\HeaderA{xmap.plot}{Utility methods for quick graph generation}{xmap.plot}
\aliasA{xmap.points}{xmap.plot}{xmap.points}
\begin{Description}\relax
These methods attempt to provide a simpler interface for generating X:Map graphs.
\end{Description}
\begin{Usage}
\begin{verbatim}
  xmap.plot( x, y, species=c("homo_sapiens","mus_musculus","rattus_norvegicus"), 
             chr, xlim, ylim, main, sub, 
             type=c("scatter", "line", "bar", "step", "area", "steparea"), 
             xlab, ylab = "value", col, dp=2, projectid )
  xmap.points( x, y, type=c("scatter", "line", "bar", "step", "area", "steparea"),
             xlab, col, dp=2, graphid )
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] The points for the x-axis of this plot.  These points must be offsets from the start of the graph, and not their actual chromosomal location 
\item[\code{y}] The points for the y-axis of this plot.  Points where min\textgreater{}y or y \textgreater{}max will not be displayed 
\item[\code{species}] The species that this graph is to be drawn on 
\item[\code{chr}] A string representing the chromosome this graph is to be drawn on 
\item[\code{xlim}] A range object describing the min and max BP for this graph.  If ommitted, we call range on the x parameter 
\item[\code{ylim}] The maximum and minimum Y value for the graph.  If ommitted, we call range on the y parameter 
\item[\code{main}] The main title 
\item[\code{sub}] A sub-title for this graph 
\item[\code{type}] The type of graph you wish to draw 
\item[\code{xlab}] The label for this plot 
\item[\code{ylab}] The label for the yaxis of this graph 
\item[\code{col}] The colour of the graph defined as an integer in the format 0xAARRGGBB.  See \code{\LinkA{xmap.col}{xmap.col}} 
\item[\code{dp}] The number of decimal places you want to save for the y-coordinates 
\item[\code{projectid}] The projectid (returned by \code{\LinkA{xmap.project.new}{xmap.project.new}} and as a list from \code{\LinkA{xmap.project.list}{xmap.project.list}}.  If this is not passed, on the first time of calling a new project will be created, and will be used on all subsequent calls) 
\item[\code{graphid}] The graphid returned by \code{\LinkA{xmap.graph.new}{xmap.graph.new}} or \code{\LinkA{xmap.graph.list}{xmap.graph.list}}.  If this is not passed, it will use the last graph generated by \code{\LinkA{xmap.plot}{xmap.plot}}. 
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Tim Yates
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{xmap.col}{xmap.col}}\\
\code{\LinkA{xmap.project.new}{xmap.project.new}}\\
\code{\LinkA{xmap.project.list}{xmap.project.list}}\\
\code{\LinkA{xmap.project.load}{xmap.project.load}}\\
\code{\LinkA{xmap.project.save}{xmap.project.save}}\\
\code{\LinkA{xmap.project.delete}{xmap.project.delete}}\\
\code{\LinkA{xmap.graph.new}{xmap.graph.new}}\\
\code{\LinkA{xmap.graph.list}{xmap.graph.list}}\\
\code{\LinkA{xmap.graph.load}{xmap.graph.load}}\\
\code{\LinkA{xmap.graph.save}{xmap.graph.save}}\\
\code{\LinkA{xmap.graph.delete}{xmap.graph.delete}}\\
\code{\LinkA{xmap.plot.new}{xmap.plot.new}}\\
\code{\LinkA{xmap.plot.list}{xmap.plot.list}}\\
\code{\LinkA{xmap.plot.load}{xmap.plot.load}}\\
\code{\LinkA{xmap.plot.save}{xmap.plot.save}}\\
\code{\LinkA{xmap.plot.delete}{xmap.plot.delete}}\\
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
  
  x <- seq( 1000, 100000, by = 1000 )
  y <- runif( length( x ), -10, 10 )

  # This will create a new project, and graph, and add a plot to it
  xmap.plot( x, y, species="homo_sapiens", "1", main="A quick graph", 
             sub="Sub heading", type="area", xlab="Plot 1", col=0xAAFFBB00 )

  # This will add another plot to the same graph
  xmap.points( x, y, type="area", xlab="Plot 2", col=0xAA0000FF )
  
\end{ExampleCode}
\end{Examples}

