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

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.

1	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))