\name{plot.responses}
\alias{plot.responses}
\title{plot.responses}
\description{Plot the detected transcriptional responses for a given subnetwork. }
\usage{
\method{plot}{responses}(x, subnet.id, nc = 3, plot.names = TRUE, plot.mode = "network", xaxis = TRUE, yaxis = TRUE, plot.type = "twopi", mar = c(5, 4, 4, 2), horiz = TRUE, \dots)
}
\arguments{
  \item{x}{ Result from NetResponse (detect.responses function). }
  \item{subnet.id}{ Subnet id. }
  \item{nc}{ Number of columns for an array of images. }
  \item{plot.names}{ Plot node names (TRUE) or indices (FALSE).}
  \item{plot.mode}{network: plot responses as a subnetwork graph;
matrix, heatmap: plot subnetwork expression matrix. For both, expression of
each gene is shown relative to the mean expression level of the gene; boxplot.data: feature-wise boxplots for hard sample-to-response assignments; response.barplot: estimated response centroids as barplot including 95\% confidence intervals for the means.
}
  \item{xaxis, yaxis}{Logical. Plot row/column names.}
  \item{plot.type}{ Network plot mode. For instance, 'neato' or 'twopi'.}
  \item{mar}{ Figure margins. }
  \item{horiz}{ Logical. Horizontal barplot.}
  \item{...}{Further arguments for plot function.}
}
\value{  Used for its side-effects. }
\references{ See citation("netresponse") }
\seealso{\code{\link{plot.scale}}}
\author{Leo Lahti \email{leo.lahti@iki.fi}}
\examples{
#res <- detect.responses(D, netw)
#vis <- plot.responses(res, subnet.id)
}
\keyword{utilities}