plot.ppp | R Documentation |
Plot a two-dimensional spatial point pattern
## S3 method for class '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,
minsize=NULL, zerosize=NULL,
zap=0.01,
show.window=show.all, show.all=!add, do.plot=TRUE,
multiplot=TRUE)
x |
The spatial point pattern to be plotted.
An object of class |
main |
text to be displayed as a title above the plot. |
... |
extra arguments that will be passed to the plotting functions
|
clipwin |
Optional. A window (object of class |
chars |
the plotting character(s) used to plot points.
Either a single character, an integer,
or a vector of single characters or integers.
Ignored if |
cols |
the colour(s) used to plot points.
Either an integer index from 1 to 8 (indexing the standard colour
palette), a character string giving the name of a colour,
or a string giving the hexadecimal representation of a colour,
or a vector of such integers or strings.
See the section on Colour Specification in the help for |
use.marks |
logical flag; if |
which.marks |
Index determining which column of marks to use,
if the marks of |
add |
logical flag; if |
type |
Type of plot: either |
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 |
symap |
The graphical symbol map to be applied to the marks.
An object of class |
maxsize |
Maximum physical size of the circles/squares plotted
when |
meansize |
Average physical size of the circles/squares plotted
when |
markscale |
physical scale factor determining the sizes of the
circles/squares plotted when |
minsize |
Minimum physical size of the circles/squares plotted
when |
zerosize |
Physical size of the circle/square representing a mark value of zero,
when |
zap |
Fraction between 0 and 1.
When |
show.window |
Logical value indicating whether to plot the observation
window of |
show.all |
Logical value indicating whether to plot everything
including the main title and the observation window of |
do.plot |
Logical value determining whether to actually perform the plotting. |
multiplot |
Logical value giving permission to display multiple plots. |
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.
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
If marks(x)
is a factor, then
each level of the factor is
represented by a different plot character.
If marks(x)
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).
If marks(x)
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 by
points(..., pch=i)
.
If there are several columns of marks, and if which.marks
is
missing or NULL
, then
if add=FALSE
and 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
plot.listof
, which calls plot.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.
If the argument symap
is given, then it determines the
graphical display of the points. It should be a symbol map
(object of class "symbolmap"
) created by the function
symbolmap
.
If symap
is not given, then the
following arguments can be used to specify how the points are plotted:
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(marks(x))
, 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
are incompatible with each other (and incompatible with
symap
).
The arguments minsize
and zerosize
are incompatible
with each other (and incompatible with symap
).
Together, these arguments 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 + zerosize
(if m
is positive) or a square of side
abs(m) * markscale + zerosize
(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
.
If minsize
is given, then the
minimum mark value, mmean=mean(abs(marks(x)))
,
will be scaled to have physical size minsize
.
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.
(Invisible) object of class "symbolmap"
giving the correspondence between
mark values and plotting characters.
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.
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
.
The behaviour of plot.ppp
is different from the
behaviour of the base R graphics functions
points
and symbols
.
In the base graphics functions points
and symbols
,
arguments such as col
, pch
and cex
can be vectors which specify the representation of each successive point.
For example col[3]
would specify the colour of the third point
in the sequence of points. If there are 100 points then
col
should be a vector of length 100.
In the spatstat function plot.ppp
,
arguments such as col
, pch
and cex
specify
the mapping from point characteristics to graphical parameters
(called the symbol map).
For example col[3]
specifies the colour of the third type of point in a
pattern of points of different types. If there are 4 types of points
then col
should be a vector of length 4.
To modify a symbol map, for example to change the colours used
without changing anything else, use update.symbolmap
.
.
ppp.object
,
plot
,
par
,
points
,
text.ppp
,
plot.owin
,
symbols
.
See also the command iplot
in the spatstat.gui package.
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)
plot(longleaf, minsize=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'
## outline colour is 'fg'
sy <- symbolmap(pch=21, bg=colmap, fg=colmap, range=ra)
plot(longleaf, symap=sy)
## or more compactly..
plot(longleaf, bg=terrain.colors(20), pch=21, cex=1)
## plot only the colour map (since the symbols have fixed size and shape)
plot(longleaf, symap=sy, leg.args=list(colour.only=TRUE))
## 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")
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