configurationAsScreenPlot: Screen plot of the plate configuration of a cellHTS object
In cellHTS2: Analysis of cell-based screens - revised version of cellHTS

Description Usage Arguments Details Value Author(s) References See Also Examples

Screen plot displaying the plate configuration of a cellHTS object.

1 2	configurationAsScreenPlot(x, verbose=interactive(), posControls, negControls, legend=FALSE, main="")

`x`	a configured `cellHTS` object (i.e. `state(x)['configured']` must be `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.
`legend`	logical defining whether to include a legend.
`main`	character giving a figure caption.

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.

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

Ligia Bras ligia@ebi.ac.uk

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

plotScreen, writeReport