main.tex

%
%  Nature Neuroscience Template - Root Document File
%
%  Author: Joe Monaco <jmonaco@jhu.edu>
%  Created: Jan 23, 2011.
%  Last updated: September 25, 2015.
%
%  This work is licensed under the Creative Commons Attribution 4.0
%  International License. To view a copy of this license, visit
%  http://creativecommons.org/licenses/by/4.0/.
%
\documentclass[12pt]{article}

\usepackage[utf8]{inputenc}
\usepackage{graphicx}
\usepackage{amssymb,amsmath}
\usepackage{lipsum}
\usepackage{sectsty}
\usepackage{fullpage}
\usepackage{microtype}
\usepackage[pagewise]{lineno}
\usepackage{acronym}
\usepackage[hidelinks]{hyperref}

% Nature citation format
\usepackage[nospace]{cite}
\usepackage{citesupernumber}
\usepackage{numberlabel}  % nature.sty is deprecated

% Customizing captions and float behavior
\usepackage[format=plain,labelformat=empty,font=small]{caption}
\usepackage{placeins}

% For creating nice looking tables
\usepackage{booktabs}
\usepackage{multirow}

% Choose your font: uncomment one of the below font packages or add your own
% \usepackage{pslatex} % for TNR
\usepackage{palatino} % for Palatino
% \usepackage{fontspec} % forces XeLaTeX engine, use \setmainfont (etc) below
% \setmainfont[Mapping=tex-text,Ligatures=TeX]{Adobe Caslon Pro} % choose any system font
% \setmainfont[Mapping=tex-text]{Hoefler Text} % ...such as Hoefler Text

% Set the manuscript title(s): full title is in titletext.tex and a shorter (4-5
% words) running title can also be provided below
\renewcommand{\title}{\input{titletext}}
\newcommand{\runningtitle}{Lorem Ipsum Dolor}

% Define the author lists, affiliations, and corresponding author information
\newcommand{\authorlistplain}{
  First~Author, Second~Author, Corresponding~Author
}
\newcommand{\authorlistannotated}{
  First~Author$^{1}$,
  Second~Author$^{2}$,
  Corresponding~Author$^{3\ast}$
}
\newcommand{\authoraffiliations}{
  $^1$Lorem Ipsum Institute,
      Dolor University,
      Springfield, MO, USA; \\
  $^2$Biomedical Engineering Dept.,
      Lectus University,
      Springfield, MA, USA; \\
  $^3$Dept. of Neuroscience,
      Adipiscing Elit University,
      Springfield, MI, USA; \\
}
\newcommand{\correspondinglastname}{Author}
\newcommand{\correspondingaddress}{
  Dr. Corresponding Author \\
  Adipiscing Elit University \\
  Department of Neuroscience \\
  Springfield, MI 54545, USA \\
  cauthor@adi.edu \\
}

% To render a selective list of manuscript sections, provide an includeonly command
% with a comma-separated list of sections to include. (Comment out all includeonly
% commands to render everything.) The available sections are any of the included
% files in the document: title, abstract, text, endnotes, legends, methods, references,
% figures, supp/legends, supp/guide, supp/figures, and supp/tables. Note that the
% presence of includeonly screws up latexdiff even when commented out, which is why
% the command names are obfuscated (and the stars should be removed when uncommenting.)
%
% \incl***udeonly{text,references}
% \incl***udeonly{legends,figures}
% \incl***udeonly{methods}
% \incl***udeonly{supp/guide}
% \incl***udeonly{supp/figures,supp/tables}

% To exclude the main figures from the manuscript file, uncomment this line:
% \def \excludefigures {}

% Annotation and inline comment command(s): change the author=XXX parameters and add
% extra commands for additional authors to comment. Add `disable' to the package
% parameters to turn off all annotations
\usepackage[disable,shadow,linecolor=black,textsize=small]{todonotes}
\newcommand{\note}[1]{\todo[author=JDM,color=orange!40,linecolor=black]{#1}}
\newcommand{\comment}[1]{\todo[inline,author=JDM,color=orange!40,linecolor=black]{#1}}
% \newcommand{\xyznote}[1]{\todo[author=XYZ,color=green!30,linecolor=black]{#1}}

% Set case of figure panel labels
\newcommand{\panelcase}{\lowercase}
% \newcommand{\panelcase}{\uppercase}

