controlDensityPerPlate: Plotting the control density per plate

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

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

Usage

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

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

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

RNAither documentation built on Nov. 8, 2020, 8:06 p.m.