commit e0d3f59babc78b6fb01cf70b9291e0b456f76e35 Author: Jeff Date: Fri Jun 21 09:19:32 2024 +0200 initial diff --git a/compendium.pdf b/compendium.pdf new file mode 100644 index 0000000..32401e0 Binary files /dev/null and b/compendium.pdf differ diff --git a/compendium.tex b/compendium.tex new file mode 100644 index 0000000..059263f --- /dev/null +++ b/compendium.tex @@ -0,0 +1,55 @@ +% MAIN FILE + +\input{jjpackages.tex} + + +\usepackage{forest} +\tikzset{ + comment/.append style={label={[font=\small]0:#1}}, +} +\forestset{ + /tikz/label position=below left, + /tikz/label distance=.1em, + dot/.style={tikz+={\fill[fill=#1] (.child anchor) circle[radius=2pt];}}, + dot/.default=black, + bar/.style={tikz+={\draw[color=#1,line width=2pt] let \p1 = (!u.parent anchor), \p2 = (.child anchor) in ($(\x1, \y2 - 0.5em)!0.5!(\x2, \y2)$) -- ($(\x1, \y2 + 0.5em)!0.5!(\x2, \y2)$);}}, + bar/.default=black, +} +\definecolor{treeedgeclr}{RGB}{80, 80, 80} + + +\usepackage{pdfpages} + + +%opening +\title{Botanik \& Systematik der Pflanzen} + \author{Jeff Jonczyk} + +\begin{document} + +\maketitle + +\section*{Einleitung} + +\newpage + +\tableofcontents + +\newpage + +\section[Systematik der Pflanzen]{Spezieller Teil: Systematik der Pflanzen} +\subsection{Prokaryota, Eukaryota \& Archea} + +\begin{figure}[!ht] + \centering + \input{trees/basetree.tex} +\end{figure} + + + + +\section[Allgemeine Phylogenetik]{Allgemeiner Teil: Phylogenetik} + + + +\end{document} diff --git a/forest/base.tex b/forest/base.tex new file mode 100644 index 0000000..f244df4 --- /dev/null +++ b/forest/base.tex @@ -0,0 +1,37 @@ +%base tree +\begin{forest} + % BEGIN treeconf.tex + where n children=0{tier=word}{}, + for tree = { + %s sep=-0.1em, + grow = 0, % 0 deg = right + reversed, + align=left, + parent anchor=east, + child anchor=west, + anchor=west, + edge path={ + \noexpand\path[draw, ptclredge, line width=1.2pt, \forestoption{edge}] + (!u.parent anchor) |- (.child anchor)\forestoption{edge label}; + }, + before typesetting nodes={ + if content={}{shape=coordinate}{} + }, + } % END treeconf.tex + [[ + [Prokaryota] + [ + [Archea] + [,label=Eukaryota, dot[ + [, label=Planta, dot + [Rhodophyta (Rotalgen)] + [, label=Grünpflanzen, dot + [Chlorophyta] + [Embryophyta] + ] + ] + [] + ]] + ] + ]] +\end{forest} \ No newline at end of file diff --git a/forest/phyloforest-template.tex b/forest/phyloforest-template.tex new file mode 100644 index 0000000..716a76f --- /dev/null +++ b/forest/phyloforest-template.tex @@ -0,0 +1,26 @@ +% phyloforest-template.tex +% Template for a phylogenetic tree using forest + +\begin{forest} + % + where n children=0{tier=word}{}, + for tree = { + s sep=-0.1em, + grow = 0, % 0 deg = right + reversed, + align=left, + parent anchor=east, + child anchor=west, + anchor=west, + edge path={ + \noexpand\path[draw, ptclredge, line width=1.2pt, \forestoption{edge}] + (!u.parent anchor) |- (.child anchor)\forestoption{edge label}; + }, + before typesetting nodes={ + if content={}{shape=coordinate}{} + }, + } % + + % TREE CONTENT + +\end{forest} \ No newline at end of file diff --git a/forest/test.forest b/forest/test.forest new file mode 100644 index 0000000..9da6485 --- /dev/null +++ b/forest/test.forest @@ -0,0 +1,8 @@ +[ + [Procaryota] + [ + [Eucaryota] + [Archea] + [some more garbage] + ] +] \ No newline at end of file diff --git a/forest/test.tex b/forest/test.tex new file mode 100644 index 0000000..109d03d --- /dev/null +++ b/forest/test.tex @@ -0,0 +1,72 @@ +%c reated by phylo-tree from test.forest + + +\documentclass[tikz, crop, border=5pt]{standalone} +\usepackage{forest} + +\usepackage{fontspec,xltxtra,xunicode} + +% English Fonts +\setmainfont[BoldFont={Fira Sans}]{Fira Sans Light} + +% 中文字体 +\usepackage{xeCJK} +\setCJKmainfont[BoldFont=Hiragino Sans GB W6]{Hiragino Sans GB W3} +\xeCJKsetup{CJKecglue = {\hskip 0pt plus 0.08\baselineskip}, xCJKecglue = {false}} +\punctstyle{plain} +\defaultfontfeatures{Mapping=tex-text,Scale=MatchLowercase} + +\definecolor{red}{RGB}{188,36,46} +\definecolor{black}{RGB}{26,25,25} +\definecolor{grey}{RGB}{129,130,132} +\definecolor{green}{RGB}{32,128,108} +\definecolor{purple}{RGB}{160,90,150} + +\tikzset{ + comment/.append style={label={[font=\small]0:#1}}, +} +\forestset{ + /tikz/label position=below left, + /tikz/label distance=.1em, + dot/.style={tikz+={\fill[fill=#1] (.child anchor) circle[radius=2pt];}}, + dot/.default=black, + bar/.style={tikz+={\draw[color=#1,line width=2pt] let \p1 = (!u.parent anchor), \p2 = (.child anchor) in ($(\x1, \y2 - 0.5em)!0.5!