complete_trace: return properties of a single path in two given networks...

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

Description

This function is equivalent to the complete_network function, but it analyses a single path returning information about the: path type, the enumeration of traversed nodes, the traversed node taxa, the original path length and the augmented path length.

Usage

	complete_trace(g1,g2,
					  taxnames,
					  node1,
					  node2,
					  maxdistance=0,
					  maxtime=3600,
					  maxnode=0,
					  maxcores=1
					) 

Arguments

g1	the original network X
g2	the augmented network Y with additional nodes (all the original nodes from X must be present in the augmented network Y)
taxnames	the taxon name of the nodes added to the original graph (default: we select all nodes that are not in g1)
node1	the from node (either the node name or the node number) of the path to investigate
node2	the to node (either the node name or the node number) of the path to investigate
maxnode	the maximum number of augmented nodes in network Y to take into account (default=0, no maximum number of augmented nodes to take into account. The augmented nodes are sorted by distance to the investigated node pairs by the algorithm.)
maxtime	the maximum search time per pathway (default=3600 seconds)
maxdistance	the maximum search distance to the added nodes in network Y (default=0, no maximum distance for augmented nodes to take into account)
maxcores	maximum number of cores to use (default=1, use 0 to use half of the total cores available )

Value

This function returns a list containing the from and to node names, the path type (Shortcut, Detour, Dead end and Equal paths or disconnected node), the original path length, the augmented path length, the traversed path nodes and the path_visited_taxa (taxa of each visited node).

Examples

## Searching the sample data for the path type between node x1 and x5
data(Sample_1)
##
## Not run: complete_trace(g1,g2,node1="x1", node2="x5")
## Expected results:
## $from
## [1] "x1"
## $to
## [1] "x5"
## $path_type
## [1] "Detour"
## $original_path_length
## [1] 2
## $augmented_path_length
## [1] 3
## $path
## [1] "x1" "x14" "x6" "x5" 
## $path_visited_taxa
## [1] 1 2 1 1

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