diff --git a/example.tex b/example.tex index 571b2cb..31a6c8f 100644 --- a/example.tex +++ b/example.tex @@ -1,29 +1,37 @@ \documentclass[a4paper]{tufte-handout} -\title{An Example of the Usage of the Tufte-Handout Style\thanks{Inspired by Edward~R. Tufte!}} +\title{Protocol number X - Title Y} -\author[The Tufte-LaTeX Developers]{The Tufte-\LaTeX\ Developers} +%\author[]{Daniel Klapak ,Sarah Broadfoot ,Gregory Penner,Anup Singh ,Eshwar Inapuri [https://doi.org/10.1371/journal.pone.0205460] } -\date{03 February 2022} % without \date command, current date is supplied +\date{04 April 2022} % without \date command, current date is supplied -%\geometry{showframe} % display margins for debugging page layout \usepackage[utf8]{inputenc} \usepackage[english]{babel} \usepackage[sfdefault, light]{FiraSans} \usepackage[T1]{fontenc} +\usepackage{parskip} \usepackage{textcomp} +\usepackage{array} +\usepackage{enumitem,amssymb} +\newlist{todolist}{itemize}{2} +\setlist[todolist]{label=$\square$} \usepackage{graphicx} % allow embedded images \setkeys{Gin}{width=\linewidth,totalheight=\textheight,keepaspectratio} - \graphicspath{{graphics/}} % set of paths to search for images +\graphicspath{ {./images/} } % set of paths to search for images \usepackage{amsmath} % extended mathematics \usepackage{booktabs} % book-quality tables \usepackage{units} % non-stacked fractions and better unit spacing \usepackage{multicol} % multiple column layout facilities \usepackage{lipsum} % filler text \usepackage{fancyvrb} % extended verbatim environments +\usepackage{multicol} +\setlength{\columnsep}{0.75cm} \fvset{fontsize=\normalsize}% default font size for fancy-verbatim environments + + % Standardize command font styles and environments \newcommand{\doccmd}[1]{\texttt{\textbackslash#1}}% command name -- adds backslash automatically \newcommand{\docopt}[1]{\ensuremath{\langle}\textrm{\textit{#1}}\ensuremath{\rangle}}% optional command argument @@ -35,262 +43,126 @@ \newenvironment{docspec}{\begin{quote}\noindent}{\end{quote}}% command specification environment \begin{document} + \footnotesize \maketitle% this prints the handout title, author, and date + +\vspace{-2em} + \begin{abstract} \noindent -This document describes the Tufte handout \LaTeX\ document style. -It also provides examples and comments on the style's use. -Only a brief overview is presented here; -for a complete reference, see the sample book. + \footnotesize +Summary of the Current experiment can be provided here in this paragraph \end{abstract} -%\printclassoptions - -The Tufte-\LaTeX\ document classes define a style similar to the -style Edward Tufte uses in his books and handouts. Tufte's style is known -for its extensive use of sidenotes, tight integration of graphics with -text, and well-set typography. This document aims to be at once a -demonstration of the features of the Tufte-\LaTeX\ document classes -and a style guide to their use. - -\section{Page Layout}\label{sec:page-layout} -\subsection{Headings}\label{sec:headings} -This style provides \textsc{a}- and \textsc{b}-heads (that is, -\Verb|\section| and \Verb|\subsection|), demonstrated above. - -The Tufte-\LaTeX\ classes will emit an error if you try to use -\linebreak\Verb|\subsubsection| and smaller headings. - -% let's start a new thought -- a new section -\newthought{In his later books},\cite{Tufte2006} Tufte -starts each section with a bit of vertical space, a non-indented paragraph, -and sets the first few words of the sentence in \textsc{small caps}. To -accomplish this using this style, use the \Verb|\newthought| command: -\begin{docspec} - \doccmd{newthought\{In his later books\}, Tufte starts\ldots} -\end{docspec} - -\subsection{Sidenotes}\label{sec:sidenotes} -One of the most prominent and distinctive features of this style is the -extensive use of sidenotes. There is a wide margin to provide ample room -for sidenotes and small figures. Any \Verb|\footnote|s will automatically -be converted to sidenotes.