# 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:
```bash
pip install -r requirements.txt
```
3. Use the provided command-line interface to generate visualizations by running:
```bash
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.
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