volcanoPlot {RNAither} | R Documentation

## Making a volcano plot

### Description

Makes a volcano plot of the data.

### Usage

    volcanoPlot(header, dataset, col4plotx, col4ploty, col4anno, plotTitle, sigLevel, showPlot)

### Arguments

`header` | the header of a dataset file generated with `generateDatasetFile`
`dataset` | an R data frame generated with `generateDatasetFile`
`col4plotx` | a character vector specifying the name of the column containing the intensity values, usually `SigIntensity`
`col4ploty` | a character vector specifying the name of the dataset column containing the corresponding p-values
`col4anno` | a character string specifying the name of the dataset column to be used to define the replicate, e.g. `"GeneName"` or `"Internal_GeneID"`.
`plotTitle` | the plot title
`sigLevel` | the significance level for the p-value, indicating where a horizontal green line will be drawn
`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 intensity values against the negative decadic logarithm of the p-values. A green horizontal line is drawn at the specified significance level.

The plot is saved in 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

`Ttest`

### Examples

    data(exampleHeader, package="RNAither")
    data(pValVec1, package="RNAither")
    data(scoredDataset1, package="RNAither")

    ##for details on the generation of pValVec1 and scoredDataset1, see the example of the Ttest function linked above.

    scoredHits1 <- hitselectionPval(scoredDataset1, pValVec1, "SigIntensity", "pValue.ttest_l", 0.05,
    "GeneName", "pvalue_testfile1.txt")

    hitDataset1 <- scoredHits1[[1]]
    hitvector1 <- scoredHits1[[2]]

    volcano_name <- volcanoPlot(header, hitDataset1, "SigIntensity", "pValue.ttest_l", "GeneName",
    "Volcano Plot", 0.05, 1)

[Package RNAither version 2.28.0 Index]