richplot: richplot

In guokai8/EnrichR: Functional Enrichment analysis

Description

plot the sigificant terms and shared genes with network format

Usage

richplot(
  resultFis,
  top = 50,
  pvalue.cutoff = 0.05,
  padj.cutoff = 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 = layout.fruchterman.reingold,
  savefig = FALSE,
  filename = "network",
  width = 7,
  height = 7,
  node.alpha = 0.7,
  repel = TRUE,
  segment.size = 0.2
)

Arguments

resultFis	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
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
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

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