Network editing: removing vertices and connecting their neighbours

Description

This function removes vertices given as vids and connects their neighbours as long as the shortest path beween the neighbours are below the reconnect.threshold.

Usage

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vertexDeleteReconnect(graph, vids, reconnect.threshold = vcount(graph),
  copy.attr = NULL)

Arguments

graph

A reaction network.

vids

Vertex ids to be removed.

reconnect.threshold

If the shortest path between vertices is larger than this threshold, they are not reconnected.

copy.attr

A function, or a list of functions, combine edge attributes. Edge attributes of new edges (between reconnected neighbours) are obtained by combining original edges attributes along the shortest path between reconnected neighbors.

Value

A modified graph.

Author(s)

Ahmed Mohamed

See Also

Other Network processing methods: expandComplexes, makeReactionNetwork, rmSmallCompounds, simplifyReactionNetwork

Examples

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 ## Remove all reaction vertices from a bipartite metabolic network
	##  keeping only metabolite vertices.
 data(ex_sbml)
 graph <- vertexDeleteReconnect(ex_sbml, vids=which(V(ex_sbml)$reactions))

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