gnet: Draw network with ggplot2 style

Description Usage Arguments Author(s)

Description

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

Usage

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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 16, 2020, 10:24 p.m.