\footnote{This is a sidenote that was entered -using the \texttt{\textbackslash footnote} command.} If you'd like to place ancillary -information in the margin without the sidenote mark (the superscript -number), you can use the \Verb|\marginnote| command.\marginnote{This is a -margin note. Notice that there isn't a number preceding the note, and -there is no number in the main text where this note was written.} - -The specification of the \Verb|\sidenote| command is: -\begin{docspec} - \doccmd{sidenote[\docopt{number}][\docopt{offset}]\{\docarg{Sidenote text.}\}} -\end{docspec} - -Both the \docopt{number} and \docopt{offset} arguments are optional. If you -provide a \docopt{number} argument, then that number will be used as the -sidenote number. It will change of the number of the current sidenote only and -will not affect the numbering sequence of subsequent sidenotes. - -Sometimes a sidenote may run over the top of other text or graphics in the -margin space. If this happens, you can adjust the vertical position of the -sidenote by providing a dimension in the \docopt{offset} argument. Some -examples of valid dimensions are: -\begin{docspec} - \ttfamily 1.0in \qquad 2.54cm \qquad 254mm \qquad 6\Verb|\baselineskip| -\end{docspec} -If the dimension is positive it will push the sidenote down the page; if the -dimension is negative, it will move the sidenote up the page. - -While both the \docopt{number} and \docopt{offset} arguments are optional, they -must be provided in order. To adjust the vertical position of the sidenote -while leaving the sidenote number alone, use the following syntax: -\begin{docspec} - \doccmd{sidenote[][\docopt{offset}]\{\docarg{Sidenote text.}\}} -\end{docspec} -The empty brackets tell the \Verb|\sidenote| command to use the default -sidenote number. - -If you \emph{only} want to change the sidenote number, however, you may -completely omit the \docopt{offset} argument: -\begin{docspec} - \doccmd{sidenote[\docopt{number}]\{\docarg{Sidenote text.}\}} -\end{docspec} - -The \Verb|\marginnote| command has a similar \docarg{offset} argument: -\begin{docspec} - \doccmd{marginnote[\docopt{offset}]\{\docarg{Margin note text.}\}} -\end{docspec} - -\subsection{References} -References are placed alongside their citations as sidenotes, -as well. This can be accomplished using the normal \Verb|\cite| -command.\sidenote{The first paragraph of this document includes a citation.} - -The complete list of references may also be printed automatically by using -the \Verb|\bibliography| command. (See the end of this document for an -example.) If you do not want to print a bibliography at the end of your -document, use the \Verb|\nobibliography| command in its place. - -To enter multiple citations at one location,\cite{Tufte2006,Tufte1990} you can -provide a list of keys separated by commas and the same optional vertical -offset argument: \Verb|\cite{Tufte2006,Tufte1990}|. -\begin{docspec} - \doccmd{cite[\docopt{offset}]\{\docarg{bibkey1,bibkey2,\ldots}\}} -\end{docspec} - -\section{Figures and Tables}\label{sec:figures-and-tables} -Images and graphics play an integral role in Tufte's work. -In addition to the standard \docenv{figure} and \docenv{tabular} environments, -this style provides special figure and table environments for full-width -floats. - -Full page--width figures and tables may be placed in \docenv{figure*} or -\docenv{table*} environments. To place figures or tables in the margin, -use the \docenv{marginfigure} or \docenv{margintable} environments as follows -(see figure~\ref{fig:marginfig}): - -\begin{marginfigure}% - \includegraphics[width=\linewidth]{helix} - \caption{This is a margin figure. The helix is defined by - $x = \cos(2\pi z)$, $y = \sin(2\pi z)$, and $z = [0, 2.7]$. The figure was - drawn using Asymptote (\url{http://asymptote.sf.net/}).