R: Plot a List of Things

plot.listof {spatstat} | R Documentation

## Plot a List of Things

### Description

Plots a list of things

### Usage

      ## S3 method for class 'listof'
    plot(x, ..., 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, panel.vpad=0.2,
       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

`x` | An object of the class `"listof"`. Essentially a list of objects.
`...` | Arguments passed to `plot` when generating each plot panel.
`main` | Overall heading for the plot.
`arrange` | Logical flag indicating whether to plot the objects side-by-side on a single page (`arrange=TRUE`) or plot them individually in a succession of frames (`arrange=FALSE`).
`nrows,ncols` | Optional. The number of rows/columns in the plot layout (assuming `arrange=TRUE`). You can specify either or both of these numbers.
`main.panel` | Optional. A character string, or a vector of character strings, giving the headings for each of the objects.
`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 Spacing between plots.
`hsep,vsep` | Additional horizontal and vertical separation between plot panels, expressed in the same units as `mar.panel`.
`panel.begin,panel.end` | Optional. Functions that will be executed before and after each panel is plotted. See Details.
`panel.args` | Optional. Function that determines different plot arguments for different panels. See Details.
`panel.begin.args` | Optional. List of additional arguments for `panel.begin` when it is a function.
`panel.end.args` | Optional. List of additional arguments for `panel.end` when it is a function.
`panel.vpad` | Amount of extra vertical space that should be allowed for the title of each panel, if a title will be displayed. Expressed as a fraction of the height of the panel. Applies only when `equal.scales=FALSE` (the default) and requires that the height of each panel can be determined.
`plotcommand` | Optional. Character string containing the name of the command that should be executed to plot each panel.
`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.
`adorn.size` | Relative width (as a fraction of the other panels' widths) of the margin plots.
`equal.scales` | Logical value indicating whether the components should be plotted at (approximately) the same physical scale.
`halign,valign` | Logical values indicating whether panels in a column should be aligned to the same x coordinate system (`halign=TRUE`) and whether panels in a row should be aligned to the same y coordinate system (`valign=TRUE`). These are applicable only if `equal.scales=TRUE`.

### Details

This is the `plot` method for the class `"listof"`.

An object of class `"listof"` (defined in the base R package) represents a list of objects, all belonging to a common class. The base R package defines a method for printing these objects, `print.listof`, but does not define a method for `plot`. So here we have provided a method for `plot`.

In the spatstat package, various functions produce an object of class `"listof"`, essentially a list of spatial objects of the same kind. These objects can be plotted in a nice arrangement using `plot.listof`. See the Examples.

The argument `panel.args` determines extra graphics parameters for each panel. It should be a function that will be called as `panel.args(i)` where `i` is the panel number. Its return value should be a list of graphics parameters that can be passed to the relevant `plot` method. These parameters override any parameters specified in the `...` arguments.

The arguments `panel.begin` and `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 `plot` command. Alternatively they may be functions that will be called as `panel.begin(i, y, main=main.panel[i])` and `panel.end(i, y, add=TRUE)` where `i` is the panel number and `y = x[[i]]`.

If all entries of `x` are pixel images, the function `image.listof` is called to control the plotting. The arguments `equal.ribbon` and `col` can be used to determine the colour map or maps applied.

If `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 `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 `x`. This means that the objects will be plotted at 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 exactly equal physical scales, and exactly aligned on the device, under the following conditions:

- every component of `x` is a spatial object whose position can be shifted by `shift`;

- `panel.begin` and `panel.end` are either `NULL` or they are spatial objects whose position can be shifted by `shift`;

- `adorn.left`, `adorn.right`, `adorn.top` and `adorn.bottom` are all `NULL`.

Another special case is when every component of `x` is an object of class `"fv"` representing a function. If `equal.scales=TRUE` then all these functions will be plotted with the same axis scales (i.e. with the same `xlim` and the same `ylim`).

### Value

Null.

### Spacing between plots

The spacing between individual plots is controlled by the parameters `mar.panel`, `hsep` and `vsep`.

If `equal.scales=FALSE`, the plot panels are logically separate plots. The margins for each panel are determined by the argument `mar.panel` which becomes the graphics parameter `mar` described in the help file for `par`. One unit of `mar` corresponds to one line of text in the margin. If `hsep` or `vsep` are present, `mar.panel` is augmented by `c(vsep, hsep, vsep, hsep)/2`.

If `equal.scales=TRUE`, all the plot panels are drawn in the same coordinate system which represents a physical scale. The unit of measurement for `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 `mar.panel[2,4]` is one-sixth of the greatest width of any object plotted in the same column of panels. If `hsep` or `vsep` are present, they are interpreted in the same units as `mar.panel[2]` and `mar.panel[1]` respectively.

### Error messages

If the error message ‘Figure margins too large’ occurs, this generally means that one of the objects had a much smaller physical scale than the others. Ensure that `equal.scales=FALSE` and increase the values of `mar.panel`.

### Author(s)

Adrian Baddeley Adrian.Baddeley@curtin.edu.au

and Rolf Turner r.turner@auckland.ac.nz

### See Also

`print.listof`, `contour.listof`, `image.listof`, `density.splitppp`

### Examples

    # Intensity estimate of multitype point pattern
     plot(D <- density(split(amacrine)))
     plot(D, main="", equal.ribbon=TRUE,
          panel.end=function(i,y,...){contour(y, ...)})

    # 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')

[Package spatstat version 1.54-0 Index]