scientific-writer 2.3.1__py3-none-any.whl

scientific_writer/.claude/skills/scientific-schematics/references/tikz_guide.md

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+# TikZ Guide for Scientific Diagrams
+
+## Overview
+
+TikZ (TikZ ist kein Zeichenprogramm - "TikZ is not a drawing program") is a powerful LaTeX package for creating high-quality vector graphics. This guide focuses on using TikZ for scientific diagrams, flowcharts, and schematics in research publications.
+
+## Basic TikZ Structure
+
+### Minimal Example
+
+```latex
+\documentclass{article}
+\usepackage{tikz}
+
+\begin{document}
+
+\begin{tikzpicture}
+  % Your drawing commands here
+  \draw (0,0) -- (2,0);  % Line from (0,0) to (2,0)
+  \node at (1,0.5) {Label};  % Text at position
+\end{tikzpicture}
+
+\end{document}
+```
+
+### Required Packages and Libraries
+
+```latex
+\usepackage{tikz}
+\usetikzlibrary{
+  shapes.geometric,  % Rectangles, circles, diamonds, etc.
+  shapes.arrows,     % Arrow shapes
+  arrows.meta,       % Modern arrow tips
+  positioning,       % Relative positioning (above, below, right of)
+  calc,             % Coordinate calculations
+  fit,              % Fitting boxes around multiple nodes
+  backgrounds,      % Background layers
+  decorations.pathreplacing  % Braces and decorations
+}
+```
+
+## Coordinate Systems
+
+### Cartesian Coordinates
+
+```latex
+\draw (0,0) -- (3,2);     % From origin to (3,2)
+\draw (1,1) circle (0.5); % Circle at (1,1) with radius 0.5
+```
+
+### Relative Coordinates
+
+```latex
+\draw (0,0) -- ++(2,0)    % Move 2 right from (0,0), update position
+           -- ++(0,2)     % Move 2 up from current position
+           -- ++(-2,0);   % Move 2 left from current position
+
+\draw (0,0) -- +(1,1);    % Move to (1,1) but don't update position
+```
+
+### Polar Coordinates
+
+```latex
+\draw (0,0) -- (30:2);    % Angle 30°, distance 2
+\draw (0,0) -- (90:1.5);  % Angle 90°, distance 1.5
+```
+
+### Named Coordinates
+
+```latex
+\coordinate (A) at (0,0);
+\coordinate (B) at (3,2);
+\draw (A) -- (B);
+```
+
+## Drawing Basic Shapes
+
+### Lines and Paths
+
+```latex
+% Straight line
+\draw (0,0) -- (2,0);
+
+% Multiple connected segments
+\draw (0,0) -- (1,1) -- (2,0) -- (0,0);
+
+% Closed path
+\draw (0,0) -- (1,1) -- (2,0) -- cycle;
+
+% Curved path (Bezier)
+\draw (0,0) .. controls (1,1) and (2,1) .. (3,0);
+
+% Smooth curve through points
+\draw plot[smooth] coordinates {(0,0) (1,2) (2,1) (3,3)};
+```
+
+### Rectangles and Circles
+
+```latex
+% Rectangle: (lower-left) rectangle (upper-right)
+\draw (0,0) rectangle (2,1);
+
+% Circle: (center) circle (radius)
+\draw (1,1) circle (0.5);
+
+% Ellipse: (center) ellipse (x-radius and y-radius)
+\draw (1,1) ellipse (1 and 0.5);
+
+% Rounded rectangle
+\draw[rounded corners=5pt] (0,0) rectangle (2,1);
+```
+
+### Arcs and Curves
+
+```latex
+% Arc: (start) arc (start-angle:end-angle:radius)
+\draw (0,0) arc (0:90:1);       % Quarter circle
+\draw (0,0) arc (0:180:1.5);    % Semicircle
+
+% Partial ellipse arc
+\draw (0,0) arc (0:270:1.5 and 1);
+```
+
+## Nodes - The Foundation of Diagrams
+
+### Basic Nodes
+
+```latex
+% Simple node
+\node at (0,0) {Text};
+
+% Node with name for referencing
+\node (A) at (0,0) {Node A};
+\node (B) at (2,0) {Node B};
+\draw (A) -- (B);  % Connect nodes
+
+% Node on a path
+\draw (0,0) -- node {middle} (2,0);
