plot.ppp
plot a Spatial Point Pattern
Plot a two-dimensional spatial point pattern
Usage
# S3 method for ppp
plot(x, main, …, 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
- x
The spatial point pattern to be plotted. An object of class
"ppp"
, or data which can be converted into this format byas.ppp()
.- main
text to be displayed as a title above the plot.
- …
extra arguments that will be passed to the plotting functions
plot.default
,points
and/orsymbols
. Not all arguments will be recognised.- clipwin
Optional. A window (object of class
"owin"
). Only this subset of the image will be displayed.- chars
plotting character(s) used to plot points.
- cols
the colour(s) used to plot points.
- use.marks
logical flag; if
TRUE
, plot points using a different plotting symbol for each mark; ifFALSE
, only the locations of the points will be plotted, usingpoints()
.- which.marks
Index determining which column of marks to use, if the marks of
x
are a data frame. A character or integer vector identifying one or more columns of marks. Ifadd=FALSE
then the default is to plot all columns of marks, in a series of separate plots. Ifadd=TRUE
then only one column of marks can be plotted, and the default iswhich.marks=1
indicating the first column of marks.- add
logical flag; if
TRUE
, just the points are plotted, over the existing plot. A new plot is not created, and the window is not plotted.- type
Type of plot: either
"p"
or"n"
. Iftype="p"
(the default), both the points and the observation window are plotted. Iftype="n"
, only the window is plotted.- legend
Logical value indicating whether to add a legend showing the mapping between mark values and graphical symbols (for a marked point pattern).
- leg.side
Position of legend relative to main plot.
- leg.args
List of additional arguments passed to
plot.symbolmap
orsymbolmap
to control the legend. In addition to arguments documented underplot.symbolmap
, and graphical arguments recognised bysymbolmap
, the list may also include the argumentsep
giving the separation between the main plot and the legend, orsep.frac
giving the separation as a fraction of the relevant dimension (width or height) of the main plot.- symap
Optional. The graphical symbol map to be applied to the marks. An object of class
"symbolmap"
; seesymbolmap
.- maxsize
Maximum physical size of the circles/squares plotted when
x
is a marked point pattern with numerical marks. Incompatible withmeansize
andmarkscale
. Ignored ifsymap
is given.- meansize
Average physical size of the circles/squares plotted when
x
is a marked point pattern with numerical marks. Incompatible withmaxsize
andmarkscale
. Ignored ifsymap
is given.- markscale
physical scale factor determining the sizes of the circles/squares plotted when
x
is a marked point pattern with numerical marks. Mark value will be multiplied bymarkscale
to determine physical size. Incompatible withmaxsize
andmeansize
. Ignored ifsymap
is given.- zap
Fraction between 0 and 1. When
x
is a marked point pattern with numerical marks,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 thanzap * max(abs(marks(x)))
will not be plotted.- show.window
Logical value indicating whether to plot the observation window of
x
.- show.all
Logical value indicating whether to plot everything including the main title and the observation window of
x
.- do.plot
Logical value determining whether to actually perform the plotting.
- multiplot
Logical value giving permission to display multiple plots.
Details
This is the plot
method for
point pattern datasets (of class "ppp"
, see ppp.object
).
First the observation window Window(x)
is plotted
(if show.window=TRUE
).
Then the points themselves are plotted,
in a fashion that depends on their marks,
as follows.
- unmarked point pattern:
If the point pattern does not have marks, or if
use.marks = FALSE
, then the locations of all points will be plotted using a single plot character- multitype point pattern:
If
x$marks
is a factor, then each level of the factor is represented by a different plot character.- continuous marks:
If
x$marks
is a numeric vector, the marks are rescaled to the unit interval and each point is represented by a circle with diameter proportional to the rescaled mark (if the value is positive) or a square with side length proportional to the absolute value of the rescaled mark (if the value is negative).- other kinds of marks:
If
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 \(i\)th smallest mark value bypoints(..., pch=i)
.
If there are several columns of marks, and if which.marks
is
missing or NULL
, then
if
add=FALSE
andmultiplot=TRUE
the default is to plot all columns of marks, in a series of separate plots, placed side-by-side. The plotting is coordinated byplot.listof
, which callsplot.ppp
to make each of the individual plots.Otherwise, only one column of marks can be plotted, and the default is
which.marks=1
indicating the first column of marks.
Plotting of the window Window(x)
is performed by
plot.owin
. This plot may be modified
through the ...
arguments. In particular the
extra argument 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 points
, except for the case of
continuous marks, where it is performed by symbols
.
Their plotting behaviour may be modified through the ...
arguments.
The argument 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 par("pch")
).
For a multitype point pattern, chars
should be a vector
of integers or characters, of the same length
as levels(x$marks)
, and then the \(i\)th level or type
will be plotted using character chars[i]
.
If chars
is absent, but there is an extra argument
pch
, then this will determine the plotting character for
all points.
The argument cols
determines the colour or colours used to
display the points. For an unmarked point pattern,
cols
should be a character string
determining a colour. For a multitype point pattern, cols
should be a character vector, of the same length
as levels(marks(x))
: that is, there is one colour for each
possible mark value. The \(i\)th level or type will
be plotted using colour cols[i]
. For a point pattern with
continuous marks, 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 cols
is absent, the colours used to plot the
points may be determined by the extra argument fg
(for multitype point patterns) or the extra argument col
(for all other cases). Note that specifying 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 spatstat.options(transparent=FALSE)
.
The arguments maxsize
, meansize
and 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 diameter;
the size of a square is its side length.
If markscale
is given, then a mark value of m
is plotted as a circle of diameter m * markscale
(if m
is positive) or a square of side abs(m) * markscale
(if m
is negative). If maxsize
is given, then the
largest mark in absolute value, mmax=max(abs(marks(x)))
,
will be scaled to have physical size maxsize
.
If meansize
is given, then the
average absolute mark value, mmean=mean(abs(marks(x)))
,
will be scaled to have physical size meansize
.
The user can set the default values of these plotting parameters
using spatstat.options("par.points")
.
To zoom in (to view only a subset of the point pattern at higher
magnification), use the graphical arguments
xlim
and ylim
to specify the rectangular field of view.
The value returned by this plot function is an object of
class "symbolmap"
representing the mapping from mark values
to graphical symbols. See symbolmap
.
It can be used to make a suitable legend,
or to ensure that two plots use the same graphics map.
Value
(Invisible) object of class "symbolmap"
giving the correspondence between
mark values and plotting characters.
Removing White Space Around The Plot
A frequently-asked question is: How do I remove the white space around
the plot? Currently plot.ppp
uses the base graphics system of
R, so the space around the plot is controlled by parameters
to par
. To reduce the white space, change the
parameter mar
. Typically, par(mar=rep(0.5, 4))
is
adequate, if there are no annotations or titles outside the window.
Drawing coordinate axes and axis labels
Coordinate axes and axis labels are not drawn, by default.
To draw coordinate axes, set axes=TRUE
.
To draw axis labels, set ann=TRUE
and give values to the
arguments xlab
and ylab
. See the Examples.
Only the default style of axis is supported;
for more control over the placement and style of axes,
use the graphics commands
axis
and mtext
.
See Also
ppp.object
,
plot
,
par
,
points
,
text.ppp
,
plot.owin
,
symbols
.
See also the command iplot
in the spatstat.gui package.
Examples
# NOT RUN {
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)")
## coordinate axes and labels
plot(humberside, axes=TRUE)
plot(humberside, ann=TRUE, xlab="Easting", ylab="Northing")
plot(humberside, axes=TRUE, ann=TRUE, xlab="Easting", ylab="Northing")
# }