find_all_paths {OmnipathR} | R Documentation |
Finds all paths up to length 'maxlen' between specified groups of vertices. This function is needed only becaues igraph's 'all_shortest_paths' finds only the shortest, not any path up to a defined length.
find_all_paths( graph, start, end, attr = NULL, mode = 'OUT', maxlen = 2, progress = TRUE )
graph |
An igraph graph object. |
start |
Integer or character vector with the indices or names of one or more start vertices. |
end |
Integer or character vector with the indices or names of one or more end vertices. |
attr |
Character: name of the vertex attribute to identify the vertices by. Necessary if 'start' and 'end' are not igraph vertex ids but for example vertex names or labels. |
mode |
Character: IN, OUT or ALL. Default is OUT. |
maxlen |
Integer: maximum length of paths in steps, i.e. if maxlen = 3, then the longest path may consist of 3 edges and 4 nodes. |
progress |
Logical: show a progress bar. Default is FALSE. |
List of vertex paths, each path is a character or integer vector.
interactions <- import_omnipath_interactions() graph <- interaction_graph(interactions) paths <- find_all_paths( graph = graph, start = c('EGFR', 'STAT3'), end = c('AKT1', 'ULK1'), attr = 'name' )