minimal.Rnw

%% LyX 2.1.4 created this file.  For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
\documentclass{article}
\usepackage[sc]{mathpazo}
\usepackage[T1]{fontenc}
\usepackage{geometry}
\geometry{verbose,tmargin=2.5cm,bmargin=2.5cm,lmargin=2.5cm,rmargin=2.5cm}
\setcounter{secnumdepth}{2}
\setcounter{tocdepth}{2}
\usepackage{url}
\usepackage[unicode=true,pdfusetitle,
 bookmarks=true,bookmarksnumbered=true,bookmarksopen=true,bookmarksopenlevel=2,
 breaklinks=false,pdfborder={0 0 1},backref=false,colorlinks=false]
 {hyperref}
\hypersetup{
 pdfstartview={XYZ null null 1}}
\begin{document}
<<setup, include=FALSE, cache=FALSE>>=
library(knitr)
library(gTrack)
library(gUtils)
# set global chunk options
opts_chunk$set(fig.path='knitr_figure/minimal-', fig.align='center', fig.show='hold')
options(formatR.arrow=TRUE,width=90)
@

\title{A Minimal Demo of knitr}

\author{Yihui Xie}

\maketitle
You can test if \textbf{knitr} works with this minimal demo. OK, let's
get started with some boring random numbers:

<<boring-random>>=
set.seed(1121)
(x=rnorm(20))
mean(x);var(x)
@

<<test-gTrack>>=
gr <- GRanges(c(1,1), IRanges(c(5,6), width=1), strand=c("+","-"), A=c(5,8), B=c(3,2), seqinfo= gUtils::si)
g <- gTrack(gr, height=7, xaxis.chronly = TRUE, y.field="A", bars=TRUE, xaxis.suffix = "bp")
plot(g, windows=GRanges(1, IRanges(5,6)))
@

The first element of \texttt{x} is \Sexpr{x[1]}. Boring boxplots
and histograms recorded by the PDF device:

<<boring-plots, fig.width=4, fig.height=4, out.width='.4\\linewidth'>>=
## two plots side by side (option fig.show='hold')
par(mar=c(4,4,.1,.1),cex.lab=.95,cex.axis=.9,mgp=c(2,.7,0),tcl=-.3,las=1)
boxplot(x)
hist(x,main='')
@

Do the above chunks work? You should be able to compile the \TeX{}
document and get a PDF file like this one: \url{https://github.com/yihui/knitr/releases/download/doc/knitr-minimal.pdf}.
The Rnw source of this document is at \url{https://github.com/yihui/knitr/blob/master/inst/examples/knitr-minimal.Rnw}.
\end{document}