How-to: switch to a journal's format

Figures are drawn at their printed size from the start. So when the journal changes, you do not redraw the figures: you switch the journal preset and run the checks again. A preset is a YAML file with that journal's figure widths, maximum height, font, text sizes, line widths and panel tag style, and the values preflight checks against.

1. The presets included

Preset	Width	Font	Text	Panel tags	Source
journal_generic	180 mm	Arial	6–8 pt	a, b, c	The range most life-science journals accept (for drafts before a journal is chosen)
journal_nature	183 mm (single column 89; 1.5 columns 120, 136)	Arial, else Helvetica	5–7 pt	a, b, c · 8 pt bold	Nature's guide for final submissions
journal_science	184 mm (single column 89; 1.5 columns 127)	Myriad, else Arial	at least 6 pt	A, B, C · 9 pt bold	Science's guide for revised manuscripts

Each file's header gives the guide's address and the date it was checked, and values the guide does not give are marked "not stated". Journal guides change, so check the header's date and address before submitting.

2. Switching

In the config's project.style, replace the page preset with the journal preset. This one line is all.

project:
  style: ["default", "print", "journal_nature"]   # before: page_a4_portrait_narrow

Then build with the checks.

fa build <project> --preflight

Values written in the config itself come before the preset (merge order: bundle < preset < config). So a panel whose text sizes are set in the config keeps them when the preset changes, and preflight points out where they do not meet that journal's limits.

3. How many columns a figure spans

A journal preset names its column widths (page.columns_mm, e.g. Nature 1: 89, 1.5: 120, 2: 183 mm). A figure says how many columns it spans, and the preset gives the width:

figures:
  page_columns: 1      # 1, 1.5 or 2; leave it out for the full (double-column) width

The span stays when the journal changes, so a single-column figure is drawn at Nature's 89 mm or the generic 85 mm without editing its width. Which span a figure needs is your decision: a figure moved from two columns to one usually needs its layout changed as well (for example a 2x2 grid of facets stacked as 4x1), and those are config keys too. Build it with --preflight; crowded or clipped text at the narrower width is what the checks report.

4. What preflight points out

Check	Key in the journal preset
Text too small, lines too thin	print_check.min_font_pt, min_line_pt
Text too large (panel tags aside)	preflight.max_font_pt
A figure not at a journal column width	preflight.allowed_widths_mm, width_tol_mm (choose one with figures.page_columns)
A figure taller than the page	page.content_height_mm
Tag case and size	preflight.panel_tag_case, panel_tag_size_pt
Fonts the PDF may not use, fonts not installed	preflight.allowed_fonts

To fix them, change the values pointed out in the config. Each key's comment gives its unit and which way to adjust it, and fa param explain <project> <key> shows where a value came from.

5. Good to know

• Fonts. A preset gives not one font but an ordered list (rcparams: font.sans-serif). If the first is not installed, the next is used. To use a commercial font such as Myriad, install it.
• Maths text. matplotlib draws exponents (10²) and subscripts (H₂O₂) in the DejaVu font by default. The journal presets set these to the same font too, with mathtext.* in rcparams. The rcparams: block is applied to matplotlib when the config is loaded, so you can also write it in the config itself.
• Scripts that draw their own tags. In figures that use place_panel_tags, the tags follow the preset. A script that writes the tag letters itself reads figures.panel_tag_case ("lower" or "upper") for their case, and gives the tags gid=PANEL_TAG_GID so preflight recognises them as tags.
• Rules that are not checked. Science, for example, asks you not to use red and green together. Preflight's colour check measures whether two colours can be told apart under simulated colour-vision deficiency, so a red-green pair that can be told apart passes. Check the guide's written rules yourself.