psyclaw 0.28.0 → 0.28.2

package/vendor/nature-skills/skills/nature-figure/references/common-patterns.md

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+# Common Patterns — Nature Figure Making
+
+## Contents
+
+- [Pattern 1: Ultra-wide multi-metric bar panel](#pattern-1-ultra-wide-multi-metric-bar-panel)
+- [Pattern 2: Dedicated legend panel](#pattern-2-dedicated-legend-panel)
+- [Pattern 3: Categorical bars without x-tick labels](#pattern-3-categorical-bars-without-x-tick-labels)
+- [Pattern 4: Dynamic y-axis tightening](#pattern-4-dynamic-y-axis-tightening)
+- [Pattern 5: Alpha-graduated ablation bars (same color, varying opacity)](#pattern-5-alpha-graduated-ablation-bars-same-color-varying-opacity)
+- [Pattern 6: Hatch encoding for print-safe grayscale](#pattern-6-hatch-encoding-for-print-safe-grayscale)
+- [Pattern 7: Semantic or family color mapping](#pattern-7-semantic-or-family-color-mapping)
+- [Pattern 8: In-bar text with luminance-aware color](#pattern-8-in-bar-text-with-luminance-aware-color)
+- [Pattern 9: Fill-between trend with hatch (print-safe)](#pattern-9-fill-between-trend-with-hatch-print-safe)
+- [Pattern 10: Annotate events on trend lines](#pattern-10-annotate-events-on-trend-lines)
+- [Pattern 11: Grouped bars across multiple datasets (grouped-within-grouped)](#pattern-11-grouped-bars-across-multiple-datasets-grouped-within-grouped)
+- [Pattern 12: Schematic hero panel with supporting quant row](#pattern-12-schematic-hero-panel-with-supporting-quant-row)
+- [Pattern 13: Dark image plate with repeated views](#pattern-13-dark-image-plate-with-repeated-views)
+- [Pattern 14: Clinical triptych](#pattern-14-clinical-triptych)
+- [Pattern 15: Asymmetric hero panel](#pattern-15-asymmetric-hero-panel)
+- [Pattern 16: Direct labels inside filled regions](#pattern-16-direct-labels-inside-filled-regions)
+- [Related files](#related-files)
+
+
+Reusable layout and encoding patterns used across publication-grade scripts.
+
+---
+
+## Pattern 1: Ultra-wide multi-metric bar panel
+
+For 3–4 metrics compared across many methods, use a wide canvas so bars and labels don't crowd.
+
+```python
+fig = plt.figure(figsize=(45, 12))   # or (28, 6) for fewer metrics
+gs = gridspec.GridSpec(1, n_metrics)
+
+for i, metric in enumerate(metrics):
+    ax = fig.add_subplot(gs[i])
+    ax.bar(x, values[metric], color=colors, ...)
+    ax.set_ylabel(metric, fontsize=54, labelpad=12)
+    ax.set_xticks([])
+
+# Last panel: legend only
+ax_leg = fig.add_subplot(gs[-1])
+ax_leg.legend(handles, labels, fontsize=38, loc='center', frameon=False)
+ax_leg.set_axis_off()
+
+fig.tight_layout(pad=2)
+```
+
+**Rule**: Width often 3–4× height. Allows left-to-right narrative scanning.
+
+---
+
+## Pattern 2: Dedicated legend panel
+
+When the legend is large, give it its own axis so data panels stay clean.
+
+```python
+fig, axes = plt.subplots(1, n_data + 1, figsize=(...))
+
+for i, ax in enumerate(axes[:-1]):
+    bars = ax.bar(...)
+    if i == 0:
+        handles, labels = ax.get_legend_handles_labels()
+
+# Legend-only panel
+axes[-1].legend(handles, labels, fontsize=28, loc='center', frameon=False)
+axes[-1].set_axis_off()
+```
+
+---
+
+## Pattern 3: Categorical bars without x-tick labels
+
+When methods are named in the legend, hide x-ticks entirely.
+
+```python
+ax.set_xticks([])        # removes ticks and labels
+# Alternatively:
+ax.set_xticklabels([])   # keeps tick marks, removes labels
+```
+
+---
+
+## Pattern 4: Dynamic y-axis tightening
+
+Never use 0–100 when all values are in 80–95.
