find_all_paths {OmnipathR} | R Documentation

## All paths between two groups of vertices

### Description

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.

### Usage

    find_all_paths(
        graph,
        start,
        end,
        attr = NULL,
        mode = 'OUT',
        maxlen = 2,
        progress = TRUE
    )

### Arguments

`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.

### Value

List of vertex paths, each path is a character or integer vector.

### See Also

- `interaction_graph`

- `enzsub_graph`

- `giant_component`

### Examples

    interactions <- import_omnipath_interactions()
    graph <- interaction_graph(interactions)
    paths <- find_all_paths(
        graph = graph,
        start = c('EGFR', 'STAT3'),
        end = c('AKT1', 'ULK1'),
        attr = 'name'
    )

[Package OmnipathR version 3.2.0 Index]