megaLogo

Table of Contents

• megalogo
  • Table of Contents
    • Introduction and Overview
    • Software Requirements and Dependencies
    • Installation
    • General Usage

• script: megalogo.py

Introduction and Overview

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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 Tonya Brunetti.

Example:

Software Requirements and Dependencies

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For script megalogo.py:

• python >= v3.9
• pandas
• numpy
• matplotlib
• logomaker

Installation

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There is no installation required, please just clone the repository:

git clone https://github.com/meganstumpf/megalogo.git

Then cd into the code directory where all scripts will be present:

cd code  

General Usage

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For using the megalogo.py script, general use is as follows:

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  

Which can also be executed by running the following within the code directory:

./run_test_data.sh

For all possible arguments available, you can run the following:

python3 megalogo.py --help

which will show the following options and their defaults:

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)