ggnetwork-methods: ggnetwork method

In hurlab/RichR: Function Enrichment analysis and Network construction

ggnetwork method

Description

ggnetwork

Usage

ggnetwork(
  object,
  gene,
  top = 50,
  pvalue = 0.05,
  padj = NULL,
  usePadj = TRUE,
  low = "orange",
  high = "red",
  weightcut = 0.2,
  useTerm = TRUE,
  writeCyt = FALSE,
  cytoscapeFile = NULL,
  cytoscapeFormat = "graphml",
  label.color = "black",
  label.size = 2,
  node.shape = NULL,
  layout = "fruchtermanreingold",
  savefig = FALSE,
  visNet = FALSE,
  smooth = TRUE,
  nodeselect = FALSE,
  edit = FALSE,
  savehtml = FALSE,
  filename = NULL,
  width = 7,
  height = 7,
  segment.size = 0.2,
  node.alpha = 0.7,
  sep = ",",
  ...
)

Arguments

object	richResult,GSEAResult object or dataframe
gene	vector contains gene names or dataframe with DEGs information
top	number of terms to display
pvalue	cutoff value of pvalue (if padj set as NULL)
padj	cutoff value of p adjust value
usePadj	use p adjust value as color or not (should use with padj)
low	color used for small value
high	color used for large value
weightcut	cutoff valule for edge
writeCyt	write out the cytoscape file
cytoscapeFile	output cytoscape File
cytoscapeFormat	output file format ("edgelist", "pajek", "ncol", "lgl", "graphml", "dimacs", "gml", "dot","leda")
label.color	label color
label.size	label size
layout	layout for the network (layout.fruchterman.reingold)
savefig	save the figure or not
filename	figure output name
width	figure width
height	figure height
segment.size	size for label segment
node.alpha	alpha-transparency scales
label.font	label font

Value

ggplot2 object

Examples

## Not run: 
  hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
  gene<-sample(unique(hsako$GeneID),1000)
  res<-richKEGG(gene,kodata = hsako)
  ggnetwork(res)

## End(Not run)

hurlab/RichR documentation built on Feb. 5, 2024, 8:07 p.m.