Capra_Lab_Cell_Press_journal_format_latexTemplate

Forfatter
Colin Brand, Evonne McArthur, Capra Lab
Sidst opdateret
6 måneder siden
Licens
Creative Commons CC BY 4.0
Resumé
More details and instructions can be found here: https://github.com/CapraLab/lab-manuscript-template. The goal of this template is to make formatting and writing a scientific manuscript easier and more standardized for Cell Press journals, building upon a previous LaTeX template for manuscripts. While this should be appropriate as a template, there is ultimately no one-size-fits-all for writing a paper. However, this will hopefully serve as a great place to start.
Tags
Academic Journal
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Capra_Lab_Cell_Press_journal_format_latexTemplate
%%% ------------ OVERVIEW OF THIS TEMPLATE ------------ %%%
% This is a Capra Lab Manuscript template! It was developed by the Capra
% Lab and converted to a LaTex document by Evonne McArthur 2/2022 and last
% edited 2/2022. 

% To use this template, you should probably read the whole compiled document
% because it contains lots of great tips. Once you are ready to go, you 
% should delete the tips in each section (\abstractTips \introTips \resultsTips 
% \captionTips \methodsTips \discussionTips and \generalTips). Then you should
% delete the REMOVEME_tips.tex file and the call to that file in this document
% (\input{REMOVEME_tips}). Then add your own content to the relevant subfiles.

% Figures should be uploaded to the ./main_figs and ./supplement/suppl_figs
% folders. Tables should be uploaded to ./supplement/suppl_tabs. When you work
% with main text figures, you should create a "code name" for them. You will
% follow the format in 4maintextFigs.tex to add a function that will generate
% the figure. When you want that figure to appear in the manuscript call that
% function (e.g. \codename).

% Note that this document contains info about how to customize these things:
% fontsize, font (to Arial), line spacing, line numbers, left vs. justified
% aligned, number or author-date citations, natbib vs bibLaTeX citations,
% sideways tables and figures, figure references and more!

% See these resources for more LaTeX tips:
%https://en.m.wikibooks.org/wiki/LaTeX
%https://tobi.oetiker.ch/lshort/lshort.pdf
%https://gangw.cs.illinois.edu/latex.pdf
%https://web.mit.edu/rsi/www/pdfs/new-latex.pdf
%http://hoffman.physics.harvard.edu/Hoffman-example-paper.pdf

%%% ------------ READ IN PACKAGES & SETUP ------------ %%%

% Basics, font size, page setup, link format, line spacing/numbering
\documentclass[11pt]{article} % font size
\usepackage[english]{babel}
\usepackage[a4paper,margin=1in]{geometry} % page setup
\usepackage{authblk} % author affiliations
\usepackage[colorlinks=true, linkcolor=black, citecolor=black, urlcolor=blue, filecolor=blue,breaklinks=true]{hyperref} % Hyperlinks, needed for biblatex, other option: allcolors=blue
\setcounter{secnumdepth}{0} % disable section numbering, generates a few warnings but these should not effect the document
\usepackage{setspace} % linespacing
\usepackage{lineno} % line numbering
\renewcommand\linenumberfont{\normalfont\scriptsize\fontspec{Arial}\color{black}}
\usepackage{csquotes} % Recommended for biblatex, must load after lineno or will get a warning
\usepackage{ragged2e}% for left aligning
\setlength{\RaggedRightParindent}{\parindent} % for paragraph indent with left aligning
\usepackage{array} % used to soft wrap text in Table S3

% Write math as font
\usepackage[no-math]{fontspec}
\setmainfont{Arial}
\usepackage[defaultmathsizes]{mathastext}
\usepackage{amsmath}

% Figure references and bolding them https://tex.stackexchange.com/questions/87903/bold-cross-references
\usepackage[capitalise, noabbrev, nameinlink]{cleveref}
\usepackage[labelsep=period]{caption} % change separator to period instead of colon
\crefdefaultlabelformat{#2#1#3}
\Crefname{figure}{Figure}{Figures}
\Crefname{table}{Table}{Tables}
\Crefname{section}{\textbf{Section}}{\textbf{Sections}}
\newcommand{\crefrangeconjunction}{--} % change conjunction b/w figures
\newcommand{\crefpairconjunction}{, }
\newcommand{\creflastconjunction}{, }
\newcommand{\crefmiddleconjunction}{, }

% Figures, Tables and captions
\usepackage{graphicx}
\graphicspath{{./main_figs/}{./supplement/suppl_figs/}} % paths for figs
\DeclareGraphicsExtensions{.pdf,.jpeg,.JPG,.png,.PNG, .eps, .tiff}
\usepackage{subcaption} % for subcaptions (panels), and add parentheses
\DeclareCaptionLabelFormat{bold}{{(#2)}} % bold subpanel letter in caption
\captionsetup{subrefformat=bold} % bold subpanel letter in caption
\renewcommand{\thesubfigure}{\Alph{subfigure}} % Make subpanel numbering capitalized
\newcommand{\labelphantom}[1]{%  To make subpanel references easier from https://tex.stackexchange.com/a/255790/121424 
  \parbox{0pt}{\phantomsubcaption\label{#1}}%
}
\usepackage{pgffor} % for function to make figures with subpanels
\usepackage{alphalph} % for function to make figures with subpanels
\usepackage[labelfont=bf, textfont=bf, singlelinecheck=off, textfont=footnotesize]{caption} % boldness of captions
\usepackage{booktabs}
\usepackage{multirow}
\usepackage{rotating}

