plot.ppp.Rd
\name{plot.ppp}
\alias{plot.ppp}
\title{plot a Spatial Point Pattern}
\description{
Plot a two-dimensional spatial point pattern
}
\usage{
\method{plot}{ppp}(x, main, \dots, clipwin=NULL,
chars=NULL, cols=NULL,
use.marks=TRUE, which.marks=NULL,
add=FALSE, type=c("p","n"),
legend=TRUE,
leg.side=c("left", "bottom", "top", "right"),
leg.args=list(),
symap=NULL, maxsize=NULL, meansize=NULL, markscale=NULL,
zap=0.01,
show.window=show.all, show.all=!add, do.plot=TRUE,
multiplot=TRUE)
}
\arguments{
\item{x}{
The spatial point pattern to be plotted.
An object of class \code{"ppp"},
or data which can be converted into
this format by \code{\link{as.ppp}()}.
}
\item{main}{
text to be displayed as a title above the plot.
}
\item{\dots}{
extra arguments that will be passed to the plotting functions
\code{\link{plot.default}}, \code{\link{points}} and/or
\code{\link{symbols}}.
}
\item{clipwin}{
Optional. A window (object of class \code{"owin"}).
Only this subset of the image will be displayed.
}
\item{chars}{
plotting character(s) used to plot points.
}
\item{cols}{
the colour(s) used to plot points.
}
\item{use.marks}{
logical flag; if \code{TRUE}, plot points using a different
plotting symbol for each mark;
if \code{FALSE}, only the locations of the points will be plotted,
using \code{\link{points}()}.
}
\item{which.marks}{
Index determining which column of marks to use,
if the marks of \code{x} are a data frame.
A character or integer vector identifying one or more
columns of marks.
If \code{add=FALSE} then
the default is to plot all columns of marks, in a series of separate
plots.
If \code{add=TRUE} then only one column of marks can be plotted,
and the default is \code{which.marks=1}
indicating the first column of marks.
}
\item{add}{
logical flag; if \code{TRUE},
just the points are plotted, over the existing plot.
A new plot is not created, and
the window is not plotted.
}
\item{type}{
Type of plot: either \code{"p"} or \code{"n"}.
If \code{type="p"} (the default), both the points and the observation window
are plotted. If \code{type="n"}, only the window is plotted.
}
\item{legend}{
Logical value indicating whether to add a legend showing the mapping
between mark values and graphical symbols (for a marked point pattern).
}
\item{leg.side}{
Position of legend relative to main plot.
}
\item{leg.args}{
List of additional arguments passed to \code{\link{plot.symbolmap}}
or \code{\link{symbolmap}} to control the legend.
In addition to arguments documented under
\code{\link{plot.symbolmap}}, and graphical arguments recognised
by \code{\link{symbolmap}}, the list may also include the argument
\code{sep} giving the separation between the main plot and the
legend, or \code{sep.frac} giving the separation as a fraction
of the relevant dimension (width or height) of the main plot.
}
\item{symap}{
Optional. The graphical symbol map to be applied to the marks.
An object of class \code{"symbolmap"}; see
\code{\link{symbolmap}}.
}
\item{maxsize}{
\emph{Maximum} physical size of the circles/squares plotted
when \code{x} is a marked point pattern with
numerical marks.
Incompatible with \code{meansize} and \code{markscale}.
Ignored if \code{symap} is given.
}
\item{meansize}{
\emph{Average} physical size of the circles/squares plotted
when \code{x} is a marked point pattern with
numerical marks.
Incompatible with \code{maxsize} and \code{markscale}.
Ignored if \code{symap} is given.
}
\item{markscale}{
physical scale factor determining the sizes of the
circles/squares plotted when \code{x} is a marked point pattern with
numerical marks. Mark value will be multiplied by \code{markscale}
to determine physical size.
Incompatible with \code{maxsize} and \code{meansize}.
Ignored if \code{symap} is given.
}
\item{zap}{
Fraction between 0 and 1.
When \code{x} is a marked point pattern with numerical marks,
\code{zap} is the smallest mark value
(expressed as a fraction of the maximum possible mark) that will
be plotted.
Any points which have marks smaller in absolute value
than \code{zap * max(abs(marks(x)))} will not be plotted.
}
\item{show.window}{
Logical value indicating whether to plot the observation
window of \code{x}.
