writeReport {cellHTS}R Documentation

Create a directory with HTML pages of linked tables and plots documenting the contents of a cellHTS object

Description

Creates a directory with HTML pages of linked tables and plots documenting the contents of a cellHTS object.

Usage

writeReport(x, outdir=x$name, force=FALSE, plotPlateArgs=FALSE, imageScreenArgs=NULL)

Arguments

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.

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.

Value

The function is called for its side-effect. It returns the character outdir with the path to the output directory.

Author(s)

Ligia Bras ligia@ebi.ac.uk, Wolfgang Huber huber@ebi.ac.uk

See Also

plotPlate, imageScreen

Examples

 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)))

[Package cellHTS version 1.2.0 Index]