tool.subgraph.find {Mergeomics} | R Documentation |
tool.subgraph.find
finds the edge lists between given seed nodes
and their neighbors
tool.subgraph.find(seeds, edgemap, heads, visited)
seeds |
seed nodes' indices |
edgemap |
list of adjacent edge information for entire graph.
|
heads |
list of either head (destination) or tail (source) nodes of the entire graph |
visited |
flag holding already visited node indices during neighborhood searching |
neighbors |
neighbor edge lists of seed nodes (for either tails or heads) |
Neighbor edge lists of the seed nodes should be obtained separately for tail and head nodes.
Ville-Petteri Makinen
data(job_kda_analyze) depth <- 1 direction <- 0 ## Take one or multiple center nodes (seeds) to search the neighborhoods: ## e.g. take the first node in the graph as the seed, find its neighborhood: center.node = job.kda$graph$nodes[1] ## Convert center node (seed) names to indices: nodes <- job.kda$graph$nodes ranks <- match(center.node, nodes) ranks <- ranks[which(ranks > 0)] ## we already know that rank is 1, since we took the first node in the graph ## as an example: ranks <- as.integer(ranks) ## Find edges to adjacent nodes. (both up- and down-stream searches) visited <- ranks foundT <- tool.subgraph.find(ranks, job.kda$graph$tail2edge, job.kda$graph$heads, visited) foundH <- tool.subgraph.find(ranks, job.kda$graph$head2edge, job.kda$graph$tails, visited)