gene-similarity 0.1.0

A package for visualizing gene similarity

Gene Similarity Visualization Project

This project provides various visualizations of gene similarity based on a similarity matrix calculated between different genes.

Features

• Heatmap: Visualizes gene similarity values as a color-coded grid.
• Clustered Dendrogram: Displays hierarchical clustering of genes based on their similarity.
• Network Graph: Visualizes gene pairs as nodes and edges with thickness representing similarity.
• 3D Similarity Matrix: A 3D surface plot where each point represents similarity between two genes.
• Bubble Chart: Represents gene pairs with bubble sizes proportional to similarity values.
• Bar Plot: Shows the average similarity between each gene and all other genes.

Sample Charts

Here are some sample visualizations generated by the project:

1. Heatmap

2. Bubble Chart

3. Network Graph

4. Bar Plot

Requirements

To run the project, the following packages are required (available in requirements.txt):

• seaborn
• matplotlib
• pandas
• click
• numpy
• scipy
• networkx

Usage

1. Clone the repository.

2. Install the necessary dependencies by running:

   pip install -r requirements.txt
   

3. Use the provided command-line interface to generate visualizations by running:

   python -m gene_similarity -f sample_genes_2.fa -l output_folder
   

This will generate various visualizations of gene similarity based on the input data.