\HeaderA{genome.plot}{Pan-genomic representation of a normalized arrayCGH}{genome.plot}
\methaliasA{genome.plot.arrayCGH}{genome.plot}{genome.plot.arrayCGH}
\methaliasA{genome.plot.default}{genome.plot}{genome.plot.default}
\begin{Description}\relax
Displays a pan-genomic representation of a normalized arrayCGH.
\end{Description}
\begin{Usage}
\begin{verbatim}
  ## S3 method for class 'arrayCGH':
  genome.plot(arrayCGH, x="PosOrder", y="LogRatio",
    chrLim=NULL, col.var=NULL, clim=NULL, cex=NULL, pch=NULL, ...)  
  ## Default S3 method:
  genome.plot(data, pch=NULL, cex=NULL, xlab="", ylab="", ...)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arrayCGH}] an object of type \code{arrayCGH}
\item[\code{data}] a data frame with two columns: 'x' and 'y', and optionally
a column data\$chrLim giving the limits of each chromosome
\item[\code{x}] a variable name from \code{arrayCGH\$cloneValues} giving the order position
of the clones along the genome (defaults to 'PosOrder')
\item[\code{y}] a variable name from \code{arrayCGH\$cloneValues} to be plotted along the
genome (defaults to 'LogRatio')
\item[\code{chrLim}] an optional variable name from \code{arrayCGH\$cloneValues}
giving the limits of each chromosome
\item[\code{col.var}] a variable name from \code{arrayCGH\$cloneValues}
defining the color legend
\item[\code{clim}] a numeric vector of length 2: color range limits (used if \code{col.var} is numeric)
\item[\code{cex}] a numerical value giving the amount by which plotting text
and symbols should be scaled relative to the default: see \code{\LinkA{par}{par}}
\item[\code{xlab}] a title for the x axis: see \code{\LinkA{title}{title}}
\item[\code{ylab}] a title for the y axis: see \code{\LinkA{title}{title}}
\item[\code{pch}] either an integer specifying a symbol or a single character
to be used as the default in plotting points: see \code{\LinkA{par}{par}} 
\item[\code{...}] further arguments to be passed to \code{plot}
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
if \code{col.var} is a numeric variable, \code{y} colors are
proportionnal to \code{col.var} values; if it is a character variable
or a factor, one color is assigned to each different value of
\code{col.var}. If \code{col.var} is NULL, colors are proportionnal to
\code{y} values.
\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{flag}{flag}}, \code{\LinkA{report.plot}{report.plot}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(spatial)

## default color code: log-ratios
## Not run: 
genome.plot(edge.norm, chrLim="LimitChr")
## End(Not run)

## color code determined by a qualitative variable: ZoneGNL (DNA copy number code)
edge.norm$cloneValues$ZoneGNL <- as.factor(edge.norm$cloneValues$ZoneGNL)
## Not run: 
genome.plot(edge.norm, col.var="ZoneGNL")
## End(Not run)
## comparing profiles with and without normalization
## aggregate data without normalization (flags)

gradient.nonorm <- norm.arrayCGH(gradient, flag.list=NULL, var="LogRatio",
FUN=median, na.rm=TRUE)
gradient.nonorm <- sort.arrayCGH(gradient.nonorm)

## Not run: 
genome.plot(gradient.nonorm, pch=20, main="Genomic profile without
normalization", chrLim="LimitChr")   
x11()
genome.plot(gradient.norm, pch=20, main="Genomic profile with
normalization", chrLim="LimitChr")   
## End(Not run)
\end{ExampleCode}
\end{Examples}

