load_network: is a helper function to load networks from files

In SDDE: Shortcuts, Detours and Dead Ends (SDDE) Path Types in Genome Similarity Networks

Description

This function allows the user to load the network files. Note that standard igraph functions can be also used.

Usage

load_network(filename_or_df, filename_tax_or_df, edge_weight)

Arguments

filename_or_df	the file containing an undirected list of nodes in tabular format (node1, node2, edge weight)
filename_tax_or_df	an additional file containing taxa information for each node
edge_weight	how to treat the edge weight: 'equal', 'proportional' or 'inverse' (default: equal)

Value

This function return generic igraph objects suitable for use in the SDDE package.

Examples

	## Load a network from files. 
	## Not run: 
		network=load_network('graph.txt','graph_tax.txt','equal')
		info_network(network$g1,network$g2);
	
## End(Not run)
	# We expect the network to be a series of nodes as tab-separated values.
	#
	# Example graph.txt:
	# node1	node2  edge weight	
	# x1	x2	   	1
	# x2	x3		1
	# x3	x6		1
	# x1	x5		1
	# x5	x6		1	
	#
	# Example graph_tax.txt
	# x1	plasmid 
	# x2	plasmid
	# x3	bacteria
	# x4	plasmid
	# x5	bacteria
	# x6	virus

SDDE documentation built on May 1, 2019, 9:01 p.m.