From e0c6872cf40896c7be36b11dcc744620f10adf1d Mon Sep 17 00:00:00 2001 From: Norbert Preining Date: Mon, 2 Sep 2019 13:46:59 +0900 Subject: Initial commit --- .../doc/text-en/pgfmanual-en-gd-phylogenetics.tex | 83 ++++++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 graphics/pgf/base/doc/text-en/pgfmanual-en-gd-phylogenetics.tex (limited to 'graphics/pgf/base/doc/text-en/pgfmanual-en-gd-phylogenetics.tex') diff --git a/graphics/pgf/base/doc/text-en/pgfmanual-en-gd-phylogenetics.tex b/graphics/pgf/base/doc/text-en/pgfmanual-en-gd-phylogenetics.tex new file mode 100644 index 0000000000..486b930ce5 --- /dev/null +++ b/graphics/pgf/base/doc/text-en/pgfmanual-en-gd-phylogenetics.tex @@ -0,0 +1,83 @@ +% Copyright 2013 by Sarah Mäusle and Till Tantau +% +% This file may be distributed and/or modified +% +% 1. under the LaTeX Project Public License and/or +% 2. under the GNU Free Documentation License. +% +% See the file doc/generic/pgf/licenses/LICENSE for more details. + + +\section{Graph Drawing Layouts: Phylogenetic Trees} +\label{section-library-graphdrawing-phylogenetics} + +{\noindent {\emph{by Sarah Mäusle and Till Tantau}}} + +\ifluatex +\else + This section of the manual can only be typeset using Lua\TeX. + \expandafter\endinput +\fi + +\tikzset{/graph drawing/phylogenetic inner node/.style={ + /tikz/.cd, + draw, circle, inner sep=0pt, minimum size=5pt} +} +\tikzset{/graph drawing/phylogenetic edge/.style={ + /tikz/.cd, + thick, rounded corners,edge node={node[auto,font=\tiny, inner sep=2pt]{}}} +} + +\includeluadocumentationof{pgf.gd.phylogenetics.library} +\includeluadocumentationof{pgf.gd.phylogenetics.PhylogeneticTree} + + +\subsection{Generating a Phylogenetic Tree} + +... \todosp{I guess something should be added here, right?} + +When a phylogenetic tree is generated, new nodes and edges get created. In +order to give you a chance at styling them, the following styles are executed: + +\begin{stylekey}{/graph drawing/phylogenetic inner node} + The style is added every newly created inner node. In this manual, this key + is set to: + % +\begin{codeexample}[code only] +\pgfgdset{phylogenetic inner node/.style={ + /tikz/.cd, draw, circle, inner sep=0pt, minimum size=5pt + } +} +\end{codeexample} + % +\end{stylekey} + +\begin{stylekey}{/graph drawing/phylogenetic edge=\meta{length}} + The style is added every newly created phylogenetic edge. The \meta{length} + will be set to the computed evolutionary length of the edge. In this + manual, this key is set to: + % +\begin{codeexample}[code only] +\pgfgdset{phylogenetic edge/.style={ + /tikz/.cd, thick, rounded corners + } +} +\end{codeexample} + % +\end{stylekey} + +\includeluadocumentationof{pgf.gd.phylogenetics.AuthorDefinedPhylogeny} +\includeluadocumentationof{pgf.gd.phylogenetics.SokalMichener1958} +\includeluadocumentationof{pgf.gd.phylogenetics.BalancedMinimumEvolution} +\includeluadocumentationof{pgf.gd.phylogenetics.BalancedNearestNeighbourInterchange} + + +\subsection{Laying out the Phylogram} + +\includeluadocumentationof{pgf.gd.phylogenetics.Maeusle2012} + + +%%% Local Variables: +%%% mode: latex +%%% TeX-master: "pgfmanual-pdftex-version" +%%% End: -- cgit v1.2.3