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<!DOCTYPE html>
<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
<meta charset="utf-8">
<meta name="generator" content="quarto-1.7.32">
<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
<title>readme</title>
<style>
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</head>
<body class="fullcontent quarto-light">
<div id="quarto-content" class="page-columns page-rows-contents page-layout-article">
<main class="content" id="quarto-document-content">
<div data-align="center">
<p><img src="https://i.postimg.cc/50yrsgpH/megalogo-smaller.jpg" width="200px"> <br></p>
<h1>
megaLogo
</h1>
<p><img src="https://img.shields.io/github/license/meganstumpf/megalogo?style=flat.png" class="img-fluid" alt="GitHub License"> <img src="https://img.shields.io/github/release-date/meganstumpf/megalogo?style=flat.png" class="img-fluid" alt="GitHub Release Date"> <img src="https://img.shields.io/github/v/release/meganstumpf/megalogo?style=flat.png" class="img-fluid" alt="GitHub Release"></p>
</div>
<section id="table-of-contents" class="level2">
<h2 class="anchored" data-anchor-id="table-of-contents">Table of Contents</h2>
<ul>
<li><a href="#megalogo">megalogo</a>
<ul>
<li><a href="#table-of-contents">Table of Contents</a>
<ul>
<li><a href="#introduction-and-overview">Introduction and Overview</a></li>
<li><a href="#software-requirements-and-dependencies">Software Requirements and Dependencies</a></li>
<li><a href="#installation">Installation</a></li>
<li><a href="#general-usage">General Usage</a></li>
</ul></li>
</ul></li>
<li>script: <a href="https://github.com/meganstumpf/megalogo/blob/master/code/megalogo.py">megalogo.py</a></li>
</ul>
</section>
<section id="introduction-and-overview" class="level2">
<h2 class="anchored" data-anchor-id="introduction-and-overview">### Introduction and Overview</h2>
<p>This repository contains code to create large logoplots for deep mutational scanning data with customizability. These plots visualize the absence/presence of amino acid mutations at all mutated codon positions above specified quality and count filters. Made in collaboration with <a href="https://github.com/tbrunetti">Tonya Brunetti</a>.</p>
<section id="example" class="level4">
<h4 class="anchored" data-anchor-id="example">Example:</h4>
<div data-align="left">
<p><img src="https://raw.githubusercontent.com/meganstumpf/megalogo/main/outputs/sample.png" width="400"></p>
</div>
</section>
</section>
<section id="software-requirements-and-dependencies" class="level2">
<h2 class="anchored" data-anchor-id="software-requirements-and-dependencies">### Software Requirements and Dependencies</h2>
<p>For script <code>megalogo.py</code>:</p>
<ul>
<li><a href="https://www.python.org/downloads/">python >= v3.9</a><br>
</li>
<li><a href="https://pandas.pydata.org/docs/getting_started/install.html#installing-from-pypi">pandas</a><br>
</li>
<li><a href="https://numpy.org/install/">numpy</a><br>
</li>
<li><a href="https://matplotlib.org/stable/users/installing/index.html#installation">matplotlib</a></li>
<li><a href="https://pypi.org/project/logomaker/">logomaker</a></li>
</ul>
</section>
<section id="installation" class="level2">
<h2 class="anchored" data-anchor-id="installation">### Installation</h2>
<p>There is no installation required, please just clone the repository:</p>
<pre><code>git clone https://github.com/meganstumpf/megalogo.git</code></pre>
<p>Then cd into the <code>code</code> directory where all scripts will be present:</p>
<pre><code>cd code </code></pre>
</section>
<section id="general-usage" class="level2">
<h2 class="anchored" data-anchor-id="general-usage">### General Usage</h2>
<p>For using the <code>megalogo.py</code> script, general use is as follows:</p>
<pre><code>python3 megalogo.py --input ../test_data/megalogo_test_data.csv --sampleName sample --annotConfig ../ref/annotations_config.csv --refAA ../ref/wildtype.csv --codonStartPos 1 --output ../outputs/sample.png </code></pre>
<p><br></p>
<p>Which can also be executed by running the following within the <code>code</code> directory:</p>
<pre><code>./run_test_data.sh</code></pre>
<p>For all possible arguments available, you can run the following:</p>
<pre><code>python3 megalogo.py --help</code></pre>
<p>which will show the following options and their defaults:</p>
<pre><code>usage: megalogo.py [-h] --input INPUT [--sampleName SAMPLENAME] [--annotConfig ANNOTCONFIG] [--codonStartPos CODONSTARTPOS] [--codonEndPos CODONENDPOS]
[--aaSpacing AASPACING] [--minAnnotLabel MINANNOTLABEL] [--refAA REFAA] --output OUTPUT
Generates logo plot for predefined input matrix
optional arguments:
-h, --help show this help message and exit
--input INPUT
Path to input csv matrix containing data to plot (default: None)
--sampleName SAMPLENAME
String indicating the name to give to sample (default: sample_1)
--annotConfig ANNOTCONFIG
Path to csv containing annotations. Example file located in ref folder of github repo (default: None)
--codonStartPos CODONSTARTPOS
The position of which codon position you want to start at (must be present in your csv matrix provided to --input; default is to plot every
position in your matrix) (default: None)
--codonEndPos CODONENDPOS
The position of which codon position you want to end at (must be present in your csv matrix provided to --input; default is to plot every
position in your matrix) (default: None)
--aaSpacing AASPACING
The number of amino acids to show per line on the logo plot (default: 65)
--minAnnotLabel MINANNOTLABEL
The minimum length of consecutive amino acids under an annotation bar; anything smaller (non-inclusive) than this value will not have text
written in the bar, to help prevent text from overflowing into margins (default: 7)
--refAA REFAA
Path to csv containing reference amino acids with POSITION and REF_AA columns (default: None)
--output OUTPUT
Path to save the output logoplot image (default: None)</code></pre>
</section>
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