netmap: Plot network of Terms

Description Usage Arguments Author(s)

Description

Plot network of Terms

Usage

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netmap(
  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.font = 2,
  vertex.label.color = "black",
  vertex.label.cex = 0.5,
  layout = layout.fruchterman.reingold,
  visNet = FALSE,
  smooth = TRUE,
  nodeselect = FALSE,
  editvis = FALSE,
  savevis = FALSE,
  savefig = FALSE,
  filename = "network",
  ...
)

Arguments

df

DGE files (DESeq2 result files) or vector contains gene names

rhs

Enrichment analsyis result

top

number of Terms you want to display

pvalue.cutoff

the cut-off P value for selecting significant Terms

padj.cutoff

the cut-off P adjust value for selecting significant Terms

low

color used for small value

high

color used for large value

weightcut

the weight cut value for remove edges

useTerm

use the Term description or not(defalutTRUE)

writeCyt

export file for Cyt software

vertex.label.color

color of label(defaultblack)

vertex.label.cex

size of label(default0.5)

layout

layout format (defultlayout.fruchterman.reingold)

visNet

use VisNetwork method to display network(defaultFALSE)

smooth

use smooth edge for visNetwork

nodeselect

select some interesting node(defaultFALSE)

editvis

choose to edit network(defaultFALSE)

savevis

save visnetwork to html

savefig

save figure to pdf

filename

output filename

Author(s)

Kai Guo


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