Our review
Generates publication-ready matplotlib figures for topological data analysis (TDA) according to the trajectory_tda project's visualization conventions.
Strengths
- Enforces consistent style constants, color rules, and output paths.
- Provides ready-to-use templates for persistence diagrams, barcodes, null histograms, and landscape comparisons.
- Automatically handles high-resolution PDF/PNG export with proper naming.
Limitations
- Specific to the trajectory_tda codebase and its conventions.
- Requires existing constants and template functions to be present.
- Not suitable for non-TDA or non-matplotlib visualizations.
Use when creating publication figures for TDA analyses within the trajectory_tda project.
Avoid for exploratory one-off plots or projects with different plotting standards.
Security analysis
SafeThe skill is purely instructional, providing templates and style guidance for generating matplotlib figures. It does not execute any code, invoke shell commands, or perform network operations.
No concerns found
Examples
/tda-figure-spec persistence-diagram P01-B/tda-figure-spec null-histogram P01-A/tda-figure-spec barcode P01-C/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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