---

name: fixture-graph
description: >
Generate publication-quality figures from code analysis data.
Multi-backend: Graphviz, Mermaid, NetworkX/D3, matplotlib, plotly, seaborn.
Supports aerospace, nuclear, military, and mathematics visualization types.
Integrates pydeps, pyreverse, python-control, and lean4-prove.
allowed-tools: Bash, Read
triggers:
# General
- generate figures
- create diagram
- make chart
- publication figure
- IEEE figure
# Architecture & Code
- architecture diagram
- dependency graph
- class diagram
- UML diagram
- module dependencies
- workflow diagram
- pipeline diagram
# Metrics & Data
- metrics visualization
- bar chart
- pie chart
- line chart
- heatmap
- correlation matrix
# Hierarchical
- treemap
- sunburst chart
- fault tree
- breakdown chart
# Network & Graph
- force directed graph
- network diagram
- system topology
- PERT network
- critical path
# Control Systems (Aerospace/Nuclear)
- bode plot
- nyquist plot
- root locus
- frequency response
- stability analysis
- control system
# Field Visualizations (Nuclear/Physics)
- contour plot
- flux distribution
- temperature field
- vector field
- flow field
- phase portrait
- streamlines
# Engineering
- sankey diagram
- energy flow
- mass balance
- parallel coordinates
- DOE analysis
- design space
- radar chart
- spider chart
# Project Management (Military/Aerospace)
- gantt chart
- project schedule
- timeline
# Mathematics
- polar plot
- phase space
- dynamical system
- differential equations
# GPU/Hardware Performance
- roofline plot
- roofline analysis
- GPU performance
- memory bandwidth
- compute intensity
- throughput latency
- inference benchmark
# LLM/ML Metrics
- scaling law
- scaling plot
- training curves
- loss curves
- confusion matrix
- ROC curve
- AUC curve
- precision recall
- PR curve
- attention heatmap
- attention weights
- embedding visualization
- t-SNE plot
- UMAP plot
- embedding scatter
- feature importance
- calibration plot
- reliability diagram
# Biology/Bioinformatics
- violin plot
- gene expression
- volcano plot
- differential expression
- survival curve
- Kaplan-Meier
- manhattan plot
- GWAS
- genome wide
# Formal Methods
- formal verification
- lean4 theorem
- requirement proof
metadata:
short-description: Publication-quality figures for aerospace, nuclear, military, mathematics

---

Fixture-Graph Skill

⚡ Quick Start for Agents

Don't get overwhelmed by 50+ commands! Use domain navigation:

# Step 1: Find your domain
fixture-graph domains

# Step 2: List commands for your domain
fixture-graph list --domain ml        # ML/LLM projects
fixture-graph list --domain control   # Aerospace/control systems
fixture-graph list --domain bio       # Bioinformatics

# Step 3: Or get recommendations by data type
fixture-graph recommend --data-type classification
fixture-graph recommend --data-type time_series
fixture-graph recommend --show-types  # See all data types

Domain Quick Reference

Domain	Use For	Key Commands
core	Any project	metrics, workflow, architecture, deps
ml	ML/LLM evaluation	confusion-matrix, roc-curve, training-curves, scaling-law
control	Aerospace, control systems	bode, nyquist, rootlocus, state-space
field	Nuclear, thermal, physics	contour, vector-field, heatmap
project	Scheduling, requirements	gantt, pert, radar, sankey
math	Pure mathematics	3d-surface, complex-plane, phase-portrait
bio	Bioinformatics, medical	violin, volcano, survival-curve, manhattan
hierarchy	Breakdowns, fault trees	treemap, sunburst, force-graph

---

Generate publication-quality figures from code analysis data for academic papers.

Architecture

Multi-backend design for maximum compatibility:

Backend	Use Case	Output Formats
Graphviz	Deterministic layouts, CI-friendly	PDF, PNG, SVG, DOT
Mermaid	Quick documentation, GitHub-compatible	PDF, PNG, SVG, MMD
NetworkX	Graph manipulation, D3 export	JSON, PDF, PNG
matplotlib/seaborn	Publication charts (IEEE settings)	PDF, PNG, SVG
plotly	Interactive Sankey, sunburst, treemap	PDF, PNG, HTML
pydeps	Python module dependencies	via Graphviz
pyreverse	UML class diagrams	via Graphviz
lean4-prove	Formal theorem verification	.lean files

D3-Style Scientific Visualizations

Advanced visualization types for scientific and engineering papers:

