Publication figure house style

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Enforces the lab's publication house style on every matplotlib/seaborn figure: a fixed Okabe-Ito color cycle, perceptually-uniform colormaps, explicit journal widths, vector PDF export at 300 dpi, despining, sentence-case labels with units, and named uncertainty. Apply whenever generating figure code intended for a manuscript, journal submission, or paper. These are non-negotiable overrides of library defaults — the base model would otherwise emit tab10 colors, a 6.4x4.8 figure, a framed legend, and a 100-dpi PNG.

Rules (the complete spec)

Color

1. Set the categorical color cycle to the Okabe-Ito palette — EXACTLY these 8 hex codes in

THIS order, then install them as the prop cycle: python okabe_ito = ['#E69F00', '#56B4E9', '#009E73', '#F0E442', '#0072B2', '#D55E00', '#CC79A7', '#000000'] plt.rcParams['axes.prop_cycle'] = plt.cycler(color=okabe_ito) Never rely on the default tab10 cycle. The order is fixed (orange first, sky-blue second).

1. Continuous / sequential data (heatmaps, intensity images): use a perceptually-uniform

colormap — viridis, plasma, or cividis. NEVER jet or rainbow.

1. Diverging data (correlation matrices, signed differences): cmap='RdBu_r' with center=0.

NEVER a red-green diverging map.

1. For colorblind/grayscale safety on line plots, add redundant non-color encoding: distinct

linestyle and/or marker per series, not color alone.

Size & format

1. Always pass figsize explicitly. Single-column default is (3.5, 2.5) inches.
2. Journal full widths in millimeters — single / double column:

• Nature: 89 / 183 mm (≈ 3.5 / 7.2 in)
• Science: 55 / 175 mm (≈ 2.2 / 6.9 in)
• Cell: 85 / 178 mm (≈ 3.35 / 7.0 in)

Convert mm to inches by dividing by 25.4.

1. Save as a VECTOR PDF at dpi=300 with tight bounding box:

fig.savefig('figure1.pdf', dpi=300, bbox_inches='tight'). Also acceptable: EPS, SVG. NEVER JPEG/JPG for plots or line art (compression artifacts). TIFF/PNG only for photos.

Axes & labels

1. Remove the top and right spines on every axes:

ax.spines['top'].set_visible(False); ax.spines['right'].set_visible(False) — or sns.despine().

1. Axis labels in SENTENCE CASE with the unit in parentheses: ax.set_xlabel('Time (hours)'),

ax.set_ylabel('Response (uM)'). Never ALL-CAPS, never unit-less.

1. Legends carry no frame: ax.legend(frameon=False).

Multi-panel

1. Label each panel with a BOLD UPPERCASE letter (A, B, C, D) at the top-left, placed in axes

coordinates: ax.text(-0.15, 1.05, 'A', transform=ax.transAxes, fontsize=10, fontweight='bold').

1. Keep figsize, fonts, palette, and styling identical across all panels of one figure.

Statistics

1. Always show uncertainty — error bars or a confidence band — and NAME the type

(SD, SEM, or 95% CI) in a comment, label, or caption. Show individual points when feasible.

Worked examples (BEFORE base default -> AFTER house style)

Color cycle

BEFORE:

python
ax.plot(x, y1, label='control')   # tab10 blue
ax.plot(x, y2, label='treated')   # tab10 orange

AFTER:

python
okabe_ito = ['#E69F00', '#56B4E9', '#009E73', '#F0E442',
             '#0072B2', '#D55E00', '#CC79A7', '#000000']
plt.rcParams['axes.prop_cycle'] = plt.cycler(color=okabe_ito)
ax.plot(x, y1, label='control')   # now #E69F00
ax.plot(x, y2, label='treated')   # now #56B4E9

Continuous colormap

BEFORE: ax.imshow(arr, cmap='jet'); fig.colorbar(...) AFTER: im = ax.imshow(arr, cmap='viridis'); fig.colorbar(im, ax=ax)

Diverging colormap

BEFORE: sns.heatmap(df.corr(), cmap='coolwarm') (uncentered, generic) AFTER: sns.heatmap(df.corr(), cmap='RdBu_r', center=0, annot=True, fmt='.2f', square=True)

