\HeaderA{plot.monomvn}{Plotting bmonomvn output}{plot.monomvn}
\keyword{hplot}{plot.monomvn}
\begin{Description}\relax
Functions for visualizing the output from \code{\LinkA{bmonomvn}{bmonomvn}},
particularly the posterior standard deviation estimates of the mean
vector and covariance matrix, and samples from the solution to a
Quadratic Program
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'monomvn':
plot(x, which=c("mu", "S", "Snz", "Sinz", "QP"),
     xaxis=c("numna", "index"), main=NULL, uselog=FALSE, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a \code{"monomvn"}-class object that must be named \code{x}
for generic plotting 
\item[\code{which}] determines the parameter whose standard deviation
to be visualized: the mean vector (\code{"mu"} for \code{sqrt(\$mu.var)});
the covariance \code{matrix} (\code{"S"} for \code{sqrt(\$S.var)}),
or \code{"S\{i\}nz"} for \code{sqrt(\$S\{i\}.nz)}, which both result in
an \code{\LinkA{image}{image}} plot; or the distribution of solutions
\code{\$W} to a Quadratic Program that may be obtained by
supplying \code{QP = TRUE} as input to \code{\LinkA{bmonomvn}{bmonomvn}} 
\item[\code{xaxis}] indicates how x-axis (or x- and y-axis in the case
of \code{which = "S" || "S\{i\}nz"}) should be displayed.  The default option
\code{"numna"} shows the (ordered) number of missing entries
(\code{NA}s) in the corresponding column, whereas \code{"index"}
simply uses the column index; see details below 
\item[\code{main}] optional text to be added to the main title of the plots;
the default of \code{NULL} causes the automatic generation of a
title 
\item[\code{uselog}] a logical which, when \code{TRUE}, causes the log
of the standard deviation to be plotted instead 
\item[\code{...}] passed to \code{\LinkA{plot.default}{plot.default}}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Currently, this function only provides a visualization of the
posterior standard deviation estimates of the parameters, and
the distributions of samples from the posterior of the solution
to a specified Quadratic Program.  Therefore
it only works on the output from \code{\LinkA{bmonomvn}{bmonomvn}}

All types of visualization (specified by \code{which}) are presented
in the order of the number of missing entries in the columns of the
data passed as input to  \code{\LinkA{bmonomvn}{bmonomvn}}.
In the case of \code{which = "mu"}
this means that y-values are presented in the order \code{x\$o}, where
the x-axis is either \code{1:length(x\$o)} in the case of
\code{xaxis = "index"}, or \code{x\$na[x\$o]} in the case of \code{xaxis
    = "numna"}.  When \code{which = "S"} is given the resulting
\code{\LinkA{image}{image}} plot is likewise ordered by \code{x\$o} where the
x- and y-axis are as above, except that in the case
where \code{xaxis = "numna"} the repeated counts of \code{NA}s are
are adjusted by small increments so that x and y arguments to
\code{\LinkA{image}{image}} are distinct.  Since a \code{\LinkA{boxplot}{boxplot}} is
used when \code{which = "QP"} it may be that \code{xaxis = "index"}
is preferred
\end{Details}
\begin{Value}
The only output of this function is beautiful plots
\end{Value}
\begin{Author}\relax
Robert B. Gramacy \email{bobby@statslab.cam.ac.uk}
\end{Author}
\begin{References}\relax
\url{http://www.statslab.cam.ac.uk/~bobby/monomvn.html}
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{bmonomvn}{bmonomvn}}, \code{\LinkA{print.monomvn}{print.monomvn}},
\code{\LinkA{summary.monomvn}{summary.monomvn}}
\end{SeeAlso}

