tikz-scientific-figures

name

tikz-scientific-figures

description

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.

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 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 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 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.