\HeaderA{plot.confband.text}{Add Selected Text to an M vs A Plot}{plot.confband.text}
\keyword{aplot}{plot.confband.text}
\begin{Description}\relax
`text' draws the strings given in the vector `labs' at the
coordinates given by `M' and `A'
\end{Description}
\begin{Usage}
\begin{verbatim}
plot.confband.text(x, M, crit1=0.025, crit2=crit1, nclass=10,
labs=NULL, output=FALSE, ...)  
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] a vector giving the x-coordinates of the points in the scatter
plot. In the microarray context, this could be a vector of
average log intensities. ie A
\item[\code{M}] a vector giving the y-coordinates of the points in the scatter
plot. In the microarray context, this could be a vector of log
intensity ratios.
\item[\code{crit1}] The number of points to be highlighted on the M vs A plot.
If crit1 < 1, the crit1*100\% spots with the smallest M values
will be highlighted. If crit1 >= 1, the crit spots  with the
smallest M values are highlighted.
\item[\code{crit2}] Similar to "crit1".   If crit2 < 1, the crit2*100\%
spots with the largest M values will be highlighted. If crit2 >= 1,
the crit2 spots with the largest M values are highlighted.
\item[\code{nclass}] A single number giving the approximate number of
intensity depedent groups to consider.
\item[\code{labs}] one or more character strings or expressions specifying the
text to be written.  If this string is not specified, by
default the index of the vector `M' will be used.
\item[\code{output}] logical, defaulting to `FALSE'. If `TRUE' a vector
containning the index to the vector `M' that are  
highlighted.
\item[\code{...}] graphical parameters may also be supplied as arguments
to the function (see \code{\LinkA{par}{par}}).
\end{ldescription}
\end{Arguments}
\begin{Note}\relax
An M vs A plot must be constructed \bold{prior} to the execution of this function.
\end{Note}
\begin{SeeAlso}\relax
\code{\LinkA{plot.mva}{plot.mva}}, \code{\LinkA{stat.ma}{stat.ma}},
\code{\LinkA{lines}{lines}}, \code{\LinkA{matlines}{matlines}},
\code{\LinkA{plot.confband.lines}{plot.confband.lines}}, \code{\LinkA{plot.confband.points}{plot.confband.points}} .
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}data(MouseArray)
## mouse.setup <- init.grid()
## mouse.data <- init.data()

plot.mva(mouse.data, mouse.setup) ## an M vs A plot

mouse.lratio <- stat.ma(mouse.data, mouse.setup)

plot.confband.text(mouse.lratio$A, mouse.lratio$M)
## 2.5% of the spots with the largest and smallest M values are
## highlighted on the M vs A plot, and each spot is assigned the
## default label of its corresponding index value. 
\end{ExampleCode}
\end{Examples}

