Publication-Grade Figure Rules

A checklist for correct, legible, internally-consistent scientific figures. This skill does not impose a visual house style — frame, font, and palette are parameters. Before plotting, follow the Notebook call below and invoke apply_figure_style().

Open Science Notebook call

Every notebook_execute request whose code uses a function named in this skill includes this skill ID:

{ "kernelSkillIds": ["figure-style"], "code": "apply_figure_style()\n..." }

kernelSkillIds contains the skill ID; function calls belong in code. This request is complete as written: call the named functions directly and do not add an import or discovery step.

§0 Scope

Load trigger (same rule as the system prompt's "Publication-grade plots" section): this skill is for final-deliverable figures — those shipping in a report, paper, or export, or saved as an artifact the user will keep — not for exploratory/intermediate plots (quick looks, EDA, sanity checks), which are drawn plainly without it. Once loaded, "every plot" below means every plot you render toward the deliverable.

§1–§3, §8, and §9 are correctness — they apply to every plot, in every context, and have no aesthetic content. §4–§7 are guidance — defaults that produce a clean result but that a deliberate alternative can override (individual rules inside §4–§7 that state a factual/perceptual invariant — e.g. §4.4 semantic-zero centering, §4.5 CVD, §6.9 leader anchoring — still bind). On its own, this skill is the inner tier (make one plot good); figure-composer and paper-narrative supply multi-panel and whole-paper context.

§1 Data fidelity & self-consistency

1.1 Excluded rows. A row marked excluded or flagged in the source data is either omitted entirely or drawn with a visually distinct open/hatched marker and named in the key. It never enters a summary statistic plotted alongside the included rows.

1.2 Comparable conditions only. Arms measured under non-comparable conditions (different N, epoch budget, initialization, protocol) are not plotted as visual peers. Separate them with a facet break or a marker on the label, and state the difference once in the caption.

1.3 Self-consistency. Every key, threshold, and title inside the figure must be satisfied by every plotted row. Before saving, walk each categorical outcome label back to the rule that defines it; if a row's value contradicts its label or the title, the figure is wrong, not the data.

1.4 Claim-titles must be true. A sentence-title (§5.1) is tested against every category on the axis before rendering. If any contradicts it, qualify the title ("on 3 of 4 pairs") or downgrade it to a description.

1.5 State n and what was held fixed. Every panel that draws a summary mark states n and the unit of replication, and every small-multiple that holds a variable fixed states the fixed value — in the panel or, when §2 budget is tight, in the caption.

1.6 Reference structure is reference. A tree, ordering, or topology drawn as context (a scale bar, a category strip) uses an established reference, not one inferred from the plotted data. Infer the structure only when the structure is the result.

1.7 One number per claim. A quantitative claim (runtime, accuracy, count) has exactly one canonical value across every panel, caption, and the abstract. Define what it measures and use that value everywhere.

§2 Label economy — floor and ceiling

The figure shows the pattern; the caption carries the context. Design for a general scientific reader, not the author.

2.1 Floor (non-removable). Every distinct mark, series, glyph, or comparator must be identifiable from the figure alone. The caption explains why it matters, not what it is. A label is non-removable if deleting it leaves a reader asking "what is that?"; it is removable only if the question becomes "why is that there?". Comparator labels name the thing ("prior method", "no joint training"), never a bare role word ("baseline", "previous"). Any term a general scientist can't parse gets a one-word gloss.

2.2 Ceiling. Per panel: title + axis labels + tick labels + series identity (labeled once per row of small multiples) + at most 2–3 result annotations. Count the strings; >6 beyond axes/ticks means you're over. The ceiling counts narrative annotations (callouts, value labels, brackets) — identity labels are floor, not budget.

2.3 Move to the caption: n=, what's-held-fixed, abbreviation expansions, non-comparable footnotes, exclusion rationale, methodological caveats.