+
+```python
+margin = (values.max() - values.min()) * 0.1   # 10% padding
+ax.set_ylim([values.min() - margin, values.max() + margin])
+
+# Manual ticks at clean round numbers
+ax.set_yticks([0.75, 0.80, 0.85, 0.90])
+ax.tick_params(axis='y', labelsize=36, length=10, width=2)
+```
+
+---
+
+## Pattern 5: Alpha-graduated ablation bars (same color, varying opacity)
+
+```python
+import numpy as np
+
+blue_rgb = (0.215686, 0.458824, 0.729412)   # #3775BA as float tuple
+n_ablations = len(ablation_configs)
+alphas = np.linspace(0.2, 1.0, n_ablations)
+colors = [(blue_rgb[0], blue_rgb[1], blue_rgb[2], a) for a in alphas]
+# Full method → alpha=1.0, most ablated → alpha=0.2
+```
+
+---
+
+## Pattern 6: Hatch encoding for print-safe grayscale
+
+Add hatching so bars remain distinct when printed in black-and-white.
+
+```python
+hatches = ['/', '\\\\', '.', 'x', 'o', '+']
+for bar_container, hatch in zip(grouped_bars, hatches):
+    for patch in bar_container:
+        patch.set_hatch(hatch)
+        patch.set_edgecolor('black')
+        patch.set_linewidth(1.5)
+```
+
+---
+
+## Pattern 7: Semantic or family color mapping
+
+Always map colors consistently across all panels in a figure:
+
+```python
+method_colors = {
+    'ResNet1d18': '#484878',   # baseline_dark
+    'ResNet1d34': '#7884B4',   # baseline_mid
+    'ECGFounder': '#B4C0E4',   # baseline_soft
+    'CSFM-Tiny':  '#E4E4F0',   # ours_tiny
+    'CSFM-Base':  '#E4CCD8',   # ours_base
+    'CSFM-Large': '#F0C0CC',   # ours_large
+}
+colors = [method_colors[m] for m in methods]
+```
+
+Prefer coherent hue families over alternating saturated blue/green/red just because categories differ.
+Green and red should usually be reserved for **directional annotations**, not primary series identity:
+
+```python
+ax.scatter(x_gain, y_gain, marker='^', color='#2E9E44', s=90, zorder=6)  # improvement
+ax.scatter(x_drop, y_drop, marker='v', color='#E53935', s=90, zorder=6)  # degradation
+```
+
+---
+
+## Pattern 8: In-bar text with luminance-aware color
+
+```python
+def annotate_bars(ax, bars, colors, fmt='{:.2f}', fontsize=32, offset=-0.10):
+    for bar, color in zip(bars, colors):
+        c = color.lstrip('#')
+        r, g, b = int(c[0:2],16)/255, int(c[2:4],16)/255, int(c[4:6],16)/255
+        lum = 0.299*r + 0.587*g + 0.114*b
+        textcolor = 'white' if lum < 0.5 else 'black'
+        value = bar.get_height()
+        ax.text(bar.get_x() + bar.get_width()/2,
+                value + offset,
+                fmt.format(value),
+                ha='center', va='bottom',
+                fontsize=fontsize, color=textcolor)
+```
+
+---
+
+## Pattern 9: Fill-between trend with hatch (print-safe)
+
+```python
+ax.fill_between(x, 0, cumsum_series,
+                color=fill_color,
+                hatch='\\\\\\',   # triple backslash for dense hatch
+                edgecolor='black',
+                label=label_name)
+# Visually erase the border artifacts:
+ax.fill_between(x, 0, cumsum_series,
+                facecolor='none',
+                edgecolor='white',
+                linewidth=2)
+```
+
+---
+
+## Pattern 10: Annotate events on trend lines
+
+```python
+def mark_events(ax, x_labels, y_cumsum, events_dict, dy_fraction=0.1):
+    """Add labeled arrows at event dates on a trend line."""
