volcanoPlot-methods: Draw a Volcano Plot

In a4Base: Automated Affymetrix Array Analysis Base Package

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.

Usage

## S4 method for signature 'tTest,missing,missing'
volcanoPlot(
  x,
  y,
  pointLabels,
  topPValues = 10,
  topLogRatios = 10,
  smoothScatter = TRUE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  newpage = TRUE,
  additionalPointsToLabel = NULL,
  additionalLabelColor = "red"
)

## S4 method for signature 'tTest,missing,character'
volcanoPlot(
  x,
  y,
  pointLabels,
  topPValues = 10,
  topLogRatios = 10,
  smoothScatter = TRUE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  newpage = TRUE,
  additionalPointsToLabel = NULL,
  additionalLabelColor = "red"
)

## S4 method for signature 'limma,missing,missing'
volcanoPlot(
  x,
  y,
  pointLabels,
  topPValues = 10,
  topLogRatios = 10,
  smoothScatter = TRUE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  newpage = TRUE,
  additionalPointsToLabel = NULL,
  additionalLabelColor = "red"
)

## S4 method for signature 'limma,missing,character'
volcanoPlot(
  x,
  y,
  pointLabels,
  topPValues = 10,
  topLogRatios = 10,
  smoothScatter = TRUE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  newpage = TRUE,
  additionalPointsToLabel = NULL,
  additionalLabelColor = "red"
)

## S4 method for signature 'numeric,numeric,character'
volcanoPlot(
  x,
  y,
  pointLabels,
  topPValues = 10,
  topLogRatios = 10,
  smoothScatter = TRUE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  newpage = TRUE,
  additionalPointsToLabel = NULL,
  additionalLabelColor = "red"
)

## S4 method for signature 'numeric,numeric,missing'
volcanoPlot(
  x,
  y,
  pointLabels,
  topPValues = 10,
  topLogRatios = 10,
  smoothScatter = TRUE,
  xlab = NULL,
  ylab = NULL,
  main = NULL,
  sub = NULL,
  newpage = TRUE,
  additionalPointsToLabel = NULL,
  additionalLabelColor = "red"
)

Arguments

x	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 gene
y	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
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 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"

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.

Author(s)

Tobias Verbeke, based on code by Willem Talloen

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.