evalrx 0.1.2__py3-none-any.whl

evalrx/agent_assets/skills/nature-figure/references/design-theory.md

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+# Nature Figure Design Theory
+
+Derived from scripts in the [figures4papers](https://github.com/ChenLiu-1996/figures4papers) repository
+(published in *Nature Machine Intelligence* and top ML/bioinformatics venues).
+
+---
+
+## 1) Typography
+
+### Font stack (priority order)
+- **Nature standard**: `font.family = 'sans-serif'`, `font.sans-serif = ['Arial']`
+- **Fallback stack**: `['Arial', 'Helvetica', 'DejaVu Sans', 'sans-serif']`
+- **Helvetica** (equivalent) also appears in many scripts as `font.family = 'helvetica'`
+- SVG/PDF editable text: always set `svg.fonttype = 'none'`
+- LaTeX math labels: `text.usetex = True` only when LaTeX is installed
+
+### Font size hierarchy
+| Context | font.size | axes.linewidth |
+|---------|-----------|---------------|
+| Journal-final dense multi-panel figure at publication width | 7–9 | 0.8–1.2 |
+| Large comparison bar panels (figsize > 28in wide) | 24 | 3 |
+| Compact subfigures / analytic plots | 15–16 | 2 |
+| Axis labels on large panels | 32–54 (override per-label) | — |
+| In-bar annotations | 32–36 | — |
+| Legend text on large panels | 28–38 | — |
+| Tick labels | 20–36 | — |
+
+When targeting the final dimensions of a two-column `Nature` figure page, start smaller than
+slide-sized preview figures. The sampled 2026 papers routinely landed in the `7–9 pt` final-text
+regime for dense composites.
+
+---
+
+## 2) Axes & Spines
+
+```python
+plt.rcParams['axes.spines.right'] = False   # always off
+plt.rcParams['axes.spines.top'] = False     # always off
+plt.rcParams['legend.frameon'] = False      # frameless legends everywhere
+```
+
+- Keep only left + bottom spines — minimalist, Nature-approved.
+- No grid lines by default; use sparse y-ticks to guide the eye.
+
+---
+
+## 3) Color Palette
+
+Semantic: blue = proposed method, green = positive variants, red/pink = baselines, neutral = reference/background.
+For dense multi-panel figures, however, **family consistency beats maximal hue separation**.
+
+```python
+# Values synced to the CVD-validated EvalRX dataviz palette (family
+# semantics unchanged; see the notice in README.md). Ramps and the 5
+# chromatic series slots were re-validated with the dataviz checker.
+PALETTE = {
+    # Proposed / key method
+    "blue_main":      "#2a78d6",   # blue — hero method (categorical slot 1)
+    "blue_secondary": "#6da7ec",   # medium blue — second author method
+
+    # Positive / improvement shades (light → dark, validated ordinal ramp)
+    "green_1": "#7ec07e",
+    "green_2": "#4ca74b",
+    "green_3": "#008300",
+
+    # Baseline / contrast shades (light → dark, validated ordinal ramp)
+    "red_1":      "#ee9999",
+    "red_2":      "#e97675",
+    "red_strong": "#e34948",
+
+    # Neutral support (ink ladder)
+    "neutral_light": "#c3c2b7",
+    "neutral_mid":   "#898781",
+    "neutral_dark":  "#52514e",
+    "neutral_black": "#0b0b0b",
+
+    # Accent / callout (use sparingly)
+    "gold":   "#eda100",
+    "teal":   "#1baf7a",
+    "violet": "#4a3aa7",
+    "magenta":"#e87ba4",
+}
+
+DEFAULT_COLOR_ORDER = [
+    "#2a78d6",   # blue_main
+    "#008300",   # green_3
+    "#e34948",   # red_strong
+    "#1baf7a",   # teal
+    "#4a3aa7",   # violet
+    "#898781",   # neutral_mid — reference/background series only
+]
+```
+
+### Unified-family rule (recommended for NMI-style pages)
+
+Publication figures should read like **one figure**, not six unrelated plots. Prefer one cool family for
+baselines and one lilac/rose family for the proposed method line.
