cnetplot {enrichplot}R Documentation

cnetplot

Description

Gene-Concept Network

Usage

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", ...)

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

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

Arguments

x

enrichment result

showCategory

number of enriched terms to display

foldChange

fold Change

layout

layout of the network

...

additional parameters

colorEdge

whether coloring edge by enriched terms

circular

whether using circular layout

node_label

select which labels to be displayed. one of 'category', 'gene', 'all' and 'none', default is "all".

Details

plot linkages of genes and enriched concepts (e.g. GO categories, KEGG pathways)

Value

ggplot object

Author(s)

Guangchuang Yu

Examples

library(DOSE)
data(geneList)
de <- names(geneList)[1:100]
x <- enrichDO(de)
cnetplot(x)

[Package enrichplot version 1.8.1 Index]