volcanoplotter: Workhorse function for the different volcanoPlot methods
In a4Base: Automated Affymetrix Array Analysis Base Package

Description Usage Arguments Value Author(s)

Workhorse function for the different volcanoPlot methods. 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.

volcanoplotter(
  logRatio,
  pValue,
  pointLabels,
  topPValues = 10,
  topLogRatios = 10,
  logTransformP = TRUE,
  smoothScatter = TRUE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  newpage = TRUE,
  additionalPointsToLabel = NULL,
  additionalLabelColor = "red"
)

`logRatio`	numeric vector of log ratios
`pValue`	numeric vector of P values
`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
`logTransformP`	if `TRUE` (default) -log10(pValue) is used for the plot instead of the raw P values
`smoothScatter`	use color saturation to indicate dots that are in densely populated regions of the graph; defaults to `TRUE`
`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)
`newpage`	should the graph be drawn to a new grid page? Defaults to `TRUE`. This argument is useful for including several volcano plots in one layout.
`additionalPointsToLabel`	Entrez IDs of genes of interest, that will be highlighted on the plot; the color of highlighting is determined by the 'additionalLabelColor' argument.
`additionalLabelColor`	Color used to highlight the 'additionalPointsToLabel'; defaults to "red"