gnn-visualization - SKILL.md Agent Skill

name: gnn-visualization description: GNN graph and matrix visualization generation. Use when creating network graph plots, matrix heatmaps, state space diagrams, or other visual representations of GNN models.

GNN Visualization (Step 8)

Purpose

Generates static visualizations of GNN models including network graphs, matrix heatmaps, state space diagrams, and connection maps using matplotlib and networkx.

Key Commands

# Run visualization
python src/8_visualization.py --target-dir input/gnn_files --output-dir output --verbose

# As part of pipeline
python src/main.py --only-steps 8 --verbose

API

from pathlib import Path
from visualization import (
    GNNVisualizer, MatrixVisualizer,
    generate_graph_visualization, generate_matrix_visualization,
    generate_visualizations, process_visualization,
)

# Use the GNNVisualizer class
viz = GNNVisualizer(output_dir="output/")
viz.generate_graph_visualization(graph_data)
viz.generate_matrix_visualization(matrix_data)

# Standalone functions
generate_graph_visualization(graph_data, output_dir="output/")
generate_matrix_visualization(matrix_data, output_dir="output/")

# Run full visualization step (used by pipeline)
process_visualization(Path("input/gnn_files"), Path("output/8_visualization_output"), verbose=True)

Key Exports

GNNVisualizer — main visualization class
MatrixVisualizer — matrix-specific visualization
generate_graph_visualization — network graph plots
generate_matrix_visualization — matrix heatmaps
process_visualization — pipeline processing (JSON-first when step-3 *_parsed.json exists)

Safe-to-Fail Pattern

Visualization uses a four-tier recovery system:

Full visualizer with all dependencies
Matrix-only visualizer
Basic plots
HTML recovery report

Dependencies

# matplotlib + networkx (included in core)
uv sync

# For additional viz backends
uv sync

Output

PNG/SVG images in output/8_visualization_output/
HTML recovery reports when matplotlib unavailable

MCP Tools

This module registers tools with the GNN MCP server (see mcp.py):

get_visualization_module_info
get_visualization_options
list_visualization_artifacts
process_visualization

References

AGENTS.md — Module documentation
README.md — Usage guide
SPEC.md — Module specification

Documentation

README: Module Overview
AGENTS: Agentic Workflows
SPEC: Architectural Specification
SKILL: Capability API