Plotting the control density per plate

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Description

Plots the density of positive and negative controls (if applicable) for each plate.

Usage

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controlDensityPerPlate(header, dataset, channel, plotTitle, plotDesign, 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

plotDesign

1 or 2. 1 will generate one window containing all plots, 2 will generate a series of plots

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

Generates a series of plots for each experiment and each plate, showing the density of positive and negative controls (if applicable). The plots are saved as pdf and png files named after the experiment name specified in the header concatenated with the plotTitle.

The function returns a list of length 3 containing:

plotName

the plot name

c(minOfScreens, numOfScreens)

a vector with the number of the first experiment and of the last experiment

c(minOfPlates, numOfPlates)

a vector with the number of the first plate and the number of the last plate

See Also

controlDensity, controlDensityPerScreen

Examples

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

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

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