configurationAsScreenPlot {cellHTS2} | R Documentation

## Screen plot of the plate configuration of a cellHTS object

### Description

Screen plot displaying the original plate configuration used in the screening stored in a given `cellHTS` object.

### Usage

    configurationAsScreenPlot(x, verbose=interactive(), posControls, negControls)

### Arguments

`x` | a configured `cellHTS` object (i.e. `state(x)['configured']=TRUE`).
`verbose` | a logical value, if TRUE, the function reports some of its intermediate progress. The default is `interactive()`.
`posControls` | a list or vector of regular expressions specifying the name of the positive controls. See details.
`negControls` | a vector of regular expressions specifying the name of the negative controls. See details.

### Details

This function calls the function `plotScreen` to create a screen plot showing the plate configuration (as defined by the plate configuration file used to configure the `cellHTS` object – see function `configure`) used for the RNAi experiment stored in `x`.

`posControls` and `negControls` should be given as vectors of regular expression patterns specifying the name(s) of the positive(s) and negative(s) controls, respectivey, as provided in the plate configuration file (and acccessed via `wellAnno(x)`).

By default, if `posControls` is not given, "pos" will be taken as the annotation name for the wells containing positive controls. Similarly, if `negControls` is missing, by default "neg" will be considered as the name used to annotate the negative controls. The content of `posControls` and `negControls` will be passed to `regexpr` for pattern matching within the well annotation given in column `controlStatus` of the `featureData` slot of the `cellHTS` object.

### Value

Invisibly, a vector with the color map used to display the well annotation in the image plot.

### Author(s)

Ligia Bras ligia@ebi.ac.uk

### References

Boutros, M., Bras, L.P. and Huber, W. (2006) Analysis of cell-based RNAi screens, Genome Biology 7, R66.

### See Also

`plotScreen`, `writeReport`

### Examples

        data(KcViab)
        # see the plate configuration for the first 20 plates of the screen:
        configurationAsScreenPlot(KcViab[1:(20*prod(pdim(KcViab))),])

[Package cellHTS2 version 2.2.5 Index]