a4 (version 1.20.0)

volcanoplotter: Workhorse function for the different volcanoPlot methods

Description

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.

Usage

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")

Arguments

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".

Value

• a volcanoplot is drawn to the current device

See Also

volcanoPlot-methods