\HeaderA{riplot}{Ratio intensity plot for 2-dye Microarray experiment}{riplot}
\keyword{hplot}{riplot}
\begin{Description}\relax
This function only works for 2-dye array at this time. It will
plot the log-ratio (log2(R/G)) versus log-intensity (log2(R*G)/2)
figure for Micro Array experiment. Ideal RI plot will be points
scattered around the y=0 horizontal line.

This function works for \code{madata}. This function and 
\code{\LinkA{arrayview}{arrayview}} assume the data is
on log2 based scale. So if your rawdata is not pre-transformed, you should
not do riplot on the raw data.
\end{Description}
\begin{Usage}
\begin{verbatim}
riplot(object, title, xlab, ylab, array, color = "blue",highlight.flag = TRUE, 
    flag.color = "Red", idx.highlight, highlight.color = "Green", 
    rep.connect = FALSE, onScreen=TRUE) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] An object of class \code{madata}.
\item[\code{title}] The title for figures. The default figure title is "RI
plot for array number X". If the user wants to provide titles, be
sure to provide a string array with the same number of elements as
the number of arrays.
\item[\code{xlab}] The xlab for figures. The default figure xlab is 
"expression(log[2](R*G))". One xlab would be used for all plot, 
thus unlike title, user (if one wants) need to provide only one name.
\item[\code{ylab}] The ylab for figures. The default figure ylab is 
"expression(log[2](R/G))". One ylab would be used for all plot, 
thus unlike title, user (if one wants) need to provide only one name.
\item[\code{array}] A list of arrays numbers for which you want to draw an RI
plot.
\item[\code{color}] The color for the points in scatter plot. Default is blue.
\item[\code{highlight.flag}] A logical parameter to indicate whether to
highlight the bad spots or not.
\item[\code{flag.color}] The color for bad spots, default is red.
\item[\code{idx.highlight}] A vector for highlighted spots other than bad
spots.
\item[\code{highlight.color}] The color for highlighted spots. Default is green.
\item[\code{rep.connect}] A logical value to represent whether to connect the
dots between the replicates or not.
\item[\code{onScreen}] A logical value to represent whether to display the
plots on screen or not. If TRUE, x11() (in Unix/Windows) or
macintosh() (in Mac) will be called inside the function. Otherwise,
it will plot the figure on the current device. Default is TRUE.
\end{ldescription}
\end{Arguments}
\begin{Note}\relax
This function will plot one figure for each array. So if you have many
arrays, there will be many figures generated.
\end{Note}
\begin{Author}\relax
Hao Wu
\end{Author}
\begin{Examples}
\begin{ExampleCode}
## Not run: 
data(kidney)
# riplot raw data on screen
riplot(kidney.raw)
graphics.off()
# riplot raw data array 1 and 3 and output to postscript file
postscript(file="kidneyRIplot.ps")
riplot(kidney.raw, array=c(1,3), onScreen=FALSE)
## End(Not run)\end{ExampleCode}
\end{Examples}

