\HeaderA{plotAlongChromLegend}{Plot a legend for genomic features}{plotAlongChromLegend}
\keyword{hplot}{plotAlongChromLegend}
\begin{Description}\relax
Plot a legend for genomic features
\end{Description}
\begin{Usage}
\begin{verbatim}
plotAlongChromLegend(vpr, nr=2, 
    featureColorScheme=1, 
    featureExclude=c("chromosome", "nucleotide_match", "insertion"),
    mainLegend, cexLegend=0.35, cexMain=1)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{vpr}] vector specifying where to place the legend in figure (set up by using the 
\code{viewport} function from the grid package.  When this function is called directly 
by the user this argument should be left missing.
\item[\code{nr}] numeric scalar, specifying the number of rows to plot legend over 
(default value is 2).
\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
\code{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{mainLegend}] character vector specifying legend title.
\item[\code{cexLegend}] numeric scalar specifying the magnification to be used for the legend 
text relative to the current text size.
\item[\code{cexMain}] numeric scalar specifying the magnification to be used for the legend 
title relative to the current text size.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function is usually called by \code{plotAlongChrom} when \code{doLegend} is TRUE.  It can also be called directly by the user to produce a separate legend.  

The following features are included in the legend (unless excluded using the \code{featuredExclude} option): \code{"chromosome"}, \code{"nucleotide\_match"}, \code{"pseudogene"}, \code{"uORF"}, \code{"nc\_primary\_transcript"}, \code{"region"}, \code{"repeat\_family"}, \code{"repeat\_region"}, \code{"transposable\_element"}, \code{"transposable\_element\_gene"}, \code{"ARS"}, \code{"centromere"}, \code{"telomere"}, \code{"insertion"}, \code{"CDS"}, \code{"CDS\_dubious"}, \code{"ncRNA"}, \code{"tRNA"}, \code{"snRNA"}, \code{"rRNA"}, \code{"snoRNA"}, \code{"binding\_site"} and \code{"TF\_binding\_site"}.
\end{Details}
\begin{Author}\relax
Wolfgang Huber <huber@ebi.ac.uk>
\end{Author}
\begin{Examples}
\begin{ExampleCode}## plotAlongChromLegend(mainLegend="Legend")\end{ExampleCode}
\end{Examples}