+```
+
+### Node Shapes
+
+```latex
+% Rectangle (default)
+\node[draw, rectangle] at (0,0) {Rectangle};
+
+% Circle
+\node[draw, circle] at (2,0) {Circle};
+
+% Ellipse
+\node[draw, ellipse] at (4,0) {Ellipse};
+
+% Diamond (requires shapes.geometric library)
+\node[draw, diamond] at (6,0) {Diamond};
+
+% Rounded rectangle
+\node[draw, rounded corners] at (8,0) {Rounded};
+```
+
+### Node Styling
+
+```latex
+% Size
+\node[minimum width=3cm, minimum height=1cm] {Wide node};
+
+% Colors
+\node[fill=blue!20, draw=blue!80] {Colored};
+
+% Line style
+\node[draw, thick, dashed] {Dashed border};
+\node[draw, ultra thick] {Thick border};
+
+% Text styling
+\node[font=\large\bfseries] {Bold Large Text};
+```
+
+### Node Anchors
+
+Nodes have anchor points for precise connections:
+
+```latex
+\node[draw] (A) at (0,0) {Node};
+
+% Anchor points: north, south, east, west, 
+%                north east, north west, south east, south west
+%                center
+
+\draw[red] (A.north) -- ++(0,0.5);    % From top of node
+\draw[blue] (A.east) -- ++(0.5,0);    % From right side
+\draw[green] (A.south) -- ++(0,-0.5); % From bottom
+```
+
+## Positioning
+
+### Absolute Positioning
+
+```latex
+\node[draw] at (0,0) {A};
+\node[draw] at (3,2) {B};
+```
+
+### Relative Positioning (positioning library)
+
+```latex
+\node[draw] (A) {Node A};
+\node[draw, right=of A] (B) {Node B};
+\node[draw, below=of A] (C) {Node C};
+\node[draw, above right=of A] (D) {Node D};
+
+% With custom distance
+\node[draw] (A) {A};
+\node[draw, right=2cm of A] (B) {B};
+\node[draw, below=1.5cm of A] (C) {C};
+```
+
+### Positioning Patterns
+
+```latex
+% Chained positioning
+\node[draw] (A) {A};
+\node[draw, right=of A] (B) {B};
+\node[draw, right=of B] (C) {C};
+\node[draw, right=of C] (D) {D};
+
+% Grid layout
+\node[draw] (A) at (0,2) {A};
+\node[draw] (B) at (2,2) {B};
+\node[draw] (C) at (0,0) {C};
+\node[draw] (D) at (2,0) {D};
+
+% Circular arrangement
+\foreach \i in {0,1,...,7} {
+  \node[draw, circle] at ({360/8 * \i}:2) {\i};
+}
+```
+
+## Arrows and Connections
+
+### Arrow Styles (arrows.meta library)
+
+```latex
+% Modern arrow tips
+\draw[-Stealth] (0,0) -- (2,0);        % Stealth arrow tip
+\draw[-Latex] (0,0.5) -- (2,0.5);      % LaTeX arrow tip
+\draw[-Triangle] (0,1) -- (2,1);       % Triangle tip
+
+% Both ends
+\draw[Stealth-Stealth] (0,1.5) -- (2,1.5);
+
+% Larger arrows
+\draw[-{Stealth[length=5mm, width=3mm]}] (0,2) -- (2,2);
+
+% Multiple arrows
+\draw[-{Stealth}{Stealth}] (0,2.5) -- (2,2.5);
+```
+
+### Connection Paths
+
+```latex
+\node[draw] (A) {A};
+\node[draw, right=3cm of A] (B) {B};
+
+% Straight arrow
+\draw[-Stealth] (A) -- (B);
+
+% Horizontal then vertical
+\draw[-Stealth] (A) -| (B);
+
+% Vertical then horizontal
+\draw[-Stealth] (A) |- (B);
+
+% Curved (Bezier)
+\draw[-Stealth] (A) to[bend left=30] (B);
+\draw[-Stealth] (A) to[bend right=30] (B);
+
+% Out and in angles
+\draw[-Stealth] (A) to[out=45, in=135] (B);
+```
+
+### Edge Labels
+
+```latex
+\node[draw] (A) {A};
+\node[draw, right=3cm of A] (B) {B};
+
+% Label above
+\draw[-Stealth] (A) -- node[above] {label} (B);
+
+% Label below
+\draw[-Stealth] (A) -- node[below] {label} (B);
+
+% Label at specific position (0=start, 0.5=middle, 1=end)
+\draw[-Stealth] (A) -- node[pos=0.25, above] {quarter} (B);
+
+% Sloped text
+\draw[-Stealth] (A) -- node[above, sloped] {sloped} (B);
