ggnetplot: richplot for Enrichment result

In hurlab/RichR: Function Enrichment analysis and Network construction

richplot for Enrichment result

Description

richplot for Enrichment result

richplot for Enrichment result

Usage

## S4 method for signature 'data.frame'
ggnetplot(
  object,
  top = 50,
  pvalue = 0.05,
  padj = NULL,
  usePadj = TRUE,
  useTerm = TRUE,
  low = "orange",
  high = "red",
  writeCyt = FALSE,
  cytoscapeFile = "network-file-for-cytoscape.txt",
  label.color = "black",
  label.size = 2,
  node.shape = NULL,
  layout = "fruchtermanreingold",
  savefig = FALSE,
  filename = "network",
  width = 7,
  height = 7,
  node.alpha = 0.7,
  repel = TRUE,
  segment.size = 0.2,
  sep = ","
)

## S4 method for signature 'GSEAResult'
ggnetplot(
  object,
  top = 50,
  pvalue = 0.05,
  padj = NULL,
  usePadj = TRUE,
  useTerm = TRUE,
  low = "orange",
  high = "red",
  writeCyt = FALSE,
  cytoscapeFile = "network-file-for-cytoscape.txt",
  label.color = "black",
  label.size = 2,
  node.shape = NULL,
  layout = "fruchtermanreingold",
  savefig = FALSE,
  filename = "network",
  width = 7,
  height = 7,
  node.alpha = 0.7,
  repel = TRUE,
  segment.size = 0.2,
  sep = ","
)

Arguments

object	richResult or dataframe
top	number of terms to show (default: 50)
pvalue	cutoff p value for enrichment result
padj	cutoff p adjust value for enrichment result
usePadj	use adjust p value for the color or not
useTerm	use terms for nodes (default: TRUE)
low	color used for small value
high	color used for large value
writeCyt	write out the cytoscape file
cytoscapeFile	output cytoscape File
label.color	label color
label.size	label size
node.shape	shape of the node
layout	layout method ('fruchtermanreingold','kamadakawai','target','circle')
savefig	save figures or not
filename	output figure name
width	width for output figure
height	height for output figure
node.alpha	alpha-transparency scales
repel	use ggrepel text function or not
segment.size	segment size for ggrepel text
sep	character string used to separate the genes when concatenating

Author(s)

Kai Guo

Examples

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

## End(Not run)
## Not run: 
hsako<-buildAnnot(species="human",keytype="SYMBOL",anntype = "KEGG")
hsako<-as.data.frame(hsako)
name=sample(unique(hsako$GeneID),1000)
gene<-rnorm(1000)
names(gene)<-name
res<-richKEGG(gene,object = hsako)
ggnetplot(res)

## End(Not run)

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