}
\item{show.all}{
Logical value indicating whether to plot everything
including the main title and the observation window of \code{x}.
}
\item{do.plot}{
Logical value determining whether to actually perform the plotting.
}
\item{multiplot}{
Logical value giving permission to display multiple plots.
}
}
\value{
(Invisible) object of class \code{"symbolmap"}
giving the correspondence between
mark values and plotting characters.
}
\details{
This is the \code{plot} method for
point pattern datasets (of class \code{"ppp"}, see \code{\link{ppp.object}}).
First the observation window \code{Window(x)} is plotted
(if \code{show.window=TRUE}).
Then the points themselves are plotted,
in a fashion that depends on their marks,
as follows.
\describe{
\item{unmarked point pattern:}{
If the point pattern does not have marks, or if \code{use.marks = FALSE},
then the locations of all points will be plotted
using a single plot character
}
\item{multitype point pattern:}{
If \code{x$marks} is a factor, then
each level of the factor is
represented by a different plot character.
}
\item{continuous marks:}{
If \code{x$marks} is a numeric vector,
the marks are rescaled to the unit interval and
each point is represented by a circle
with \emph{diameter} proportional to the rescaled mark
(if the value is positive) or a square with \emph{side length}
proportional to the absolute value of the rescaled mark
(if the value is negative).
}
\item{other kinds of marks:}{
If \code{x$marks} is neither numeric nor a factor,
then each possible mark will be represented by a
different plotting character. The default is to
represent the \eqn{i}th smallest mark value by
\code{points(..., pch=i)}.
}
}
If there are several columns of marks, and if \code{which.marks} is
missing or \code{NULL}, then
\itemize{
\item
if \code{add=FALSE} and \code{multiplot=TRUE}
the default is to plot all columns of marks, in a series of separate
plots, placed side-by-side. The plotting is coordinated by
\code{\link{plot.listof}}, which calls \code{plot.ppp} to make each of
the individual plots.
\item
Otherwise, only one column of marks can be plotted,
and the default is \code{which.marks=1}
indicating the first column of marks.
}
Plotting of the window \code{Window(x)} is performed by
\code{\link{plot.owin}}. This plot may be modified
through the \code{...} arguments. In particular the
extra argument \code{border} determines
the colour of the window, if the window is not a binary mask.
Plotting of the points themselves is performed
by the function \code{\link{points}}, except for the case of
continuous marks, where it is performed by \code{\link{symbols}}.
Their plotting behaviour may be modified through the \code{...}
arguments.
The argument \code{chars} determines the plotting character
or characters used to display the points (in all cases except
for the case of continuous marks). For an unmarked point pattern,
this should be a single integer or character determining a
plotting character (see \code{par("pch")}).
For a multitype point pattern, \code{chars} should be a vector
of integers or characters, of the same length
as \code{levels(x$marks)}, and then the \eqn{i}th level or type
will be plotted using character \code{chars[i]}.
If \code{chars} is absent, but there is an extra argument
\code{pch}, then this will determine the plotting character for
all points.
The argument \code{cols} determines the colour or colours used to
display the points. For an unmarked point pattern,
\code{cols} should be a character string
determining a colour. For a multitype point pattern, \code{cols}
should be a character vector, of the same length
as \code{levels(marks(x))}: that is, there is one colour for each
possible mark value. The \eqn{i}th level or type will
be plotted using colour \code{cols[i]}. For a point pattern with
continuous marks, \code{cols} can be either a character string
or a character vector specifying colour values: the range of mark
values will be mapped to the specified colours.
If \code{cols} is absent, the colours used to plot the
points may be determined by the extra argument \code{fg}
(for multitype point patterns) or the extra argument \code{col}
(for all other cases). Note that specifying \code{col} will also
apply this colour to the window itself.
The default colour for the points is a semi-transparent grey,
if this is supported by the plot device. This behaviour can be
suppressed (so that the default colour is non-transparent)
by setting \code{spatstat.options(transparent=FALSE)}.
The arguments \code{maxsize}, \code{meansize} and \code{markscale}
incompatible. They control the physical size of the circles and
squares which represent the marks in a point pattern with continuous
marks. The size of a circle is defined as its \emph{diameter};
the size of a square is its side length.