+
+```python
+PALETTE_NMI_PASTEL = {
+    "baseline_dark": "#484878",
+    "baseline_mid":  "#7884B4",
+    "baseline_soft": "#B4C0E4",
+    "ours_tiny":  "#E4E4F0",
+    "ours_base":  "#E4CCD8",
+    "ours_large": "#F0C0CC",
+    "delta_up":   "#2E9E44",
+    "delta_down": "#E53935",
+}
+
+DEFAULT_COLOR_ORDER_NMI_PASTEL = [
+    "#484878",   # baseline_dark
+    "#7884B4",   # baseline_mid
+    "#B4C0E4",   # baseline_soft
+    "#E4E4F0",   # ours_tiny
+    "#E4CCD8",   # ours_base
+    "#F0C0CC",   # ours_large
+]
+```
+
+Rules:
+1. Keep related baselines in one cool family.
+2. Keep `Tiny / Base / Large` or sibling variants in one hero family.
+3. Reserve green/red for arrows, gains, drops, thresholds, or signed biological direction.
+4. Never remap the same method to a different hue family in another panel.
+5. If in doubt, reduce saturation before adding more categories.
+
+### Modality-specific palette discipline from sampled 2026 Nature figures
+
+- **Imaging plates**: grayscale context + 1–2 fluorescent accent channels on black.
+- **Schematic/material pages**: derive the palette from the physical objects in the schematic,
+  then reuse softened versions of those colors in the support plots.
+- **Clinical composites**: dark baseline/reference series, restrained warm/cool follow-up hues,
+  pale background bands in forest plots.
+- **Genomics / systems pages**: neutral grey scaffolds plus a small number of biologically
+  meaningful highlight families, often one red and one blue.
+
+### Ablation alpha encoding
+When ablating components of one method, use a **single color with varying alpha**:
+```python
+color = (0.215686, 0.458824, 0.729412)   # blue_secondary as RGB tuple
+alphas = np.linspace(0.2, 1.0, n_variants)
+colors = [(color[0], color[1], color[2], a) for a in alphas]
+# alpha=1.0 → full method, alpha=0.2 → minimal/ablated variant
+```
+
+---
+
+## 4) Layout and Composition
+
+### Figure sizes
+| Figure type | Typical figsize |
+|-------------|----------------|
+| Journal-width composite page / asymmetric multi-panel | (7.0–7.4, 5.5–7.8) |
+| Multi-metric bar (3–4 metrics + legend) | (28–45, 6–12) |
+| Compact single bar | (9–16, 5–8) |
+| Trend / line multi-panel | (14, 4) or (9, 8) |
+| Heatmap single | (8–20, 5–9) |
+| Radar polar | (12, 10) |
+| 3D / illustration multi-panel | (24, 8) |
+
+**Rule**: Width ≈ 3–4× height for comparison bars; prevents vertical crowding and allows left-to-right narrative reading.
+
+### Dedicated legend panel
+For multi-axis figures, the **last subplot is legend-only**:
+```python
+ax_legend = fig.add_subplot(1, n+1, n+1)
+ax_legend.legend(handles, labels, fontsize=..., loc='center', frameon=False)
+ax_legend.set_axis_off()
+```
+
+### Dynamic y-axis scaling
+Never use fixed 0–100 when values sit in a narrow band.
+Tighten limits to data range: e.g., `ax.set_ylim([data.min() - margin, data.max() + margin])`.
+
+### Nature page archetypes from sampled 2026 papers
+
+`Nature` figures were not uniformly dashboard-like. They repeatedly used a few strong page
+archetypes:
+
+| Archetype | Layout signal | Practical rule |
+|-----------|---------------|----------------|
+| Schematic-led composite | One wide story panel with smaller quant panels below | Give the schematic the visual hierarchy; supporting plots should validate, not compete |
+| Dark image plate | Repeated black tiles with fluorescent channels | Use black only inside the image plate region; keep scale bars, gutters, and channel labels high-contrast |
+| Clinical triptych | Top longitudinal row, middle forest row, bottom summary row | Reuse the same column logic across outcomes and put the shared legend above the row |
+| Asymmetric hero layout | One dominant circular/schematic panel plus small support plots | Let one panel span multiple grid cells; equal panel sizes are not required |
+
+### Panel labels and gutters
+
+- Use small bold lowercase panel letters near the top-left edge.
+- Keep gutters tight but real; increase spacing when dark and light modalities touch.
