imageScreen {cellHTS2} | R Documentation |
Experiment-wide quality control plot of a scored cellHTS
object.
imageScreen(object, ar = 3/5, zrange, map = FALSE, anno)
object |
a cellHTS object that has already been scored (i.e. state(object)['scored']=TRUE ). |
ar |
the desired aspect ration for the image plot (i.e. number of columns per number of rows) |
zrange |
the range of values to be mapped into the color
scale. If missing, zrange will be set to the range of the score values stored in slot assayData of object . |
map |
a logical value that determines whether an image map should be created using tooltips to indicate the annotation at each position. It only makes sense to set it to TRUE when the function is called from writeReport function, so the default is FALSE . |
anno |
optional input giving the annotation information for the mapping. It should be a vector of the same size as
the total number of featured in object . See details. |
This function creates an image plot that gives an overview of the whole set of score values stored in slot assayData
of a scored cellHTS
object.
When the annotation mapping is performed, by default, anno
is set to:
object
is annotated) The content of column named GeneSymbol
or named GeneID
(if the former is not available) of the featureData
slot of object
;
object
is not annotated.
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.
normalizePlates
,
summarizeChannels
,
scoreReplicates
,
summarizeReplicates
,
Data
writeReport
data(KcViabSmall) x <- KcViabSmall x <- normalizePlates(x, scale="multiplicative", log=FALSE, method="median", varianceAdjust="none") x <- scoreReplicates(x, sign="-", method="zscore") x <- summarizeReplicates(x, summary="min") imageScreen(x, zrange=c(-5,5))