configurationAsScreenPlot {cellHTS2} | R Documentation |
Screen plot displaying the plate configuration of a cellHTS
object.
configurationAsScreenPlot(x, verbose=interactive(), posControls, negControls)
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. |
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.
data("KcViab") configurationAsScreenPlot(KcViab)