BioNet (version 1.32.0)

saveNetwork: Save undirected network in various formats

Description

The function saves a graph in a Cytoscape readable format: either in XGMML format, or as two tables, one for the nodes with attributes and one for the edges with attributes, or as .sif file. Or other standard formats like tab separated, .tgf, .net

Usage

saveNetwork(network, name="network", file, type=c("table", "XGMML", "sif", "tab", "tgf", "net"))

Arguments

network

Network to save.

name

Name of the network, only needed for the XGMML format.

file

File to save to.

type

Type in which graph shall be saved.

Details

The format types are "XGMML", "table", "sif", "tab", "tgf" and "net". XGMML (eXtensible Graph Markup and Modeling Language) is an XML format based on GML which is used for graph description. Edges, nodes and their affiliated attributes are all saved in one file. In the table format two tables are created, one for the nodes with attributes and one for the edges with attributes. The sif format creates a .sif file for the network and an node attribute (.NA) or edge attribute (.EA) for each attribute. The name of the attribute is the filename. Tab writes only the edges of the network in a tabular format. Tgf save the network to simple .tgf format. The net format writes a Pajek readable file of the network and the ET type saves the edge tags to file.

Examples

library(DLBCL)
#create small network
library(igraph)
data(interactome) 
interactome <- igraph.from.graphNEL(interactome)
small.net <- subNetwork(V(interactome)[1:16]$name, interactome)
E(small.net)$e.weight <- rep(1,length(E(small.net)))
V(small.net)$n.weight <- rep(2,length(V(small.net)))
summary(small.net)
## Not run: saveNetwork(small.net, file="example_network", name="small.net", type="XGMML")