Writing scientific papers in LaTex (Tips and Tricks)

• TeX Engine Settings
• Aesthetics
  • Balancing Columns on the Last Page in a Two-Column Document
  • Highlighting
    • Round label
    • Grey highlight
• Meta
  • Finding weird Unicode
  • Highlight updates or inline comments
• Math
• Glossaries
• Bibliography
  • Clean bib files
  • Use Biblatex
• Tables
  • Hide columns
• SI-units
• Clever reference
• Figures
  • Color schemes
  • ETH Figure Tool
  • Python to Tikz
  • Extract data from existing figures
  • Indicate lines in a plot
• Preparing for submission
  • Clean-up Project
    • LaTeX cleaner's main features:
  • Shortening a Paper
  • Reducing space after caption
    • Biblatex hacks
• Updating manuscript
  • Change color of single reference using biblatex

TeX Engine Settings

Settings in VSCode with increased memory size (pgfplots) and shell escape:

{
			"name": "lualatexmk",
			"command": "latexmk",
			"args": [
                "-shell-escape",                // <---- added this line
                "--extra-mem-bot=10000000",     // <---- added this line
                "--extra-mem-top=10000000",     // <---- added this line
				"-synctex=1",
				"-interaction=nonstopmode",
				"-file-line-error",
				"-lualatex",
				"-outdir=%OUTDIR%",
				"%DOC%"
			],
			"env": {}
		}

Aesthetics

Balancing Columns on the Last Page in a Two-Column Document

In LaTeX, when using a two-column format, the last page may sometimes have only one full column, leaving an unbalanced layout. To ensure both columns are evenly distributed, use the balance package. Adding \balance before the last content forces LaTeX to split the text evenly across both columns. This results in a cleaner and more professional layout, avoiding a single long column with excessive white space. If fine-tuning is needed, manual adjustments with \vfill and \newpage can be used. Example:

\usepackage{balance}  % Include in the preamble
\balance  % Place before the last content

Highlighting

Round label

\usepackage{tikz}
\usepgfplotslibrary{external}

\definecolor{mycolor}{RGB}{112,45,128}
\newcommand{\roundlabel}[1]{\tikzexternaldisable \tikz[baseline=(char.base)]{
            \node[rectangle, rounded corners=0.65mm,inner sep=0.65mm,fill=mycolor, draw=mycolor, text=white, font=\itshape](char) {#1};}\tikzexternalenable}

Example usgae: \roundlabel{Message 5/Conclusion:}

Grey highlight

\newcommand{\syntaxHighlight}[1]{\colorbox{black!10}{#1}}

Example usage: \syntaxHighlight{chapters/contributors.tex}

Meta

Finding weird Unicode

Add in the preamble the following to easily find a weird unicode in Overleaf.

\DeclareUnicodeCharacter{2500}{\color{red} FIX ME!!!!}

Highlight updates or inline comments

\usepackage[dvipsnames]{xcolor} %required package
\newcommand{\update}[1]{{\color{YellowOrange} #1}} %usage \update{this is changed.}

\usepackage[dvipsnames,svgnames, table]{xcolor} % Required to specify custom colors

\usepackage{listofitems}
\usepackage{pgffor}

\makeatletter
% Define your own list of colors
\def\myColorList{LimeGreen,BrickRed,Fuchsia,Bittersweet,YellowOrange, YellowGreen, WildStrawberry}
\readlist\ColorList\myColorList


\newcommand{\defineauthors}[1]{
    Personal commands for comments are:
    \begin{itemize}
    \foreach \x [count=\xi from 1] in {#1} {   
        \item \textcolor{\ColorList[\xi]}{\textbackslash\unexpanded\expandafter{\x}\{\}}
        }
    
    \end{itemize}

    \foreach \x [count=\xi from 1] in {#1} { 
    \expandafter\xdef\csname\x\endcsname####1{\noexpand\textcolor{\ColorList[\xi]}{[\unexpanded\expandafter{\x}: ####1]}}%
    }
}
\makeatother

%usage after begin document
\defineauthors{all, gilles, emma, ozlem, lianet, nicola}

Math

Typesetting and defining symbols:

\usepackage{xifthen}
\newcommand{\prob}[1][]{%requires xifthen package%
\ifthenelse{\isempty{#1}}%
      {\ensuremath{P}}%
    {\ensuremath{P\left\(#1\right\)}}%
}
\newcommand{\vect}[1]{\boldsymbol{\mathrm{#1}}}
\newcommand{\mat}[1]{\boldsymbol{\mathrm{#1}}}
\newcommand{\MSE}{\mathrm{MSE}}
\newcommand{\tr}{\mathrm{tr}}
\newcommand{\moddef}{\mathrm{mod}}
\newcommand{\diag}{\mathrm{diag}}
\newcommand{\vecop}{\text{vec}}
\newcommand{\CP}{L}
\newcommand{\hddots}{\hdots}
\newcommand*{\inC}[1]{\in\mathbb{C}^{#1}}
\newcommand{\norm}[1]{\left\lVert#1\right\rVert}
\newcommand{\abs}[1]{\left\lvert#1\right\rvert}
\newcommand{\expt}[1]{\mathbb{E} \left\{#1\right\}}
\newcommand{\cn}[2]{\ensuremath{\sim\mathcal{C}\mathcal{N}\left(#1,#2\right)}}

Glossaries

\usepackage[xindy, toc, numberedsection, acronym]{glossaries}
\usepackage{hyperref}
\loadglsentries{abbr.tex}
\makeglossaries 

More information: https://www.overleaf.com/learn/latex/Glossaries Base LaTex file is located here.