(\x2, \y2)$) -- ($(\x1, \y2 + 0.5em)!0.5!(\x2, \y2)$);}}, + bar/.default=black, +} + +\begin{document} + +\begin{forest} + where n children=0{tier=word}{}, + for tree={ + s sep=-0.1em, % make siblings closer + grow=0, % 0 degrees is to the right + reversed, % tree_direction + align=left, + parent anchor=east, + child anchor=west, + anchor=west, + edge path={ + \noexpand\path[draw, grey, line width=1pt, \forestoption{edge}] + (!u.parent anchor) |- (.child anchor)\forestoption{edge label}; + }, + before typesetting nodes={ + if content={}{shape=coordinate}{} + }, + } +[ + [a] + [ + [b] + [b + [c] + [c + [d] + [d] + ] + ] + ] +] +\end{forest} + +\end{document} diff --git a/forest/treeconf.tex b/forest/treeconf.tex new file mode 100644 index 0000000..bd3150d --- /dev/null +++ b/forest/treeconf.tex @@ -0,0 +1,18 @@ +% BEGIN treeconf.tex +where n children=0{tier=word}{}, +for tree = { + s sep=-0.1em, + grow = 0, % 0 deg = right + reversed, + align=left, + parent anchor=east, + child anchor=west, + anchor=west, + edge path={ + \noexpand\path[draw, ptclredge, line width=1.2pt, \forestoption{edge}] + (!u.parent anchor) |- (.child anchor)\forestoption{edge label}; + }, + before typesetting nodes={ + if content={}{shape=coordinate}{} + }, +} % END treeconf.tex \ No newline at end of file diff --git a/jjpackages.tex b/jjpackages.tex new file mode 100644 index 0000000..7c95979 --- /dev/null +++ b/jjpackages.tex @@ -0,0 +1,104 @@ +%####################################### +% jjpackages.tex +% generic include for common LaTeX packages +% @author Jeff J +% usage: \input{jjpackages.tex} +% +% v0.1 2024-05 +%####################################### + + +% ### DOCUMENTCLASS & LANGUAGE ######### + +\documentclass[a4paper, 12pt, german]{article} +\usepackage{geometry} + +\usepackage[utf8]{inputenc} +\usepackage[T1]{fontenc} + +\usepackage[german]{babel} + + +% ### MISC ############################# + +\usepackage{hyperref} +% \usepackage[implicit=false]{hyperref} % disable color conversions for printing +\hypersetup{ + pdftitle = {Botanik \& Systematik der Pflanzen}, + pdfauthor = {Jeff Jonczyk}, + pdfsubject = {}, + pdfkeywords = {}, + colorlinks = false, + urlcolor = blue, + linkcolor = cyan, + citecolor = brown, + filecolor = magenta + pagebackref = true + linktoc = all + } + +\usepackage{url} +\usepackage{pdfpages} + +\usepackage{ragged2e} +\usepackage{parskip} +% \usepackage[skip=12pt, indent=30pt, parfill=50pt]{parskip} +\usepackage{setspace} + + +% ### FONTS & COLORS ################### + +\usepackage[table]{xcolor} + +%\usepackage{lmodern} %modern font-family +%\usepackage{mathptmx} %times ff that also works in math mode + +\usepackage{titlesec} % allows heading customisation + +% options for stiketrough +% \usepackage{soul} +% \usepackage{ulem} +% \usepackage{cancel} + + +% ### COMMENTS & CODE ################## + +% \usepackage{comment} +\usepackage{verbatim} + +%\usepackage{minted} + + +% ### IMAGES & FIGURES ################# + +\usepackage{graphicx} +%\usepackage{wrapstuff} + + +% ### TABLES ########################### + +\usepackage{multirow} + + +% ### LISTS ############################ + +% \usepackage{enumerate} +% \usepackage{paralist} % provides compactitem, compactenum enviroments + +\usepackage{enumitem} + + +% ### REFERENCES ####################### + +%\usepackage{cleveref} % ! For some reason must be loaded after ansmath; see below +%\usepackage{showkeys} + + +% ### MATH ############################# + +\usepackage{amsmath} +\usepackage{pgfplots} + + + +\usepackage{cleveref} % technically belongs to REFERENCES, but must be loaded after ansmath diff --git a/trees/basetree.tex b/trees/basetree.tex new file mode 100644 index 0000000..c24762f --- /dev/null +++ b/trees/basetree.tex @@ -0,0 +1,35 @@ +% phyloforest-template.tex +% Template for a phylogenetic tree using forest +\begin{forest} + % + where n children=0{tier=word}{}, + for tree = { + s sep=-0.1em, + grow = 0, % 0 deg = right + reversed, + align=left, + parent anchor=east, + child anchor=west, + anchor=west, + edge path={ + \noexpand\path[draw, treeedgeclr, line width=1.2pt, \forestoption{edge}] + (!u.parent anchor) |- (.child anchor)\forestoption{edge label}; + }, + before typesetting nodes={ + if content={}{shape=coordinate}{} + }, + } % + [, label=Animalia, dot + [Ctenophora] + [, label=NOTE, bar=red + [\color{green}{Porifera}] + [, label=\color{green}{Parahoxozoa}, dot=red + [Placozoa] + [, label=Planulozoa, dot=red + [Bilateria] + [Cnidaria] + ] + ] + ] + ] +\end{forest}