# Draw a Volcano Plot

### Description

This function draws a volcano plot, a graph that allows to simultaneously assess the statistical and biological significance of differential expression for the given genes.

### Arguments

`x` |
either an object of class 'tTest', 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 |

`y` |
should not be given if an object of class 'tTest' 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 |

`topPValues` |
top n points that will be included in the points to label based on their low P Values |

`topLogRatios` |
top n points that will be included in the points to label based on their high absolute values of the log ratio |

`smoothScatter` |
use color saturation to indicate dots that are in densely
populated regions of the graph; defaults to |

`xlab` |
label for the x axis (string) |

`ylab` |
label for the y axis (string) |

`main` |
main title for the graph (string) |

`sub` |
subtitle for the graph (string) |

### Details

The set of genes for which labels are displayed is the *union* of the set of
genes that have lowest P-values (`topPValues`

) and the set of genes
that display the highest absolute values for the log ratios (`topLogRatios`

).

### Value

The volcano plot is drawn to the current device.

### Methods

tTest,missing,missing

- x = "tTest", y = "missing", pointLabels = "missing"
volcanoPlot for an object resulting from

`tTest`

tTest,missing,character

- x = "tTest", y = "missing", pointLabels = "character"
volcanoPlot for an object resulting from

`tTest`

numeric,numeric,character

- x = "numeric", y = "numeric", pointLabels = "character"
volcanoPlot for arbitrary numeric vectors containing log ratio values and p values respectively

numeric,numeric,missing

- x = "numeric", y = "numeric", pointLabels = "missing"
volcanoPlot for arbitrary numeric vectors containing log ratio values and p values respectively

limma,missing,missing

- x = "limma", y = "missing", pointLabels = "missing"
volcanoPlot for an object resulting from

`limma2Groups`

limma,missing,character

- x = "tTest", y = "missing", pointLabels = "missing"
volcanoPlot for an object resulting from

`limma2Groups`

### Author(s)

Tobias Verbeke, based on code by Willem Talloen