plotSpatialEffects {cellHTS2} | R Documentation |
The function plots the per-plate row and column effects estimated by the B score method or by the spatial normalization.
plotSpatialEffects(object, channel = 1, plates)
object |
a cellHTS object that has been normalized using the B score method or other spatial normalization (see details). |
channel |
a numeric value giving the channel of object to plot. |
plates |
a vector of integers giving the plate numbers to plot. If missing, the function considers all of the plates. |
The function plots the plate plots
displaying the row and column offsets (stored in slot rowcol.effects
of the cellHTS
object) within the plates in plates
, and for channel channel
, as determined by the B score method
or spatial normalization
.
Before plotting the spatial offsets, the values within the chosen channel (argument channel
) are transformed in order to be confined in the range [0, 1], as follows:
yt = (y - min(y))/(max(y) - min(y))
Here, yt are the transformed values, and y the estimated spatial effects.
The maximum and the minimum values are calculated using all the values in
plateEffects(object)$rowcol[,,channel]
.
Ligia P. Bras ligia@ebi.ac.uk
plotPlate
,
Bscore
,
spatialNormalization
,
normalizePlates
,
summarizeChannels
data(KcViabSmall) x <- normalizePlates(KcViabSmall, scale="multiplicative", log=TRUE, method="Bscore", save.model = TRUE) ## see plate plots with the row and column estimated offsets for plates 1 and 3: plotSpatialEffects(x, plates=c(1,3))