HTSanalyzeR (version 2.24.0)

plotEnrichMap: Plot and save an enrichment map for results of 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 and save an enrichment map for GSEA or Hypergeometric test results.

To use this function for objects of class GSCA:

plotEnrichMap(object, resultName="GSEA.results", gscs, ntop=NULL, allSig=TRUE, gsNameType="id", displayEdgeLabel=TRUE, layout= "layout.fruchterman.reingold", filepath=".", filename="test.png", output="png", ...)

Usage

plotEnrichMap(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)

Details

See help(viewEnrichMap) for more details about the enrichment map for GSEA.

See Also

viewEnrichMap

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
# plotEnrichMap(KcViab_GSCA, gscs=c("GO_MF"), allSig=TRUE, ntop=NULL, gsNameType="id", 
# displayEdgeLabel=FALSE,layout="layout.fruchterman.reingold", filepath="~", 
# filename="GO_MF.pdf",output="pdf", width=8, height=8)
# ## End(Not run)