plotOverrepresentation: Plot overlap of gene sets and core set

In GiANT: Gene Set Uncertainty in Enrichment Analysis

Plot overlap of gene sets and core set

Description

Plots a Venn diagramm of the overlaps of the core set and gene sets in an overrepresentation analysis.

Usage

plotOverrepresentation(
	object,
	signLevel = object$signLevel,
	subset = NULL,
	aggregate = FALSE,
	ask = FALSE,
	...)

Arguments

object	A result of a call to geneSetAnalysis using the predefined analysis analysis.customOverrepresentation or analysis.overrepresentation.
signLevel	Only results with significance level smaller than the given value are included in the venn diagram.
subset	Indices for the results that should be included in the diagram.
aggregate	Specifies whether all gene sets should be plotted in a single Venn diagram (which is possible for at most four gene sets) or whether there should be one Venn diagram for each gene set.
ask	If set to true, the plot function will prompt for a user input for each new plot that is shown on an interactive device (see par("ask")). If aggregate = TRUE, ask is ignored.
...	Further parameters to be passed to vennDiagram.

Value

No return value, called for creating a plot.

See Also

geneSetAnalysis, predefinedAnalyses, gsAnalysis

Examples

	data(exampleData)
  # use the absolute correlation as a gene-level statistic
  stat <- abs(apply(countdata,1,cor,y = labels))
  # define the core set as the 25% genes with the highest correlation
  coreSet <- rownames(countdata)[tail(order(stat), 25)]
  
  # perform an overrepresentation analysis
  resOverrep <- geneSetAnalysis(
  	dat = countdata,
  	geneSets = pathways,
  	analysis = analysis.customOverrepresentation(),
  	coreSet = coreSet,
  	adjustmentMethod = "fdr")
  
  # plot a Venn diagram
  plotOverrepresentation(resOverrep, subset = 1:3, aggregate = TRUE)

GiANT documentation built on Sept. 11, 2024, 9:16 p.m.