plot.fv: Plot Function Values

Description

Plot method for the class "fv".

Usage

# S3 method for fv
plot(x, fmla, ..., subset=NULL, lty=NULL, col=NULL, lwd=NULL,
           xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL,
           clip.xlim=TRUE, ylim.covers=NULL,
           legend=!add, legendpos="topleft", legendavoid=missing(legendpos),
           legendmath=TRUE, legendargs=list(),
           shade=fvnames(x, ".s"), shadecol="grey",
           add=FALSE, log="",
           mathfont=c("italic", "plain", "bold", "bolditalic"), 
           limitsonly=FALSE, do.plot=TRUE)

Arguments

Value

Invisible: either NULL, or a data frame giving the meaning of the different line types and colours.

Details

This is the plot method for the class "fv".

An object of class "fv" is a convenient way of storing several different statistical estimates of a summary function; see fv.object. The default behaviour, executed by plot(x), displays these different estimates as curves with different colours and line styles, and plots a legend explaining them.

The use of the argument fmla is like plot.formula, but offers some extra functionality.

The left and right hand sides of fmla are evaluated, and the results are plotted against each other (the left side on the \(y\) axis against the right side on the \(x\) axis).

The left and right hand sides of fmla may be the names of columns of the data frame x, or expressions involving these names. If a variable in fmla is not the name of a column of x, the algorithm will search for an object of this name in the environment where plot.fv was called, and then in the enclosing environment, and so on.

Multiple curves may be specified by a single formula of the form cbind(y1,y2,...,yn) ~ x, where x,y1,y2,...,yn are expressions involving the variables in the data frame. Each of the variables y1,y2,...,yn in turn will be plotted against x. See the examples.

Convenient abbreviations which can be used in the formula are

the symbol . which represents all the columns in the data frame that will be plotted by default;
the symbol .x which represents the function argument;
the symbol .y which represents the recommended value of the function.

For further information, see fvnames.

The value returned by this plot function indicates the meaning of the line types and colours in the plot. It can be used to make a suitable legend for the plot if you want to do this by hand. See the examples.

The argument shade can be used to display critical bands or confidence intervals. If it is not NULL, then it should be a subset index for the columns of x, that identifies exactly 2 columns. When the corresponding curves are plotted, the region between the curves will be shaded in light grey. See the Examples.

The default values of lty, col and lwd can be changed using spatstat.options("plot.fv").

Use type = "n" to create the plot region and draw the axes without plotting any curves.

Use do.plot=FALSE to suppress all plotting. The return value is a data frame giving the meaning of the different line types and colours which would have been plotted.

Use limitsonly=TRUE to suppress all plotting and just compute the \(x\) and \(y\) limits. This can be used to calculate common \(x\) and \(y\) scales for several plots.

To change the kind of parenthesis enclosing the explanatory text about the unit of length, use spatstat.options('units.paren')

Examples

Run this code

   K <- Kest(cells)
   # K is an object of class "fv"

   plot(K, iso ~ r)                # plots iso against r

   plot(K, sqrt(iso/pi) ~ r)   # plots sqrt(iso/r)  against r

   plot(K, cbind(iso,theo) ~ r)   # plots iso against r  AND theo against r

   plot(K, .  ~ r)            # plots all available estimates of K against r

   plot(K, sqrt(./pi) ~ r)   # plots all estimates of L-function
                             # L(r) = sqrt(K(r)/pi)

   plot(K, cbind(iso,theo) ~ r, col=c(2,3))
                                   # plots iso against r  in colour 2
                                   # and theo against r in colour 3

   plot(K, iso ~ r, subset=quote(r < 0.2))
                                   # plots iso against r for r < 10

   # Can't remember the names of the columns? No problem..
   plot(K, sqrt(./pi) ~ .x)

   # making a legend by hand
   v <- plot(K, . ~ r, legend=FALSE)
   legend("topleft", legend=v$meaning, lty=v$lty, col=v$col)

   # significance bands
   KE <- envelope(cells, Kest, nsim=19)
   plot(KE, shade=c("hi", "lo"))

   # how to display two functions on a common scale
   Kr <- Kest(redwood)
   a <- plot(K, limitsonly=TRUE)
   b <- plot(Kr, limitsonly=TRUE)
   xlim <- range(a$xlim, b$xlim)
   ylim <- range(a$ylim, b$ylim)
   opa <- par(mfrow=c(1,2))
   plot(K, xlim=xlim, ylim=ylim)
   plot(Kr, xlim=xlim, ylim=ylim)
   par(opa)
   # For a shortcut, try plot(anylist(K, Kr), equal.scales=TRUE)