2.4 Titles are takeaways. A reader seeing only the title knows what the panel shows. "Robust to gene dropout" passes; "Fewer genes" fails. Test: read it aloud cold — if the listener asks "fewer genes what?", rewrite. For a row of small multiples that vary one thing, drop per-panel titles for one row-header.

2.5 Value-on-mark only for the headline number — the one a reader would quote. Everything else is read off the axis.

2.6 When in doubt, delete the label and re-read. If the message survives, it stays deleted.

§3 Axes, scales, small multiples

When an existing axes needs a frame different from the figure-wide setting, call set_frame(ax, style=...).

3.1 Axis padding. Axis limits clear the data by ≥ one marker radius on every side; markers and text never touch a spine. ax.margins(0.04) after plotting, or extend the limit past any annotation.

3.2 Axis breaks over wasted range. When data occupy <40 % of an axis, break the axis or start it at the data floor with a clear non-zero tick. Never draw a reference line, threshold, or annotation inside a broken-axis gap — the gap has no coordinate.

3.3 Log axes get human-readable ticks — 10², 10³, or 1k / 10k / 100k, not raw exponents. Never draw filled bars on a log-scaled value axis (bar length encodes ratio to an arbitrary floor); use points + median tick instead.

3.4 Shared axes across small multiples. A row or column of small multiples shows tick labels once (leftmost / bottommost panel); interior panels keep ticks but drop labels. When the panels share a y-axis and differ only by x-variable, render them as abutting subplots (wspace≤0.06) with one row-header title.

3.5 Fill the box. A panel's data envelope occupies ≥75 % of its allotted rectangle. If a panel's natural aspect leaves dead bands, reshape the grid (rowspan, stacked complementary panels) — don't pad the panel.

3.6 Direction of goodness. When higher- or lower-is-better is not obvious from the axis label, place a small upright cue ("higher = better") in the margin — once per row of panels, never per panel, and never only in the caption. A directional glyph embedded in rotated text rotates with it; set the cue upright. goodness_arrow(ax, ...) places this cue.

3.7 Physical width. A single-row figure at 300 dpi fits the venue's double-column width. Adding a schematic or labels does not push data panels narrower than they were before.

§4 Color

4.1 Threading. Once a color is bound to an entity (a method, a feature, a condition), reuse that exact color for every mark representing that entity across the figure — line, fill, marker, text, heatmap row. Color is the cross-reference; a reader should never have to consult a legend twice.

4.2 Limit hues. Use as few distinct hues as the data require. When the figure compares a focal series against others, make the focal series visually dominant (saturated, heavier weight) and render comparators with lower visual weight (desaturated, lighter, or thinner). The focal hue must not coincide with any hue in a categorical palette used in the same figure. The focal series must remain identifiable even when its mark is zero-width or coincident with others — via outline, marker, or a light tinted band. Use focal_palette(...) to bind the focal and comparator colors to the ordered labels.

4.3 Hierarchical categories. When categories nest (groups within groups), the outer level picks the hue family and the inner level samples within it.

4.4 Continuous and diverging. Use a perceptually uniform sequential map for generic continuous values; a single-hue ramp for ordinal rank or size; a diverging map for signed quantities — always centered at the semantically meaningful zero (0, 1.0, or median), never the data midpoint.

4.5 CVD safety. Never rely on a red/green contrast for a binary or opposing distinction. Any binary pair should remain distinguishable in deuteranopia simulation. Reserve one alarm hue for error/anomaly/perturbation marks and do not reuse it as a data-series color.

4.6 Two palettes, two legends. When a figure uses two categorical color systems, each legend sits adjacent to the first panel where its palette applies.

§5 Typography

5.1 Sentence titles. A panel title states the comparison in plain language, regular weight, left-aligned. Metric names go on the axis, not in the title.

