plotSpatialEffects {cellHTS} | R Documentation |
The function plots the per-plate row and column effects estimated by the B score method.
plotSpatialEffects(x, whichChannel = 1, plateRange)
x |
a cellHTS object that has already been normalized using the B score method (see details). |
whichChannel |
a numeric value giving the channel of x to plot. |
plateRange |
a numeric vector giving the plate numbers to plot. If missing, the function considers all the plates. |
The function plots the plate plots displaying the row and column offsets (stored in slot rowcol.effects
of the cellHTS
object x
) within the plates in plateRange
, and for channel whichChannel
, as determined by the B score method.
Before plotting the spatial offsets, the values within the chosen channel (whichChannel
) 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 of the values in
x$rowcol.effects[,,,whichChannel]
.
Ligia P. Bras ligia@ebi.ac.uk
plotPlate
,
Bscore
,
normalizePlates
,
summarizeChannels
data(KcViabSmall) x = normalizePlates(KcViabSmall, normalizationMethod="Bscore", save.model = TRUE) ## see plate plots with the row and column estimated offsets for plates 1 and 3: plotSpatialEffects(x, plateRange=c(1,3))