If \code{markscale} is given, then a mark value of \code{m}
is plotted as a circle of diameter \code{m * markscale}
(if \code{m} is positive) or a square of side \code{abs(m) * markscale}
(if \code{m} is negative). If \code{maxsize} is given, then the
largest mark in absolute value, \code{mmax=max(abs(marks(x)))},
will be scaled to have physical size \code{maxsize}.
If \code{meansize} is given, then the
average absolute mark value, \code{mmean=mean(abs(marks(x)))},
will be scaled to have physical size \code{meansize}.
The user can set the default values of these plotting parameters
using \code{\link{spatstat.options}("par.points")}.
To zoom in (to view only a subset of the point pattern at higher
magnification), use the graphical arguments
\code{xlim} and \code{ylim} to specify the rectangular field of view.
The value returned by this plot function is an object of
class \code{"symbolmap"} representing the mapping from mark values
to graphical symbols. See \code{\link{symbolmap}}.
It can be used to make a suitable legend,
or to ensure that two plots use the same graphics map.
}
\section{Removing White Space Around The Plot}{
A frequently-asked question is: How do I remove the white space around
the plot? Currently \code{plot.ppp} uses the base graphics system of
\R, so the space around the plot is controlled by parameters
to \code{\link{par}}. To reduce the white space, change the
parameter \code{mar}. Typically, \code{par(mar=rep(0.5, 4))} is
adequate, if there are no annotations or titles outside the window.
}
\seealso{
\code{\link{iplot}},
\code{\link{ppp.object}},
\code{\link{plot}},
\code{\link{par}},
\code{\link{points}},
\code{\link{plot.owin}},
\code{\link{symbols}}
}
\examples{
plot(cells)
plot(cells, pch=16)
# make the plotting symbols larger (for publication at reduced scale)
plot(cells, cex=2)
# set it in spatstat.options
oldopt <- spatstat.options(par.points=list(cex=2))
plot(cells)
spatstat.options(oldopt)
# multitype
plot(lansing)
# marked by a real number
plot(longleaf)
# just plot the points
plot(longleaf, use.marks=FALSE)
plot(unmark(longleaf)) # equivalent
# point pattern with multiple marks
plot(finpines)
plot(finpines, which.marks="height")
# controlling COLOURS of points
plot(cells, cols="blue")
plot(lansing, cols=c("black", "yellow", "green",
"blue","red","pink"))
plot(longleaf, fg="blue")
# make window purple
plot(lansing, border="purple")
# make everything purple
plot(lansing, border="purple", cols="purple", col.main="purple",
leg.args=list(col.axis="purple"))
# controlling PLOT CHARACTERS for multitype pattern
plot(lansing, chars = 11:16)
plot(lansing, chars = c("o","h","m",".","o","o"))
## multitype pattern mapped to symbols
plot(amacrine, shape=c("circles", "squares"), size=0.04)
plot(amacrine, shape="arrows", direction=c(0,90), size=0.07)
## plot trees as trees!
plot(lansing, shape="arrows", direction=90, cols=1:6)
# controlling MARK SCALE for pattern with numeric marks
plot(longleaf, markscale=0.1)
plot(longleaf, maxsize=5)
plot(longleaf, meansize=2)
# draw circles of diameter equal to nearest neighbour distance
plot(cells \%mark\% nndist(cells), markscale=1, legend=FALSE)
# inspecting the symbol map
v <- plot(amacrine)
v
## variable colours ('cols' not 'col')
plot(longleaf, cols=function(x) ifelse(x < 30, "red", "black"))
## re-using the same mark scale
a <- plot(longleaf)
juveniles <- longleaf[marks(longleaf) < 30]
plot(juveniles, symap=a)
## numerical marks mapped to symbols of fixed size with variable colour
ra <- range(marks(longleaf))
colmap <- colourmap(terrain.colors(20), range=ra)
## filled plot characters are the codes 21-25
## fill colour is indicated by 'bg'
sy <- symbolmap(pch=21, bg=colmap, range=ra)
plot(longleaf, symap=sy)
## or more compactly..
plot(longleaf, bg=terrain.colors(20), pch=21, cex=1)
## clipping
plot(humberside)
B <- owin(c(4810, 5190), c(4180, 4430))
plot(B, add=TRUE, border="red")
plot(humberside, clipwin=B, main="Humberside (clipped)")
}
\author{
\spatstatAuthors.
}
\keyword{spatial}
\keyword{hplot}
