Created
July 22, 2013 20:45
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BiocStyle + knitr; try `library("knitr"); library("BiocStyle"); knit("knitr.Rnw"); tools::texi2pdf("knitr.tex")`
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\NeedsTeXFormat{LaTeX2e} | |
\ProvidesPackage{Bioconductor}[2013/07/01 Bioconductor vignette style] | |
%% -I would wish to know how to make this work- | |
%% \DeclareOption{pdftitle}{\PassOptionsToPackage{pdftitle}{hyperref}} | |
%% \DeclareOption{pdfauthor}{\PassOptionsToPackage{pdfauthor}{hyperref}} | |
%% \ExecuteOptions{pdftitle,pdfauthor} | |
%% \ProcessOptions | |
\PassOptionsToPackage{usenames,dvipsnames}{color} | |
\RequirePackage{color} | |
\definecolor{BiocBlue}{RGB}{24,129,194} | |
\definecolor{BiocGreen}{RGB}{135,177,63} | |
\RequirePackage[% | |
pdfpagelabels,% | |
plainpages=false,% | |
pdfborder={0 0 0},% | |
bookmarks=true,% | |
bookmarksopen=true,% | |
bookmarksnumbered=true,% | |
linktoc=section,% | |
linkcolor=BiocBlue,% | |
citecolor=BiocBlue,% | |
urlcolor=BiocBlue,% | |
citebordercolor={.7 .7 .7},% | |
linkbordercolor={.7 .7 .7},% | |
urlbordercolor={.7 .7 .7},% | |
raiselinks,% | |
pdfusetitle,% | |
pdftex]{hyperref} | |
\pdfpageattr{/Group << /S /Transparency /I true /CS /DeviceRGB>>} %fixes incorrect color rendering in acroread | |
\RequirePackage[left=2cm,top=2.5cm,bottom=2.5cm,right=2cm]{geometry} | |
\RequirePackage{graphicx} | |
\RequirePackage{helvet} | |
\renewcommand{\familydefault}{\sfdefault} | |
\RequirePackage{cite} | |
\pagestyle{empty} | |
% | |
\RequirePackage{sectsty} | |
\sectionfont{\sffamily\bfseries\color{BiocBlue}\sectionrule{0pt}{0pt}{-1ex}{1pt}} | |
\subsectionfont{\sffamily\bfseries\color{BiocBlue}} | |
\subsubsectionfont{\sffamily\bfseries\color{BiocBlue}} | |
% | |
%% Page layout | |
\RequirePackage{titling} %% captures \title{} as \thetitle for subsequent use | |
\RequirePackage{fancyhdr} | |
\pagestyle{fancy} | |
\fancyhf{} % clear all header and footer fields | |
\fancyhead[LE,RO]{\thepage} | |
\fancyhead[LO,RE]{\thetitle} | |
\renewcommand{\headrule}{} | |
% | |
\usepackage{enumitem} | |
\setlist{nolistsep} | |
%% Alter some LaTeX defaults for better treatment of floats | |
%% See p.105 of "TeX Unbound" for suggested values | |
\setcounter{topnumber}{2} | |
\setcounter{bottomnumber}{2} | |
\setcounter{totalnumber}{4} | |
\setcounter{dbltopnumber}{2} | |
\renewcommand\topfraction{0.9} | |
\renewcommand\bottomfraction{0.5} | |
\renewcommand\textfraction{0.1} | |
\renewcommand\floatpagefraction{0.9} | |
\renewcommand\dbltopfraction{0.9} | |
\renewcommand\dblfloatpagefraction{0.8} | |
% | |
\RequirePackage{Sweave} | |
% | |
\newcommand{\email}[1]{\href{mailto:#1}{\texttt{#1}}} | |
\newcommand{\file}[1]{'#1'} | |
\newcommand{\software}[1]{\textsl{#1}} | |
\newcommand\R{\software{R}} | |
\newcommand\Bioconductor{\software{Bioconductor}} | |
\newcommand\Biocpkg[1]{% | |
{\href{http://bioconductor.org/packages/release/bioc/html/#1.html}% | |
{\textsl{#1}}}} | |
\newcommand\Biocannopkg[1]{% | |
{\href{http://bioconductor.org/packages/release/data/annotation/html/#1.html}% | |
{\textsl{#1}}}} | |
\newcommand\Biocexptpkg[1]{% | |
{\href{http://bioconductor.org/packages/release/data/experiment/html/#1.html}% | |
{\textsl{#1}}}} | |
\newcommand\Rpkg[1]{% | |
{\href{http://cran.fhcrc.org/web/packages/#1/index.html}% | |
{\textsl{#1}}}} | |
\newcommand{\Rpackage}[1]{\textit{#1}} | |
\newcommand{\Rfunction}[1]{\texttt{#1}} | |
\newcommand{\Robject}[1]{\texttt{#1}} | |
\newcommand{\Rclass}[1]{\textit{#1}} | |
\newcommand{\Rcode}[1]{\texttt{#1}} | |
% | |
\newcommand{\comment}[1]{\textsl{\textcolor{Gray}{#1}}} | |
\newcommand{\warning}[1]{\textsl{\textcolor{Red}{warning: #1}}} | |
\newcommand{\fixme}[1]{\textsl{\textcolor{Bittersweet}{fixme: #1}}} | |
% | |
\newcommand{\incfig}[4]{% | |
\begin{figure}[tbp] | |
\begin{center} | |
\includegraphics[width=#2]{#1} | |
\caption[#3]{\label{#1}\textbf{#3} #4} | |
\end{center} | |
\end{figure} | |
} | |
\endinput |
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\documentclass{article} | |
\usepackage{Bioconductor-patched} | |
<<style, eval=TRUE, echo=FALSE, results="asis">>= | |
BiocStyle::latex() | |
@ | |
\author{Sebastian Gibb% | |
\thanks{\email{mail@sebastiangibb.de}} | |
} | |
\date{\today} | |
\title{Minimal Example} | |
\begin{document} | |
<<boring-random>>= | |
set.seed(1121) | |
(x=rnorm(20)) | |
mean(x);var(x) | |
@ | |
\end{document} |
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\documentclass{article} | |
<<style, eval=TRUE, echo=FALSE, results="asis">>= | |
BiocStyle::latex() | |
@ | |
\author{Sebastian Gibb% | |
\thanks{\email{mail@sebastiangibb.de}} | |
} | |
\date{\today} | |
\title{Minimal Example} | |
\begin{document} | |
<<boring-random>>= | |
set.seed(1121) | |
(x=rnorm(20)) | |
mean(x);var(x) | |
@ | |
\end{document} |
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\documentclass{article} | |
\usepackage{Bioconductor-patched} | |
\author{Sebastian Gibb% | |
\thanks{\email{mail@sebastiangibb.de}} | |
} | |
\date{\today} | |
\title{Minimal Example} | |
\begin{document} | |
<<boring-random>>= | |
set.seed(1121) | |
(x=rnorm(20)) | |
mean(x);var(x) | |
@ | |
\end{document} |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
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\documentclass{article} | |
<<style, eval=TRUE, echo=FALSE, results=tex>>= | |
BiocStyle::latex() | |
@ | |
\author{Sebastian Gibb% | |
\thanks{\email{mail@sebastiangibb.de}} | |
} | |
\date{\today} | |
\title{Minimal Example} | |
\begin{document} | |
<<boring-random>>= | |
set.seed(1121) | |
(x=rnorm(20)) | |
mean(x);var(x) | |
@ | |
\end{document} |
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