Making a volcano plot

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Description

Makes a volcano plot of the data.

Usage

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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

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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)

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