plot.anylist.Rd
\name{plot.anylist}
\alias{plot.anylist}
\title{Plot a List of Things}
\description{
Plots a list of things
}
\usage{
\method{plot}{anylist}(x, \dots, main, arrange=TRUE,
nrows=NULL, ncols=NULL, main.panel=NULL,
mar.panel=c(2,1,1,2), hsep=0, vsep=0,
panel.begin=NULL, panel.end=NULL, panel.args=NULL,
panel.begin.args=NULL, panel.end.args=NULL,
plotcommand="plot",
adorn.left=NULL, adorn.right=NULL, adorn.top=NULL, adorn.bottom=NULL,
adorn.size=0.2, equal.scales=FALSE, halign=FALSE, valign=FALSE)
}
\arguments{
\item{x}{
An object of the class \code{"anylist"}.
Essentially a list of objects.
}
\item{\dots}{
Arguments passed to \code{\link{plot}} when generating each
plot panel.
}
\item{main}{
Overall heading for the plot.
}
\item{arrange}{
Logical flag indicating whether to plot the objects
side-by-side on a single page (\code{arrange=TRUE})
or plot them individually in a succession of frames
(\code{arrange=FALSE}).
}
\item{nrows,ncols}{
Optional. The number of rows/columns in the plot layout
(assuming \code{arrange=TRUE}).
You can specify either or both of these numbers.
}
\item{main.panel}{
Optional. A character string, or a vector of character strings,
giving the headings for each of the objects.
}
\item{mar.panel}{
Size of the margins outside each plot panel.
A numeric vector of length 4 giving the bottom, left, top,
and right margins in that order. (Alternatively the vector
may have length 1 or 2 and will be replicated to length 4).
See the section on \emph{Spacing between plots}.
}
\item{hsep,vsep}{
Additional horizontal and vertical separation between plot panels,
expressed in the same units as \code{mar.panel}.
}
\item{panel.begin,panel.end}{
Optional. Functions that will be executed before and after each panel is
plotted. See Details.
}
\item{panel.args}{
Optional. Function that determines different plot arguments
for different panels. See Details.
}
\item{panel.begin.args}{
Optional. List of additional arguments for \code{panel.begin}
when it is a function.
}
\item{panel.end.args}{
Optional. List of additional arguments for \code{panel.end}
when it is a function.
}
\item{plotcommand}{
Optional.
Character string containing the name of the command that should be
executed to plot each panel.
}
\item{adorn.left,adorn.right,adorn.top,adorn.bottom}{
Optional. Functions (with no arguments) that will be executed to
generate additional plots at the margins (left, right, top and/or
bottom, respectively) of the array of plots.
}
\item{adorn.size}{
Relative width (as a fraction of the other panels' widths)
of the margin plots.
}
\item{equal.scales}{
Logical value indicating whether the components
should be plotted at (approximately) the same physical scale.
}
\item{halign,valign}{
Logical values indicating whether panels in a column
should be aligned to the same \eqn{x} coordinate system
(\code{halign=TRUE}) and whether panels in a row should
be aligned to the same \eqn{y} coordinate system (\code{valign=TRUE}).
These are applicable only if \code{equal.scales=TRUE}.
}
}
\value{
Null.
}
\details{
This is the \code{plot} method for the class \code{"anylist"}.
An object of class \code{"anylist"} represents
a list of objects intended to be treated in the same way.
This is the method for \code{plot}.
In the \pkg{spatstat} package, various functions produce
an object of class \code{"anylist"}, essentially a list of
objects of the same kind.
These objects can be plotted in a nice arrangement
using \code{plot.anylist}. See the Examples.
The argument \code{panel.args} determines extra graphics parameters
for each panel. It should be a function that will be called
as \code{panel.args(i)} where \code{i} is the panel number.
Its return value should be a list of graphics parameters that can
be passed to the relevant \code{plot} method. These parameters
override any parameters specified in the \code{\dots} arguments.
