ZScorePlot {RNAither} | R Documentation

## 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)

[Package RNAither version 2.35.0 Index]