+```
+
+## Styles and Customization
+
+### Defining Custom Styles
+
+```latex
+\begin{tikzpicture}[
+  % Define styles within tikzpicture options
+  process/.style={rectangle, draw, fill=blue!20, 
+                  minimum width=3cm, minimum height=1cm},
+  decision/.style={diamond, draw, fill=orange!20, aspect=2},
+  arrow/.style={-Stealth, thick}
+]
+
+\node[process] (p1) {Process};
+\node[decision, below=of p1] (d1) {Decision?};
+\draw[arrow] (p1) -- (d1);
+
+\end{tikzpicture}
+```
+
+### Global Style Definitions
+
+```latex
+% In preamble or separate file
+\tikzset{
+  process/.style={
+    rectangle, 
+    rounded corners,
+    draw=black, 
+    thick,
+    fill=blue!20,
+    minimum width=3cm,
+    minimum height=1cm,
+    text width=2.5cm,
+    align=center
+  },
+  decision/.style={
+    diamond,
+    draw=black,
+    thick,
+    fill=orange!20,
+    minimum width=2cm,
+    aspect=2,
+    align=center
+  },
+  data/.style={
+    trapezium,
+    trapezium left angle=70,
+    trapezium right angle=110,
+    draw=black,
+    thick,
+    fill=green!20,
+    minimum width=2cm,
+    minimum height=1cm
+  }
+}
+```
+
+### Color Definitions (Okabe-Ito Colorblind-Safe Palette)
+
+```latex
+\definecolor{okabe-orange}{RGB}{230, 159, 0}
+\definecolor{okabe-blue}{RGB}{86, 180, 233}
+\definecolor{okabe-green}{RGB}{0, 158, 115}
+\definecolor{okabe-yellow}{RGB}{240, 228, 66}
+\definecolor{okabe-dblue}{RGB}{0, 114, 178}
+\definecolor{okabe-vermillion}{RGB}{213, 94, 0}
+\definecolor{okabe-purple}{RGB}{204, 121, 167}
+\definecolor{okabe-black}{RGB}{0, 0, 0}
+
+% Use in styles
+\node[fill=okabe-blue!30, draw=okabe-dblue] {Text};
+```
+
+## Advanced Techniques
+
+### Loops and Repetition
+
+```latex
+% Simple loop
+\foreach \x in {0,1,2,3,4} {
+  \node[draw] at (\x,0) {\x};
+}
+
+% Loop with calculations
+\foreach \x in {0,1,...,5} {
+  \draw (\x,0) circle (0.2);
+}
+
+% Multiple variables
+\foreach \x/\y/\label in {0/0/A, 1/1/B, 2/0/C} {
+  \node[draw] at (\x,\y) {\label};
+}
+
+% Nested loops
+\foreach \x in {0,1,2} {
+  \foreach \y in {0,1,2} {
+    \node[draw] at (\x,\y) {\x,\y};
+  }
+}
+```
+
+### Calculations (calc library)
+
+```latex
+% Midpoint
+\coordinate (A) at (0,0);
+\coordinate (B) at (4,3);
+\coordinate (M) at ($(A)!0.5!(B)$);  % Midpoint between A and B
+\node[draw] at (M) {Middle};
+
+% Point along path
+\coordinate (C) at ($(A)!0.25!(B)$);  % 25% from A to B
+
+% Perpendicular point
+\coordinate (P) at ($(A)!0.5!(B)$);
+\coordinate (Q) at ($(P)!1cm!90:(B)$);  % 1cm perpendicular to AB
+```
+
+### Backgrounds and Layers
+
+```latex
+\begin{tikzpicture}
+  % Main content
+  \node[draw] (A) {Node A};
+  \node[draw, right=of A] (B) {Node B};
+  
+  % Background layer
+  \begin{scope}[on background layer]
+    \node[fill=gray!20, rounded corners, fit=(A) (B),
+          inner sep=10pt] {};
+  \end{scope}
+\end{tikzpicture}
+```
+
+### Scope for Local Styling
+
+```latex
+\begin{tikzpicture}
+  % Normal drawing
+  \draw (0,0) -- (1,0);
+  
+  % Apply style only within scope
+  \begin{scope}[thick, blue]
+    \draw (0,0.5) -- (1,0.5);
+    \draw (0,1) -- (1,1);
+  \end{scope}
+  
+  % Back to normal
+  \draw (0,1.5) -- (1,1.5);
+\end{tikzpicture}
+```
+
+## Common Scientific Diagram Patterns
+
+### Flowchart Pattern
+
+```latex
+\begin{tikzpicture}[
+  node distance=1.5cm and 2cm,
