Our review
This skill scaffolds publication-ready matplotlib code for topological data analysis figures, following the trajectory_tda project's visualization conventions.
Strengths
- Enforces consistent style constants (sizes, colors, fonts) imported from the codebase.
- Provides templates for persistence diagrams, barcodes, null histograms, and landscape comparisons.
- Automates saving output as PDF and PNG at the appropriate DPI.
- Prevents ad-hoc colors or dimensions by requiring the use of defined constants.
Limitations
- Tightly coupled to the trajectory_tda codebase, making it unusable outside that project.
- Relies on existing figure templates in the visualization module.
- Produces code scaffolding, not the final rendered figures directly.
When you need to generate a TDA figure for a paper or supplement within the trajectory_tda project.
For quick exploration or for visualizations outside this project, where the enforced conventions would be too restrictive.
Security analysis
SafeThe skill is a descriptive specification for generating matplotlib figures. It does not instruct any dangerous actions, command execution, or data exfiltration. It only provides coding conventions and templates, posing no execution risk.
No concerns found
Examples
/tda-figure-spec persistence-diagram P01-B/tda-figure-spec null-histogram P01-AUse /tda-figure-spec landscape-comparison P02-S1 to scaffold the landscape figure for the supplement./tda-figure-spec — Generate Publication-Ready TDA Figures
Scaffold matplotlib figure code following the established trajectory_tda/viz/ conventions.
Uses PUBLICATION_RC, DPI, FIGSIZE_*, STATE_COLORS, and _save_figure from the
codebase — never ad-hoc sizes or colours.
Usage
/tda-figure-spec [figure-type] [paper-number]
Example: /tda-figure-spec persistence-diagram P01-B
Example: /tda-figure-spec null-histogram P01-A
Example: /tda-figure-spec (interactive)
Style constants (always import from trajectory_tda/viz/constants.py)
from trajectory_tda.viz.constants import (
DPI, FIGSIZE_FULL, FIGSIZE_WIDE, FIGSIZE_HALF, FIGSIZE_SQUARE,
PUBLICATION_RC, STATE_COLORS, STATES, STATE_LABELS, REGIME_LABELS,
)
import matplotlib.pyplot as plt
plt.rcParams.update(PUBLICATION_RC)
Figure size guide
| Use case | Constant | Size |
|---|---|---|
| Single full-width plot | FIGSIZE_FULL | 190mm × 120mm |
| Wide two-panel | FIGSIZE_WIDE | 190mm × 104mm |
| Half-width single panel | FIGSIZE_HALF | 90mm × 120mm |
| Square heatmap | FIGSIZE_SQUARE | 90mm × 90mm |
Save function (always use this pattern)
def _save_figure(fig, output_dir: Path, name: str) -> None:
output_dir.mkdir(parents=True, exist_ok=True)
fig.savefig(output_dir / f"{name}.pdf", format="pdf")
fig.savefig(output_dir / f"{name}.png", format="png", dpi=DPI)
Colour rules
- State space: always
STATE_COLORSdict — nevertab10or default cycle - Observations:
#2d6a2e(green); Null:steelblue; Dim 0: green; Dim 1:#1a237e - Regimes:
plt.cm.tab10withREGIME_LABELSorder - Sequential/diverging:
viridis,plasma,RdBu_r— neverjet
Annotation standards
- p-values: write
p=0.003, notp<0.01 - Axes: remove top and right spines; keep bottom and left
- Legends:
frameon=False - Subplot labels:
ax.text(0.02, 0.97, "(a)", transform=ax.transAxes, ...)
Figure templates available
| Template | When to use |
|---|---|
| plot_persistence_diagram(diagram, dim, ax) | Scatter birth-death pairs |
| plot_barcode(diagram, dim, ax) | Feature lifetimes sorted by persistence |
| plot_null_histogram(observed, null_dist, p_value, dim, ax) | Permutation test result |
| plot_landscape_comparison(obs, null, grid, ax) | L² landscape distance (mandatory) |
Output paths
| Context | Path | Naming |
|---|---|---|
| Production paper figure | papers/PXX/figures/ | fig{N}_{desc}.{pdf\|png} |
| Supplement | papers/PXX/figures/ | figS{N}_{desc}.{pdf\|png} |
| Working / exploratory | figures/{domain}/ | YYYYMMDD_{desc}.png |
Working figures must not be saved to papers/PXX/figures/ — that is for production only.
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