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>

===Diagram===
<code>
\usepackage{tikz}
\usetikzlibrary{positioning,shapes,snakes,arrows}
\begin{tikzpicture}[->,>=stealth',shorten >=1pt,auto,node distance=3cm,
   bin/.style={rectangle,minimum width=1.9cm,minimum height=0.15cm,line width=0.015cm,fill=blue!50,draw,font=\sffamily\normalsize\bfseries},
   read/.style={draw=none,fill=orange!50,font=\sffamily\tiny\bfseries},
   count/.style={text centered,draw=none,font=\sffamily\scriptsize\bfseries},
   protein/.style={circle,fill=red!50,text centered,draw,font=\sffamily\tiny\bfseries},
   rate/.style={ellipse,text centered,draw=none,fill=green!80,font=\sffamily\small\bfseries},
   hyper/.style={ellipse,text centered,draw=none,fill=pink!80,font=\sffamily\small\bfseries}]
    \matrix[nodes={draw, ultra thick, fill=red!20}, row sep=0cm,column sep=0cm,ampersand replacement=\&] {
      \node[bin](1){};\&      \node[bin](2){};\&      \node[bin](3){};\&      \node[bin](4){};\&      \node[bin](5){};\\
    };
    \node[hyper](input)[rectangle,fill=none,above = 2.9cm of 3]{Input Reads};
    \node[read](read1)[above right=0.2cm and -1.8cm of 1]{ACCTAC...................};
    \node[read](read1)[above right=0.2cm and 1.3cm of 1]{...................CTGAGT};
    \node[read](read1)[above right=0.2cm and -1.5cm of 4]{GTTACA...................};
    \node[read](read1)[above right=0.4cm and -1.8cm of 1]{...................TGATTC};
    \node[read](read1)[above right=0.4cm and 1.2cm of 3]{...................CACTTT};
    \node[count](x1)[below=0.3cm of 1]{$X_1=2$};
    \node[count](x2)[below=0.3cm of 2]{$X_2=2$};
    \node[count](x3)[below=0.3cm of 3]{$X_3=1$};
    \node[count](x4)[below=0.3cm of 4]{$X_4=2$};
    \node[count](x5)[below=0.3cm of 5]{$X_5=2$};
    \node[rate](lambda1)[below=1cm of x1]{$\lambda^z_1$};
    \node[rate](lambda2)[below=1cm of x2]{$\lambda^z_2$};
    \node[rate](lambda3)[below=1cm of x3]{$\lambda^z_3$};
    \node[rate](lambda4)[below=1cm of x4]{$\lambda^z_4$};
    \node[rate](lambda5)[below=1cm of x5]{$\lambda^z_5$};
    \node[hyper](fun)[fill=red!80,below=2.5cm of x3]{$\mu_i=f(M_i,GC_i)$};
    \node[rate](lambday1)[below=6cm of x1]{$\lambda^y_1$};
    \node[rate](lambday2)[below=6cm of x2]{$\lambda^y_2$};
    \node[rate](lambday3)[below=6cm of x3]{$\lambda^y_3$};
    \node[rate](lambday4)[below=6cm of x4]{$\lambda^y_4$};
    \node[rate](lambday5)[below=6cm of x5]{$\lambda^y_5$};
    \node[count](y1)[below=1cm of lambday1]{$Y_1=3$};
    \node[count](y2)[below=1cm of lambday2]{$Y_2=5$};
    \node[count](y3)[below=1cm of lambday3]{$Y_3=3$};
    \node[count](y4)[below=1cm of lambday4]{$Y_4=2$};
    \node[count](y5)[below=1cm of lambday5]{$Y_5=2$};
  %  \matrix[nodes={draw, ultra thick, fill=red!20}, row sep=0cm,column sep=0cm,ampersand replacement=\&] {
      \node[bin](bin1)[below=0.3cm of y1]{};\&      \node[bin](bin2)[below=0.3cm of y2]{};\&      \node[bin](bin3)[below=0.3cm of y3]{};\&      \node[bin](bin4)[below=0.3cm of y4]{};\&      \node[bin](bin5)[below=0.3cm of y5]{};\\
  %  };
%    \matrix[nodes={draw, ultra thick, fill=red!20}, row sep=0cm,column sep=0cm,ampersand replacement=\&] {      \node[bin](bin1){};\&      \node[bin](bin2){};\&      \node[bin](bin3){};\&      \node[bin](bin4){};\&      \node[bin](bin5){};\\   };
    \node[protein](protein1)[above right=-0.3cm and -1cm of bin2]{protein};
    \node[read](read1)[below right=0.2cm and -0.7cm of bin1]{ACCGAC...................};
    \node[hyper](fig)[below=0.1cm of chip,fill=none,rectangle]{\scriptsize \textit{Fig. 2: The hierarchical Bayesian model for bin-level couts.}};

    \path[every node/.style={font=\sffamily\small}]
    (lambda1) edge  (x1)
    (fun) edge  (lambday5)
    (lambday5) edge  (y5);

    \node[rate](B1)[above left=0.5cm and -0.5cm of lambday1]{$B_1=0$};
    \node[rate](B5)[above left=0.5cm and -0.50cm of lambday5]{$B_5=0$};
    \path[every node/.style={font=\sffamily\small}]
    (B1)edge(lambday1)
    (B5)edge(lambday5);

  \end{tikzpicture}
  </code>
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