cellHTS2 (version 2.36.0)

plotSpatialEffects: Plate plot with the row and column offsets estimated by the a spatial normalization method

Description

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

Usage

plotSpatialEffects(object, channel = 1, plates)

Arguments

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.

Details

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:

$$y^t = \frac{(y - min(y))}{max(y)-min(y)}$$

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].

See Also

plotPlate, Bscore, spatialNormalization, normalizePlates, summarizeChannels

Examples

    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))