\name{plotCtPairs}
\Rdversion{1.1}
\alias{plotCtPairs}
\title{Pairwise scatterplot of multiple sets of Ct values from qPCR data.}

\description{
Produces a plot of high-throughput qPCR Ct values from N number of samples plotted pairwise against each other in an N by N plot. The Ct values will be in the upper triangle, and the correlation between samples in the lower. Features can be marked based on for example feature class or type.
}

\usage{
plotCtPairs(q, cards = TRUE, lower.panel = panel.Ct.cor, upper.panel = panel.Ct.scatter, Ct.max = 35, col = "type", pch = 20, cex.cor = 2, cex.pch = 1, diag = TRUE, ...)
}

\arguments{
  \item{q}{object of class qPCRset. }
  \item{cards}{vector, the cards to plot against each other.}
  \item{lower.panel}{function, to use for plotting the lower triangle.}
  \item{upper.panel}{function, to use for plotting the upper triangle.}
  \item{Ct.max}{numeric, Ct values above this limit will be excluded when calculating the correlation.}
  \item{col}{vector with the colour(s) to use for the points, or a character string ("type" or "class") indicating whether points should be coloured according to \code{featureType} or \code{featureClass} of \code{q}.}
  \item{pch}{integer or single character, which plotting symbol to use for the points.}
  \item{cex.cor}{numeric, the expansion factor for the text in \code{panel.Ct.cor}.}
  \item{cex.pch}{numeric, the expansion factor for the points in \code{panel.Ct.scatter}.}
  \item{diag}{logical, should the diagonal line y=x be plotted.}
  \item{\dots}{any other arguments are passed to the panel functon or \code{pairs}.}
}

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

\value{A figure is generated in the current graphics device.}

\author{Heidi Dvinge}

\seealso{\code{\link{pairs}} or \code{\link{plotCtScatter}} for plotting just two samples.
}

\examples{
# Load example data
data(qPCRraw)
# Various types of plot
plotCtPairs(qPCRraw, cards=1:4)
plotCtPairs(qPCRraw, col="black")
plotCtPairs(qPCRraw, Ct.max=40)
}

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