dDAGinduce: Function to generate a subgraph of a direct acyclic graph...

In dnet: Integrative Analysis of Omics Data in Terms of Network, Evolution and Ontology

Description

dDAGinduce is supposed to produce a subgraph induced by given vertices, given a direct acyclic graph (DAG; an ontology). The input is a graph of "igraph" or "graphNET" object, a list of the vertices of the graph, and the mode defining the paths to the root of DAG. The resultant subgraph inherits the class from the input one. The induced subgraph contains exactly the vertices of interest and their defined paths to the root of DAG.

Usage

dDAGinduce(
g,
nodes_query,
path.mode = c("all_paths", "shortest_paths", "all_shortest_paths")
)

Arguments

g	an object of class "igraph" or "graphNEL"
nodes_query	the vertices for which the calculation is performed
path.mode	the mode of paths induced by nodes in query. It can be "all_paths" for all possible paths to the root, "shortest_paths" for only one path to the root (for each node in query), "all_shortest_paths" for all shortest paths to the root (i.e. for each node, find all shortest paths with the equal lengths)

Value

• subg: an induced subgraph, an object of class "igraph" or "graphNEL"

Note

For the mode "shortest_paths", the induced subgraph is the most concise, and thus informative for visualisation when there are many nodes in query, while the mode "all_paths" results in the complete subgraph.

See Also

dDAGroot

Examples

## Not run: 
# 1) load HPPA as igraph object
ig.HPPA <-dRDataLoader(RData='ig.HPPA')
g <- ig.HPPA

# 2) randomly select vertices as the query nodes
# the query nodes can be igraph vertex sequences
nodes_query <- sample(V(g),5)
# more commonly, the query nodes can be term id
nodes_query <- sample(V(g),5)$name

# 3) obtain the induced subgraph
# 3a) based on all possible paths (i.e. the complete subgraph induced)
subg <- dDAGinduce(g, nodes_query, path.mode="all_paths")
# 3b) based on shortest paths (i.e. the most concise subgraph induced)
subg <- dDAGinduce(g, nodes_query, path.mode="shortest_paths")

## End(Not run)

Example output

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Loading required package: supraHex
Loading required package: hexbin
'ig.HPPA' (from package 'dnet' version 1.1.4) has been loaded into the working environment (at 2019-08-05 13:06:20)

dnet documentation built on Feb. 20, 2020, 3:01 p.m.