cellHTS (version 1.42.0)

plotSpatialEffects: Plate plot with the row and column offsets estimated by the B score method

Description

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

Usage

plotSpatialEffects(x, whichChannel = 1, plateRange)

Arguments

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.

Details

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:

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

Here, $yt$ are the transformed values, and $y$ the estimated spatial effects. The maximum and the minimum values are calculated using all of the values in x$rowcol.effects[,,,whichChannel].

See Also

plotPlate, Bscore, normalizePlates, summarizeChannels

Examples

    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))