\name{makeFabiaDataBlocks}
\alias{makeFabiaDataBlocks}
\title{Generation of Bicluster Data with Bicluster Blocks}
\description{

  \code{makeFabiaDataBlocks}: \R implementation of  \code{makeFabiaDataBlocks}.
}
\usage{

makeFabiaDataBlocks(n,l,p,f1,f2,of1,of2,sd_noise,sd_z_noise,
              mean_z,sd_z,sd_l_noise,mean_l,sd_l)


}
\arguments{
  \item{n}{number of observations.}
  \item{l}{number of samples.}
  \item{p}{number of biclusters.}
  \item{f1}{nn/f1 max. additional samples are active in a bicluster.}
  \item{f2}{n/f2 max. additional observations that form a pattern in a bicluster.}
  \item{of1}{minimal active samples in a bicluster.}
  \item{of2}{minimal observations that form a pattern in a bicluster.}
  \item{sd_noise}{Gaussian zero mean noise std on data matrix.}
  \item{sd_z_noise}{Gaussian zero mean noise std for deactivated hidden factors.}
  \item{mean_z}{Gaussian mean for activated factors.}
  \item{sd_z}{Gaussian std for activated factors.}
  \item{sd_l_noise}{Gaussian zero mean noise std if no observation patterns are present.}
  \item{mean_l}{Gaussian mean for observation patterns.}
  \item{sd_l}{Gaussian std for observation patterns.}
}
\details{

  Bicluster data is generated for visualization because the biclusters
  are now in block format. That means observations and samples that
  belong to a bicluster are consecutive. This allows visual inspection
  because the use can identify blocks and whether they have been found
  or reconstructed.

  Essentially the data generation model is the sum of
  outer products of sparse vectors:
   \deqn{X  =  \sum_{i=1}^{p} \lambda_i  z_i^T  +  U}
  where the number of summands  \eqn{p}
  is the number of biclusters.
  The matrix factorization is
  \deqn{X =  L  Z  +  U}
  and noise free
  \deqn{Y  =  L  Z}

   Here \eqn{\lambda_i} are from \eqn{R^n}, \eqn{z_i} from
   \eqn{R^l}, \eqn{L} from \eqn{R^{n \times p}},
   \eqn{Z} from \eqn{R^{p \times l}}, and \eqn{X}, \eqn{U}, \eqn{Y}
   from \eqn{R^{n \times l}}.



   Sequentially \eqn{L_i} are generated using
   \code{n}, \code{f2}, \code{of2}, \code{sd_l_noise}, \code{mean_l},
   \code{sd_l}.
   \code{of2} gives the minimal observations participating in a
   bicluster to which between 0 and \eqn{n/f2} observations are added,
   where the number is uniformly chosen. \code{sd_l_noise} gives the
   noise of observations not participating in the
   bicluster. \code{mean_l} and \code{sd_l} determines the Gaussian from
   which the values are drawn for the observations that participate in
   the bicluster.  The sign of the mean is randomly chosen for each
   component.

   Sequentially \eqn{Z_i} are generated using
   \code{l}, \code{f1}, \code{of1}, \code{sd_z_noise}, \code{mean_z},
   \code{sd_z}.
   \code{of1} gives the minimal samples participating in a
   bicluster to which between 0 and \eqn{l/f1} samples are added,
   where the number is uniformly chosen. \code{sd_z_noise} gives the
   noise of samples not participating in the
   bicluster. \code{mean_z} and \code{sd_z} determines the Gaussian from
   which the values are drawn for the samples that participate in
   the bicluster.

   \eqn{U} is the overall Gaussian zero mean
   noise generated by \code{sd_noise}.



  Implementation in \R.

}
\value{
  \item{Y}{the noise data from \eqn{R^{n \times l}}.}
  \item{X}{the noise free data from \eqn{R^{n \times l}}.}
  \item{ZC}{list where i-th element gives samples belonging to i-th bicluster.}
  \item{LC}{list where i-th element gives observations belonging to i-th
    bicluster.} 
    }
\seealso{
\code{\link{fabia}},
\code{\link{fabias}},
\code{\link{fabiap}},
\code{\link{fabi}},
\code{\link{fabiasp}},
\code{\link{mfsc}},
\code{\link{nmfdiv}},
\code{\link{nmfeu}},
\code{\link{nmfsc}},
\code{\link{plot}},
\code{\link{extractPlot}},
\code{\link{extractBic}},
\code{\link{plotBicluster}},
\code{\link{Factorization}},
\code{\link{projFuncPos}},
\code{\link{projFunc}},
\code{\link{estimateMode}},
\code{\link{makeFabiaData}},
\code{\link{makeFabiaDataBlocks}},
\code{\link{makeFabiaDataPos}},
\code{\link{makeFabiaDataBlocksPos}},
\code{\link{matrixImagePlot}},
\code{\link{summary}},
\code{\link{show}},
\code{\link{showSelected}},
\code{\link{fabiaDemo}},
\code{\link{fabiaVersion}}
}
\author{Sepp Hochreiter}
\examples{


#---------------
# TEST
#---------------

dat <- makeFabiaDataBlocks(n = 100,l= 50,p = 3,f1 = 5,f2 = 5,
  of1 = 5,of2 = 10,sd_noise = 3.0,sd_z_noise = 0.2,mean_z = 2.0,
  sd_z = 1.0,sd_l_noise = 0.2,mean_l = 3.0,sd_l = 1.0)

X <- dat[[1]]
Y <- dat[[2]]

matrixImagePlot(Y)
dev.new()
matrixImagePlot(X)


\dontrun{
#---------------
# DEMO
#---------------

dat <- makeFabiaDataBlocks(n = 1000,l= 100,p = 10,f1 = 5,f2 = 5,
  of1 = 5,of2 = 10,sd_noise = 3.0,sd_z_noise = 0.2,mean_z = 2.0,
  sd_z = 1.0,sd_l_noise = 0.2,mean_l = 3.0,sd_l = 1.0)

Y <- dat[[1]]
X <- dat[[2]]

matrixImagePlot(Y)
dev.new()
matrixImagePlot(X)

}
}
\keyword{datagen}
\concept{biclustering}
\concept{sparse coding}
\concept{sparse matrix factorization}