Graph Type	Engineering Use	Backend
Sankey diagrams	Energy/mass flow balances, reactor coolant	plotly/matplotlib
Heatmaps	Field distributions, neutron flux, temp	seaborn/matplotlib
Treemaps	Component breakdown, zone hierarchies	plotly/squarify
Sunburst charts	Fault hierarchies, module structure	plotly
Force-directed	System topology, P&ID, fault trees	NetworkX
Parallel coordinates	Multi-dimensional DOE analysis	pandas/plotly
Chord diagrams	Fuel cycle flows, interdependencies	NetworkX

Control Systems & Engineering Plots

Specialized visualizations for aerospace, nuclear, and control systems:

Graph Type	Engineering Use	Backend
Bode plots	Frequency response, stability margins	python-control/scipy
Nyquist plots	Stability analysis, gain/phase margins	python-control/scipy
Root locus	Pole placement, gain tuning	python-control/scipy
Polar plots	Antenna patterns, wind roses	matplotlib
Contour plots	Neutron flux, temperature fields, stress	matplotlib
Vector fields	Flow fields, gradients, velocity	matplotlib
Phase portraits	Dynamical systems, stability regions	matplotlib
Radar charts	Multi-attribute comparison	matplotlib
Gantt charts	Project scheduling, milestones	matplotlib
PERT networks	Critical path analysis	matplotlib/networkx

GPU/Hardware Performance Visualizations

Specialized visualizations for GPU, CUDA, and hardware performance papers:

Graph Type	Use Case	Backend
Roofline plots	Compute vs memory bound analysis, kernel optimization	matplotlib
Throughput/Latency	Inference benchmarks, batching analysis	matplotlib
Scaling law plots	Parameter/compute/data scaling (Chinchilla-style)	matplotlib
Training curves	Multi-run loss/accuracy with std shading	matplotlib

LLM/ML Visualization Types

Specialized visualizations for machine learning and LLM papers:

Graph Type	Use Case	Backend
Confusion matrix	Classification evaluation, error analysis	matplotlib
ROC curves	Binary classification, AUC comparison	matplotlib
Attention heatmaps	Transformer attention visualization	matplotlib
Embedding scatter	t-SNE/UMAP token/document embeddings	sklearn/umap
Precision-Recall curves	Multi-class classification metrics	matplotlib
Feature importance	Model interpretability, XGBoost/RF	matplotlib
Calibration plots	Probability calibration (reliability)	matplotlib

Biology/Bioinformatics Visualizations

Specialized visualizations for biological and medical research:

Graph Type	Use Case	Backend
Violin plots	Gene expression, distribution comparison	matplotlib
Volcano plots	Differential expression, fold change	matplotlib
Survival curves	Kaplan-Meier, clinical outcomes	matplotlib
Manhattan plots	GWAS, genome-wide association	matplotlib

Commands

deps - Dependency Graph

Generate dependency graph from Python project.

./run.sh deps --project /path/to/package --output deps.pdf
./run.sh deps -p ./src -o deps.svg --backend mermaid --depth 3
./run.sh deps -p ./src -o deps.json --backend networkx --format json

Options:
- --project, -p: Path to Python package/module (required)
- --output, -o: Output file (default: dependencies.pdf)
- --format, -f: Output format (pdf, png, svg, dot, json)
- --depth, -d: Maximum dependency depth (default: 2)
- --backend, -b: graphviz, mermaid, networkx

uml - UML Class Diagram

Generate UML class diagram using pyreverse.

./run.sh uml --project ./src --output classes.pdf

Requires: pip install pylint

architecture - Architecture Diagram

Generate architecture diagram from project or /assess JSON.

./run.sh architecture --project ./assess_output.json --output arch.pdf
./run.sh architecture -p /path/to/project -o arch.svg --backend mermaid

metrics - Metrics Chart

Generate publication-quality metrics chart with IEEE styling.

./run.sh metrics --input data.json --output metrics.pdf --type bar
./run.sh metrics -i data.json -o chart.pdf --type pie --title "Issue Distribution"

Chart types: bar, hbar, pie, line

Input formats:

// Simple dict
{"Feature A": 42, "Feature B": 28}

// With "metrics" key
{"metrics": {"LOC": 1500, "Functions": 45}}

// List format
[{"name": "A", "value": 10}, {"name": "B", "value": 20}]

table - LaTeX Table

Generate LaTeX table with proper escaping.