} - \label{fig:marginfig} -\end{marginfigure} -\begin{Verbatim} -\begin{marginfigure} - \includegraphics{helix} - \caption{This is a margin figure.} -\end{marginfigure} -\end{Verbatim} - -The \docenv{marginfigure} and \docenv{margintable} environments accept an optional parameter \docopt{offset} that adjusts the vertical position of the figure or table. See the ``\nameref{sec:sidenotes}'' section above for examples. The specifications are: -\begin{docspec} - \doccmd{begin\{marginfigure\}[\docopt{offset}]}\\ - \qquad\ldots\\ - \doccmd{end\{marginfigure\}}\\ - \mbox{}\\ - \doccmd{begin\{margintable\}[\docopt{offset}]}\\ - \qquad\ldots\\ - \doccmd{end\{margintable\}}\\ -\end{docspec} - -Figure~\ref{fig:fullfig} is an example of the \Verb|figure*| -environment and figure~\ref{fig:textfig} is an example of the normal -\Verb|figure| environment. - -\begin{figure*}[h] - \includegraphics[width=\linewidth]{sine.pdf}% - \caption{This graph shows $y = \sin x$ from about $x = [-10, 10]$. - \emph{Notice that this figure takes up the full page width.}}% - \label{fig:fullfig}% -\end{figure*} - -\begin{figure} - \includegraphics{hilbertcurves.pdf} -% \checkparity This is an \pageparity\ page.% - \caption{Hilbert curves of various degrees $n$. - \emph{Notice that this figure only takes up the main textblock width.}} - \label{fig:textfig} - %\zsavepos{pos:textfig} - \setfloatalignment{b} -\end{figure} - -Table~\ref{tab:normaltab} shows table created with the \docpkg{booktabs} -package. Notice the lack of vertical rules---they serve only to clutter -the table's data. - -\begin{table}[ht] - \centering - \fontfamily{ppl}\selectfont - \begin{tabular}{ll} - \toprule - Margin & Length \\ - \midrule - Paper width & \unit[8\nicefrac{1}{2}]{inches} \\ - Paper height & \unit[11]{inches} \\ - Textblock width & \unit[6\nicefrac{1}{2}]{inches} \\ - Textblock/sidenote gutter & \unit[\nicefrac{3}{8}]{inches} \\ - Sidenote width & \unit[2]{inches} \\ - \bottomrule - \end{tabular} - \caption{Here are the dimensions of the various margins used in the Tufte-handout class.} - \label{tab:normaltab} - %\zsavepos{pos:normaltab} +\vspace{-2em} + +\section{Chemicals used :} +\vspace{-1em} +\begin{table}[h!] + \footnotesize + \centering + \begin{tabular}{||c | c | c | c||} + \hline + Chemical name & Provider & Mol wt.(g/mol) & Additional safety requirements \\ [0.5ex] + \hline\hline + 1 & 6 & 87837 & 787 \\ + 2 & 7 & 78 & 5415 \\ + 3 & 545 & 778 & 7507 \\ + 4 & 545 & 18744 & 7560 \\ + 5 & 88 & 788 & 6344 \\ [1ex] + \hline + \end{tabular} \end{table} -\section{Full-width text blocks} - -In addition to the new float types, there is a \docenv{fullwidth} -environment that stretches across the main text block and the sidenotes -area. - -\begin{Verbatim} -\begin{fullwidth} -Lorem ipsum dolor sit amet... -\end{fullwidth} -\end{Verbatim} +\vspace{-1em} -\begin{fullwidth} -\small\itshape\lipsum[1] -\end{fullwidth} +\section{Experiment}\label{sec:page-layout} +\vspace{-1em} +\begin{multicols}{2} +\subsection{Buffers and solutions}\label{sec:headings} +\begin{todolist} +\item Carboxyl-coated or silica-coated magnetic beads in TE buffer (X µl per sample)\\ +\item TE buffer (X µl per sample)\\ +\item Isopropanol (X µl per sample) \\ +\item 80\% ethanol (X µl per sample) \\ +\item Lysis buffer (. X µl per sample) find composition\\ -\section{Typography}\label{sec:typography} +\end{todolist} -\subsection{Typefaces}\label{sec:typefaces} -If the Palatino, \textsf{Helvetica}, and \texttt{Bera Mono} typefaces are installed, this style -will use them automatically. Otherwise, we'll fall back on the Computer Modern -typefaces. -\subsection{Letterspacing}\label{sec:letterspacing} -This document class includes two new commands and some improvements on -existing commands for letterspacing. -When setting strings of \allcaps{ALL CAPS} or \smallcaps{small caps}, the -letter\-spacing---that is, the spacing between the letters---should be -increased slightly.