Tikz diagrams

TikZ Diagrams

Generate publication-ready TikZ/PGF diagrams for academic papers.

Diagram Types

System Architecture

• Layered block diagrams with labeled components
• Arrows showing data/control flow between modules
• Color-coded subsystems with legend
• Typical use: software systems, ML pipelines, hardware architectures

Neural Network Diagrams

• Layer-by-layer visualization (input, hidden, output)
• Convolutional filter stacks, attention blocks, skip connections
• Annotated dimensions (e.g., 128x128x64)
• Uses custom node styles for different layer types

Note on PlotNeuralNet-style diagrams: For simple neural network diagrams (basic layer stacks, small architectures), this skill handles them well. However, for publication-quality 3D layered architecture diagrams (the style popularized by PlotNeuralNet with isometric 3D blocks, color-coded layer types, and detailed dimension annotations), defer to the dedicated plotneuralnet skill instead. That skill specializes in generating PlotNeuralNet-compatible Python/LaTeX code that produces the distinctive 3D CNN/transformer visualizations commonly seen in top-tier ML publications. Use this skill for flowchart-style NN diagrams; use plotneuralnet for 3D architectural visualizations.

Flowcharts and Pipelines

• Decision diamonds, process rectangles, start/end ovals
• Conditional branching with labeled yes/no paths
• Linear pipelines with sequential processing steps
• Data transformation chains with intermediate representations

Experimental Setup

• Equipment arrangement diagrams
• Participant flow (CONSORT-style)
• Measurement configurations
• Stimulus presentation timelines

State Machines

• States as rounded rectangles or circles
• Transitions as labeled arrows with conditions
• Initial/final state markers
• Guard conditions and actions on transitions

Data Flow Diagrams

• Sources, sinks, processes, and data stores
• Directional arrows with data labels
• Hierarchical decomposition levels

Comparison Frameworks

• Side-by-side or matrix layouts
• Feature grids with visual indicators
• Venn diagrams for overlap visualization

Timeline and Gantt Charts

• Horizontal timeline with milestones
• Gantt bars for parallel tasks and dependencies
• Phase markers with date labels

Tree Structures

• Uses forest package for linguistic/parse trees
• Hierarchical classification trees
• Decision trees with split conditions
• Taxonomy diagrams

Mathematical Plots (pgfplots)

• Line plots, bar charts, scatter plots
• Error bars and confidence bands
• Multiple axes and grouped plots
• Axis labels with LaTeX math notation

Required Packages

Package	Purpose
tikz	Core drawing engine
pgfplots	Data-driven plots and charts
forest	Tree and hierarchy diagrams
tikz-cd	Commutative diagrams (category theory)
circuitikz	Circuit diagrams
tikz-timing	Timing diagrams

Common TikZ Libraries

• arrows.meta: modern arrow tips
• positioning: relative node placement
• shapes.geometric: diamonds, ellipses, trapezoids
• calc: coordinate arithmetic
• fit: bounding boxes around node groups
• backgrounds: shaded regions behind nodes
• decorations.pathreplacing: braces and brackets

Style Conventions

Reference references/tikz-patterns.md for reusable patterns. Follow these defaults:

• Colors: Use a consistent palette (e.g., blue!60, red!60, green!60). Define named colors at the top of the file for easy theming.
• Fonts: Use \sffamily\small for node labels. Match the document font family.
• Line widths: thick for primary flow, thin for secondary. Avoid ultra thick.
• Arrow tips: Use arrows.meta style: -{Stealth[length=3mm]} or -{Latex[length=2.5mm]}.
• Node spacing: Minimum 1.5cm between nodes for readability.
• Grayscale fallback: Every diagram must remain legible in grayscale (use patterns or dashes alongside color).

Style presets

This skill consumes TikZ style macros (colors, fonts, line widths, arrowheads) that replace the defaults in references/tikz-patterns.md. Named presets are defined once in references/figure-styles.md: do not duplicate those definitions here, load that file when a preset is needed.