5.2 Role-mapped size ladder. A figure uses at most three font sizes, mapped to role not space: titles/axis-labels/series-identity at the base size; legend/annotation text one step down; tick labels one step further. Panel letters are the only exception (bold, larger). If a label doesn't fit at its role's size, fix the layout or shorten the text — don't reach for an intermediate size. apply_figure_style(sizes=(8,7,6)) sets the ladder. When one secondary metadata line is necessary, build the two-line text with two_tier_label(name, meta).

5.3 Nomenclature. Species, gene, and variable names that scientific convention italicizes are italicized. Abbreviated codes inherit the rule; expand once on first appearance.

5.4 Magnitude suffixes. Large counts use k / M / B (4.2B, 120 kb), not comma-grouped full numerals.

5.5 Numeric annotations. On-mark numbers use at most 2 significant figures — unless 2-sf rounding would make two distinct rows print the same value, in which case show the digit that separates them. Text on a filled mark reaches ≥4.5:1 contrast; if it doesn't, place the text outside the mark.

5.6 No internal codes. Axis labels use plain-language names; codebase abbreviations appear only in parentheses after the readable name or in the caption. Comparator series are labeled with what they are, not a role word.

5.7 Panel letters. Bold, top-left, outside the axes box. Case follows the target venue's convention; panel_letter(ax, 'a', case=...) handles either.

§6 Chart-family guidance (by data shape)

6.1 Categorical × numeric. Show the distribution, not just the summary. Chart choice follows n: jittered strip with a median tick for small n; box or violin for large n; bar + overlaid raw points or bar + interval when the mean is the message. Use strip_with_median(...) for the jittered-strip form and bar_with_points(...) for bars with raw points or an interval. The errorbar='ci95' interval is the t-distribution 95% CI of the mean (half-width t_{0.975,n−1}·s/√n), so it is valid at small n. Error bars and raw-point overlays are alternatives — showing both is usually redundant. A category absent from a group is marked (n.d., —, or a hatched ghost) at its slot; an empty slot reads as zero. A zero-valued bar gets a visible stub or dot at the baseline.

6.2 Single-observation categories. A filled dot with a thin neutral stem to the semantic zero (lollipop). Value labels sit beside the dot.

6.3 Continuous series. Mean-per-x as a line with markers; individual runs as thin translucent lines or points behind it. Label each series with direct text at the right end of its line in preference to a legend box; end_of_line_labels(...) places those labels. Summary glyphs (per-bin mean/median) use a shape that cannot be mistaken for a raw observation, identical across series, drawn below the raw points in z-order.

6.4 Distributions on shared support. When two distributions overlap heavily, stack them as small panels with a shared x-axis or use a ridgeline. Overlay only when the separation is visually clear.

6.5 Matrices. When a heatmap is small enough to read (< ~200 cells), print the value in every cell. State the threshold once in the colorbar label.

6.6 Embeddings. Dimensionality-reduction scatters (UMAP, t-SNE, PCA) drop ticks and tick labels; a small corner arrow pair names the axes. Clusters are labeled by thin leader lines to text in surrounding whitespace.

6.7 Paired prediction vs. observation. Stack the two as adjacent tracks with identical x and color; let the alignment carry the comparison. Target regions are translucent spans registered in the legend.

6.8 Insets. Connect a detail inset to its source region visibly — a bounding box with connector lines, or a translucent wedge.

6.9 Label the extremes. On a scatter of named observations, direct-label at least the maximum, minimum, and any flagged point with a thin leader line. After rendering, verify every leader endpoint terminates within one marker radius of the row it names.

§7 Layout & narrative

7.1 Show what is measured before the result. A reader should grasp what's being compared before seeing the comparison — via a plain-language title, a labeled schematic, or panel ordering. Any schematic uses the same words and glyphs as the data panels' labels.

7.2 One figure, one message. A multi-panel figure has a single sentence it is trying to make true. Every panel either states it, supports it, or bounds it; panels that do none of these belong in supplement.

