# 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 by`as.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/or`symbols`

.- 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; if`FALSE`

, only the locations of the points will be plotted, using`points()`

.- 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. If`add=FALSE`

then the default is to plot all columns of marks, in a series of separate plots. If`add=TRUE`

then only one column of marks can be plotted, and the default is`which.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"`

. If`type="p"`

(the default), both the points and the observation window are plotted. If`type="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`

or`symbolmap`

to control the legend. In addition to arguments documented under`plot.symbolmap`

, and graphical arguments recognised by`symbolmap`

, the list may also include the argument`sep`

giving the separation between the main plot and the legend, or`sep.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"`

; see`symbolmap`

.- maxsize
*Maximum*physical size of the circles/squares plotted when`x`

is a marked point pattern with numerical marks. Incompatible with`meansize`

and`markscale`

. Ignored if`symap`

is given.- meansize
*Average*physical size of the circles/squares plotted when`x`

is a marked point pattern with numerical marks. Incompatible with`maxsize`

and`markscale`

. Ignored if`symap`

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 by`markscale`

to determine physical size. Incompatible with`maxsize`

and`meansize`

. Ignored if`symap`

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 than`zap * 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 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.

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.

##### See Also

`iplot`

,
`ppp.object`

,
`plot`

,
`par`

,
`points`

,
`text.ppp`

,
`plot.owin`

,
`symbols`

##### 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)")
# }
```

*Documentation reproduced from package spatstat, version 1.62-2, License: GPL (>= 2)*