\HeaderA{plotChr}{Plot Smoothed Sense/Anti-sense of Specified Chromosomes}{plotChr}
\keyword{hplot}{plotChr}
\begin{Description}\relax
For a given chromosome, plot the smooths of the sense and the 
anti-sense from 5' to 3' (left to right on x-axis).
\end{Description}
\begin{Usage}
\begin{verbatim}
plotChr(chrN, senseObj, cols = rep("black", length(senseObj[[1]])), log = FALSE, xloc = c("equispaced", "physical"), geneSymbols = FALSE, ngenes = 20, lines.at = NULL, lines.col = "red")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{chrN}] The desired chromosome, e.g. for humans it would be a character string in the set of c(1:22, "X", "Y").
\item[\code{senseObj}] The result of \code{Makesense}.
\item[\code{cols}] A vector of colors for the lines in the plot, typically specified according to a certain pheotype of samples.
\item[\code{log}] Logical, whether log-transformation should be taken on the smoothed expressions.
\item[\code{xloc}] Determines whether the "Representative Genes" 
will be displayed according to their relative 
positions on the chromosome (physical), or spaced 
evenly (equispaced).  Default is equispaced.
\item[\code{geneSymbols}] Logical, whether to use Affy IDs or 
Gene Symbols for "Representative Genes", default is 
Affy IDs.
\item[\code{ngenes}] Desired number of "Representative Genes". The 
number of actual displayed genes may differ.
\item[\code{lines.at}] A vector of Affy IDs. Vertical lines will 
be drawn at specified genes.
\item[\code{lines.col}] A vector of colors associated with 
\code{lines.at}.
\end{ldescription}
\end{Arguments}
\begin{Author}\relax
Robert Gentleman and Xiaochun Li
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{Makesense}{Makesense}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
example(Makesense)

if (interactive())
  op <- par(ask=TRUE)

cols <- ifelse(expressionSet133a$cov1=="test 1", "red", "green")
plotChr("21", esetobj, cols)

# plot on log-scale:

plotChr("21", esetobj, cols, log=TRUE)

# genesymbol instead of probe names:

plotChr("21", esetobj, cols, log=TRUE, geneSymbols=TRUE)

# add vertical lines at genes of interest:

gs <- c("220372_at", "35776_at", "200943_at")
plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs)

# add vertical lines at genes of interest
# with specified colors:

gs <- c("220372_at", "35776_at", "200943_at")
cc <- c("blue", "cyan","magenta")
plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs,
lines.col=cc)
if (interactive())
  par(op)
\end{ExampleCode}
\end{Examples}

