controlDensity: Plotting the control density

Description Usage Arguments Value See Also Examples

Description

Plots the density of positive and negative controls (if applicable) for all controls contained in the dataset.

Usage

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controlDensity(header, dataset, channel, plotTitle, showPlot, supHisto)

Arguments

header

the header of a dataset file generated with generateDatasetFile

dataset

an R data frame generated with generateDatasetFile

channel

a character string specifying the name of the column containing the values for computing the density, e.g. "SigIntensity"

plotTitle

the plot title

showPlot

0 or 1. 1 will open one or several plot windows in the R GUI, 0 will only save the plot(s) without opening windows

supHisto

0 or 1. 1 will additionally superimpose a colour histogram of the values for the positive and negative controls. Otherwise choose 0.

Value

Plots the density of positive and negative controls (if applicable) for all controls contained in the dataset. The plot is saved as a pdf and a png file named after the experiment name specified in the header concatenated with the plotTitle.

The function returns the plot name.

See Also

controlDensityPerScreen, controlDensityPerPlate

Examples

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data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")

controlDensity(header, dataset, "SigIntensity", "Control density", 1, 1)


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