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,
map, logical value indicating whether tooltips with the
annotation should be added to the plot (default value is FALSE),
anno, gene annotation for the image map.
posControls and negControls should be given as a vector
of regular expression patterns specifying the name of the positive(s)
and negative(s) controls, respectively, as provided in the plate
configuration file (and stored in x$wellAnno). The length of
these vectors should be equal to the number of reporters used in the
screen (dim(x$xraw)[4] or to dim(x$xnorm)[4], in case
x contains multi-channel data that have been normalized by
combining the values from two or more channels).
By default, if posControls is not given, "pos" will be taken as
the name for the wells containing positive controls. Similarly, if
negControls is missing, by default "neg" will be considered as
the name used to annotate the negative controls.
The content of posControls and negControls will be
passed to regexpr for pattern matching
within the well annotation given in x$wellAnno (see
examples). If no controls are available for a given channel, use
"" or NA for that channel. For example,
posControls = c("", "(?i)^diap$") means that channel 1 has no
positive controls, while "diap" is the positive control for channel 2.
The arguments posControls and negControls are
particularly useful in multi-channel data since the controls might be
reporter-specific, or after normalizing multi-channel data.
In case of a two-way assay, where two types of "positive" controls are used in the screen ("activators" and "inhibitors"), posControls should be defined as a list with two components (called act and inh), each of which should be vectors of regular expressions of the same length as the current number of reporters (as explained above).
By default, tooltips doing the mapping between the probe annotation and the plate wells are not added to the plate plots and to the overall screen plot. If the cellHTS object x is annotated, the probe annotation is based on the information contained whether in x$geneAnno$GeneSymbol, or x$geneAnno$GeneID, if the former is missing. Otherwise, the mapping simply uses the well identifiers.