netmap: Plot network of Terms

Description Usage Arguments Author(s)

View source: R/netmap.R

Description

Plot network of Terms

Usage

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netmap(df, rhs, top = 50, pvalue.cutoff = 0.05, padj.cutoff = NULL,
  weightcut = 0.2, useTerm = TRUE, writeCyt = FALSE,
  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

smooth

use smooth edge for visNetwork

nodeselect

select some interesting node(default:FALSE)

editvis

choose to edit network(default:FALSE)

savevis

save visnetwork to html

savefig

save figure to pdf

filename

output filename

df:

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

rhs:

Enrichment analsyis result

pvalue.cutoff:

the cut-off P value for selecting significant Terms

padj.cutoff:

the cut-off P adjust value for selecting significant Terms

weightcut:

the weight cut value for remove edges

useTerm:

use the Term description or not(defalut:TRUE)

writeCyt:

export file for Cyt software

vertex.label.color:

color of label(default:black)

vertex.label.cex:

size of label(default:0.5)

layout:

layout format (defult:layout.fruchterman.reingold)

visNet:

use VisNetwork method to display network(default:FALSE)

top:

number of Terms you want to display

Author(s)

Kai Guo


hurlab/RichR documentation built on July 30, 2018, 10:13 p.m.