\HeaderA{smcPlot}{Plot PGSEA results}{smcPlot}
\keyword{hplot}{smcPlot}
\begin{Description}\relax
This basic function will plot results from PGSEA with easy altering of margins, colors, and text.
\end{Description}
\begin{Usage}
\begin{verbatim}
smcPlot(m, ff = NULL, skip = "NO", scale = c(-3, 3), na.color = par("bg"), margins = NULL, r.cex = NULL, c.cex = NULL, show.grid = F, cnames = TRUE, rnames = TRUE,grid.lty=3, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{m}] matrix - your results from PGSEA (or any other numeric matrix of data)
\item[\code{ff}] factor - this factor corresponds to the subtypes of your samples and will control the column names
\item[\code{skip}] character - which subtype(s) to skip from"ff"
\item[\code{scale}] vector, length 2 - this vector sets the minimum and maximum values for the graph scale (at bottom of plot)
\item[\code{na.color}] character - color to display in the result of an NA
\item[\code{margins}] vector, length 4 - this vector gives the expansion values for the margins
\item[\code{r.cex}] numeric - number giving the amount by which row names should be scaled relative to the default
\item[\code{c.cex}] numeric - number giving the amount by which column names should be scaled relative to the default 
\item[\code{show.grid}] boolean - show grid outlines within plot?
\item[\code{cnames}] boolean or character - vector of alternatvie column names 
\item[\code{rnames}] boolean or character - vector of alternative row names
\item[\code{grid.lty}] numeric - line type of the grid lines
\item[\code{...}] additional graphical parameters passed along to the plotting function 
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Karl Dykema <karl.dykema@vai.org>
\end{Author}
\begin{Examples}
\begin{ExampleCode}

library(PGSEA)
datadir <- system.file("data", package = "PGSEA")
sample <- readGmt(file.path(datadir, "sample.gmt"))
data(nbEset)

pg <- PGSEA(nbEset,cl=sample,ref=1:5)
sub <- factor(c(rep(NA,5),rep("NeuroB",5),rep("NeuroB_MYC+",5)))

smcPlot(pg,sub,scale=c(-10,10),col=.rwb,margins=c(1,1,8,13))

\end{ExampleCode}
\end{Examples}

