plotPlateLibrary: Plate plot of the raw data of the four consecutive 96-well...

In cellHTS: Analysis of cell-based screens

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 [e-mail]

See Also

plotPlate, getLibraryPlate

Examples

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

cellHTS documentation built on Oct. 5, 2016, 4:40 a.m.