visualization the attention across genes #108
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Reorganize documentation by adding README.md and visualization directory, remove outdated tutorial scripts, and update PyG dataset and training modules. Add requirements.txt for dependency management.
…sualization modules - Delete main.py and reorganize notebook structure - Add new clustering analysis scripts (gene, cell, and combined clustering) - Add dataset processing and comparison utilities - Update spatial and gene visualization modules with improved documentation - Enhance visualization functions with better parameter descriptions and type hints
- Add compare_cell_clustering.py to evaluate clustering vs annotated cell types - Add run_gene_cell_clustering.py and run_gene_clustering.py for modular analysis - Rename main.py to process_dataset.py for clarity - Add test_dendrogram_ordering.py for clustering validation - Add gene_cell_clustering.py visualization module - Update existing visualization modules and spatial plotting functionality
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