6(8): e23378
</span>
<span class="year">
2011
</span>
</a>
</li>
<li>
<a class="publink"
href="http://dx.doi.org/10.1111/j.1365-2656.2011.01812.x">
<img class="pubimage" src="images/daniel-jae.gif"/>
<span class="title">
The role of body mass in diet contiguity and food-web structure
</span>
<span class="authors">
Stouffer DB, Rezende EL, Amaral LAN
</span>
<span class="journal">
J. Anim. Ecol.
</span>
<span class="volumepage">
80(3): 632-639
</span>
<span class="year">
2011
</span>
</a>
</li>
<li>
<a class="publink"
href="http://dx.doi.org/10.1073/pnas.1014353108">
<img class="pubimage" src="images/daniel-pnas.gif"/>
<span class="title">
Compartmentalization increases food-web persistence
</span>
<span class="authors">
Stouffer DB, Bascompte J
</span>
<span class="journal">
Proc. Natl. Acad. Sci. USA
</span>
<span class="volumepage">
108(9): 3648-3652
</span>
<span class="year">
2011
</span>
</a>
</li>
<li>
<a class="publink"
href="http://dx.doi.org/10.1038/nature09040">
<img class="pubimage" src="images/dean-nature.jpg"/>
<span class="title">
The role of mentorship in protégé performance
</span>
<span class="authors">
Malmgren RD, Ottino JM, Amaral LAN
</span>
<span class="journal">
Nature
</span>
<span class="volumepage">
465(7298): 622-626
</span>
<span class="year">
2010
</span>
</a>
</li>
<li>
<a class="publink"
href="http://dx.doi.org/10.1126/science.1174562">
<img class="pubimage" src="images/dean-science.gif"/>
<span class="title">
On universality in human correspondence activity
</span>
<span class="authors">
Malmgren RD, Stouffer DB, Campanharo ASLO, Amaral LAN
</span>
<span class="journal">
Science
</span>
<span class="volumepage">
325(5948): 1696-1700
</span>
<span class="year">
2009
</span>
</a>
</li>
<li>
<a class="publink"
href="http://arxiv.org/abs/0905.0106">
<img class="pubimage" src="images/dean-arxiv.png"/>
<span class="title">
Characterizing individual communication patterns
</span>
<span class="authors">
Malmgren RD, Hofman JM, Amaral LAN, Watts DJ
</span>
<span class="journal">
Proc. ACM SIGKDD
</span>
<span class="volumepage">
607-616
</span>
<span class="year">
2009
</span>
</a>
</li>
<li>
<a class="publink"
href="http://dx.doi.org/10.1073/pnas.0800332105">
<img class="pubimage" src="images/dean-pnas.png"/>
<span class="title">
A Poissonian explanation for heavy tails in e-mail
communication
</span>
<span class="authors">
Malmgren RD, Stouffer DB, Motter AE, Amaral LAN
</span>
<span class="journal">
Proc. Natl. Acad. Sci. USA
</span>
<span class="volumepage">
105(47): 18153-18158
</span>
<span class="year">
2008
</span>
</a>
</li>
<li>
<a class="publink"
href="http://dx.plos.org/10.1371/journal.pone.0001683">
<img class="pubimage" src="images/mike-plosone.png"/>
<span class="title">
Effectiveness of Journal Ranking Schemes as a Tool for
Locating Information
</span>
<span class="authors">
Stringer MJ, Sales-Pardo M, Amaral LAN
</span>
<span class="journal">
PLoS ONE
</span>
<span class="volumepage">
3(2): e168
</span>
<span class="year">
2008
</span>
</a>
</li>
</ul>
</div>
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