\inputencoding{latin1}
\HeaderA{plotProfile}{Plot genomic profile and cytogenetic banding}{plotProfile}
\methaliasA{plotProfile.profileCGH}{plotProfile}{plotProfile.profileCGH}
\keyword{hplot}{plotProfile}
\begin{Description}\relax
Plot genomic profile with breakpoints, outliers, smoothing
line and cytogenetic banding.
\end{Description}
\begin{Usage}
\begin{verbatim}

## S3 method for class 'profileCGH':
plotProfile(profileCGH, variable="LogRatio", Chromosome=NULL,
                       Smoothing=NULL, GNL="ZoneGNL", Bkp=FALSE,
                       labels=TRUE, plotband=TRUE, unit=0,
                       colDAGLAD=c("black","blue","red","green","yellow"),
                       pchSymbol=c(20,13),
                       colCytoBand=c("white","darkblue"),
                       colCentro="red", text=NULL, main="", ylim=NULL, ...)



\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{profileCGH}] Object of class \code{\LinkA{profileCGH}{profileCGH}}
\item[\code{variable}] The variable to be plot.
\item[\code{Chromosome}] A numeric vector with chromosome number to be
plotted. Use 23 and 24 for chromosome X and Y respectively. If
\code{NULL}, all the genome is plotted.
\item[\code{Smoothing}] The variable used to plot the smoothing line. If
\code{NULL}, nothing is plotted.
\item[\code{GNL}] The variable used to plot the Gain, Normal and Loss color code.
\item[\code{Bkp}] If \code{TRUE}, the breakpoints are represented by a
vertical red dashed line.
\item[\code{labels}] If \code{TRUE}, the labels of the cytogenetic banding
are written.
\item[\code{plotband}] If \code{TRUE}, the cytogenetic banding are plotted.
\item[\code{unit}] Give the unit of the PosBase. For example if \code{unit=3},
PosBase are in Kb, if \code{unit=6}, PosBase are in Mb, ...
\item[\code{colDAGLAD}] Color code to plot Deletion, Amplification, Gain,
Lost and Normal status.
\item[\code{pchSymbol}] A vector of two elements to specify the symbol tu be
used for plotting point. pchSymbol[2] is the symbol for outliers.
\item[\code{colCytoBand}] Color code for cytogenetic banding.
\item[\code{colCentro}] Color code for centromere.
\item[\code{text}] A list with the parameters to be passed to the function
\code{\LinkA{text}{text}}.
\item[\code{main}] title of the plot.
\item[\code{ylim}] range of the y-axis
\item[\code{...}] 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
" "
\end{Details}
\begin{Value}
A plot
\end{Value}
\begin{Note}\relax
People interested in tools dealing with array CGH analysis can
visit our web-page \url{http://bioinfo.curie.fr}.
\end{Note}
\begin{Author}\relax
Philippe Hupé, \email{glad@curie.fr}.
\end{Author}
\begin{SeeAlso}\relax
" "
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

### Cytogenetic banding information
data(cytoband)

###
data(snijders)

### Creation of "profileCGH" object
profileCGH <- as.profileCGH(gm13330)


###########################################################
###
###  glad function as described in Hupé et al. (2004)
###
###########################################################

res <- glad(profileCGH, mediancenter=FALSE,
                smoothfunc="lawsglad", bandwidth=10, round=2,
                model="Gaussian", lkern="Exponential", qlambda=0.999,
                base=FALSE,
                lambdabreak=8, lambdacluster=8, lambdaclusterGen=40,
                type="tricubic", param=c(d=6),
                alpha=0.001, msize=5,
                method="centroid", nmax=8,
                verbose=FALSE)

### Genomic profile on the whole genome
plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing="Smoothing", plotband=FALSE)

### Genomic profile on the whole genome and cytogenetic banding
plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing="Smoothing")

### Genomic profile for chromosome 1
text <- list(x=c(90000,200000),y=c(0.15,0.3),labels=c("NORMAL","GAIN"), cex=2)
plotProfile(res, unit=3, Bkp=TRUE, labels=TRUE, Chromosome=1,
Smoothing="Smoothing", plotband=FALSE, text=text)

### Genomic profile for chromosome 1 and cytogenetic banding with labels
text <- list(x=c(90000,200000),y=c(0.15,0.3),labels=c("NORMAL","GAIN"), cex=2)
plotProfile(res, unit=3, Bkp=TRUE, labels=TRUE, Chromosome=1,
Smoothing="Smoothing", text=text, main="Chromosome 1")


\end{ExampleCode}
\end{Examples}