Scripting files to format the file, remove duplicates, merge different abbr files is located here.

Bibliography

Clean bib files

• Clean-up your bib files: https://flamingtempura.github.io/bibtex-tidy/
• I also always enable the "Enclose values in double braces" option to keep the capitalization in titles.
• My default setup

Use Biblatex

No cite or natbib package is required. For more info check: https://www.overleaf.com/learn/latex/Bibliography_management_with_biblatex. Always be aware there is a difference in citation style and bibliography style.

\usepackage[backend=biber,style=ieee]{biblatex}
%\usepackage[backend=biber,language=dutch]{biblatex}
\addbibresource{bib.bib}
\AtBeginBibliography{\footnotesize}

\begin{document}

\printbibliography
\end{document}

Tables

• Handy table generator: https://www.tablesgenerator.com/
• I prefer to use the Booktabs table style. An example can be found in the following link: https://nhigham.com/2019/11/19/better-latex-tables-with-booktabs/

Hide columns

%% to hide a column in table 
\usepackage{array}
\newcolumntype{H}{>{\setbox0=\hbox\bgroup}c<{\egroup}@{}}

SI-units

\usepackage[per-mode=symbol]{siunitx}  %usage \SI{35}{\meter\squared}
\DeclareSIUnit{\dBm}{dBm}	% add SI unit "dBm"

Clever reference

\usepackage[capitalise]{cleveref}  %usage \cref{fig:figureReference}

• Standard figure reference gives (\ref) gives: 1
• Cleveref figure references gives (\cref): fig. 1

Figures

Color schemes

https://sronpersonalpages.nl/~pault/#sec:qualitative

ETH Figure Tool

https://www.bsaver.io/misc/pretty-figures

Python to Tikz

tikzplotlib

Extract data from existing figures

https://automeris.io/WebPlotDigitizer/

Indicate lines in a plot

%draw arc
\draw (x0, y0) arc
    [
        start angle=50,
        end angle=310,
        x radius=0.1cm,
        y radius =0.6cm
    ] ;
    
%draw line 
\draw[] (x1, y1) -- (x2, y2);

%add text
\node[] (x3,  y3) {my text};

example:

Preparing for submission

Clean-up Project

LaTeX cleaner from Google Research.

Usage:

pip install arxiv_latex_cleaner
arxiv_latex_cleaner ./ --keep_bib --verbose
tar -jcvf arxiv.tar.gz gwffzkzgrjgpqksqdkfgtvzkfnjwghny_arXiv/

LaTeX cleaner's main features:

• Removes all auxiliary files (.aux, .log, .out, etc.).
• Removes all comments from your code (yes, those are visible on arXiv and you do not want them to be). These also include \begin{comment}\end{comment}, \iffalse\fi, and \if0\fi environments.
• Optionally removes user-defined commands entered with commands_to_delete (such as \todo{} that you redefine as the empty string at the end).
• Optionally allows you to define custom regex replacement rules through a cleaner_config.yaml file.

There is a 50MB limit on arXiv submissions, so to make it fit:

• Removes all unused .tex files (those that are not in the root and not included in any other .tex file).
• Removes all unused images that take up space (those that are not actually included in any used .tex file).
• Optionally resizes all images to im_size pixels, to reduce the size of the submission. You can allowlist some images to skip the global size using images_allowlist.
• Optionally compresses .pdf files using ghostscript (Linux and Mac only). You can allowlist some PDFs to skip the global size using images_allowlist.

Shortening a Paper

Reducing space after caption

\setlength{\belowcaptionskip}{-20pt} % in the preamble

Biblatex hacks

• You can check how many times a certain reference is cited in the text. In this example, every reference which is only cited once is colored red.

\usepackage[backend=biber, style=ieee, citestyle=numeric-comp, maxcitenames=1,mincitenames=1, maxbibnames=1, minbibnames=1,isbn=false, doi=false,citecounter=true]{biblatex}
\addbibresource{bib.bib}
\AtBeginBibliography{\footnotesize}
\renewcommand{\finentrypunct}{%
  \addperiod\space
  \ifnum \value{citecounter} < 2
  \color{red}
  \else
   \color{Green}
    \fi
  (Cited \arabic{citecounter})%
}

• The number of names shown in the bibliography can be altered by the maxbibnames=1, minbibnames=1 option.
• What if linebreaking of titles in bibliography not working correctly. Possible solutions:
  • remove \usepackage{ulem}
  • remove \usepackage{cite}
  • remove \usepackage{natbib}

Updating manuscript

Change color of single reference using biblatex

% Example bib entry
@article{biodegradables,
	title        = {{Recent Advances in Biodegradable Green Electronic Materials and Sensor Applications}},
	author       = {Min, JinKi and Jung, Yeongju and Ahn, Jiyong and Lee, Jae Gun and Lee, Jinwoo and Ko, Seung Hwan},
	year         = 2023,
	journal      = {Advanced Materials},
	volume       = 35,
	number       = 52,
	pages        = 2211273,
	doi          = {https://doi.org/10.1002/adma.202211273},
}

% Define start and reset color
\makeatletter
\newcommand{\startcolor}{%
  \color{RoyalBlue}\global\let\default@color\current@color
}
\newcommand{\resetcolor}{%
  \color{black}\global\let\default@color\current@color
}
\makeatother

% Make a highlighted category
\DeclareBibliographyCategory{highlighted}

% Add specific bib entries to category
\addtocategory{highlighted}{biodegradables}
\addtocategory{highlighted}{other_bib_item}
\addtocategory{highlighted}{another_bib_item}

\AtEveryBibitem{%
  \ifcategory{highlighted}{\startcolor}{\resetcolor}
}