+    x_index = {label: i for i, label in enumerate(x_labels)}
+    y_lo, y_hi = ax.get_ylim()
+    dy = dy_fraction * (y_hi - y_lo)
+    for date, label in events_dict.items():
+        if date not in x_index:
+            continue
+        i = x_index[date]
+        stars = label.count('*')
+        clean_label = label.replace('*', '')
+        y_data = y_cumsum[i]
+        ax.annotate(
+            clean_label,
+            xy=(i, y_data),
+            xytext=(i, y_data + (1 + 0.8 * stars) * dy),
+            ha='center', va='bottom', fontsize=11,
+            arrowprops=dict(arrowstyle='-|>', lw=1.3, color='black',
+                            shrinkA=0, shrinkB=0, mutation_scale=15)
+        )
+```
+
+---
+
+## Pattern 11: Grouped bars across multiple datasets (grouped-within-grouped)
+
+```python
+num_methods = len(methods)
+xtick_positions = []
+
+for dataset_idx, dataset_name in enumerate(datasets):
+    x_start = dataset_idx * (num_methods + 1)   # gap of 1 between groups
+    ax.bar(
+        np.arange(num_methods) + x_start,
+        values[dataset_name],
+        color=method_colors,
+        label=methods if dataset_idx == 0 else ['_nolegend_'] * num_methods,
+    )
+    xtick_positions.append(np.mean(np.arange(num_methods)) + x_start)
+
+ax.set_xticks(xtick_positions)
+ax.set_xticklabels(datasets)
+```
+
+---
+
+## Pattern 12: Schematic hero panel with supporting quant row
+
+Use when one mechanism or fabrication story needs to lead, with 2–4 smaller evidence plots below.
+
+```python
+fig = plt.figure(figsize=(7.2, 6.2))
+gs = fig.add_gridspec(
+    2, 4,
+    height_ratios=[2.2, 1.0],
+    hspace=0.18, wspace=0.28,
+)
+
+ax_top = fig.add_subplot(gs[0, :])    # hero schematic
+ax_b = fig.add_subplot(gs[1, 0])
+ax_c = fig.add_subplot(gs[1, 1:3])
+ax_d = fig.add_subplot(gs[1, 3])
+
+# top panel should carry the main palette and the main visual narrative
+```
+
+Rules:
+
+- Allocate `45–60%` of total height to the hero schematic.
+- Reuse softened versions of the same colors in the lower plots.
+- Keep support plots quieter than the hero panel.
+
+---
+
+## Pattern 13: Dark image plate with repeated views
+
+Use for microscopy, volume rendering, or fluorescence-heavy panels.
+
+```python
+fig = plt.figure(figsize=(7.2, 6.5))
+gs = fig.add_gridspec(3, 5, hspace=0.08, wspace=0.04)
+
+for r in range(3):
+    for c in range(5):
+        ax = fig.add_subplot(gs[r, c])
+        ax.set_facecolor('black')
+        ax.set_xticks([])
+        ax.set_yticks([])
+        for spine in ax.spines.values():
+            spine.set_visible(False)
+```
+
+Rules:
+
+- Use black only within the image plate cells.
+- Put channel labels, scale bars and small crop guides directly on the plate.
+- Keep crop geometry and scale-bar placement consistent across the grid.
+
+---
+
+## Pattern 14: Clinical triptych
+
+Use for outcome-over-time figures that combine trajectories, effect sizes, and summary proportions.
+
+```python
+fig = plt.figure(figsize=(7.2, 6.8))
+gs = fig.add_gridspec(
+    3, 3,
+    height_ratios=[1.0, 1.35, 0.8],
+    hspace=0.28, wspace=0.32,
+)
+
+axes_top = [fig.add_subplot(gs[0, i]) for i in range(3)]
+axes_mid = [fig.add_subplot(gs[1, i]) for i in range(3)]
+axes_bot = [fig.add_subplot(gs[2, i]) for i in range(3)]
+
+# Put one shared legend strip above axes_top rather than repeating legends.
+```
+
+Rules:
+
+- Keep the three columns semantically parallel.
+- Use a dashed vertical reference line in the forest-plot row.
+- Group shading in the forest-plot row should be pale and subordinate.
+
+---
+
+## Pattern 15: Asymmetric hero panel
+
+Use when one panel is conceptually central and should dominate.
+
+```python
+fig = plt.figure(figsize=(7.2, 5.8))
+gs = fig.add_gridspec(3, 4, hspace=0.25, wspace=0.28)
+
+ax_a = fig.add_subplot(gs[0, :2])
+ax_b = fig.add_subplot(gs[0, 2])
+ax_c = fig.add_subplot(gs[1, :2])
+ax_d = fig.add_subplot(gs[1, 2])
+ax_e = fig.add_subplot(gs[:, 3])      # hero panel spans all rows
+ax_f = fig.add_subplot(gs[2, :2])
+```
+
+Rule: do not normalize every subplot to the same size if the science does not have equal importance.
+
+---
+
+## Pattern 16: Direct labels inside filled regions
+
+Use when the same categorical structure repeats and a legend would become too large.