+  process/.style={rectangle, rounded corners, draw, thick, 
+                  fill=blue!20, minimum width=3cm, minimum height=1cm},
+  decision/.style={diamond, draw, thick, fill=orange!20, aspect=2},
+  arrow/.style={-Stealth, thick}
+]
+
+\node[process] (start) {Start};
+\node[process, below=of start] (step1) {Process Step};
+\node[decision, below=of step1] (decision) {Decision?};
+\node[process, below left=of decision] (yes) {Yes Path};
+\node[process, below right=of decision] (no) {No Path};
+\node[process, below=3cm of decision] (end) {End};
+
+\draw[arrow] (start) -- (step1);
+\draw[arrow] (step1) -- (decision);
+\draw[arrow] (decision) -| node[near start, above] {yes} (yes);
+\draw[arrow] (decision) -| node[near start, above] {no} (no);
+\draw[arrow] (yes) |- (end);
+\draw[arrow] (no) |- (end);
+
+\end{tikzpicture}
+```
+
+### Block Diagram Pattern
+
+```latex
+\begin{tikzpicture}[
+  block/.style={rectangle, draw, thick, fill=blue!20, 
+                minimum width=2.5cm, minimum height=1cm},
+  arrow/.style={-Stealth, thick}
+]
+
+\node[block] (input) {Input};
+\node[block, right=2cm of input] (process) {Process};
+\node[block, right=2cm of process] (output) {Output};
+
+\draw[arrow] (input) -- node[above] {data} (process);
+\draw[arrow] (process) -- node[above] {result} (output);
+
+% Feedback loop
+\draw[arrow] (output.north) |- ++(0,1) -| 
+             node[near end, above] {feedback} (process.north);
+
+\end{tikzpicture}
+```
+
+### Network Diagram Pattern
+
+```latex
+\begin{tikzpicture}[
+  node/.style={circle, draw, thick, fill=blue!20, minimum size=1cm},
+  edge/.style={-Stealth, thick}
+]
+
+% Nodes
+\node[node] (1) at (0,0) {1};
+\node[node] (2) at (2,1.5) {2};
+\node[node] (3) at (2,-1.5) {3};
+\node[node] (4) at (4,0) {4};
+
+% Edges
+\draw[edge] (1) -- (2);
+\draw[edge] (1) -- (3);
+\draw[edge] (2) -- (4);
+\draw[edge] (3) -- (4);
+\draw[edge, bend left] (2) to (3);
+
+\end{tikzpicture}
+```
+
+### Timeline Pattern
+
+```latex
+\begin{tikzpicture}
+  % Timeline axis
+  \draw[thick, -Stealth] (0,0) -- (10,0) node[right] {Time};
+  
+  % Events
+  \foreach \x/\label in {1/Baseline, 3/Week 4, 5/Week 8, 7/Week 12, 9/Final} {
+    \draw[thick] (\x,0.1) -- (\x,-0.1);
+    \node[below] at (\x,-0.1) {\label};
+    \node[circle, fill=blue!20, draw, inner sep=2pt] at (\x,0) {};
+  }
+  
+  % Interventions as bars
+  \draw[thick, blue] (1,0.5) -- (5,0.5) node[midway, above] {Treatment A};
+  \draw[thick, red] (5,0.8) -- (9,0.8) node[midway, above] {Treatment B};
+  
+\end{tikzpicture}
+```
+
+## CircuitikZ for Circuit Diagrams
+
+CircuitikZ extends TikZ specifically for electrical circuits:
+
+```latex
+\usepackage{circuitikz}
+
+\begin{circuitikz}[american]
+  % Voltage source
+  \draw (0,0) to[V, v=$V_s$] (0,2)
+  
+  % Resistors
+        to[R, l=$R_1$] (2,2)
+        to[R, l=$R_2$] (4,2)
+  
+  % Capacitor
+        to[C, l=$C_1$] (4,0)
+  
+  % Close circuit
+        to[short] (0,0);
+  
+  % Ground
+  \draw (0,0) node[ground] {};
+  
+\end{circuitikz}
+```
+
+## Best Practices for Scientific Diagrams
+
+### 1. Consistent Node Spacing
+
+```latex
+% Define node distance globally
+\begin{tikzpicture}[node distance=2cm and 3cm]
+  % All nodes will be spaced consistently
+\end{tikzpicture}
+```
+
+### 2. Use Styles for Consistency
+
+```latex
+% Define styles once, use everywhere
+\tikzset{
+  myprocess/.style={/* styling */},
