plotSpatialEffects {cellHTS2} | R Documentation

## 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:

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]`.

### Author(s)

Ligia P. Bras ligia@ebi.ac.uk

### 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))

[Package cellHTS2 version 2.46.1 Index]