gnet: Draw network with ggplot2 style

In guokai8/EnrichR: Functional Enrichment analysis

Description

gnet provides method to draw the enrichment results with a ggplot2 style network

Usage

gnet(
  df,
  rhs,
  top = 50,
  pvalue.cutoff = 0.05,
  padj.cutoff = NULL,
  low = "orange",
  high = "red",
  weightcut = 0.2,
  useTerm = TRUE,
  writeCyt = FALSE,
  cytoscapeFile = "network-file-for-cytoscape.txt",
  vertex.label.color = "black",
  vertex.label.cex = 2,
  vertex.node.shape = NULL,
  layout = layout.fruchterman.reingold,
  savefig = FALSE,
  filename = "network",
  width = 7,
  height = 7,
  segment.size = 0.2,
  node.alpha = 0.7,
  ...
)

Arguments

df	Differential expression result or vector of genes
rhs	Enrichment results
top	number of terms to show (default: 50)
pvalue.cutoff	cutoff p value for enrichment result
padj.cutoff	cutoff p adjust value for enrichment result
low	color used for small value
high	color used for large value
weightcut	cutoff value for the edges
useTerm	use terms for nodes (default: TRUE)
writeCyt	write out the cytoscape file
cytoscapeFile	output cytoscape File
vertex.label.color	label color
vertex.label.cex	label size
vertex.node.shape	vector of shape and names of the vector should be the terms (default: 20)
layout	layout method
savefig	save figures or not
filename	output figure name
width	width for output figure
height	height for output figure
segment.size	size for label segment
node.alpha	alpha-transparency scales

Author(s)

Kai Guo

guokai8/EnrichR documentation built on May 18, 2020, 5:29 a.m.