bp2.minimum.spanning.tree: Solve minimum spanning trees for follower lists
In microbiome/biopax2: BioPAX level 2 S4 object model

Description Usage Arguments Value Note Author(s) Examples

Solves minimum spanning tree for a graph of BioPAX classes based on follower list returned by bp2.find.followers. This is useful for solving minimum distances between model objects. The types of relations that are considered are selected

1 2	tree <- bp2.minimum.spanning.tree(follower.list, root, max.depth=length(follower.list)) bp2.print.tree(tree)

`follower.list`	Follower list representation of bp2 model object ids as returned by `bp2.follower.list objects.`
`root`	Index of root vertex in follower.list
`max.depth`	Maximum distance from root, after which the algorithm is terminated.
`tree`	Spanning tree `data.frame` returned by `bp2.minimum.spanning.tree`

Returns data.frame that contains columns of same length than follower.list: id, parent and distance. id is the index in the follower.list, parent is the id of parent vertex for the given id and dist is the distance from root.

This function is not very useful for general use until bp2.find.followers supports configuration of include.slots argument separately for different class types. Use bp2.find.nodes for constructing interesting graphs based on BioPAX data.

Ossi Koivistoinen

my.bp2 <- bp2.create.model(...)
complexes <- bp2.get.instances.of(my.bp2@all.objects, "bp2.complex")
followers <- bp2.find.followers(pathways, include.slots=''components,physicalEntity'') 
tree <- bp2.minimum.spanning.tree(followers, 1)
bp2.print.tree(tree)