\cite{Bringhurst2005} The \Verb|\allcaps| command has proper letterspacing for -strings of \allcaps{FULL CAPITAL LETTERS}, and the \Verb|\smallcaps| command -has letterspacing for \smallcaps{small capital letters}. These commands -will also automatically convert the case of the text to upper- or -lowercase, respectively. +\vspace{-1em} -The \Verb|\textsc| command has also been redefined to include -letterspacing. The case of the \Verb|\textsc| argument is left as is, -however. This allows one to use both uppercase and lowercase letters: -\textsc{The Initial Letters Of The Words In This Sentence Are Capitalized.} +\subsection{Equipment and Setup}\label{sec:sidenotes} +\begin{todolist} +\item Fume hood\\ +\item Magnetic stand \\ +\item Minifuge \\ +\item Heat block \\ +\item Pipettes\\ +\end{todolist} +\vspace{-1em} -\section{Installation}\label{sec:installation} -To install the Tufte-\LaTeX\ classes, simply drop the -following files into the same directory as your \texttt{.tex} -file: -\begin{quote} - \ttfamily - tufte-book.cls\\ - tufte-common.def\\ - tufte-handout.cls\\ - tufte.bst -\end{quote} -% TODO add instructions for installing it globally +\end{multicols} +\vspace{-1em} +\begin{table} + \centering + \footnotesize + \begin{tabular}{||c | c | c | c||} + \hline + \centering + Reagents &Concentrations & Stock solution & For X ml \\ [1ex] + \hline\hline + GITC & 2 & 3 & 4\\ + Tris HCl & 7 & 78 & 5415 \\ + Sarkosyl & 545 & 778 & 7507 \\ + EDTA & 545 & 18744 & 7560 \\ + Antifoam (optional) & 88 & 788 & 6344 \\ [0.5ex] + \hline + \end{tabular} +\end{table} -\section{More Documentation}\label{sec:more-doc} -For more documentation on the Tufte-\LaTeX{} document classes (including commands not -mentioned in this handout), please see the sample book. - -\section{Support}\label{sec:support} - -The website for the Tufte-\LaTeX\ packages is located at -\url{https://github.com/Tufte-LaTeX/tufte-latex}. On our website, you'll find -links to our \smallcaps{svn} repository, mailing lists, bug tracker, and documentation. - -\bibliography{example} -\bibliographystyle{plainnat} - +\subsection{Sample collection and TNA purification} + +\vspace{-1em} + + \begin{table}[h!] + \footnotesize + \begin{tabular}{| m{12cm} | m{1cm} | m{3 cm}|} + \hline + Step & Time & Observations/Notes \\ [0.1ex] + \hline\hline +\begin{todolist} + \item Collect up to 106 + cultured mammalian cells in a single well of a deep-well plate + \end{todolist} & & \\ +\begin{todolist} + \item Pellet the cells via centrifugation at 500g and discard supernatant + \end{todolist} & 10 min & \\ + \hline + \end{tabular} + \end{table} + + + +\section{Observations} +\vspace{-1em} +Add observations here +\vspace{-1em} +\section{Results}\label{sec:results} +\vspace{-1em} +Add results here +\vspace{-1em} +\section{Iterations} +\vspace{-1em} +Add iterations here \end{document} diff --git a/tufte-common.def b/tufte-common.def index 1f20ed8..afe4f8c 100644 --- a/tufte-common.def +++ b/tufte-common.def @@ -443,10 +443,10 @@ %% % Set page layout geometry -\RequirePackage[letterpaper,left=0.5in,top=1in,headsep=2\baselineskip,textwidth=26pc,marginparsep=2pc,marginparwidth=12pc,textheight=44\baselineskip,headheight=\baselineskip]{geometry} +\RequirePackage[letterpaper,left=0.25in,top=0.25in,headsep=2\baselineskip,textwidth=26pc,marginparsep=2pc,marginparwidth=6pc,textheight=40\baselineskip,headheight=\baselineskip]{geometry} \ifthenelse{\boolean{@tufte@afourpaper}} - {\geometry{a4paper,left=19.8mm,top=20.4mm,headsep=2\baselineskip,textwidth=118mm,marginparsep=8.2mm,marginparwidth=49.4mm,textheight=49\baselineskip,headheight=\baselineskip}} + {\geometry{a4paper,left=9.8mm,top=10.4mm,headsep=2\baselineskip,textwidth=118mm,marginparsep=4.2mm,marginparwidth=25.4mm,textheight=40\baselineskip,headheight=\baselineskip}} {} \ifthenelse{\boolean{@tufte@bfivepaper}}