===General Setup===
\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}
===Use natbib===
\usepackage{natbib}
...
%use bib
\bibliographystyle{apalike}
\bibliography{bib file name without .bib}
When compile,
latex file.tex
bibtex file
latex file.tex
latex file.tex
dvipdf file.dvi
===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
\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}
..
<>=
...
@
Compile:
library(cacheSweave)
Sweave("foo.Rnw", driver = cacheSweaveDriver)
To control R output line length,
<<...>>=
options(width=60)
@
To control Sweave-generated figures' sizes,
<<... fig=T,width=4,height=4>>=
...
@
To formulate the Soutput, paste following in Sweave.sty
\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}}
===Set Page Format===
\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}}
===Animate===
\usepackage{animate}
\animategraphics[width=0.9\textwidth]{}{}{}{}
===Diagram===
\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=0.4cm and 1.2cm of 3]{...................CACTTT};
\node[count](x1)[below=0.3cm of 1]{$X_1=2$};
\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[count](y1)[below=1cm of lambday1]{$Y_1=3$};
% \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}