===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=0.4cm 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} </code>