7.3 Legends live in whitespace. Frameless, placed inside the figure's natural whitespace, or replaced by direct labeling. Legend entries are swatch-first, left-aligned, and resolve every visually distinct glyph on the panel.

7.4 Row-band headers for nested faceting. When small multiples are grouped, each group gets one spanning header, not repeated per-panel titles.

7.5 The figure arc. For a paper: Figure 1 renders the paper's one-sentence pitch as data — scope, not architecture. Subsequent figures cover mechanism, evidence, robustness, application. A panel is judged against the paper's pitch, not just its own figure's claim; content moves between figures if that's where the story needs it. (paper-narrative runs this review.)

7.6 Don't re-decorate a passing panel. Between revision rounds, a panel that already passes is not made more visually complex to fix nothing. Adding marks or labels to a clean panel is a regression.

§8 Anti-patterns

These are correctness failures, not style preferences:

• Red and green as opposing categories.
• Filled bars on a log-scaled value axis.
• Colorbar ticks that are evenly spaced but miss the semantic center.
• A diverging colormap whose center is the data midpoint, not the semantic zero.
• An axis title that restates the tick labels.
• Explaining the direction of goodness only in the caption.
• A "reference" line drawn at a value that is itself one of the plotted points.
• An excluded row that enters a plotted summary statistic.
• A leader line whose nearest mark is not the row it labels.

§9 Render-then-verify

After fig.savefig(...), before save_artifacts:

9.1 Geometric (bbox) check.

# A previous notebook cell may have closed the pyplot manager after capturing
# its inline image. Reattach the headless canvas when reusing that Figure.
if not hasattr(fig.canvas, "get_renderer"):
    from matplotlib.backends.backend_agg import FigureCanvasAgg
    FigureCanvasAgg(fig)
fig.canvas.draw()
r = fig.canvas.get_renderer()
texts = [(t, t.get_window_extent(r)) for t in fig.findobj(mpl.text.Text)
         if t.get_text().strip() and t.get_visible()]
spines = [(s, s.get_window_extent(r)) for ax in fig.axes
          for s in ax.spines.values() if s.get_visible()]
ticklabels = {ax: set(ax.get_xticklabels(which='both') + ax.get_yticklabels(which='both'))
              for ax in fig.axes}
overlaps  = [(a, b) for i, (a, ba) in enumerate(texts) for b, bb in texts[i+1:] if ba.overlaps(bb)]
overlaps += [(t, s) for t, bt in texts for s, bs in spines
             if bt.overlaps(bs) and t not in ticklabels[s.axes]]
# assert: overlaps == [] and every text box lies within fig.bbox

Overlap is defined between visible boxes, and a tick label sitting on its own spine is not a finding. Fix (move, shorten, stagger) and re-save until clean. This canvas guard makes the check safe when plotting and QA run in separate notebook_execute cells; do not require them to share one cell.

9.2 Perceptual check. The bbox check is geometric, not perceptual — it will not catch a low-contrast label, a leader that crosses three others, or a series color mistakable for another. When feedback identifies specific panels, inspect those panel crops first at native resolution. For full QA, crop the saved PNG to each panel and look:

fig.savefig("figure.png")
for letter, box in panel_crops(fig).items():
    print(letter, box)  # pass each box to the Agent's image-viewing tool

For each crop: Is every glyph and mark legible against its background? Does the smallest plotted element have a stroke or stub? Do any leaders cross? Could any series color be mistaken for another? Does the legend sit beside what it keys? A perceptual defect that passes §9.1 is still a defect.

For SVG, query before reading: locate the relevant element by text, ID, or attributes and inspect only its immediate context. When the figure is reproducible, remove an unwanted overlay in the producer and re-render; inspect broader SVG source only when narrow lookup cannot locate the element.

When in doubt: fewer hues, more direct labels, raw data over summary stats, and state what is being measured before showing the result.