volcanoPlot: Draw a Volcano Plot

Description

Generic function to draw a volcano plot. A volcano plot is a graph that allows to simultaneously assess the P values (statistical significance) and log ratios (biological difference) of differential expression for the given genes.

Usage

volcanoPlot(x, y, pointLabels, ...)

Arguments

either an object of class 'tTest', of class 'limma' or a numeric vector of log ratios, i.e. the log of the fold change values; the names of the logRatio vector will be used to display the names of the most interesting genes

should not be given if an object of class 'tTest' or 'limma' is passed as argument 'x'; if 'x' is a numeric vector of log ratios, 'y' should be given and should be a numeric vector of P-values indicating the statistical significance

pointLabels

Labels for points on the volcano plot that are interesting taking into account both the x and y dimensions; typically this is a vector of gene symbols; most methods can access the gene symbols directly from the object passed as 'x' argument; the argument allows for custom labels if needed

...

further arguments to specific methods

Value

The volcano plot is drawn to the current device.

References

Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix Microarrays, Chapman & Hall/CRC, pp. 148 - 153.

Examples

Run this code

if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)
  ALL$BTtype <- as.factor(substr(ALL$BT,0,1))

  tTestRes <- tTest(object = ALL,	groups = "BTtype", probe2gene = TRUE)
  volcanoPlot(tTestRes)  
}