Description Usage Arguments Examples

Functions to compute the pathway structure of different states within a network with testing pathway structure with permutation analysis. Uses shortest paths to compute the structure between nodes of differing states. Shortest paths are computed in advance where possible to reduce computational redundancy.

1 2 3 4 5 6 7 8 9 | ```
test.structure(graph, target_node, source_node, shortest.paths.in = NULL)
matrix.structure(graph, target_vec, source_vec,
pathway_structure_nodes = NULL, shortest.paths.in = NULL,
remove_intersect = T)
permutation.structure(graph, target, source, universe,
shortest.paths.in = NULL, reps = 1000, fixed_intersect = FALSE,
remove_intersect = T)
``` |

`graph` |
An |

`shortest.paths.in` |
Defaults to NULL leading to computing the shortest paths from the input graph where necessary, these may be given as computed in advance (or passed from higher functions) to reduce computational redundancy. |

`pathway_structure_nodes` |
Defaults to NULL as uses all nodes in the graph. Gives the nodes for which paths are used to evaluate pathway structure. |

`remove_intersect` |
logical. Defaults to TRUE. Whether the intersecting states are used in computing the number of upstream or downstream events. |

`target, target_node, target_vec` |
string: vector of target states for testing pathway structure. Must be a single string for target_node. These are cross referenced against V(graph)$name. |

`source, source_node, source_vec` |
string: vector of source states for testing pathway structure. Must be a single string for source_node. These are cross referenced against V(graph)$name. |

`universe` |
string vector of potential nodes to be assigned target and\/or source states. This may be V(graph)$name, and subset thereof, or a larger pool of nodes to assign states for permutation analysis. |

`reps` |
scalar numeric. Number of permutations to statistically test the structure of the network. |

`fixed_intersect` |
logical. Defaults to FALSE. Whether number of intersecting states is fixed to the same in permutations as the input states. |

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ```
#generate example graphs
library("igraph")
g1 <- make_ring(10)
V(g1)$name <- letters[1:10]
g2 <- make_star(10)
V(g2)$name <- letters[1:10]
#test pathway structure between two points
test.structure(g1, "a", "c")
test.structure(g2, "a", "c")
#test pathway structure between two vectors of points
matrix.structure(g1, letters[1:5], letters[5:7])
matrix.structure(g2, letters[1:5], letters[5:7])
#test pathway structure between two vectors of points with permutations
permutation.structure(g1, letters[1:5], letters[5:7], letters)
permutation.structure(g2, letters[1:5], letters[5:7], letters)
``` |

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