mnetmap: plot combine network of Terms

Description Usage Arguments Author(s)

View source: R/netmap_m.R

Description

plot combine network of Terms

Usage

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mnetmap(df, gores = NULL, kores = NULL, rores = NULL, pfres = NULL,
  itres = NULL, top = NULL, top.display = NULL, pvalue.cutoff = 0.05,
  padj.cutoff = NULL, visNet = F, weightcut = 0.2, useTerm = TRUE,
  layout = NULL, vertex.label.cex = 0.5, gnet = FALSE, ...)

Arguments

df:

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

gores:

GO Enrichment analsyis result

kores:

KEGG Enrichment analsyis result

rores:

Reactome Pathway Enrichment analsyis result

pfres:

PFAM Enrichment analysis result result

itres:

InterPro Enrichment analysis 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(default:the total number of all Significant number)

Author(s)

Kai Guo


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