% Reference commands - Figures (call like \[t]*fig{<key>}{<panel_string>} or
% \*figs{<key1>}{<key2>}). Keys reference figures based on figures/Figures_<key>.png
% image files that are brought in via \mainfigure commands in figures.tex.
\newcommand{\fig}[2]{Fig.~\ref{fig:#1}\panelcase{#2}}
\newcommand{\figs}[2]{Figs.~\ref{fig:#1} and \ref{fig:#2}}
\newcommand{\tfig}[2]{Figure~\ref{fig:#1}\panelcase{#2}}
% Supplementary figures
\newcommand{\suppfig}[2]{Supplementary Fig.~\ref{suppfig:#1}\panelcase{#2}}
\newcommand{\suppfigs}[2]{Supplementary Figs.~\ref{suppfig:#1} and \ref{suppfig:#2}}
\newcommand{\tsuppfig}[2]{Supplementary Figure~\ref{suppfig:#1}\panelcase{#2}}
% Supplementary tables
\newcommand{\supptable}[1]{Supplementary Table~\ref{tab:#1}}
% Equations
\newcommand{\eqn}[1]{equation~(\ref{eq:#1})}
\newcommand{\eqns}[2]{equations~(\ref{eq:#1}) and (\ref{eq:#2})}

% Figure and caption display commands:
% NOTE: Main figures should live at ./figures/Figures_<name>.png and
% supplementary figures should live at ./figures/SuppFigures_<name>.png.
% Then use the above reference commands with <name> as the figure key.
% Figure images should be single-column (89mm) or double-column (183mm) wide.
\newcommand{\panel}[1]{\panelcase{\textbf{#1}}}
\newcommand{\customfigure}[4]{
  \begin{figure}[hp]
    \centering
    \includegraphics[scale=1]{figures/#1Figures_#3.png}
    \caption{#4\label{#2fig:#3}}
  \end{figure}
  \vfill
  \clearpage
}
\newcommand{\mainfigure}[1]{
  \customfigure{}{}{#1}{\textbf{\tfig{#1}{}}}
}
\newcommand{\maincaption}[3]{
  {\bf\tfig{#1}{}} $|$ \textbf{#2.} #3
}
\newcommand{\suppcaption}[3]{
  {\bf\tsuppfig{#1}{} $|$} \textbf{#2.} #3
}
\newcommand{\suppfigurewithcaption}[3]{
  \customfigure{Supp}{supp}{#1}{\suppcaption{#1}{#2}{#3}}
}

% Set formatting for section headings
\allsectionsfont{\bfseries}
\sectionfont{\centering\Large}
\subsectionfont{\large}
\paragraphfont{\hspace*{1.5em}}

% Paragraph and line spacing
\setlength{\parindent}{0pt}
\setlength{\parskip}{4ex plus 1ex minus 0.4ex}
\frenchspacing
\raggedright

% Page setup: margins, footers, etc.
\setlength{\hoffset}{0pt}
\setlength{\textwidth}{6.5in}
\setlength{\topmargin}{0pt}
\setlength{\headheight}{0pt}
\setlength{\headsep}{0pt}
\setlength{\voffset}{0pt}
\setlength{\footskip}{5ex}
\setlength{\textheight}{9in}

% Comment this line to enable line numbering
\renewcommand{\linenumbers}{{}}

% Maximize orphan/widow penalties
\widowpenalty=10000
\clubpenalty=10000

\begin{document}

  \include{title}

  \setlength{\baselineskip}{2.6em}

  {
    \linenumbers
    \thispagestyle{empty}
    \include{abstract}
  }

  {
    \setcounter{page}{3}
    \linenumbers
    \include{text}
    \include{endnotes}
    \include{legends}
    \include{methods}
  }

  {
    \setlength{\baselineskip}{1.8em}
    \include{references}
  }

  \ifx\excludefigures\undefined
    {
      \pagestyle{empty}
      \addtolength{\hoffset}{-9mm}
      \addtolength{\textwidth}{18mm}
      \include{figures}
    }
  \fi

  % Include supplementary figure captions at end of main manuscript file for
  % final submission
  \include{supp/legends}

  % Set up the supplementary info
  \pagebreak
  \setcounter{page}{1}
  \setcounter{figure}{0}
  \include{supp/guide}
  \include{supp/figures}
  \include{supp/tables}

\end{document}