+- Leave extra bottom clearance when a dense caption will sit immediately below the figure.
+- Avoid decorative panel boxes. Alignment and whitespace should carry the structure.
+
+### Legend economy and direct labelling
+
+- Use direct labels when regions, channels, or line identities are spatially stable.
+- Prefer one shared legend strip above a row rather than repeating legends inside several axes.
+- Dense categorical area plots often read better with embedded text than with a detached legend.
+- If a legend exists, it should usually be frameless and visually quieter than the data.
+
+### X-tick suppression
+When bars represent methods and the legend already names them:
+```python
+ax.set_xticks([])   # hide x-tick labels; use legend + panel title instead
+```
+
+---
+
+## 5) Bar Chart Rules
+
+### Vertical bars (comparison)
+```python
+bars = ax.bar(
+    x_positions,
+    values,
+    yerr=std_values,
+    capsize=5,
+    color=colors,
+    label=method_names,
+    edgecolor='black',      # sharp separation
+    linewidth=1.5,
+)
+```
+
+### Horizontal bars (ablation)
+```python
+ax.barh(
+    y_positions,
+    values,
+    xerr=std_values,
+    color=[(r, g, b, alpha) for alpha in alphas],
+    ecolor='k',
+    capsize=5,
+)
+```
+
+### In-bar value annotation
+Print exact numbers inside or above bars at 32–36pt for readability without a grid:
+```python
+for bar, value in zip(bars, values):
+    luminance = compute_luminance(bar_color)
+    textcolor = 'white' if luminance < 128 else 'black'
+    ax.text(bar.get_x() + bar.get_width()/2,
+            bar.get_height() - 0.10,
+            f'{value:.2f}',
+            ha='center', va='bottom',
+            fontsize=32, color=textcolor)
+```
+
+### Hatch encoding for print-safe grayscale
+```python
+hatches = ['/', '\\', '.', 'x', 'o']
+for bar, hatch in zip(bars, hatches):
+    bar.set_hatch(hatch)
+```
+
+### Error bar styling
+```python
+error_kw = {
+    'elinewidth': 2,
+    'capthick': 2,
+    'capsize': 15,
+}
+```
+
+---
+
+## 6) Line / Trend Plots
+
+- Line width: 2–3pt with controlled alpha.
+- Marker size: 8–12pt circles.
+- For clinical or longitudinal triptychs, place one shared legend above the row rather than repeating it per axis.
+- Fading alpha for temporal progression:
+  ```python
+  from matplotlib.collections import LineCollection
+  alphas = np.linspace(0.3, 0.9, n_segments)
+  # build LineCollection with per-segment alpha
+  ```
+- `fill_between` for uncertainty bands (keep alpha low: 0.1–0.2).
+- Reference baseline as dashed horizontal line: `ax.axhline(y=..., linestyle='--', alpha=0.3, linewidth=4)`.
+- No grid; sparse y-ticks guide the eye.
+
+---
+
+## 7) Heatmap Rules
+
+```python
+import matplotlib as mpl
+
+# Diverging (positive/negative): use Red + Blue colormaps per column direction
+cmap_pos = plt.cm.Reds
+cmap_neg = plt.cm.Blues_r
+
+# Masked NaN cells show as white
+cmap.set_bad(color='white')
+
+# Normalize per column
+norm = mpl.colors.Normalize(vmin=col_min, vmax=col_max)
+
+# Remove frame
+ax.set_frame_on(False)
+
+# Remove tick marks, keep labels
+ax.tick_params(axis='x', which='both', bottom=False, top=False, length=0)
+```
+
+Cell text contrast:
+```python
+r, g, b, _ = cmap(norm(value))
+luminance = 0.299*r + 0.587*g + 0.114*b
+text_color = 'white' if luminance < 0.5 else 'black'
+```
+
+---
+
+## 8) Radar / Polar Charts
+
+- Project: `fig.add_subplot(projection='polar')`.
+- Remove default grid and spines; draw custom spokes and contour polygons.
+- Normalize per-spoke to display range (e.g., 45–90) using per-benchmark tick lists.
+- Use `ax.set_theta_zero_location('N')` to start at top.
+- Legend: `bbox_to_anchor=(1.40, 0.05)` outside right edge.
