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[read](read1)[below right=0.2cm and 1.3cm of bin1]{...................CTCAGT};
    \node[read](read1)[below right=0.2cm and -1cm of bin4]{GTTACA...................};
    \node[read](read1)[below right=0.6cm and -0.9cm of bin1]{AGCACC...................};
    \node[read](read1)[below right=0.4cm and -1.1cm of bin1]{...................TAGATC};
    \node[read](read1)[below right=0.4cm and 0.7cm of bin1]{CGCCAG...................};
    \node[read](read1)[below right=0.4cm and 0.8cm of bin3]{...................CCCCTT};
    \node[hyper](chip)[below=0.6cm of bin3,fill=none,rectangle]{ChIP Reads};
    \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)
    (lambda2) edge  (x2)
    (lambda3) edge  (x3)
    (lambda4) edge  (x4)
    (lambda5) edge  (x5)
    (fun) edge  (lambda1)
    (fun) edge  (lambda2)
    (fun) edge  (lambda3)
    (fun) edge  (lambda4)
    (fun) edge  (lambda5)
    (fun) edge  (lambday1)
    (fun) edge  (lambday3)
    (fun) edge  (lambday4)
    (fun) edge  (lambday5)
    (lambday1) edge  (y1)
    (lambday2) edge  (y2)
    (lambday3) edge  (y3)
    (lambday4) edge  (y4)
    (lambday5) edge  (y5);

    \node[rate](B1)[above left=0.5cm and -0.5cm of lambday1]{$B_1=0$};
    \node[rate](B3)[above left=0.5cm and -0.50cm of lambday3]{$B_3=0$};
    \node[rate](B4)[above left=0.5cm and -0.50cm of lambday4]{$B_4=0$};
    \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)
    (B3)edge(lambday3)
    (B4)edge(lambday4)
    (B5)edge(lambday5);


    \node [hyper](hyperx)[below=0.3cm of lambda3]{$\lambda^x_i\sim \Gamma(a,a/\mu_i)$};
    \node [hyper](poisx)[below=0.3cm of x3]{$X_i\sim Pois(\lambda_iN_x)$};
    \node [hyper](poisx)[above=0.3cm of y3]{$Y_i\sim Pois(\lambda^y_ie_0N_y)$};
    \node[hyper](hyperb)[above right =0.5cm and 1.5cm of B1]{$\lambda^y_i | B_i=j \sim \Gamma(b^j,b^j/\mu^j)$};
    \path[every node/.style={font=\sffamily\small}]
    (hyperb)edge(lambday2);
    \node[rate](B2)[above left=0.5cm and -0.50cm of lambday2]{$B_2=1$};
    \path[every node/.style={font=\sffamily\small}]
    (B2) edge (lambday2) ;
    \node [hyper](hyperx)[below=0.3cm of fun]{$\lambda^y_i|B_j=0 \sim \Gamma(b,b/\mu_i)$};

  \end{tikzpicture}
  </code>
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