Draw a Volcano Plot

Share:

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 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)

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

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.