\name{plotCtArray}
\alias{plotCtArray}

\title{Image plot of qPCR Ct values from an array format}
\description{Function for plotting high-throughput qPCR Ct values from a platform with a defined spatial layout, such as Fluidigm Dynamic Arrays. The location of Ct values in the plot corresponds to the position of each well on the array.}

\usage{
plotCtArray(q, plot = "Ct", main, col, col.range, na.col = "grey", na.value = 40, chamber.size, ...)
}

\arguments{
  \item{q}{object of class qPCRset. }
  \item{plot}{character string indicating what type of plot to produce. Currently only "Ct" is implemented.}
  \item{main}{character string, the title of the plot. Per default "Ct values".}
  \item{col}{the name of a colour scheme.}
  \item{col.range}{vector, the range of colours to use.}
  \item{na.col}{the colour used for well with NA (undetermined) Ct values.}
  \item{na.value}{numeric, if NA has been replaced by an (arbitrary) high Ct value in the data.}
  \item{chamber.size}{numeric, for adjusting the size of the reaction chamber on the card.}
  \item{\dots}{any other arguments will be passed to the \code{plot} function.}
}

%\details{
%%  ~~ If necessary, more details than the description above ~~
%}

\value{A plot is created on the current graphics device.}

\author{Heidi Dvinge}

\seealso{\code{\link{plotCtCard}} for plotting data from other high-throughput qPCR platforms.}

\examples{
	
# Locate example data
exPath <- system.file("exData", package="HTqPCR")
exFiles <- "fluidigm_sample.csv"
# Create qPCRset object
temp	<- readCtData(exFiles, path=exPath, n.features=48*48, flag=9, feature=5, type=6, Ct=7, position=1, skip=12, sep=",")
# Re-format from 1x2304 samples in input file into 48x48 as on array
raw	<- changeCtLayout(temp, sample.order=rep(1:48, each=48))
# Plot
plotCtArray(raw)
# Change colour and range
plotCtArray(raw, col=brewer.pal(11, "Spectral"), col.range=c(10,35))

}

% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{hplot}