+
+```python
+for x_text, y_text, text, color in label_specs:
+    ax.text(
+        x_text, y_text, text,
+        color=color,
+        ha='center', va='center',
+        fontsize=9, fontweight='bold',
+    )
+```
+
+Rules:
+
+- Keep labels inside stable, visually large regions.
+- Use a small white or black stroke if the fill varies strongly underneath.
+- Prefer direct labels over a mega-legend for repeated stacked-area or phase diagrams.
+
+---
+
+## Related files
+
+- [SKILL.md](../SKILL.md) — When to use this skill
+- [api.md](api.md) — Helper function signatures and PALETTE
+- [design-theory.md](design-theory.md) — Rationale behind every pattern above
+- [nature-2026-observations.md](nature-2026-observations.md) — Real Nature page archetypes behind these patterns
+- [tutorials.md](tutorials.md) — End-to-end walkthroughs
+- [chart-types.md](chart-types.md) — Radar, 3D, scatter patterns
+- [demos.md](demos.md) — Third-party demo map, copyright-aware reference use, and original reimplementation guidance

package/vendor/nature-skills/skills/nature-figure/references/demos.md

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+# figures4papers Reference Index
+
+Use this file when a user asks for a `figures4papers` look, cites the older
+`scientific-figure-making` skill, or needs a concrete Python/matplotlib reference.
+
+The retained third-party files live under `../assets/figures4papers/`. Before
+opening or adapting them, read
+`../assets/figures4papers/THIRD_PARTY_NOTICES.md`. These materials are not
+automatically covered by the root MIT License, and their inclusion does not grant
+additional reuse rights.
+
+## Use boundary
+
+1. Study layout, palette, axes, legends, and export structure as reference patterns.
+2. Reimplement with original code and the user's own data whenever the upstream
+   license or written permission does not clearly authorize copying or modification.
+3. Never reuse manuscript-specific labels, metric values, statistical results, or
+   visual assets as placeholders for real evidence.
+4. Record the external reference and implementation provenance in the internal QA
+   record when it materially influenced the result.
+5. Preserve the editable SVG/PDF/TIFF and source-data rules from `api.md` and
+   `qa-contract.md`.
+
+## Retained project map
+
+| Project | Open when | Local references |
+|---------|-----------|------------------|
+| `figure_ImmunoStruct` | Method-comparison and ablation bars | `../assets/figures4papers/figure_ImmunoStruct/` |
+| `figure_CellSpliceNet` | Compact benchmark and cross-species bars | `../assets/figures4papers/figure_CellSpliceNet/` |
+| `figure_brainteaser` | Category, rewriting, and self-correction panels | `../assets/figures4papers/figure_brainteaser/` |
+| `figure_VIGIL` | Radar, trend, ablation, and probability/manifold panels | `../assets/figures4papers/figure_VIGIL/` |
+| `figure_ophthal_review` | Time trends and composition heatmaps | `../assets/figures4papers/figure_ophthal_review/` |
+| `figure_RNAGenScape` | Heatmaps, optimization, manifold, and sweep plots | `../assets/figures4papers/figure_RNAGenScape/` |
+| `figure_Dispersion` | Conceptual sphere and observation panels | `../assets/figures4papers/figure_Dispersion/` |
+| `figure_Cflows` | Diffusion, trajectory, comparison, and ablation panels | `../assets/figures4papers/figure_Cflows/` |
+| `figure_FPGM` | Frequency-prior or distribution-style motivation | `../assets/figures4papers/figure_FPGM/` |
+
+## Prefer repository-owned implementation paths
+
+When copying is not clearly authorized, route the pattern through the repository's
+own material:
+
+| Requested pattern | Open and use |
+|-------------------|--------------|
+| Grouped bars, ablation bars, shared legends | `tutorials.md`, `common-patterns.md` |
+| Radar or polar comparison | `chart-types.md`, then implement with original code |
+| Trends, sweeps, and reference baselines | `tutorials.md`, `chart-types.md` |
+| Heatmap or annotated matrix | `tutorials.md`, `template-catalog.md` |
+| Probability or manifold concept panel | `chart-types.md` |
+| Submission typography, palette, and export | `api.md`, `design-theory.md` |
+| CSV-driven reproducible plots | `template-catalog.md`, `scripts/plot_templates.py` |
+
+## Upstream source
+
+<https://github.com/ChenLiu-1996/figures4papers>
+
+Check the current upstream license and obtain permission when required before
+redistributing, modifying, or publishing derived materials.