neighborhood: Return the neighborhood set of given vertices

In KEGGgraph: KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor

Description

The function returns the neighborhood set of given vertices in the form of list. Optionally user can choose to include the given vertices in the list, too.

Usage

neighborhood(graph, index, return.self = FALSE)

Arguments

graph	An object of graphNEL
index	Names of nodes, whose neighborhood set should be returned
return.self	logical, should the vertex itself also be returned?

Details

Let v be a vertex in a (di)graph, the out-neighborhood or successor set (N+(v), x belongs to V(G) and v->x) and the in-neighborhood or predecessor set (N-(v), x belongs to V(G) and x->v) are jointly returned.

The returned list is indexed by the given node indices, NULL is returned in case of non-existing node.

The nodes are unique, that is, duplicated nodes are removed in results.

Value

A list indexed by the given node indices, each entry containing the neighborhood set of that node (or furthermore including that node).

Author(s)

Jitao David Zhang <[e-mail]>

References

D.B. West. Introduction to Graph Theory, Second Edition. Prentice Hall, 2001

Examples

  V <- c("Hamburg","Stuttgart","Berlin","Paris","Bremen")
  E <- list("Hamburg"=c("Berlin","Bremen"),
            "Stuttgart"=c("Berlin","Paris"),
            "Berlin"=c("Stuttgart","Bremen"),
            "Paris"=c("Stuttgart"),
            "Bremen"=c("Hamburg","Berlin"))
  g <- new("graphNEL", nodes=V, edgeL=E, edgemode="directed")
  if(require(Rgraphviz) & interactive()) {
    plot(g, "neato")
  }

  ## simple uses
  neighborhood(g, "Hamburg")
  neighborhood(g, c("Hamburg", "Berlin","Paris"))

  ## in case of non-existing nodes
  neighborhood(g, c("Stuttgart","Ulm"))

  ## also applicable to non-directed graphs
  neighborhood(ugraph(g), c("Stuttgart","Berlin"))

Example output

Attaching package: 'KEGGgraph'

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

    plot

Loading required package: Rgraphviz
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: grid
$Hamburg
[1] "Berlin" "Bremen"

$Hamburg
[1] "Berlin" "Bremen"

$Berlin
[1] "Stuttgart" "Bremen"    "Hamburg"  

$Paris
[1] "Stuttgart"

$Stuttgart
[1] "Berlin" "Paris" 

$Ulm
NULL

$Stuttgart
[1] "Berlin" "Paris" 

$Berlin
[1] "Hamburg"   "Stuttgart" "Bremen"   

KEGGgraph documentation built on Nov. 8, 2020, 5:42 p.m.