+
+---
+
+## 9) Export Policy
+
+### SVG is the required primary format
+
+SVG preserves editable text (when `svg.fonttype = 'none'`), supports lossless scaling,
+and is required for any figure where text labels may need post-hoc alignment in
+Illustrator or Inkscape. Always save SVG first.
+
+```python
+import os
+os.makedirs('./figures/', exist_ok=True)
+fig.tight_layout(pad=2)   # default; use pad=1 for compact multi-panel
+
+# ── PRIMARY ── editable vector, text as <text> nodes ─────────────────────────
+fig.savefig('./figures/name.svg', bbox_inches='tight')
+
+# ── SECONDARY ── raster for quick preview / submission portals ────────────────
+fig.savefig('./figures/name.png', dpi=300, bbox_inches='tight')
+
+plt.close(fig)   # always close to free memory
+```
+
+**DPI guide (PNG only)**:
+- `dpi=300` — standard for all figure types.
+- `dpi=600` — dense bar panels with many methods.
+
+**Never** use `svg.fonttype = 'path'` (matplotlib default): it converts glyphs to bezier
+curves, breaking text editability. The mandatory three rcParams lines (see api.md) must
+be set before any `savefig` call.
+
+---
+
+## 11) Multi-Panel Information Architecture
+
+### Rule: Every panel must answer a unique scientific question
+
+In a multi-panel figure, each panel should be independently informative. Covering one panel must leave a gap that cannot be recovered from the others.
+
+**Recommended three-level progression**:
+
+| Level | Question answered | Typical encoding |
+|-------|------------------|-----------------|
+| Overview | "What is the landscape?" | Stacked bar, composition |
+| Deviation | "What is distinctive per group?" | Z-score heatmap (diverging cmap) |
+| Relationship | "How do variables co-vary?" | Scatter / bubble plot |
+
+### Anti-redundancy checklist
+
+Before finalising:
+
+- [ ] Panel b does **not** re-display the same data as panel a in a different visual form
+- [ ] Panel c adds a dimension absent from a and b (e.g., correlation, biological relationship)
+- [ ] Each panel has its own axis-label vocabulary (different x/y quantities)
+
+### Common redundancy traps
+
+| Trap | Example | Fix |
+|------|---------|-----|
+| Absolute + absolute | Stacked bar (%) + heatmap of same % | Replace heatmap with z-score deviation |
+| Subset of parent | Tumor-only ranked bar is just one column of the stacked bar | Swap for scatter: tumor % vs. immune % |
+| Two rankings | Two ranked bars on related metrics | Replace one with scatter / bubble |
+| Different chart, same data slice | Pie + stacked bar | Merge or replace one with a relationship plot |
+
+### Z-score deviation heatmap (complement to a composition bar)
+
+When panel a shows absolute composition, panel b should show **what is atypical** per group:
+
+```python
+# heat: DataFrame (cohorts × cell-type categories), values in %
+z = (heat - heat.mean(axis=0)) / heat.std(axis=0)
+im = ax.imshow(z.values, cmap="RdBu_r", aspect="auto", vmin=-2.5, vmax=2.5)
+# colorbar label:
+cbar.set_label("Z-score vs pan-cohort mean")
+```
+
+Use `RdBu_r` (red = enriched above average, blue = depleted). This diverging view is orthogonal to the absolute-percentage view in panel a.
+
+### Bubble scatter (complement to both)
+
+When a = composition, b = deviation, panel c should reveal **biological co-variation**:
+
+```python
+# x: dominant compartment (e.g., tumor %)
+# y: functional readout (e.g., immune-cell %)
+# size: third variable (e.g., stroma %)
+ax.scatter(x, y, s=stroma * scale, c=colors,
+           edgecolors="white", linewidth=0.8, alpha=0.9)
+# Quadrant reference lines at median x and median y
+ax.axvline(np.median(x), lw=1.2, ls="--", color="#767676", alpha=0.6)
+ax.axhline(np.median(y), lw=1.2, ls="--", color="#767676", alpha=0.6)
+```
+
+Label quadrants ("Immune-hot / low tumor", "Immune-desert / high tumor", …) with small grey text.
