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Visualization Module Specification

Overview

Step-8 visualization: graphs, matrices, combined analysis. Prefers step-3 {model}_parsed.json; falls back to markdown parsing.

Layout

Package / file Responsibility
core/process.py Orchestration, per-file pipeline, sampling
core/parsed_model.py load_visualization_model, step-3 path resolution
parse/markdown.py parse_gnn_content explicit raw-Markdown parser
parse/gnn_file_parser.py GNNParser (file / CSV-oriented API)
plotting/utils.py Matplotlib Agg, save/tight_layout helpers
graph/network_visualizations.py Directed vs undirected edges, ontology labels
graph/bipartite.py Variable–parameter bipartite sketch
matrix/visualizer.py MatrixVisualizer facade, module generate_matrix_visualizations
matrix/extract.py convert_to_matrix, parameter extraction
matrix/compat.py parse_matrix_data (markdown matrices), batch generate_matrix_visualizations
analysis/combined_analysis.py Combined and cross-file plots
ontology/visualizer.py Ontology table / annotations
compat/viz_compat.py Shared plt / np / sns for step 8 and analysis
Root entry points processor.py, matrix_visualizer.py, parser.py, network_visualizations.py, combined_analysis.py, ontology_visualizer.py, _viz_compat.py

Visualization types

  • Matrix heatmaps and 3D POMDP transition views
  • Connection graphs (respecting connection_type)
  • Combined analysis and generative-model schematic
  • Optional Plotly HTML network

Key exports

from visualization import process_visualization, MatrixVisualizer
from visualization.processor import parse_gnn_content, save_plot_safely
from visualization.parse import GNNParser, parse_gnn_content

Documentation