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, pdf=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. See below for further
details. |
outdir |
The directory to which the HTML report is to be
saved. Each qaProcess object should have been 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 over several pages. |
pdf |
A logical indicating whether vectorized versions of the
images should be included. Setting this to TRUE implies that
the individual QA processes have also been created with setting
pdf=TRUE . |
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 qaProcess
. The creation of such
objects is abstracted in dedicated constructor function 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 mostly called for it's side effects, that is, the
generation of a HTML quality report in outdir
. A URL to an
entry point for browsing of the report is returned.
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) url <- writeQAReport(GvHD, processes=list(qp1, qp2), outdir=dest, grouping="Patient") browseURL(url) ## End(Not run)