+
+---
+
+## 10) Reproduction Checklist
+
+To match Nature publication standards:
+
+- [ ] **MANDATORY first lines**: `font.family='sans-serif'`, `font.sans-serif=['Arial','DejaVu Sans','Liberation Sans']`, `svg.fonttype='none'`
+- [ ] **Save as SVG** (primary). PNG dpi=300 as optional raster preview.
+- [ ] Top and right spines off; frameless legend
+- [ ] Figure architecture chosen intentionally: grid, schematic-led composite, image plate, or asymmetric hero layout
+- [ ] Font size ≥ 16 base; 24 for large bar panels; 32–54 for axis labels on large panels
+- [ ] Colors from blue-green-red-neutral semantic palette
+- [ ] Black background used only for imaging plates, not for ordinary plots
+- [ ] Legends omitted or shared when direct labels or one legend strip read better
+- [ ] Y-limits tightened to data range (not 0–100 when values are 80–95)
+- [ ] X-ticks hidden when methods are named in legend
+- [ ] Legend in dedicated panel or `frameon=False`
+- [ ] `tight_layout(pad=2)` before save
+- [ ] `plt.close(fig)` after save

evalrx/agent_assets/skills/nature-figure/references/figure-contract.md

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+# Figure Contract
+
+Use this reference before writing plotting code. The goal is to make the figure
+serve the paper's scientific logic.
+
+## Privacy rule
+
+Keep the figure contract user-facing, but keep the working trail private. Do not mention
+private paths, source filenames, internal reference documents, template identifiers, or
+where a private draft came from unless the user explicitly asks for provenance.
+
+## Required contract
+
+Create a short contract in working notes or in the response:
+
+```text
+Core conclusion:
+Figure archetype:
+Target journal/output:
+Backend: Python or R
+Final size:
+Panel map:
+  a:
+  b:
+  c:
+Evidence hierarchy:
+  hero evidence:
+  validation evidence:
+  controls/robustness:
+Statistics needed:
+Source data needed:
+Image-integrity notes:
+Reviewer risk:
+```
+
+Do not start from a favorite template. Start from the conclusion, then choose the
+minimum set of panels that make the conclusion clear and defensible.
+
+## Core conclusion rules
+
+- The core conclusion should be one sentence with a verb: "Treatment X reduces
+  Y by restoring Z", not "Treatment results".
+- Every panel must answer a unique question. If covering a panel would not weaken
+  the argument, remove or merge it.
+- Separate primary evidence from supporting evidence. The primary evidence gets
+  the hero panel or the clearest axis; controls and robustness panels should be
+  visually quieter.
+- If the user provides data but no claim, infer a provisional claim from the data
+  request and ask for confirmation before final styling.
+
+## Archetype selection
+
+| Archetype | Use when | Hero panel | Supporting panels |
+|---|---|---|---|
+| `quantitative grid` | The claim is mainly numerical comparison | Optional; often a dominant summary metric | Shared axes, aligned scales, compact legends |
+| `schematic-led composite` | A workflow, mechanism, device, or experimental design must be understood first | Left or top schematic, 35-60% of area | 2-4 quantitative validation panels |
+| `image plate + quant` | Microscopy, imaging, histology, spatial overlays, segmentation, or blots lead the evidence | Image plate or representative image | Scale bars, overlays, crops, quantification |
+| `asymmetric mixed-modality figure` | The figure combines schematic, raster images, heatmaps, and quantitative plots | One panel spans rows/columns | Smaller panels ranked by evidence value |
+
+## Panel logic
+
+Use this order unless the manuscript story clearly requires another:
+
+1. Establish the system: sample, method, cohort, device, or experimental design.
+2. Show the main effect or primary comparison.
+3. Show mechanism or localization.
+4. Quantify the representative image or qualitative observation.
+5. Add robustness, controls, subgroup analysis, or sensitivity analysis.
+
+For Fig. 1 or a method figure, the first panel often defines the visual vocabulary:
+colors, symbols, workflow direction, sample classes, and scale. Reuse that vocabulary
+through the whole figure and, where possible, through the manuscript.
+
+## Aesthetic integration
+
+- Use one neutral family, one signal family, and one accent family.
+- Keep the same condition/method color across all panels.
+- Prefer direct labels for stable line identities, channels, and fixed spatial regions.
+- Use a shared legend area when repeated legends would waste space.
+- Avoid equal-sized panels when the evidence is not equally important.
