\name{writeQAReport}
\alias{writeQAReport}
\alias{writeLines,data.frame,file,missing,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-class]{flowSets}} in a single
  hyperlinked HTML document.
  
}
\usage{

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

}

\arguments{
  
  \item{set}{ A \code{\link[flowCore:flowSet-class]{flowSet}} or a list
    of several \code{\link[flowCore:flowSet-class]{flowSets}}.}
  
  \item{processes}{ A list of
    \code{\link[flowQ:qaProcess-class]{qaProcess}} objects or, in 
    the case of multiple \code{\link[flowCore:flowSet-class]{flowSets}},
    a list of lists of \code{qaProcess} objects. See below
    for further details.}

 \item{globalProcess}{ A list of \code{qaProcess} objects 
 generated by multipanel comparison qaProcess functions, when set is a list of 
  \code{\link[flowCore:flowSet-class]{flowSets}} .}

  \item{outdir}{ The directory to which the HTML report is to be
    saved. Each \code{\link[flowQ:qaProcess-class]{qaProcess}} object
    should have been created in the same directory. }

  \item{grouping}{ A character scalar indicating a variable in the
    \code{\link[flowCore:flowSet-class]{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 over several pages. }
   
   \item{pdf}{ A logical indicating whether vectorized versions of the
     images should be included. Setting this to \code{TRUE} implies that
     the individual QA processes have also been created with setting
     \code{pdf=TRUE}. }

}

\details{
  
  Both the information about graphical output generated as part of a QA
  process as well as the qunatitative or qualitative results are stored
  in objects of class
  \code{\link[flowQ:qaProcess-class]{qaProcess}}. The creation of such 
  objects is abstracted in dedicated constructor function and the user
  should call these functions directly rather than creating
  \code{\link[flowQ:qaProcess-class]{qaProcess}}
  manually. \code{\link[flowQ]{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-class]{flowSets}} can be given to
  \code{\link[flowQ]{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 mostly called for it's side effects, that is, the
  generation of a HTML quality report in \code{outdir}. A URL to an
  entry point for browsing of the report is returned.
  
}


\author{ Florian Hahne }

\seealso{ \code{\link[flowQ]{qaProcess.marginevents}},
  \code{\link[flowQ]{qaReport}},
  \code{\link[flowQ:qaProcess-class]{qaProcess}},
  \code{\link[flowQ]{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)
url <- writeQAReport(GvHD, processes=list(qp1, qp2), outdir=dest,
  grouping="Patient")
browseURL(url)
}
}

\keyword{ IO }
\keyword{ dynamic }