channelPlot: Plot signal channels against each other

In RNAither: Statistical analysis of high-throughput RNAi screens

Description

Generates plots allowing pairwise comparison of signal channels. Fits a lowess regression curve into the plots.

Usage

channelPlot(header, dataset, vecOfChannels, flag, plotTitle, showPlot, smSpan=2/3)

Arguments

header	the header of a dataset file generated with generateDatasetFile
dataset	an R data frame generated with generateDatasetFile
vecOfChannels	A vector containing the names of the signal channels to be compared, e.g. "SigIntensity"
flag	0, 1, or 2. 0 uses the data from the complete dataset, 1 makes comparisons for each experiment, 2 makes comparisons for each plate.
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.
smSpan	The smoother span of the lowess curve. This gives the proportion of points in the plot which influence the smooth at each value. Larger values give more smoothness. Optional, defaults to 2/3

Value

Saves the plots in pdf and png files named after the experiment name specified in the header concatenated with the plotTitle, the number of the comparison, and if applicable the experiment number and/or the plate number.

When flag == 0, returns the plot name (plotName).

When flag == 1, returns a list containing:

plotName	The plot name
minOfScreens	The number of the first experiment
numOfScreens	The number of the last experiment

When flag == 2, returns a list containing: the plot name, a vector with the number of the first experiment and of the last experiment, and a vector with the number of the first plate and the number of the last plate.

Examples

data(exampleHeader, package="RNAither")
data(exampleDataset, package="RNAither")
plotname <- channelPlot(header, dataset, c("SigIntensity", "NbCells"), 0, "Channel comparison", 1)

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