R: pairwise_termsim

pairwise_termsim {enrichplot}

R Documentation

pairwise_termsim

Description

Get the similarity matrix

Usage

pairwise_termsim(x, method = "JC", semData = NULL, showCategory = 30)

## S4 method for signature 'enrichResult'
pairwise_termsim(x, method = "JC", semData = NULL, showCategory = 200)

## S4 method for signature 'gseaResult'
pairwise_termsim(x, method = "JC", semData = NULL, showCategory = 200)

## S4 method for signature 'compareClusterResult'
pairwise_termsim(x, method = "JC", semData = NULL, showCategory = 200)

pairwise_termsim.enrichResult(
  x,
  method = "JC",
  semData = NULL,
  showCategory = 200
)

pairwise_termsim.compareClusterResult(
  x,
  method = "JC",
  semData = NULL,
  showCategory = 200
)

Arguments

`x`	enrichment result.
`method`	method of calculating the similarity between nodes, one of "Resnik", "Lin", "Rel", "Jiang" , "Wang" and "JC"(Jaccard similarity coefficient) methods.
`semData`	GOSemSimDATA object
`showCategory`	number of enriched terms to display

Details

This function add similarity matrix to the termsim slot of enrichment result.

Examples

## Not run: 
    library(clusterProfiler)
    library(org.Hs.eg.db)
    library(enrichplot)
    library(GOSemSim)
    library(DOSE)
    data(geneList)
    gene <- names(geneList)[abs(geneList) > 2]
    ego <- enrichGO(gene  = gene,
        universe      = names(geneList),
        OrgDb         = org.Hs.eg.db,
        ont           = "BP",
        pAdjustMethod = "BH",
        pvalueCutoff  = 0.01,
        qvalueCutoff  = 0.05,
        readable      = TRUE)
    d <- godata('org.Hs.eg.db', ont="BP")
    ego2 <- pairwise_termsim(ego, method="Wang", semData = d)
    emapplot(ego2)
    emapplot_cluster(ego2)
   
## End(Not run)

[Package enrichplot version 1.10.2 Index]