writeQAReport {flowQ} | R Documentation |
This function combines all graphical output of multiple QA processes
for one or several flowSet
s in a single
hyperlinked HTML document.
writeQAReport(set, processes, outdir = "./qaReport", grouping = NULL, pagebreaks = TRUE)
set |
A flowSet or a list of several
flowSet s |
processes |
A list of A qaProcess objects or, in
the case of multiple flowSet s, a list of
lists of qaProcess objects. |
outdir |
The directory to which the HTML report is to be
saved. Make sure that each qaProcess object was
created in the same directory. |
grouping |
A character scalar indicating a variable in the
flowSet 's phenoData that is used as a
grouping factor in the output. |
pagebreaks |
A logical indicating whether the output should be on one long page, or split on several pages. |
Both the information about graphical output and the results for a QA
process are stored in objects of class qaProcess
. The
creation of such objects is abstracted in dedicated functions and the
user should call these functions directly rather than creating
qaProcess
manually. 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
flowSet
s can be given to
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
outdir/index.html
.
The function is called for it's side effects
Florian Hahne
qaProcess.marginevents
, qaReport
,
qaProcess
, qaProcess.timeline
## Not run: 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")) ## End(Not run)