+  mydecision/.style={/* styling */}
+}
+```
+
+### 3. Named Nodes for Flexibility
+
+```latex
+% Always name nodes you'll reference
+\node (A) {Node A};  % Good
+\node at (0,0) {Node};  % Hard to reference later
+```
+
+### 4. Anchor Points for Precise Connections
+
+```latex
+% Use anchors for clean connections
+\draw (A.east) -- (B.west);  % Good
+\draw (A) -- (B);  % May not connect cleanly
+```
+
+### 5. Layer Complex Diagrams
+
+```latex
+% Draw in logical order: background -> main -> annotations
+\begin{scope}[on background layer]
+  % Background elements
+\end{scope}
+% Main diagram
+% Annotations on top
+```
+
+### 6. Modularity with \input
+
+```latex
+% Main document
+\begin{figure}
+  \centering
+  \input{figures/my_diagram.tikz}
+  \caption{My diagram}
+\end{figure}
+
+% my_diagram.tikz contains just the tikzpicture
+\begin{tikzpicture}
+  % diagram code
+\end{tikzpicture}
+```
+
+## Compilation and Optimization
+
+### Standalone Compilation
+
+Create standalone TikZ documents for faster iteration:
+
+```latex
+\documentclass[tikz, border=2mm]{standalone}
+\usepackage{tikz}
+\usetikzlibrary{shapes, arrows.meta, positioning}
+
+\begin{document}
+\begin{tikzpicture}
+  % Your diagram
+\end{tikzpicture}
+\end{document}
+```
+
+Compile to PDF:
+```bash
+pdflatex diagram.tex
+```
+
+### External Graphics (for large documents)
+
+For complex diagrams, compile separately and include:
+
+```latex
+% Enable externalization
+\usetikzlibrary{external}
+\tikzexternalize
+
+% In document
+\begin{tikzpicture}
+  % Complex diagram - compiled once, cached
+\end{tikzpicture}
+```
+
+## Troubleshooting Common Issues
+
+**Issue**: Nodes overlapping text
+- **Solution**: Increase `minimum width` or `minimum height`, or use `text width` with `align=center`
+
+**Issue**: Arrows not pointing to node edges
+- **Solution**: Use anchor points: `\draw (A.east) -- (B.west);`
+
+**Issue**: Inconsistent spacing
+- **Solution**: Set `node distance` globally in tikzpicture options
+
+**Issue**: Curved arrows going wrong direction
+- **Solution**: Adjust `bend left/right` angle or use `out` and `in` angles
+
+**Issue**: Text overflowing nodes
+- **Solution**: Add `text width=Xcm, align=center` to node style
+
+**Issue**: Compilation slow
+- **Solution**: Use `\tikzexternalize` or compile diagrams separately
+
+## Quick Reference: Common Commands
+
+```latex
+% Shapes
+\node[draw, rectangle] {Text};
+\node[draw, circle] {Text};
+\node[draw, diamond] {Text};
+\node[draw, ellipse] {Text};
+
+% Positioning
+\node[right=of A] (B) {B};
+\node[below=2cm of A] (C) {C};
+\node[above right=of A] (D) {D};
+
+% Arrows
+\draw[-Stealth] (A) -- (B);
+\draw[-Stealth] (A) to[bend left] (B);
+\draw[-Stealth] (A) -| (B);
+
+% Styling
+\node[fill=blue!20, draw=blue!80, thick] {Styled};
+\draw[thick, dashed, red] (A) -- (B);
+
+% Loops
+\foreach \x in {0,1,2,3} { \node at (\x,0) {\x}; }
+```
+
+## Further Resources
+
+- **TikZ & PGF Manual**: https://pgf-tikz.github.io/pgf/pgfmanual.pdf
+- **TeXample.net**: http://www.texample.net/tikz/
+- **CircuitikZ Manual**: https://ctan.org/pkg/circuitikz
+- **TikZ Tutorial**: https://cremeronline.com/LaTeX/minimaltikz.pdf
+
+This guide provides the foundation for creating scientific diagrams with TikZ. Combine these techniques with the templates in the `assets/` directory for publication-ready figures.
+