ZScorePlotTwo: Plot signal intensities per well (II)
In RNAither: Statistical analysis of high-throughput RNAi screens

Description Usage Arguments Value See Also Examples

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.

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

`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.

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.

plotBar, ZScorePlot

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

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