Metagenomic Data Analysis and Visualization

This repository contains R and Python scripts for performing comprehensive metagenomic data analysis. The scripts are designed to calculate Alpha & Beta Diversity and create Taxonomy pie charts from ASV and OTU data collected from 16s RNA sequences. This script was were create to create specfic data analysis for one of my project

Features

Alpha Diversity Calculation: Measure the diversity within a single sample. Beta Diversity Calculation: Measure the diversity between different samples. Taxonomy Pie Charts: Visualize the composition of microbial communities.

Installation

To run the scripts, you'll need to have R and Python installed on your system along with the necessary libraries. Follow the instructions below to set up your environment:

R Setup

Install R from CRAN. Install the required R packages:

install.packages(c("phyloseq", "vegan", "ape", "ggplot2", "reshape2", "dplyr", "ggpubr"))

Python Setup

Install Python from Python.org. Install the required Python packages using pip:

pip install numpy pandas matplotlib seaborn

Usage

Running the R Script To calculate Alpha & Beta Diversity and create Taxonomy pie charts using the R script:

source("Alpha_&_Beta_diversity.R")

Running the Python Script To perform additional analysis and visualization with the Python script:

python pie_chart.py

Example plot the script will create

Figure 1: Alpha Diversity

Figure 2: Beta Diversity

Figure 3: Taxonomy Pie Chart

License

This project is licensed under the MIT License - see the LICENSE file for detail