export_to_gephi: Export accnet or igraph object to GraphML format

In irycisBioinfo/PATO: Pangenome Analysis Toolkit

Export accnet or igraph object to GraphML format

Description

This function export a network (accnet or igraph) to universal format graphml.

Usage

export_to_gephi(data, file, cluster)

Arguments

data	accnet or igraph object
file	Filename for network

Note

Big networks (especially accnet networks) can not be visualized in R enviroment. We recomend to use external software such as Gephi or Cytoscape. Gephi can manage bigger networks and the ForceAtlas2 layout can arrange accnet networks up to 1.000 genomes. If accnet object comes from accnet_with_padj() function, the graph files will include the edges-weight proportional to the p-value that associate the protein with the genome.

irycisBioinfo/PATO documentation built on Oct. 19, 2023, 3:07 p.m.