writeReport {cellHTS} | R Documentation |
Creates a directory with HTML pages of linked tables and plots documenting the contents of a cellHTS object.
writeReport(x, outdir=x$name, force=FALSE, plotPlateArgs=FALSE, imageScreenArgs=NULL)
x |
a cell HTS object. |
outdir |
a character of length 1 with the output base directory. |
force |
a logical value, determines the behavior of the function
if outdir contains anything.
If force is TRUE , the function forcefully recursively
removes the contents of outdir of it, otherwise it casts an error. |
plotPlateArgs |
either a list with parameters for the plate plots the
per plate quality report pages, or a logical with value FALSE .
If FALSE , the plate plots are omitted, this option is
here because the production of the plate plots takes a long time.
See details. |
imageScreenArgs |
a list with parameters for the function
imageScreen . See details. |
The following elements are recognized for plotPlateArgs
and
passed on to plotPlate
:
sdcol
, the color scheme for the standard deviation plate plot,
sdrange
, the sd range to which the colors are mapped,
xcol
, the color scheme for the intensity plate plot,
xrange
, the intensity range to which the colors are mapped.
If an element is not specified, default values are used.
The following elements are recognized for imageScreenArgs
and
passed on to imageScreen
:
ar
, aspect ratio,
zrange
, range.
The function is called for its side-effect.
It returns the character outdir
with the path to the output directory.
Ligia Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk
datadir = system.file("KcViabSmall", package = "cellHTS") x = readPlateData("Platelist.txt", "KcViabSmall", path=datadir) confFile = system.file("KcViabSmall", "Plateconf.txt", package="cellHTS") logFile = system.file("KcViabSmall", "Screenlog.txt", package="cellHTS") descripFile = system.file("KcViabSmall", "DESCRIPTION.txt", package="cellHTS") x = configure(x, confFile, logFile, descripFile) writeReport(x) x = normalizePlateMedian(x, zscore="-") x = summarizeReplicates(x, summary="min") writeReport(x, force=TRUE, plotPlateArgs = list(), imageScreenArgs=list(zrange=c(-4,4)))