Differences

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--- latex_and_sweave [2012/11/20 11:13]
zuo created
+++ latex_and_sweave [2013/07/23 09:13] (current)
zuo
@@ Line 5: / Line 5: @@
 \usepackage{amsmath,mathrsfs,stmaryrd,graphicx}
 \usepackage[top=2cm,bottom=2cm,left=2cm,right=1cm]{geometry}
-\usepackage[utf8]{inputenc}%used with sweave
-\SweaveOpts{engine=R,eps=FALSE,pdf=TRUE,width=3,height=6.5,strip.white=all}%used with sweave
 \title{...}
@@ Line 23: / Line 21: @@
 </code>
-==Convert tiff to eps==
+===Use natbib===
-tiff2ps -e input.tif > output.eps
-Must output encapsulated eps; otherwise the figure can not be located correctly in the latex.
+<code>
+\usepackage{natbib}
+...
+%use bib
+\bibliographystyle{apalike}
+\bibliography{bib file name without .bib}
+</code>
-==Compile .bib==
+When compile,
+<code>
 latex file.tex
 bibtex file
@@ Line 34: / Line 39: @@
 latex file.tex
 dvipdf file.dvi
+</code>
-==Sweave==
+===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}
 ..
@@ Line 53: / Line 67: @@
 </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>

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