./run.sh table --input features.json --output table.tex --caption "Feature Comparison"

workflow - Workflow Diagram

Generate workflow/pipeline diagram with quality gates.

./run.sh workflow --stages "Scope,Analysis,Search,Learn,Draft" --output workflow.pdf
./run.sh workflow -s "A,B,C,D" -o flow.svg --no-gates --backend graphviz

theorem - Formal Verification

Generate formally verified theorem from requirement (uses lean4-prove).

./run.sh theorem --requirement "All inputs must be validated" --name input_validation --output theorem.lean

sankey - Sankey Diagram

Generate Sankey diagram for energy/mass flow balances.

./run.sh sankey --input flows.json --output sankey.pdf --title "Reactor Coolant Flow"

Input format:

[{"source": "Primary", "target": "Heat Exchanger", "value": 1000}]

heatmap - Heatmap

Generate heatmap for field distributions or correlation matrices.

./run.sh heatmap --input matrix.json --output flux.pdf --cmap plasma --title "Neutron Flux"

treemap - Treemap

Generate treemap for hierarchical size data.

./run.sh treemap --input sizes.json --output breakdown.pdf

sunburst - Sunburst Chart

Generate sunburst chart for hierarchical fault trees.

./run.sh sunburst --input hierarchy.json --output faults.pdf

force-graph - Force-Directed Graph

Generate force-directed graph for system topology.

./run.sh force-graph --input network.json --output topology.pdf

parallel-coords - Parallel Coordinates

Generate parallel coordinates for multi-dimensional DOE analysis.

./run.sh parallel-coords --input experiments.json --output doe.pdf --color-by efficiency

radar - Radar Chart

Generate radar/spider chart for multi-attribute comparison.

./run.sh radar --input attributes.json --output comparison.pdf

Input format:

{"Design A": {"Safety": 8, "Cost": 6, "Efficiency": 9}, "Design B": {"Safety": 9, "Cost": 4, "Efficiency": 7}}

bode - Bode Plot

Generate Bode plot for control systems frequency response.

./run.sh bode --num 1,2 --den 1,3,2 --output bode.pdf --freq-min 0.01 --freq-max 100

nyquist - Nyquist Plot

Generate Nyquist plot for stability analysis.

./run.sh nyquist --num 1,2 --den 1,3,2,0 --output nyquist.pdf

rootlocus - Root Locus

Generate root locus for control system gain analysis.

./run.sh rootlocus --num 1 --den 1,5,6 --output rootlocus.pdf

polar - Polar Plot

Generate polar plot for directional data (antenna patterns, wind roses).

./run.sh polar --input pattern.json --output antenna.pdf

contour - Contour Plot

Generate contour plot for field distributions (flux, temperature, stress).

./run.sh contour --input field.json --output flux.pdf --cmap plasma --levels 30

Input format:

{"x": [0, 1, 2], "y": [0, 1, 2], "z": [[0,1,2],[1,2,3],[2,3,4]]}

gantt - Gantt Chart

Generate Gantt chart for project scheduling.

./run.sh gantt --input schedule.json --output timeline.pdf

Input format:

[{"task": "Design", "start": 0, "end": 5, "progress": 100}]

pert - PERT Network

Generate PERT network diagram for critical path analysis.

./run.sh pert --input network.json --output cpm.pdf

vector-field - Vector Field

Generate vector field for flow visualization.

./run.sh vector-field --input flow.json --output velocity.pdf --streamlines

phase-portrait - Phase Portrait

Generate phase portrait for dynamical systems.

./run.sh phase-portrait --equations "dx = y; dy = -x - 0.5*y" --output damped.pdf

roofline - Roofline Plot

Generate roofline plot for GPU/hardware performance analysis.

./run.sh roofline --input kernels.json --output roofline.pdf

Input format:

{"peak_flops": 19.5e12, "peak_bandwidth": 900e9, "kernels": [{"name": "GEMM", "flops": 1e12, "bytes": 1e9}]}

scaling-law - Scaling Law Plot

Generate log-log scaling law plot (common in LLM papers).

./run.sh scaling-law --input params_vs_loss.json --output scaling.pdf --fit

confusion-matrix - Confusion Matrix

Generate confusion matrix for classification results.

./run.sh confusion-matrix --input results.json --output confusion.pdf --normalize

roc-curve - ROC Curve

Generate ROC curve with AUC for binary classification.

./run.sh roc-curve --input roc_data.json --output roc.pdf

training-curves - Training Curves

Generate multi-run training curves with std shading.

