R:cnetplot的使用

cnetplot用于Gene-Concept Network,将位于一个GO Terms下的基因用线连接起来。

cnetplot(x, showCategory = 5, foldChange = NULL, layout = "kk", ...)

## S4 method for signature 'enrichResult'
cnetplot(x, showCategory = 5, foldChange = NULL, layout = "kk", ...)

## S4 method for signature 'gseaResult'
cnetplot(x, showCategory = 5, foldChange = NULL, layout = "kk", ...)

cnetplot.enrichResult(
  x,
  showCategory = 5,
  foldChange = NULL,
  layout = "kk",
  colorEdge = FALSE,
  circular = FALSE,
  node_label = "all",
  ...
)

gene就是差异基因对应的向量,keyType指定基因ID的类型,默认为ENTREZID,  该参数的取值可以参考keytypes(org.Hs.eg.db)的结果, 建议采用ENTREZID, OrgDb指定该物种对应的org包的名字,ont代表GO的3大类别,BP, CC, MF;  pAdjustMethod指定多重假设检验矫正的方法,cufoff指定对应的阈值,readable=TRUE代表将基因ID转换为gene  symbol。

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