TikZ - LuaLaTeX - Trying to fix the library `phylogenetics`

Question

The following code shows an ugly way to fix the bad vertical positioning of the labels in a top-down phylogenetic graph. How to avoid the special fixing style done by hand? How to find the good style to be fixed?

% Source: https://tex.stackexchange.com/a/133237/6880
\documentclass[12 pt]{article}
\usepackage{tikz}
\usetikzlibrary{graphs, graphdrawing}
\usegdlibrary{phylogenetics}
\pgfgdset{
    phylogenetic inner node/.style = {
        /tikz/.cd, 
        draw, circle, 
        inner sep=0pt, 
        minimum size=5pt
    }
}
\begin{document}
\begin{tikzpicture}
\graph[
    phylogenetic tree layout,
    upgma,
    distance matrix = {
      % a b c d e f g
        0 4 9 9 9 9 9 % a 
        4 0 9 9 9 9 9 % b
        9 9 0 2 7 7 7 % c
        9 9 2 0 7 7 7 % d
        9 9 7 7 0 3 5 % e
        9 9 7 7 3 0 5 % f
        9 9 7 7 5 5 0 % g
    }]
    { a, b, c, d, e, f, g }; 
\end{tikzpicture}
\begin{tikzpicture}[
    test/.append style={font=\vphantom{Vg}}
]
\graph[
    phylogenetic tree layout,
    upgma,
    distance matrix = {
      % a b c d e f g
        0 4 9 9 9 9 9 % a 
        4 0 9 9 9 9 9 % b
        9 9 0 2 7 7 7 % c
        9 9 2 0 7 7 7 % d
        9 9 7 7 0 3 5 % e
        9 9 7 7 3 0 5 % f
        9 9 7 7 5 5 0 % g
    }]
    { a[test], b[test], c[test], d[test], e[test], f[test], g[test] }; 
\end{tikzpicture}
\end{document}

Jasper Habicht · Accepted Answer · 2023-02-21T19:50:36.567

You can set the option text height for every node so something sensible (additionally, depending on the use case, setting text depth is also a good idea):

\documentclass[border=10pt]{standalone}
\usepackage{tikz}
\usetikzlibrary{graphs, graphdrawing}
\usegdlibrary{phylogenetics}
\pgfgdset{
    phylogenetic inner node/.style={
        /tikz/.cd, draw, circle, inner sep=0pt, minimum size=5pt
    }
}
\tikzset{
    every node/.style={text height=1.25ex}
}
\begin{document}
\begin{tikzpicture}
    \graph[phylogenetic tree layout,
       upgma,
       distance matrix = {
        0 4 9 9 9 9 9 
        4 0 9 9 9 9 9
        9 9 0 2 7 7 7 
        9 9 2 0 7 7 7 
        9 9 7 7 0 3 5 
        9 9 7 7 3 0 5
        9 9 7 7 5 5 0 }]
{ a, b, c, d, e, f, g }; 
\end{tikzpicture}
\end{document}

Why does this help here? You can best see the effect by temporarily adding a border to the nodes:

\documentclass[border=10pt]{standalone}
\usepackage{tikz}
\usetikzlibrary{graphs, graphdrawing}
\usegdlibrary{phylogenetics}
\pgfgdset{
    phylogenetic inner node/.style={
        /tikz/.cd, draw, circle, inner sep=0pt, minimum size=5pt
    }
}
\tikzset{
    every node/.style={text height=1.5ex, text depth=0.33ex, draw}
}
\begin{document}
\begin{tikzpicture}
    \graph[phylogenetic tree layout,
       upgma,
       distance matrix = {
        0 4 9 9 9 9 9 
        4 0 9 9 9 9 9
        9 9 0 2 7 7 7 
        9 9 2 0 7 7 7 
        9 9 7 7 0 3 5 
        9 9 7 7 3 0 5
        9 9 7 7 5 5 0 }]
{ a, b, c, d, e, f, g }; 
\end{tikzpicture}
\end{document}

Without text depth set:

Without text height (and without text depth) set:

Using it via \begin{tikzpicture}[every node/.style={text height=1.25ex}] ... \end{tikzpicture} does the job. Thanks. — projetmbc, Feb 21 '23 at 19:48
@projetmbc Sure, this is also a way to go. I added some pictures to show what is happening and why setting text height and text depth helps in this case. — Jasper Habicht, Feb 21 '23 at 19:51

TikZ - LuaLaTeX - Trying to fix the library `phylogenetics`

1 Answers1