plotSpatialEffects {cellHTS} | R Documentation

## 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:

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]`.

### Author(s)

Ligia P. Bras ligia@ebi.ac.uk

### 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))

[Package cellHTS version 1.10.0 Index]