ggnetwork: generate network based on Enrichment results
In hurlab/RichR: Function Enrichment analysis and Network construction

ggnetwork_internal

R Documentation

generate network based on Enrichment results

Description

generate network based on Enrichment results

network for Enrichment results

Usage

ggnetwork_internal(
  object = object,
  gene = 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 = ",",
  ...
)

## S4 method for signature 'richResult'
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 = ",",
  ...
)

## S4 method for signature 'data.frame'
ggnetwork(
  object,
  gene = NULL,
  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 = ",",
  ...
)

## S4 method for signature 'GSEAResult'
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`	data.frame object
`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`	Character string giving the output file format
`label.color`	label color
`label.size`	label size
`layout`	layout method ('fruchtermanreingold','kamadakawai','target','circle')
`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
`sep`	character string used to separate the genes when concatenating
`label.font`	label font