TikZ Scientific Figures

Generate reproducible, publication-grade figures in TikZ. One figure = one standalone .tex file that compiles to PDF (intermediate only), then exports SVG + PNG as the actual deliverables. Always deliver the .tex (+ any data file) so the figure stays editable. PDF is not a deliverable and must not be registered in the figure registry.

Step 0 — check the toolchain (first run only)

bash scripts/check_env.sh

If tools are missing, show the user the printed install hints (OS-aware: macOS/Windows/Linux) and stop until the toolchain is in place. Need: a LaTeX engine (pdflatex — the scripts' default; lualatex needs luatex85), poppler (preview), and for SVG export dvisvgm + mutool (mupdf-tools). latexmk is optional — the scripts run the engine twice without it.

Cross-platform note. The recipes and TikZ code are OS-independent (identical output on macOS/Windows/Linux). The four .sh scripts are portable bash: on Windows run them from Git Bash or WSL. If no bash is available, run the underlying commands directly — compile ≈ pdflatex -interaction=nonstopmode -halt-on-error figure.tex (run twice), preview ≈ pdftoppm -png -r 200 -singlefile figure.pdf out, export_svg ≈ dvisvgm --pdf figure.pdf. On Windows, MiKTeX auto-installs missing LaTeX packages on first compile, so the "optional packages" step is usually unnecessary there.

Workflow

1. Pick the figure type and read the matching recipe (only that one):
   • data plot (line/scatter/bar/hist/box/heatmap/contour/3D/log) → references/pgfplots-recipes.md
   • circuit → references/circuitikz-recipes.md
   • flowchart / block / force / geometry → references/diagram-recipes.md
   • biology (IF/tissue, cell, pathway, gene/plasmid map) → references/biology-recipes.md
   • CS/ML (neural net, architecture, automaton, tree, graph, UML, ER, Gantt) → references/cs-recipes.md
   • chemistry (molecule, reaction, energy profile, lattice) → references/chemistry-recipes.md
   • physics (ray optics, Feynman, vector field) → references/physics-recipes.md
   • math (commutative diagram, Venn, number line) → references/math-recipes.md 2b. Composing a paper figure? Multi-panel (a)(b)(c), insets, significance markers, fit+CI bands, or labelling a real microscopy/photo image → references/figure-composition.md.
2. Start from the template. Copy assets/standalone-template.tex and assets/preamble.tex into the working dir. Keep the TUNABLES block at the top — it is what lets non-experts hand-edit later.
3. Put data in an external file (data.csv) for data plots, so "editing the plot" means editing the CSV, not the TikZ.
4. Compile, export SVG+PNG, then self-check visually (do not skip the look):

   bash scripts/compile.sh figure.tex      # -> figure.pdf (intermediate only)
   bash scripts/export_svg.sh figure.pdf   # -> figure.svg (primary vector deliverable)
   bash scripts/preview.sh figure.pdf      # -> figure.png (raster deliverable)

   On errors, match figure.log against references/common-errors.md.
5. Deliver SVG + PNG + .tex + data file together. PDF is an intermediate compile artifact only — do not deliver it, do not register it in the figure registry. State the figure's edit state (see Editing below).

Contest-Orchestrator Adapter

When this skill is invoked from contest-orchestrator, read contest-adapter.md. In that context this skill is reserved for evidence-grounded mechanism, principle, force, geometry, coordinate, vector, curve, angle and formula schematics.

• Do not use this route for data result plots; those use ModelViz followed by scipilot-figure-skill quality checks.
• Do not use this route for problem-analysis flowcharts or technical-roadmap diagrams; those use tech-route-maker.
• Read the project's model_contract.yaml, symbol_table.md, derivation registry and relevant result/source files before writing TikZ.
• Every visible variable, label, relation and geometric object must have a source locator. Do not invent formulas, variables, units or mechanisms.
• Keep .tex as the authoritative editable source and deliver SVG + PNG; PDF is only a local compilation intermediate and must not enter artifacts, registry or delivery package.
• Run preview rendering, visual inspection and AI visual QA by default for every generated figure. Check clipping, overlap, alignment, legibility, whitespace, color/gray-scale readability and clean composition in addition to compilation, source, structure and provenance checks; the user may perform a final visual inspection as an additional check.
• Register the output as kind=schematic, generator=tikz-scientific-figures.
• Return the shared node handoff fields: status, active_mode, task_card, artifacts, evidence, checks, blockers, and next_node; keep source and reports under the project workspace.
• Treat the TikZ source and compiled figure as artifacts, not proof. Every symbol and relation must be defined in the paper or model contract; captions and labels must not contain agent discussion, debugging, failed attempts, old versions or other negative echo.

Publication-grade rules (non-negotiable defaults)

• Vector output (SVG) + raster preview (PNG); PDF is compile-only intermediate, never delivered.
• Colour-blind-safe palette (Okabe–Ito / viridis) — wired into preamble.tex. Never hard-code raw red/green or use the jet colormap.
• Size to the target: 89 mm single-column / 183 mm double-column; body font 7–9 pt.
• Every axis labelled with units; error bars state SD/SE/CI; multi-panel figures numbered (a)(b)(c).
• Render math labels in LaTeX ($\alpha$, siunitx), so they match the paper.
• Ship the source: deliver .tex + data, not just an image.

If the user names a target venue (IEEE, a thesis template, etc.), adjust width, font, and compat in preamble.tex accordingly before drawing.

Editing an existing figure

Read references/editing-guide.md. Summary of the rule that must not be broken:

• Default: edit the .tex/.csv in place and recompile (model-driven or via the TUNABLES block). Never redraw from scratch when a source file exists.
• For free-form visual polish, bash scripts/export_svg.sh figure.tex exports an SVG for Inkscape/TikZiT. This forks the figure to the SVG branch (a figure.svg.frozen marker is written): from then on the SVG is authoritative and the .tex is a frozen archive — do NOT recompile the .tex over the user's SVG edits. Always tell the user which branch a figure is on.
• After exporting, launch a local visual editor that loads the SVG and saves back in place:

  bash scripts/edit_svg.sh figure.svg   # no arg => newest *.svg in the dir

  This starts a local server (127.0.0.1, ephemeral port), opens Method Draw in the browser with the SVG pre-loaded, and Ctrl/Cmd+S writes the edits back to the same figure.svg (the browser's download export stays as a fallback). Ctrl+C in the terminal stops the server. The SVG remains the authoritative source (.tex stays frozen). Needs python3; on Windows run from Git Bash or call python3 scripts/edit_server.py figure.svg directly.