
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")
viewEnrichMap(object, ...)
GSCA
)
igraph
with all attributes about the enrichement map
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.
plotEnrichMap
## 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)
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