RNAither (version 2.20.0)

channelPlot: Plot signal channels against each other

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)