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\name{SpTrellis-class}
\Rdversion{1.1}
\docType{class}
% constructor:
\alias{SpTrellis-class}
\alias{SpTrellis}
% methods:
\alias{zi}
\alias{zi,SpTrellis-method}
\alias{zo}
\alias{zo,SpTrellis-method}
\alias{right,SpTrellis-method}
\alias{left,SpTrellis-method}
\alias{restore}
\alias{restore,SpTrellis-method}
\alias{show,SpTrellis-method}
\title{Class "SpTrellis"}
\description{
A reference class to manage the trellis graphics related component of the
\code{\link{Snapshot}} functionality for visualization of genomic data.
}
\usage{
SpTrellis(trellis, debug_enabled=FALSE)
}
\arguments{
\item{trellis}{A trellis object for storing the plot of the genome area being
visualized.}
\item{debug_enabled}{\code{logical(1)} indicating whether class methods
should report debugging information to the user.}
}
\section{Fields}{
\describe{
\item{\code{trellis}:}{Object of class \code{trellis} for storing the plot
information.}
\item{debug_enabled}{\code{logical(1)} indicating whether class methods
should report debugging information to the user.}
}
}
\section{Methods}{
\describe{
\item{zi}{\code{signature(x="SpTrellis")}: zoom in}
\item{zo}{\code{signature(x="SpTrellis")}: zoom out}
\item{right}{\code{signature(x="SpTrellis")}: shift to the right}
\item{left}{\code{signature(x="SpTrellis")}: shift to the left}
\item{restore}{\code{signature(x="SpTrellis")}: restore to the
original plot}
\item{show}{\code{signature(x="SpTrellis")}: show the current plot}
\item{update}{\code{signature(x="SpTrellis")}: update the trellis
parameters of the \code{SpTrellis} object.}
}
}
\author{Chao-Jen \url{cwon2@fhcrc.org}}
\seealso{\code{\link{Snapshot}}}
\examples{
col <- c("#66C2A5", "#FC8D62")
x = numeric(1000)
x[sample(1000, 100)] <- abs(rnorm(100))
df <- data.frame(x = c(x, -x), pos = seq(1, 1e5, length.out=1000),
group = rep(c("positive", "negative"), each=1000))
cv <- lattice::xyplot(x ~ pos, df, group=group, type="s",
col=col, main="yeast chrI:1 - 2e5",
ylab="Coverage", xlab="Coordinate",
scales=list(y=list(tck=c(1,0)),
x=list(rot=45, tck=c(1,0), tick.number=20)),
panel=function(...) {
lattice::panel.xyplot(...)
lattice::panel.grid(h=-1, v=20)
lattice::panel.abline(a=0, b=0, col="grey")
})
s <- SpTrellis(cv)
s
zi(s)
zi(s)
left(s)
right(s)
zo(s)
restore(s)
}
\keyword{classes}
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