./run.sh training-curves --input runs.json --output loss.pdf --log-y

attention-heatmap - Attention Heatmap

Generate transformer attention visualization.

./run.sh attention-heatmap --input attention.json --output attn.pdf

embedding-scatter - Embedding Scatter

Generate t-SNE or UMAP visualization of embeddings.

./run.sh embedding-scatter --input embeddings.json --output tsne.pdf --method tsne

throughput-latency - Throughput vs Latency

Generate throughput vs latency plot for inference benchmarks.

./run.sh throughput-latency --input benchmarks.json --output perf.pdf

pr-curve - Precision-Recall Curve

Generate Precision-Recall curve for classification.

./run.sh pr-curve --input pr_data.json --output pr.pdf

violin - Violin Plot

Generate violin plot for distribution comparison.

./run.sh violin --input expression.json --output violin.pdf --y-label "Expression"

volcano - Volcano Plot

Generate volcano plot for differential expression analysis.

./run.sh volcano --input deseq.json --output volcano.pdf --fc 1.5 --pval 0.01

survival-curve - Kaplan-Meier Survival Curve

Generate Kaplan-Meier survival curve.

./run.sh survival-curve --input survival.json --output km.pdf

manhattan - Manhattan Plot

Generate Manhattan plot for GWAS results.

./run.sh manhattan --input gwas.json --output manhattan.pdf

feature-importance - Feature Importance

Generate feature importance bar chart.

./run.sh feature-importance --input importance.json --output features.pdf --top-n 15

calibration - Calibration Plot

Generate calibration plot (reliability diagram).

./run.sh calibration --input calibration.json --output calib.pdf

from-assess - Generate All Figures

Generate all figures from /assess output in one command.

./run.sh from-assess --input assess_output.json --output-dir ./figures/

Generates:
- architecture.pdf - System architecture diagram
- dependencies.pdf - Module dependency graph
- features.pdf - Feature distribution chart
- issues.pdf - Issue severity pie chart
- comparison.tex - Feature comparison table
- test_coverage.tex - Test coverage table

check - Backend Status

Check which backends are available.

./run.sh check

Publication Quality Settings

matplotlib figures use IEEE publication settings:
- Font: 8pt Times New Roman (serif)
- DPI: 600 for saving, 300 for display
- Column widths: Single (3.5"), Double (7.16")
- TrueType fonts for Illustrator compatibility

Integration with paper-writer

from pathlib import Path
import subprocess

def generate_figures(assess_json: Path, output_dir: Path):
    subprocess.run([
        str(FIXTURE_GRAPH_SCRIPT), "from-assess",
        "--input", str(assess_json),
        "--output-dir", str(output_dir),
    ])

Dependencies

Required:
- Python 3.10+
- typer
- numpy

Optional (enables features):

Package	Features Enabled
matplotlib	All charts, plots, diagrams
seaborn	Heatmaps, publication styling
plotly	Sankey, sunburst, treemap, interactive
networkx	Force-directed graphs, PERT
pandas	Parallel coordinates
squarify	Treemaps (matplotlib fallback)
scipy	Bode/Nyquist fallback, contours
control	Bode, Nyquist, root locus
sklearn	t-SNE for embedding scatter
umap-learn	UMAP for embedding scatter
graphviz	Dependency/architecture diagrams
pydeps	Python module dependencies
pylint	UML via pyreverse

System dependencies:
- graphviz (apt install graphviz) - Graphviz rendering
- mermaid-cli (npm install -g @mermaid-js/mermaid-cli) - Mermaid backend
- lean4-prove skill - Formal theorem verification

Installation

# Core
pip install typer numpy matplotlib

# Full installation (all features)
pip install typer numpy matplotlib seaborn plotly networkx pandas squarify scipy control pydeps pylint

# Control systems only
pip install typer numpy matplotlib scipy control

# System dependencies
apt install graphviz  # Debian/Ubuntu
npm install -g @mermaid-js/mermaid-cli

Sanity Check

./sanity.sh

Verifies:
- Python dependencies available
- CLI loads correctly
- Basic diagram generation works
- Tests pass

Research Sources

This skill's design is informed by:
- pydeps - Python module dependency visualization
- matplotlib for papers - Publication-quality figures
- Mermaid vs Graphviz - Diagram-as-code comparison
- NetworkX + D3 - Interactive graph visualization
- OverViz - AI architecture diagram generation