+\name{image.DNAbin}
+\alias{image.DNAbin}
+\title{Plot of DNA Sequence Alignement}
+\description{
+ This function plots an image of an alignment of nucleotide sequences.
+}
+\usage{
+\method{image}{DNAbin}(x, what, col, bg = "white", xlab = "", ylab = "",
+ show.labels = TRUE, cex.lab = 1, legend = TRUE, ...)
+}
+\arguments{
+ \item{x}{a matrix of DNA sequences (class \code{"DNAbin"}).}
+ \item{what}{a vector of characters specifying the bases to
+ visualize. If missing, this is set to ``a'', ``g'', ``c'', ``t'',
+ ``n'', and ``-'' (in this order).}
+ \item{col}{a vector of colours. If missing, this is set to ``red'',
+ ``yellow'', ``green'', ``blue'', ``grey'', and ``black''. If it is
+ shorter (or longer) than \code{what}, it is recycled (or shortened).}
+ \item{bg}{the colour used for nucleotides whose base is not among
+ \code{what}.}
+ \item{xlab}{the label for the \emph{x}-axis; none by default.}
+ \item{ylab}{Idem for the \emph{y}-axis. Note that by default, the
+ labels of the sequences are printed on the \emph{y}-axis (see next option).}
+ \item{show.labels}{a logical controlling whether the sequence labels
+ are printed (\code{TRUE} by default).}
+ \item{cex.lab}{a single numeric controlling the size of the sequence labels.
+ Use \code{cex.axis} to control the size of the annotations on the \emph{x}-axis.}
+ \item{legend}{a logical controlling whether the legend is plotted
+ (\code{TRUE} by default).}
+ \item{\dots}{further arguments passed to
+ \code{\link[graphics]{image.default}} (e.g., \code{cex.axis}).}
+}
+\details{
+ The idea of this function is to allow fleixble plotting and colouring
+ of a nucleotide alignment. By default, the most common bases (a, g, c,
+ t, and n) and alignment gap are plotted using a standard colour
+ scheme.
+
+ It is possible to plot only one base specified as \code{what} with a
+ chosen colour: this might be useful to check, for instance, the
+ distribution of alignment gaps (\code{image(x, "-")}) or missing data
+ (see examples).
+}
+\author{Emmanuel Paradis}
+\seealso{
+ \code{\link{DNAbin}}, \code{\link{del.gaps}}, \code{\link{clustal}}
+}
+\examples{
+data(woodmouse)
+image(woodmouse)
+image(woodmouse, "n", "blue") # show missing data
+image(woodmouse, c("g", "c"), "green") # G+C
+par(mfcol = c(2, 2))
+### barcoding style:
+for (x in c("a", "g", "c", "t"))
+ image(woodmouse, x, "black", cex.lab = 0.5, cex.axis = 0.7)
+par(mfcol = c(1, 1))
+### zoom on a portion of the data:
+image(woodmouse[11:15, 1:50], c("a", "n"), c("blue", "grey"))
+### see the guanines on a black background:
+image(woodmouse, "g", "yellow", "black")
+}
+\keyword{hplot}
+