R:cnetplot的使用

05/16/2020 16:26 • R • 阅读 619

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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