# Tikz Scientific Figures > Create publication-grade scientific figures and schematic diagrams with TikZ/PGFPlots, output as vector PDF (and SVG for visual editing). Use when the user wants a figure for a paper/thesis/report, a data plot (line, scatter, bar, error-bar, heatmap, log axis), a circuit diagram, a flowchart or block diagram, a free-body/force or geometry schematic, a biology figure (immunofluorescence/tissue, cell, signaling pathway, gene or plasmid map), a CS/ML figure (neural network, system architecture, finite-state machine, tree, graph), or a molecular structure — especially when they mention TikZ, PGFPlots, circuitikz, LaTeX figures, reproducible/vector/publication-quality plots, or editing an existing .tex figure. Produces reproducible .tex + data sources the user can re-edit. - Skill: `pm-shawn/tikz-scientific-figures` (Agent Skill, multi-file: 4 files) - Install (CLI): `npx skillmds@latest add pm-shawn/tikz-scientific-figures` - Raw SKILL.md: https://api.skillmd.com/api/skills/pm-shawn/tikz-scientific-figures/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Docs & Writing - Author: pm-shawn (https://skillmd.com/u/pm-shawn) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/pm-shawn/tikz-scientific-figures --- # TikZ Scientific Figures Generate reproducible, publication-grade figures in TikZ. One figure = one `standalone` `.tex` file that compiles to a tightly-cropped vector PDF. Always deliver the `.tex` (+ any data file) so the figure stays editable. ## Step 0 — check the toolchain (first run only) ```bash 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, then self-check visually** (do not skip the look): ```bash bash scripts/compile.sh figure.tex # -> figure.pdf (read figure.log on error) bash scripts/preview.sh figure.pdf # -> figure.preview.png — actually open & inspect it ``` On errors, match `figure.log` against `references/common-errors.md`. 5. **Deliver** the PDF + `.tex` + data file together, and state the figure's edit state (see Editing below). ## Publication-grade rules (non-negotiable defaults) - Vector output (PDF/SVG); never deliver only a raster. - 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 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.