\name{plotCtCard}
\Rdversion{1.1}
\alias{plotCtCard}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{Image plot of qPCR Ct values from a card format}
\description{Function for plotting high-throughput qPCR Ct values from a platform with a defined spatial layout, such as TaqMan Low Density Assay cards. The location of Ct values in the plot corresponds to the position of each well on the card.}

\usage{
plotCtCard(q, card = 1, plot = "Ct", main, nrow = 16, ncol = 24, col, col.range, na.col = "grey", na.value = 40, legend.cols, well.size = 3.1, zero.center = FALSE, unR = FALSE, unD = FALSE, ...)
}

\arguments{
  \item{q}{object of class qPCRset. }
  \item{card}{integer, the sample number to plot.}
  \item{plot}{character string among "Ct", "flag", "type", "class") indicating what type of plot to produce. See Details for a longer description.}
  \item{main}{character string, the title of the plot. Per deault this is the sample name corresponding to card.}
  \item{nrow}{integer, the numer of rows on the card (16 for a standard 384 well format).}
  \item{ncol}{integer, the numer of columns on the card (24 for a standard 384 well format).}
  \item{col}{vector of colors of the same length as the number of different groups for the categorical data, or the name of a colour scheme for the continuous data.}
  \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  \item{na.value}{numeric, if NA has been replaced by an (arbitrary) high Ct value in the data.}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{legend.cols}{integer, how many columns should the legend text be split into (defaults to number of labels).}
  \item{well.size}{numeric, for adjusting the size of the wells on the card.}
  \item{zero.center}{logical, should the colours be shifted to be zero-centered.}
  \item{unR}{logical, should wells from the category "Unreliable" be crossed out.}
  \item{unD}{logical, should wells from the category "Undetermined" be crossed out.}
  \item{\dots}{any other arguments will be passed to the \code{plot} and \code{points} functions.}
}

\details{This function may be used to plot the values of any well-specific information, such as the raw or normalized Ct values, or categorical data such as flag, gene class etc. The image follows the layout of an actual HTqPCR card. 
	
%The color range is used to represent the range of values for the statistic. Especially for dCt and ddCt it can be an advantage to set zero.center=TRUE to make the colour scale symmetric around 0.

If \code{unR=TRUE} these will wells will be crossed out using a diagonal cross (X), whereas \code{unD=TRUE} will be marked with a horisontal/vertical cross.}

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

\author{Heidi Dvinge}

\seealso{\code{\link{image}}}

\examples{
# Load some example data
data(qPCRraw)
# Plot Ct values from first card
plotCtCard(qPCRraw)
plotCtCard(qPCRraw, card=2, col.range=c(10,35))
plotCtCard(qPCRraw, unR=TRUE, unD=TRUE)
# Other examples
plotCtCard(qPCRraw, plot="class")
plotCtCard(qPCRraw, plot="type")
plotCtCard(qPCRraw, plot="flag")
}

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