+- Keep schematic colors and quantitative plot colors related. A schematic-led
+  figure should look like one integrated argument, not a pasted collage.
+
+## Reviewer-risk prompts
+
+Before finalizing, ask what a skeptical reviewer would challenge:
+
+- Is the sample size visible in the legend or source data?
+- Are error bars, intervals, and statistical tests defined?
+- Are axes comparable across panels that invite comparison?
+- Are representative images quantified and traceable to raw files?
+- Are image adjustments global and documented?
+- Could the same conclusion be made from fewer panels?

evalrx/agent_assets/skills/nature-figure/references/figure-legend-conventions.md

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+# Figure & Table Legend Conventions (Nat Commun 2025 CS/AI corpus)
+
+Use this file when **writing or auditing the legend text** of a figure or table.
+It complements `nature-2026-observations.md`, which covers visual/layout
+archetypes; this file covers the *words* of the caption. Distilled from a 2025
+set of 20 open-access *Nature Communications* computer-science / AI papers
+(legend conventions were consistent across all research articles). **Do not copy
+source wording.**
+
+## Legend structure — the fixed skeleton
+
+1. **`Fig. N | ` + a bold noun-phrase overall title** that names the whole
+   figure. Common openers: *Overview of …*, *Comparison of …*, *Performance of
+   …*, or a finding phrase. No terminal full stop required on the title.
+2. **`a / b / c …` panels, each described in present tense, telegraphic style**,
+   often subject-less: *"a Comparison of the four EMS paradigms. b Distributions
+   of WSIs and patches in the pre-training dataset."*
+3. **Statistics written into the legend**: sample size `n=`, error type, and
+   test — *"mean ± 95% CI (n = 1373) … one-way ANOVA with Tukey correction."*
+4. **Data-availability boilerplate** at the end: *"Source data are provided as a
+   Source Data file."*
+
+## Tense
+
+- Visual facts in **present** tense — *"are shown as cyan sticks"*, *"depicts"*.
+- Methods/how-it-was-made in **past** tense — *"was performed"*, *"was adopted
+  from"*.
+
+## Self-containment rule
+
+A legend must be readable away from the body text. Put colour/shape mappings,
+sample size, and key numeric anchors (PDB id, RMSD, units) into the legend
+itself — *"tRNA-Glu of E. coli (PDB: 2DER chain C). 76 nt, RMSD: 2.88 Å."*;
+*"Grey boxes designate what is defined by the benchmark, and orange boxes
+indicate what is unique to each solution."*
+
+## Advanced: the claim-closing sentence
+
+A legend's final sentence may advance an argument rather than only describe —
+*"…indicating that these co-folding models are not predicting poses based on
+physics but rather learning patterns in global structures."* Use sparingly, and
+only when the panel actually supports the inference.
+
+## Review/Perspective legends
+
+When a figure aggregates others' published systems, each sub-panel gets a
+one-line characterisation (often past tense, describing prior work) and the
+legend carries an attribution line — *"adapted with permission from refs. 16,17
+… by Springer Nature."* Include the permission/attribution string for any
+adapted panel.
+
+## Table captions
+
+Same shape: **`Table N | ` + noun phrase**, with detailed specs pointed to
+Methods — *"Table 1 | … Detailed specifications are provided in the Methods
+section."* Benchmark/framework papers lean on tables (multi-metric results) more
+than figures.
+
+## Length & title limits (consistency with style-guardrails)
+
+- Keep a Nature-style legend `<= 300` words.
+- Keep the `Fig. N |` title short and nominal; no numbers/results in the figure
+  *title* line (numbers live in the panels and stats).
+
+## 中文图注要点
+
+- 结构铁律:`图 N | 加粗名词短语总题` → `a/b/c` 现在时电报式分面 → 统计(n、误差、检验)写进图注 → "Source data are provided as a Source Data file." 套语。
+- 时态:视觉事实用现在时,制作方法用过去时。
+- 自足:颜色/形状映射、样本量、关键数值(PDB/RMSD/单位)都写进图注,使其脱离正文可读。
+- 进阶:图注末句可给一句推断结论,但须确有面板支撑。
+- 综述图注:聚合他人系统时逐子图一句话定性,并标注"adapted with permission from refs… by Springer Nature"授权。