RNAither (version 2.20.0)

ZScorePlotTwo: Plot signal intensities per well (II)

Description

Plots signal intensity values for each well, a black line showing the median, two green lines showing one median absolute deviation, two red lines showing two median absolute deviations.

Usage

ZScorePlotTwo(header, dataset, flag, flag2, col4plot, col4anno, plotTitle, showPlot)

Arguments

header

the header of a dataset file generated with generateDatasetFile

dataset

an R data frame generated with generateDatasetFile

flag

0, 1, or 2. 0 uses the data from the complete dataset, 1 generates one plot for each experiment, 2 generates one plot for each plate.

flag2

0 draws lines using mean and sd, 1 draws lines using median and mad.

col4plot

a character string specifying the column whose intensity values will be used for the plot

col4anno

in case showPlot == 1, a character string specifying the column used for identifying points

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.

Value

Saves the plots in pdf and png files named after the experiment name specified in the header concatenated with the plotTitle 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.

See Also

plotBar, ZScorePlot

Examples

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

plotname <- ZScorePlotTwo(header, dataset, 0, 1, "SigIntensity", "GeneName", "Data per well", 0)