\HeaderA{report.plot}{Array image and a genomic representation of a normalized arrayCGH}{report.plot}
\methaliasA{report.plot.arrayCGH}{report.plot}{report.plot.arrayCGH}
\methaliasA{report.plot.default}{report.plot}{report.plot.default}
\keyword{hplot}{report.plot}
\begin{Description}\relax
Displays an array image and a genomic representation of a normalized arrayCGH.
\end{Description}
\begin{Usage}
\begin{verbatim}
## S3 method for class 'arrayCGH':
report.plot(arrayCGH, x="PosOrder", y=c("LogRatioNorm",
  "LogRatio"), chrLim=NULL, layout=TRUE, main=NULL, zlim=NULL, ...)
## Default S3 method:
report.plot(spot.data, clone.data, design, x="PosOrder",
  y=c("LogRatioNorm", "LogRatio"), chrLim=NULL, layout=TRUE, main=NULL,
  zlim=NULL, ...) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arrayCGH}] an object of type \code{arrayCGH}.
\item[\code{spot.data}] data.frame with spot-level information to be passed
to arrayPlot.
\item[\code{clone.data}] data.frame with clone-level information to be passed
to genome.plot.
\item[\code{design}] vector of length 4 with array design: number of blocks
per column and per row, number of columns and rows per block.
\item[\code{x}] a variable name from arrayCGH\$cloneValues giving the order position
of the clones along the genome.
\item[\code{y}] a vector of one or two variable names to be plotted on the
array and along the genome. The first one is taken from
\code{arrayCGH\$arrayValues} and is plotted on the array; the second
one (or the first one if only one name was provided) is taken from
\code{arrayCGH\$cloneValues} and is plotted along the genome.
\item[\code{chrLim}] an optional variable name from arrayCGH\$cloneValues
giving the limits of each chromosome.
\item[\code{layout}] if \code{TRUE}, plot layout is set to a 1*2 matrix with
relative column widths 1 and 4.
\item[\code{main}] title for the genomic profile.
\item[\code{zlim}] numeric vector of length 2 to be passed to
\code{\LinkA{arrayPlot}{arrayPlot}}: minimum and maximum signal values for
array image display.
\item[\code{...}] further arguments to be passed to \code{\LinkA{genome.plot}{genome.plot}}.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function successively calls \code{\LinkA{arrayPlot}{arrayPlot}} and \code{\LinkA{genome.plot}{genome.plot}}.
\end{Details}
\begin{Note}\relax
People interested in tools for array-CGH analysis can
visit our web-page: \url{http://bioinfo.curie.fr}.
\end{Note}
\begin{Author}\relax
Pierre Neuvial, \email{manor@curie.fr}.
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{genome.plot}{genome.plot}}, \code{\LinkA{arrayPlot}{arrayPlot}}, \code{\LinkA{html.report}{html.report}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(spatial)

### edge: local spatial bias
## aggregate arrayCGH without normalization for comparison with
## normalized array
edge.nonorm <- norm(edge, flag.list=NULL, FUN=median, na.rm=TRUE) 
edge.nonorm <- sort(edge.nonorm, position.var="PosOrder")

layout(matrix(c(1,2,4,5,3,3,6,6), 4,2),width=c(1, 4), height=c(6,1,6,1))
report.plot(edge.nonorm, chrLim="LimitChr", layout=FALSE,
main="Pangenomic representation (before normalization)", zlim=c(-1,1),
ylim=c(-3,1))  
report.plot(edge.norm, chrLim="LimitChr", layout=FALSE,
main="Pangenomic representation (after normalization)", zlim=c(-1,1),
ylim=c(-3,1)) 

### gradient: global array Trend
## aggregate arrayCGH without normalization for comparison with
## normalized array
gradient.nonorm <- norm(gradient, flag.list=NULL, FUN=median, na.rm=TRUE) 
gradient.nonorm <- sort(gradient.nonorm)

layout(matrix(c(1,2,4,5,3,3,6,6), 4,2),width=c(1, 4), height=c(6,1,6,1))
report.plot(gradient.nonorm, chrLim="LimitChr", layout=FALSE,
main="Pangenomic representation (before normalization)", zlim=c(-2,2),
ylim=c(-3,2)) 
report.plot(gradient.norm, chrLim="LimitChr", layout=FALSE,
main="Pangenomic representation (after normalization)", zlim=c(-2,2),
ylim=c(-3,2)) 
\end{ExampleCode}
\end{Examples}

