My Research Notes

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===General Setup===

<code>
\documentclass[a4paper,12pt]{article}
\usepackage{amsmath,mathrsfs,stmaryrd,graphicx}
\usepackage[top=2cm,bottom=2cm,left=2cm,right=1cm]{geometry}

\title{...}

\author{Name\footnote{affiliation} and name\footnote{}} }
\date{}

\begin{document}
\maketitle

\begin{thebibliography}{99}
  \bibitem{} Rozowsky, J.. (2009). {\it PeakSeq enables systematic scoring of ChIP-Seq experiments relative to controls}. Nature Biotechnology, \textbf{27}(1), 66–75.
\end{thebibliography}

\end{document}
</code>

===Use natbib===

<code>
\usepackage{natbib}
...
%use bib
\bibliographystyle{apalike}
\bibliography{bib file name without .bib}
</code>

When compile,

<code>
latex file.tex
bibtex file
latex file.tex
latex file.tex
dvipdf file.dvi
</code>

===Convert tiff to eps===
tiff2ps -e input.tif > output.eps

Must output encapsulated eps; otherwise the figure can not be located correctly in the latex.

===Sweave===

in .rnw file
<code>
\usepackage[utf8]{inputenc}%used with sweave
\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=3,height=6.5,strip.white=all}%used with sweave

\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=3,height=6.5,strip.white=all}
..
<<eval=T,echo=T,fig=T,results=verbatim,cache=T>>=
...
@
</code>

Compile:

<code>
library(cacheSweave)
Sweave("foo.Rnw", driver = cacheSweaveDriver)
</code>

To control R output line length, 

<code>
<<...>>=
options(width=60)
@
</code>

To control Sweave-generated figures' sizes,

<code>
<<... fig=T,width=4,height=4>>=
...
@
</code>

To formulate the Soutput, paste following in Sweave.sty

<code>
\DefineVerbatimEnvironment{Sinput}{Verbatim} {xleftmargin=2em}
\DefineVerbatimEnvironment{Soutput}{Verbatim}{xleftmargin=2em}
\DefineVerbatimEnvironment{Scode}{Verbatim}{xleftmargin=2em}
\fvset{listparameters={\setlength{\topsep}{0pt}}}
\renewenvironment{Schunk}{\vspace{\topsep}}{\vspace{\topsep}}
</code>

===Set Page Format===
<code>

\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhead{} % clear all header fields
\fancyhead[C]{Chandler Zuo}
\fancyhead[L]{}
\fancyhead[R]{UW Madison}
\fancyfoot{} % clear all footer fields
\fancyfoot[C]{\textbf{Page \thepage}}

</code>


===Animate===
<code>
\usepackage{animate}

\animategraphics[width=0.9\textwidth]{<frame rate>}{<pdf_file_name_without_.pdf>}{<first frame>}{<last frame>}
</code>
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