\HeaderA{plotHmmStates}{Plotting the estimated hmm states and log2 ratios for each sample.}{plotHmmStates}
\aliasA{plotHmmStatesNew}{plotHmmStates}{plotHmmStatesNew}
\keyword{hplot}{plotHmmStates}
\begin{Description}\relax
This function displays the estimated hmm states and log2 ratios for
each sample.
\end{Description}
\begin{Usage}
\begin{verbatim}
plotHmmStates(aCGH.obj, sample.ind, chr = 1:num.chromosomes(aCGH.obj),
             statesres = hmm.merged(aCGH.obj), maxChrom = 23,
             chrominfo = human.chrom.info.Jul03, yScale = c(-2, 2),
             samplenames = sample.names(aCGH.obj))
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{aCGH.obj}] object of class aCGH
\item[\code{sample.ind}] index of the sample to be plotted relative to the
data matrix (i.e. column index in the file)
\item[\code{statesres}] matrix containing states informations. defaults to the states selected using the first  model selection criterionof \code{aCGH.obj}
\item[\code{chr}] vector of chromosomes to be plotted
\item[\code{yScale}] specified scale for Y-exis
\item[\code{maxChrom}] highest chromosome to show
\item[\code{chrominfo}] a chromosomal information associated with the mapping of the data
\item[\code{samplenames}] vector of sample names
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
Each chromosome is plotted on a separate  page and contains two
figures. The top figure shows the observed log2ratios and the bottom
figure shows predicted values for all clones but outliers which show
observed values. The genomic events are indicated on both figures as
following. The first clone after transition is indicated with solid
blue line and the last clone after transitions is shown with dotted
green line. Focal aberrations clones are colored orange,
amplifications are colored red and outliers are yellow.
\end{Details}
\begin{Author}\relax
Jane Fridlyand
\end{Author}
\begin{References}\relax
Application of Hidden Markov Models to the analysis of the
array CGH data, Fridlyand et.al., \emph{JMVA}, 2004
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{aCGH}{aCGH}}
\code{\LinkA{find.hmm.states}{find.hmm.states}}
\code{\LinkA{plotGenome}{plotGenome}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(colorectal)
plotHmmStates(colorectal, 1)

\end{ExampleCode}
\end{Examples}