• default: the current behavior described above (Style Conventions). Used when no style is mentioned; zero change from prior output.
• nature: preset for Nature-portfolio submissions.
• ieee: preset for IEEE submissions.

Presets resolve in one precedence order, highest first: explicit Style: line > trigger phrase > journal inference from manuscript/config.yaml > default.

Style: line (accepted input): the invocation may carry an explicit Style: line, which outranks every other selector:

Draw my two-stage pretraining and fine-tuning pipeline as a standalone TikZ figure.
Style: nature

Style: nature and Style: ieee apply that preset. Style: default, or no Style: line at all, is the no-op path: exactly the output this skill produces today, and an omitted Style: line is never an error. For any other value, do not guess and do not improvise a preset: say it is not defined, list the presets that are (default, nature, ieee), and ask which to use.

Trigger phrases: with no Style: line, prose selects a preset: "nature style", "in Nature format", "for submission to <journal>", "IEEE format".

Journal inference: with neither a Style: line nor a trigger phrase, if a target journal is set in manuscript/config.yaml, map it to a preset family: Nature portfolio titles map to nature, IEEE titles map to ieee, anything else (or no target journal) maps to default.

Scope of presets: presets restyle only, they change colors, fonts, line widths, and arrowheads. They never alter data, values, or the "(synthetic, for demonstration)" labeling used elsewhere in generated figures.

Output Format

Standalone .tex File

Every diagram is saved as a standalone file in figures/:

\documentclass[tikz,border=5pt]{standalone}
\usepackage{pgfplots}
\pgfplotsset{compat=1.18}
% ... additional packages as needed

\begin{document}
\begin{tikzpicture}
  % diagram code
\end{tikzpicture}
\end{document}

Integration with Manuscript

Generate an \input{} or \includegraphics{} reference for main.tex:

\begin{figure}[htbp]
  \centering
  \input{figures/architecture-diagram.tex}
  \caption{Overview of the proposed system architecture.}
  \label{fig:architecture}
\end{figure}

PDF Compilation

• Compile-check standalone .tex to PDF by running scripts/latex-compile.py (or scripts/latex-compile.sh on POSIX), which uses whichever TeX engine is installed (tectonic recommended, or latexmk / pdflatex from TeX Live, MiKTeX, or MacTeX)
• Verify the output renders correctly before delivering
• Report any compilation errors with suggested fixes

Workflow

1. Identify diagram type from user description
2. Determine required packages and TikZ libraries
3. Consult references/tikz-patterns.md for matching patterns
4. Load references/figure-styles.md and apply the matching preset (default, nature, or ieee), resolved by precedence (explicit Style: line, then trigger phrase, then the target journal in manuscript/config.yaml, then default); state which preset was applied and why
5. Generate TikZ code with named styles and coordinates
6. Save standalone .tex to figures/<diagram-name>.tex
7. Compile-check via scripts/latex-compile.py (uses tectonic if available, otherwise latexmk/pdflatex from TeX Live, MiKTeX, or MacTeX) and verify output
8. Generate \input{} snippet for manuscript integration
9. If Word output is needed, export the compiled figure to PDF and PNG and tell the user to place it in the document. Automated image embedding is planned, not implemented: templates/word/build-docx.js generates headings, paragraphs, and lists only, so do not claim a figure was written into their DOCX

Alt Text

Alt text is a REQUIRED output of this skill, delivered with every diagram (and every preset variant). Write one or two sentences describing the DATA content: name the stages or components and the order in which they connect, not the visual styling (colors, fonts, line weights). Presets restyle only, so all variants of one diagram share ONE data description plus at most a one-clause style note (for example "(Nature preset: sans-serif, hairline strokes)"). Do not begin with "Image of". See the Alt Text section of references/figure-styles.md. For LaTeX inclusion, offer \pdftooltip (pdfcomment package) without claiming full PDF/UA compliance; when the figure is placed in Word, templates/word/build-docx.js carries the alt text into the DOCX image accessibility properties.