Figure size / journal width

BEFORE: fig, ax = plt.subplots() (6.4 x 4.8 in default) AFTER: fig, ax = plt.subplots(figsize=(3.5, 2.5)) # single column For a Nature double-column figure: figsize=(183/25.4, 4) # 183 mm ≈ 7.2 in

Vector export

BEFORE: fig.savefig('fig.png') (raster, ~100 dpi) AFTER: fig.savefig('figure1.pdf', dpi=300, bbox_inches='tight')

Despine

BEFORE: (all four spines drawn) AFTER: ax.spines['top'].set_visible(False); ax.spines['right'].set_visible(False)

Axis labels

BEFORE: ax.set_xlabel('TIME'); ax.set_ylabel('amplitude') AFTER: ax.set_xlabel('Time (hours)'); ax.set_ylabel('Amplitude (mV)')

Legend

BEFORE: ax.legend() (framed box) AFTER: ax.legend(frameon=False)

Panel labels

BEFORE: ax.set_title('1') (numeric, inside title) AFTER: ax.text(-0.15, 1.05, 'A', transform=ax.transAxes, fontsize=10, fontweight='bold')

Uncertainty

BEFORE: ax.bar(conditions, means) (no error) AFTER:

python
ax.errorbar(conditions, means, yerr=sems, fmt='o', capsize=3)  # error bars = SEM

Colorblind redundant encoding

BEFORE: four lines distinguished by color only. AFTER:

python
styles, marks = ['-', '--', '-.', ':'], ['o', 's', '^', 'v']
for i, (yy, lbl) in enumerate(series):
    ax.plot(x, yy, linestyle=styles[i], marker=marks[i], label=lbl)  # color from Okabe-Ito cycle

Edge cases & exceptions

• More than 8 categorical series: 8 Okabe-Ito colors are the ceiling — add linestyle/marker

encoding rather than inventing a 9th color, or split into panels.

• Nature lowercases panel letters (a, b, c); most other journals use uppercase. Default to

UPPERCASE unless the target is explicitly Nature.

• Interactive Plotly figures: still export a STATIC vector/high-res raster for the manuscript

(fig.write_image('figure.png', scale=3) ≈ 300 dpi); the interactive version is not the deliverable.

• Bar charts: start the y-axis at 0 unless a non-zero baseline is scientifically justified and noted.
• A single-series heatmap that is purely positive (e.g. counts) uses viridis, NOT RdBu_r —

RdBu_r + center=0 is only for signed/diverging data.

• Photographs / microscopy: TIFF or PNG at 300-600 dpi is correct — the "no JPEG / vector PDF"

rule is for plots and line art, not pixel images.

Do / Don't

• DO install the Okabe-Ito prop cycle; DON'T leave the default tab10 cycle.
• DO use viridis/plasma/cividis; NEVER use jet or rainbow.
• DO center diverging maps at 0 with RdBu_r; NEVER use red-green diverging colors.
• DO set figsize explicitly; DON'T accept the 6.4x4.8 default.
• DO save vector PDF at dpi=300; NEVER save plots as JPEG.
• DO despine top+right; DON'T ship the full four-spine box.
• DO write 'Time (hours)'; DON'T write 'TIME' or a unit-less label.
• DO pass frameon=False; DON'T leave the boxed legend.
• DO label panels bold-uppercase in axes coords; DON'T number them in the title.
• DO show and name the uncertainty type; NEVER plot means with no error indication.

Common mistakes (the base's wrong defaults)

1. Leaving the default tab10 color cycle instead of installing Okabe-Ito.
2. Reaching for jet/rainbow/coolwarm for heatmaps.
3. Using a diverging map without center=0 (misleading neutral point).
4. Omitting figsize, producing an oversized 6.4x4.8 figure.
5. Saving .png at default dpi, or worse .jpg, for a line plot.
6. Drawing all four spines and a framed legend.
7. ALL-CAPS or unit-less axis labels.
8. Numbering panels in the title instead of bold-uppercase axes-coordinate labels.
9. Plotting summary means with no error bars / CI, or not stating the error type.
10. Distinguishing series by color alone, breaking grayscale and colorblind readability.

Quick checklist

Okabe-Ito cycle - viridis/RdBu_r(center=0) not jet - explicit figsize / journal mm - vector PDF @300 not JPEG - despine top+right - sentence-case labels with units - legend frameon=False - bold-uppercase panel labels in axes coords - named uncertainty - redundant encoding for colorblind.