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]