cnetplot: cnetplot

In enrichplot: Visualization of Functional Enrichment Result

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",
  cex_category = 1,
  cex_gene = 1,
  node_label_size = NULL,
  cex_label_category = 1,
  cex_label_gene = 1,
  ...
)

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".
cex_category	number indicating the amount by which plotting category nodes should be scaled relative to the default.
cex_gene	number indicating the amount by which plotting gene nodes should be scaled relative to the default.
node_label_size	size of node label, this parameter has been changed to cex_label_category and cex_label_gene
cex_label_category	scale of category node label size
cex_label_gene	scale of gene node label size

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)

Example output

DOSE v3.16.0  For help: https://guangchuangyu.github.io/software/DOSE

If you use DOSE in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

enrichplot documentation built on Jan. 30, 2021, 2:01 a.m.