spatialDistrib: Generate spatial plots of intensity values

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

Generate plots of plates and their intensity values.

Usage

spatialDistrib(header, dataset, plotTitle, col4plot, col4anno, showPlot)

Arguments

header	the header of a dataset file generated with generateDatasetFile
dataset	an R data frame generated with generateDatasetFile
plotTitle	the plot title
col4plot	a character string specifying the column whose values will be used for the plot
col4anno	a character string specifying the column whose values will be used for the annotation of the plot
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.

Value

For each plate, the plot will be saved as a png file named after the experiment name specified in the header concatenated with the plotTitle, the number of the experiment, and the number of the plate.

Wells containing positive controls are marked with a "P", wells containing negative controls with an "N".

Each plate will also be saved as an html file containing mouse-overs with the siRNA name for each well.

The function returns a list containing:

histoName	the plotname
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

compareReplicateSD, compareReplicateSDPerScreen

Examples

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

spatialDistrib(header, dataset, "Spatial distribution of cell counts", "NbCells", "GeneName", 1)

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