\name{volcanoPlot-methods} \alias{volcanoPlot-methods} \alias{volcanoPlot,tTest,missing,missing-method} \alias{volcanoPlot,tTest,missing,character-method} \alias{volcanoPlot,numeric,numeric,character-method} \alias{volcanoPlot,numeric,numeric,missing-method} \alias{volcanoPlot,limma,missing,missing-method} \alias{volcanoPlot,limma,missing,character-method} \title{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. } \section{Methods}{ \describe{ tTest,missing,missing \item{x = "tTest", y = "missing", pointLabels = "missing"}{volcanoPlot for an object resulting from \code{tTest}} tTest,missing,character \item{x = "tTest", y = "missing", pointLabels = "character"}{volcanoPlot for an object resulting from \code{tTest}} numeric,numeric,character \item{x = "numeric", y = "numeric", pointLabels = "character"}{volcanoPlot for arbitrary numeric vectors containing log ratio values and p values respectively} numeric,numeric,missing \item{x = "numeric", y = "numeric", pointLabels = "missing"}{volcanoPlot for arbitrary numeric vectors containing log ratio values and p values respectively} limma,missing,missing \item{x = "limma", y = "missing", pointLabels = "missing"}{volcanoPlot for an object resulting from \code{limma2Groups}} limma,missing,character \item{x = "tTest", y = "missing", pointLabels = "missing"}{volcanoPlot for an object resulting from \code{limma2Groups}} } } \arguments{ \item{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} \item{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} \item{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} \item{topPValues}{top n points that will be included in the points to label based on their low P Values} \item{topLogRatios}{top n points that will be included in the points to label based on their high absolute values of the log ratio} \item{smoothScatter}{use color saturation to indicate dots that are in densely populated regions of the graph; defaults to \code{TRUE}} \item{xlab}{label for the x axis (string)} \item{ylab}{label for the y axis (string)} \item{main}{main title for the graph (string)} \item{sub}{subtitle for the graph (string)} } \details{ The set of genes for which labels are displayed is the \emph{union} of the set of genes that have lowest P-values (\code{topPValues}) and the set of genes that display the highest absolute values for the log ratios (\code{topLogRatios}). } \value{ The volcano plot is drawn to the current device. } \author{Tobias Verbeke, based on code by Willem Talloen} \keyword{dplot}