\HeaderA{plotFeatures}{Plot genomic features for a region along a chromosome}{plotFeatures}
\keyword{hplot}{plotFeatures}
\begin{Description}\relax
Plot genomic features for a region along a chromosome
\end{Description}
\begin{Usage}
\begin{verbatim}
plotFeatures(gff, chr, xlim, strand, vpr, featureColorScheme=1, 
             featureExclude=c("chromosome", "nucleotide_match", "insertion"),            
             featureNoLabel=c("uORF", "CDS"), ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{gff}] data frame with genome annotation from the GFF file.
\item[\code{chr}] integer of length 1 specifying the chromosome to plot the features for.
\item[\code{xlim}] integer of length 2 with start and end coordinates (in bases) for plotting.
\item[\code{strand}] character scalar which should be set to either \code{+} or \code{-} to 
indicate which strand of DNA to plot the features from.
\item[\code{vpr}] which viewport to plot the features in.
\item[\code{featureColorScheme}] numeric scalar, used to select a color scheme for the 
boxes representing genomic features such as coding sequences, ncRNAs etc. 
Currently the only value supported is 1.
\item[\code{featureExclude}] character vector of names of feature types (in
gff) that should not be plotted. Default is \code{"chromosome"}, \code{"nucleotide\_match"} and 
\code{"insertion"}.  Additional possible candidates include: \code{"ARS"}, \code{"repeat\_region"},
\code{"repeat\_family"} and \code{"nc\_primary\_transcript"}.
\item[\code{featureNoLabel}] character vector, names of feature types (in
gff) that should not be labelled with their names (if they are plotted).
\item[\code{...}] additional arguments.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function is called by \code{plotAlongChrom} when the \code{gff} argument has been specified.  It should not be called directly by the user.
\end{Details}
\begin{Author}\relax
Wolfgang Huber <huber@ebi.ac.uk>
\end{Author}
\begin{Examples}
\begin{ExampleCode}\end{ExampleCode}
\end{Examples}

