\name{writeQAReport}
\alias{writeQAReport}
\alias{writeLines,data.frame,file,missing-method}


\title{ Create HTML report for (lists of) qaProcess objects }

\description{
  
  This function combines all graphical output of multiple QA processes
  for one or several \code{\link[flowCore]{flowSet}}s in a single
  hyperlinked HTML document.
  
}
\usage{

writeQAReport(set, processes, outdir = "./qaReport", grouping = NULL,
pagebreaks = TRUE)

}

\arguments{
  
  \item{set}{ A \code{\link[flowCore]{flowSet}} or a list of several
    \code{\link[flowCore]{flowSet}}s }
  
  \item{processes}{ A list of A \code{\link{qaProcess}} objects or, in
    the case of multiple \code{\link[flowCore]{flowSet}}s, a list of
    lists of \code{\link{qaProcess}} objects.}

  \item{outdir}{ The directory to which the HTML report is to be
    saved. Make sure that each \code{\link{qaProcess}} object was
    created in the same directory. }

  \item{grouping}{ A character scalar indicating a variable in the
    \code{\link[flowCore]{flowSet}}'s \code{phenoData} that is used as a
    grouping factor in the output.}

   \item{pagebreaks}{ A logical indicating whether the output should be
   on one long page, or split on several pages.}

}

\details{
  
  Both the information about graphical output and the results for a QA
  process are stored in objects of class \code{\link{qaProcess}}. The
  creation of such objects is abstracted in dedicated functions and the
  user should call these functions directly rather than creating
  \code{\link{qaProcess}} manually. \code{\link{writeQAReport}} takes
  lists of such objects and combines their information in a unified HTML
  document. A grouping factor can be specified to indicate subgroups of
  the data. In the case of multiple panels, a list of
  \code{\link[flowCore]{flowSet}}s can be given to
  \code{\link{writeQAReport}}, and the function expects a list of lists
  of processes, where each process list is specific to one panel.

  An entry point to the output of this function can be found at
  \code{outdir/index.html}.
  
}
\value{
  The function is called for it's side effects
}


\author{ Florian Hahne }

\seealso{ \code{\link{qaProcess.marginevents}}, \code{\link{qaReport}},
  \code{\link{qaProcess}}, \code{\link{qaProcess.timeline}}}
\examples{
\dontrun{
data(GvHD)
GvHD <- transform(GvHD, "FL1-H"=asinh(`FL1-H`), "FL2-H"=asinh(`FL2-H`))
dest <- tempdir()
qp1 <- qaProcess.timeline(GvHD, channel="FL1-H", outdir=dest, cutoff=1)
qp2 <- qaProcess.marginevents(GvHD, channels=c("FL1-H", "FL2-H"),
  outdir=dest, cFactor=4)
writeQAReport(GvHD, processes=list(qp1, qp2), outdir=dest,
  grouping="Patient")
browseURL(file.path(dest, "index.html"))
}
}

\keyword{ IO }
\keyword{ dynamic }