The arguments \code{panel.begin} and \code{panel.end}
determine graphics that will be plotted before and after
each panel is plotted. They may be objects
of some class that can be plotted
with the generic \code{plot} command. Alternatively they
may be functions that will be
called as \code{panel.begin(i, y, main=main.panel[i])}
and \code{panel.end(i, y, add=TRUE)} where \code{i} is the panel
number and \code{y = x[[i]]}.
If all entries of \code{x} are pixel images,
the function \code{\link{image.listof}} is called to control
the plotting. The arguments \code{equal.ribbon} and \code{col}
can be used to determine the colour map or maps applied.
If \code{equal.scales=FALSE} (the default), then the
plot panels will have equal height on the plot device
(unless there is only one column of panels, in which case
they will have equal width on the plot device). This means that the
objects are plotted at different physical scales, by default.
If \code{equal.scales=TRUE}, then the dimensions of the
plot panels on the plot device will be proportional
to the spatial dimensions of the
corresponding components of \code{x}. This means that the
objects will be plotted at \emph{approximately} equal physical scales.
If these objects have very different spatial sizes,
the plot command could fail (when it tries
to plot the smaller objects at a tiny scale), with an error
message that the figure margins are too large.
The objects will be plotted at \emph{exactly} equal
physical scales, and \emph{exactly} aligned on the device,
under the following conditions:
\itemize{
\item
every component of \code{x} is a spatial object
whose position can be shifted by \code{\link{shift}};
\item
\code{panel.begin} and \code{panel.end} are either
\code{NULL} or they are spatial objects
whose position can be shifted by \code{\link{shift}};
\item
\code{adorn.left},
\code{adorn.right},
\code{adorn.top} and
\code{adorn.bottom} are all \code{NULL}.
}
Another special case is when every component of \code{x} is an
object of class \code{"fv"} representing a function.
If \code{equal.scales=TRUE} then all these functions will
be plotted with the same axis scales
(i.e. with the same \code{xlim} and the same \code{ylim}).
}
\section{Spacing between plots}{
The spacing between individual plots is controlled by the parameters
\code{mar.panel}, \code{hsep} and \code{vsep}.
If \code{equal.scales=FALSE}, the plot panels are
logically separate plots. The margins for each panel are
determined by the argument \code{mar.panel} which becomes
the graphics parameter \code{mar}
described in the help file for \code{\link{par}}.
One unit of \code{mar} corresponds to one line of text in the margin.
If \code{hsep} or \code{vsep} are present, \code{mar.panel}
is augmented by \code{c(vsep, hsep, vsep, hsep)/2}.
If \code{equal.scales=TRUE}, all the plot panels are drawn
in the same coordinate system which represents a physical scale.
The unit of measurement for \code{mar.panel[1,3]}
is one-sixth of the greatest height of any object plotted in the same row
of panels, and the unit for \code{mar.panel[2,4]} is one-sixth of the
greatest width of any object plotted in the same column of panels.
If \code{hsep} or \code{vsep} are present,
they are interpreted in the same units as \code{mar.panel[2]}
and \code{mar.panel[1]} respectively.
}
\seealso{
\code{\link{contour.listof}},
\code{\link{image.listof}},
\code{\link{density.splitppp}}
}
\section{Error messages}{
If the error message \sQuote{Figure margins too large}
occurs, this generally means that one of the
objects had a much smaller physical scale than the others.
Ensure that \code{equal.scales=FALSE}
and increase the values of \code{mar.panel}.
}
\examples{
trichotomy <- list(regular=cells,
random=japanesepines,
clustered=redwood)
K <- lapply(trichotomy, Kest)
K <- as.anylist(K)
plot(K, main="")
# list of 3D point patterns
ape1 <- osteo[osteo$shortid==4, "pts", drop=TRUE]
class(ape1)
plot(ape1, main.panel="", mar.panel=0.1, hsep=0.7, vsep=1,
cex=1.5, pch=21, bg='white')
}
\author{\adrian
\rolf
and \ege
}
\keyword{spatial}
\keyword{hplot}
