\name{plot.fv}
\alias{plot.fv}
\title{Plot Function Values}
\description{
  Plot method for the class \code{"fv"}.
}
\usage{
 \method{plot}{fv}(x, fmla, \dots, subset=NULL, lty=NULL, col=NULL, lwd=NULL,
           xlim=NULL, ylim=NULL, xlab=NULL, ylab=NULL, 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)
}
\arguments{
  \item{x}{
    An object of class \code{"fv"}, containing the variables to be plotted
    or variables from which the plotting coordinates can be computed.
  }
  \item{fmla}{
    an R language formula 
    determining which variables or expressions are plotted.
    Either a formula object, or a string that can be parsed as a
    formula.
    See Details.
  }
  \item{subset}{
    (optional) subset of rows of the data frame that will be plotted.
  }
  \item{lty}{
    (optional) numeric vector of values of the graphical parameter
    \code{lty} controlling the line style of each plot.
  }
  \item{col}{
    (optional) numeric vector of values of the graphical parameter
    \code{col} controlling the colour of each plot.
  }
  \item{lwd}{
    (optional) numeric vector of values of the graphical parameter
    \code{lwd} controlling the line width of each plot.
  }
  \item{xlim}{
    (optional) range of x axis
  }
  \item{ylim}{
    (optional) range of y axis
  }
  \item{xlab}{
    (optional) label for x axis
  }
  \item{ylab}{
    (optional) label for y axis
  }
  \item{\dots}{
    Extra arguments passed to \code{plot.default}.
  }
  \item{ylim.covers}{
    Optional vector of \eqn{y} values that must be included in the
    \eqn{y} axis. For example \code{ylim.covers=0} will ensure that the
    \eqn{y} axis includes the origin.
  }
  \item{legend}{
    Logical flag or \code{NULL}. If \code{legend=TRUE}, the algorithm
    plots a legend in the top left corner of the plot,
    explaining the meaning of the different line types and colours.
  }
  \item{legendpos}{
    The position of the legend. Either a character string keyword
    (see \code{\link[graphics]{legend}} for keyword options)
    or a pair of coordinates in the format \code{list(x,y)}.
    Alternatively if \code{legendpos="float"}, a location will be
    selected inside the plot region, avoiding the graphics.
  }
  \item{legendavoid}{
    Whether to avoid collisions between the legend and the graphics.
    Logical value.
    If \code{TRUE}, the code will check for collisions between the
    legend box and the graphics, and will override \code{legendpos}
    if a collision occurs.
    If \code{FALSE}, the value of \code{legendpos} is always respected.
  }
  \item{legendmath}{
    Logical. If \code{TRUE}, the legend will display the
    mathematical notation for each curve. If \code{FALSE}, the legend text
    is the identifier (column name) for each curve.
  }
  \item{legendargs}{
    Named list containing additional arguments to be passed to
    \code{\link{legend}} controlling the appearance of the legend.
  }
  \item{shade}{
    A character vector giving the names of two columns of \code{x},
    or another type of index that identifies two columns.
    When the corresponding curves are plotted,
    the region between the curves will be shaded in light grey.
    The object \code{x} may or may not contain two columns which are designated
    as boundaries for shading; they are identified by \code{fvnames(x, ".s")}.
    The default is to shade between these two curves
    if they exist. To suppress this behaviour, set \code{shade=NULL}.
  }
  \item{shadecol}{
    The colour to be used in the \code{shade} plot.
    A character string or an integer specifying a colour.
  }
  \item{add}{
    Logical. Whether the plot should be added to an existing plot
  }
  \item{log}{
    A character string which contains \code{"x"} if the x axis is to
    be logarithmic, \code{"y"} if the y axis is to be logarithmic and
    \code{"xy"} or \code{"yx"} if both axes are to be logarithmic.
  }
  \item{mathfont}{
    Character string. The font to be used for mathematical
    expressions in the axis labels and the legend.
  }
  \item{limitsonly}{
    Logical. If \code{FALSE}, plotting is performed normally.
    If \code{TRUE}, no plotting is performed at all; 
    just the \eqn{x} and \eqn{y} limits of the plot are computed
    and returned. 
  }
}
\value{
  Invisible: either \code{NULL}, or a data frame giving the meaning of the
  different line types and colours.
}
\details{
  This is the \code{plot} method for the class \code{"fv"}.

  An object of class \code{"fv"} is a convenient way of storing several different
  statistical estimates of a summary function; see \code{\link{fv.object}}.
  The default behaviour, executed by \code{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 \code{fmla} is like \code{plot.formula}, but offers
  some extra functionality.

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

  The left and right hand sides of \code{fmla} may be
  the names of columns of the data frame \code{x},
  or expressions involving these names. If a variable in \code{fmla}
  is not the name of a column of \code{x}, the algorithm will search for
  an object of this name in the environment where \code{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 
  \code{cbind(y1,y2,\dots,yn) ~ x}, where \code{x,y1,y2,\dots,yn} are
  expressions involving the variables in the data frame.
  Each of the variables \code{y1,y2,\dots,yn} in turn will be plotted
  against \code{x}. 
  See the examples.

  Convenient abbreviations which can be used in the formula
  are 
  \itemize{
    \item the symbol \code{.} which represents all the
    columns in the data frame that will be plotted by default;
    \item the symbol \code{.x} which represents the function argument;
    \item the symbol \code{.y} which represents the recommended value
    of the function.
  }
  For further information, see \code{\link{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 \code{shade} can be used to display critical bands
  or confidence intervals. If it is not \code{NULL}, then it should be
  a subset index for the columns of \code{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 \code{lty}, \code{col} and \code{lwd} can
  be changed using \code{\link{spatstat.options}("plot.fv")}.

  Use \code{type = "n"} to create the plot region and draw the axes
  without plotting any data.

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

  To change the kind of parenthesis enclosing the
  explanatory text about the unit of length, use
  \code{\link{spatstat.options}('units.paren')}
}
\examples{
   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)
}
\seealso{
  \code{\link{fv.object}},
  \code{\link[spatstat.explore]{Kest}}
}
\author{
  \adrian
  and \rolf
}
\keyword{spatial}
\keyword{hplot}
 
