## Friday, December 16, 2022

### Branched Pathway in TikZ

I couldn't resist, here are some simple branched pathways using tikz. Note you can change the vertical splay and horizontal distance for the nodes by changing the node distance in the argument to tikzpicture. I also added some colors wshich really don't match, someone with more artistic tallent could do better.

\documentclass[12pt]{article}

\usepackage{tikz}
\usetikzlibrary{positioning}
\usepackage{xcolor}

\begin{document}

\begin{tikzpicture}[node distance=0.4cm and 1cm]
\node (Xo) at (0,0) {};
\node[right=of Xo] (S1) {\small $S_1$};
\node[above right=of S1] (S2) {};
\node[below right=of S1] (S3) {};

\draw[-latex, thick, blue] (Xo) -- (S1) node[pos=0.5,above,gray] {$v_1$};

\draw[-latex, thick, orange] (S1) -- (S2) node[above=0.15, left,pos=0.5,gray] {$v_2$};
\draw[-latex, thick, green!45!black] (S1) -- (S3) node[below=0.15, left,pos=0.5,gray] {$v_3$};
\end{tikzpicture}

\vspace{1cm}

\begin{tikzpicture}[node distance=0.4cm and 1cm]
%\draw [help lines,step=.1] (0,-6) grid (6,6);
\node (Xo) at (0,0) {};
\node[right=of Xo,yellow!20!red] (S1) {\small $S_1$};
\node[above right=of S1,blue!80!red] (S2) {\small $S_2$};
\node[below right=of S1,green!80!red] (S3) {\small $S_3$};

\node[above right=of S3] (S4) {};
\node[below right=of S3] (S5) {};

\draw[-latex, thick, blue] (Xo) -- (S1) node[pos=0.5,above,purple] {$v_1$};
\draw[-latex, thick, blue] (S1) -- (S2) node[above=0.15, left,pos=0.5,purple] {$v_2$};
\draw[-latex, thick, blue] (S1) -- (S3) node[below=0.15, left,pos=0.5,purple] {$v_3$};

\draw[-latex, thick, blue] (S3) -- (S4) node[below=-0.12, left,pos=0.5,purple] {$v_4$};
\draw[-latex, thick, blue] (S3) -- (S5) node[below=0.05, left,pos=0.5,purple] {$v_5$};
\end{tikzpicture}

\end{document}


## Sunday, December 11, 2022

### Experimenting with foreach loops in TikZ to draw biochemical pathways

Here is an example of a foreach loop in TikZ that can be used to draw an arbitrary long linear chain of reactions.

By setting the value of N in the following TikZ code, you can get any length linear chain. Obviously, you're limited by the width of the page. It uses the xifthen package to provide a conditional that is used to print out the last species, which is X1. There could be a better way of doing this, but this works. For example, use newcommand instead of def

\documentclass{article}

\usepackage{tikz}
\usetikzlibrary{arrows}
\usetikzlibrary{calc}
\usepackage{xifthen}

\begin{document}

\begin{tikzpicture}[>=latex', node distance=2cm]
\node (X0) {$X_o$};
\pgfmathsetmacro{\N}{4}
\foreach \x in {0,...,\N}
{
\pgfmathtruncatemacro{\nextval}{\x+1}
\ifthenelse{\x = \N}
{\def\speciesName{$X_1$}}
{\def\speciesName{\large $x_\nextval$}}

\node [right of = X\x] (X\nextval) {\speciesName};
\draw [->,ultra thick,blue] (X\x) -- node[above, black] {$v_{\nextval}$} (X\nextval);
}
\end{tikzpicture}

\end{document}


Here are some examples for N = 0, N = 2 and N = 4