plotSpatialEffects: Plate plot with the row and column offsets estimated by the a...
In cellHTS2: Analysis of cell-based screens - revised version of cellHTS

Description Usage Arguments Details Author(s) See Also Examples

The function plots the per-plate row and column effects estimated by the B score method or by the spatial normalization.

1	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))