RNAither (version 2.20.0)

ZScorePlot: Plot normalized intensity values per well

Description

Plots the normalized intensity values for each well, together with a black line showing the mean, two green lines showing the standard deviation, and two red lines showing 2 standard deviations.

Usage

ZScorePlot(header, dataset, flag, col4plot, col4anno, plotTitle, showPlot)

Arguments

header

the header of a dataset file generated with generateDatasetFile

dataset

an R data frame generated with generateDatasetFile

flag

either 1 or 2. 1 if the dataset contains values per well, 2 if the dataset contains summarized values for each siRNA (e.g. a dataset summarized with summarizeReps).

col4plot

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

col4anno

a character string specifying the column that will be used for the plot annotation

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

Plots the normalized intensity values for each well, together with a black line showing the mean, and two red lines showing 2 standard deviations. Clicking on the points shows the gene/siRNA name.The plot is saved as a pdf and a png file named after the experiment name specified in the header concatenated with the plotTitle.The function returns the plot name.

See Also

plotBar, ZScorePlotTwo

Examples

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

normedvals <- ZScore(header, dataset, list("SigIntensity", 1))
ZScorePlot(normedvals[[1]], normedvals[[2]], 1, "SigIntensity", "GeneName",
"Normed intensity values per well", 1)