HTSanalyzeR (version 2.24.0)

viewEnrichMap: Plot a figure of the enrichment map for GSEA or Hypergeometric tests

Description

This is a generic function.

When implemented as the S4 method for objects of class GSCA, this function will plot an enrichment map for GSEA or Hypergeometric test results.

To use this function for objects of class GSCA:

viewEnrichMap(object, resultName="GSEA.results", gscs, ntop=NULL, allSig=TRUE, gsNameType="id", displayEdgeLabel=TRUE, layout= "layout.fruchterman.reingold")

Usage

viewEnrichMap(object, ...)

Arguments

object

an object. When this function is implemented as the S4 method of class GSCA, this argument is an object of class GSCA.

...

other arguments. (see below for the arguments supported by the method of class GSCA)

Value

an object of igraph with all attributes about the enrichement map

Details

The idea of this function is similar to the PLoS one paper by Merico et al.

An enrichment map is a network to help better visualize and interpret the GSEA or Hypergeometric test results. In an enrichment map, the nodes represent gene sets and the edges denote the Jaccard similarity coefficient between two gene sets. Node colors are scaled according to the adjusted p-values (the darker the more significant). For GSEA, nodes are colored by the sign of the enrichment scores (red:+, blue: -). The size of nodes illustrates the size of gene sets, while the width of edges denotes the Jaccard coefficient.

References

Merico, D. et al, Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation, PloS one, 2010, e13984

See Also

plotEnrichMap

Examples

## Not run: 
# library(org.Dm.eg.db)
# library(KEGG.db)
# ##load data for enrichment analyses
# data("KcViab_GSCA")
# ##plot and save the enrichment map
# viewEnrichMap(KcViab_GSCA, gscs=c("GO_MF"), allSig=TRUE, ntop=NULL, gsNameType="id", 
# displayEdgeLabel=FALSE,layout="layout.fruchterman.reingold")
# ##append Gene set terms to results
# KcViab_GSCA<-appendGSTerms(KcViab_GSCA, goGSCs=c("GO_BP","GO_MF","GO_CC"), 
# keggGSCs=c("PW_KEGG"))
# viewEnrichMap(KcViab_GSCA, gscs=c("GO_MF"), allSig=TRUE, ntop=NULL, gsNameType="term", 
# displayEdgeLabel=FALSE,layout="layout.fruchterman.reingold")
# ## End(Not run)