Farhang Jaryani - Postdoctoral Fellow - farhang.jaryani@bcm.edu, fxjaryan@texaschildrens.org
The Gallo Brain Tumor Research Lab, Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine
This project provides various visualizations of gene similarity based on a similarity matrix calculated between different genes.
- 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.
Here are some sample visualizations generated by the project:
To run the project, the following packages are required (available in requirements.txt):
- seaborn
- matplotlib
- pandas
- click
- numpy
- scipy
- networkx
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Clone the repository.
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Install the necessary dependencies by running:
pip install -r requirements.txt
The package is available on PyPI. You can install it using
pip:pip install gene-similarity
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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.