plotPlateLibrary {cellHTS} | R Documentation

## Plate plot of the raw data of the four consecutive 96-well plates of a given 384-well plate

### Description

Given a `cellHTS` object with data from an assay where every set of four consecutive 96-well plates was combined into a 384-well plate, this function plots the raw intensities of a chosen 384-well assay plate distributed according to the 96-well plate format.

### Usage

    plotPlateLibrary(x, whichPlate = 1, whichChannel = 1, plotSd = TRUE, plotPlateArgs)

### Arguments

`x` | a cellHTS object containing the slot `libPlate` with the 96-well plate identifiers (see `getLibraryPlate`).
`whichPlate` | a number indicating the 384-well plate that we want to examine. (By default, it considers the first plate, `whichPlate = 1`).
`whichChannel` | a number indicating the channel that we want to consider. (By default, the first channel is considered: `whichChannel = 1`)
`plotSd` | a logical value indicating whether the standard deviation across replicates should be plotted (default is `plotSd = TRUE`.
`plotPlateArgs` | optional argument. If given, should be a list with parameters for the plate plots. See details.

### Details

The cellHTS object `x` contains data from a screening experiment where every set of four consecutive 96-well plates was combined into a 384-well plate. The plate identifiers for the 96-well plates are given in the slot `libPlate`, obtained by `getLibraryPlate`.

Given the channel specified by `whichChannel` and the 384-well plate number `whichPlate`, the function plots the raw intensities for each replicate in both the 96-well and the 384-well plate format. If `plotSd = TRUE`, the standard deviation across replicates is also plotted.

The following elements are recognized for `plotPlateArgs` and passed on to `plotPlate`: `sdcol`, the color scheme for the standard deviation plate plot, `sdrange`, the sd range to which the colors are mapped, `xcol`, the color scheme for the intensity plate plot, `xrange`, the intensity range to which the colors are mapped. If an element is not specified, default values are used.

### Author(s)

Ligia Braz ligia@ebi.ac.uk

### See Also

`plotPlate`, `getLibraryPlate`

### Examples

        data(KcViabSmall)
        x <- getLibraryPlate(KcViabSmall)
        plotPlateLibrary(x, whichPlate=2, plotSd=TRUE)

[Package cellHTS version 1.10.0 Index]