% Read in helper functions
\input{helperFunctions}

% Can remove, are for the tips
\usepackage[dvipsnames]{xcolor} % can remove, for coloring the tips
\usepackage{changepage} % can remove, for width on the tips
\usepackage{enumitem} % can remove, for width on the tips

 % soft wrap URLs and use same font as document
\usepackage{xurl}
\urlstyle{same}

%%% ------------ REFERENCES FORMAT ------------ %%% 
\usepackage[backend=biber, citestyle=numeric-comp, bibstyle=authoryear, sorting=none, natbib=true, url=false, minbibnames=10, maxbibnames=10, uniquename=false, uniquelist=false, giveninits=true]{biblatex}

% add numbers to authoryear bibstyle in References
\defbibenvironment{bibliography}
  {\list
    {\printtext[labelnumberwidth]{%
       \printfield{labelprefix}%
       \printfield{labelnumber}}}
    {\setlength{\labelwidth}{\labelnumberwidth}%
     \setlength{\leftmargin}{\labelwidth}%
     \setlength{\labelsep}{\biblabelsep}%
     \addtolength{\leftmargin}{\labelsep}%
     \setlength{\itemsep}{\bibitemsep}%
     \setlength{\parsep}{\bibparsep}}%
     \renewcommand*{\makelabel}[1]{##1}}
  {\endlist}
  {\item}

% add a period to each numbered reference
\DeclareFieldFormat{labelnumberwidth}{#1.}

% last names first
\DeclareNameAlias{author}{family-given}

% clear the month, issue number, and ISSN from references
\AtEveryBibitem{\clearfield{month}}
\AtEveryBibitem{\clearfield{number}}
\AtEveryBibitem{\clearfield{issn}}

% remove quotes from article title
\DeclareFieldFormat[article]{title}{#1}

% deitalicize journal title
\DeclareFieldFormat{journaltitle}{#1\isdot}

% axe "In:" before journal name
\renewbibmacro{in:}{}

% italicize volume number
\renewbibmacro*{volume+number+eid}{%
  \printfield{volume}%
}
\DeclareFieldFormat[article]{volume}{\mkbibitalic{#1}}

% format DOI
\DeclareFieldFormat{doi}{\url{https://doi.org/#1}}

% removes "pp" from pages
\DefineBibliographyStrings{english}{%
  page             = {},
  pages            = {},
} 

% add a space between entries
\setlength\bibitemsep{\baselineskip}

% add bibliography resource
\addbibresource{example.bib}

%%% ------------ FONT COLOR FORMAT ------------ %%% 
\usepackage{xcolor}
\usepackage{caption}

% Define a custom colors using the hexadecimal code
\definecolor{sectioncolor}{HTML}{9c4847}
\definecolor{black}{HTML}{000000}
\definecolor{linkcolor}{HTML}{008ebe}

% Set custom colors
\usepackage{titlesec}
\titleformat{\section}
{\color{sectioncolor}\normalfont\Large\bfseries}
{\thesection}{1em}{}

\titleformat{\subsection}
{\color{sectioncolor}\normalfont\large\bfseries}
{\thesubsection}{1em}{}

% Redefine the figures title color
\DeclareCaptionFont{figuretitlecolor}{\color{sectioncolor}}
\DeclareCaptionFont{figurecaptioncolor}{\color{black}}
\captionsetup[figure]{labelfont=bf, textfont=figurecaptioncolor, font=figuretitlecolor}

% Redefine the tables title color
\DeclareCaptionFont{tabletitlecolor}{\color{sectioncolor}}
\DeclareCaptionFont{tablecaptioncolor}{\color{black}\footnotesize}
\captionsetup[table]{labelfont=bf, textfont=tablecaptioncolor, font=tabletitlecolor}

\hypersetup{
    colorlinks=true,
    linkcolor=linkcolor,
    urlcolor=linkcolor,
    citecolor=linkcolor
}

%%% ------------ TITLE PAGE FORMATTING ------------ %%% 

% left align title, authors, and affiliations
\makeatletter
\renewcommand\maketitle{\par
  \begingroup
    \flushleft
    \Large{\@title}\par
  \endgroup
  \vspace{0.5em}
  \begin{flushleft}
    \@author
  \end{flushleft}
}
\makeatother

% left align abstract title and justify abstract body
\renewenvironment{abstract}{
  \begin{flushleft}
    \textbf{\abstractname}
  \end{flushleft}
  \vspace{-1.5em}
  \par
  \noindent\justify
  \parfillskip=0pt
}{
  \par 
}

%%% ------------ DOCUMENT ORGANIZATION ------------ %%%

\input{1titlepage}
\begin{document}
    \setstretch{1.15} %\onehalfspace
    \linenumbers
    \input{REMOVEME_tips}

    \maketitle
    \makeAbstract
    \clearpage
    \input{2intro} 
    \input{3results}
    \input{5discussion}
    \input{6methods}

    \begin{singlespace}
        \printbibliography
    \end{singlespace}
    \clearpage
    
    %\section*{Supplementary Information}
    \setcounter{page}{1} % Set page at 1
    \input{supplement/0suppl_text}
    \clearpage
    \input{supplement/1suppl_figs}
    \input{supplement/2suppl_tabs}

\end{document}