Search paths between resources

searchPath allows to search the first k-th shortest paths between resources.

searchPath(graph, ...)

# S4 method for class 'igraph'
searchPath(graph, by, k = 1, include = NULL, exclude = NULL, res.name = NULL)

Arguments

graph

An igraph object.

...

Unused.

by

A formula specifying the path to search.

k

Numeric scalar. The kth shortest paths to search. (Default: 1)

include

Character vector. Nodes to cross in the path. (Default: NULL)

exclude

Character vector. Nodes to avoid in the path. (Default: NULL)

res.name

Character vector. Names of resources to include in the graph. (Default: NULL)

Value

A message.

Examples

# Retrieve resource graph
graph <- ariadne()

# Search first 5 paths from ko to ec
searchPath(graph, ko ~ ec, k = 5)
#> Path 1:
#> ko -(KEGG)-> ec
#> 
#> Path 2:
#> ko -(ChocoPhlAn)-> uniref90 -(UniProt)-> ec
#> 
#> Path 3:
#> ko -(ChocoPhlAn)-> uniref50 -(UniProt)-> ec
#> 
#> Path 4:
#> ko -(ChocoPhlAn)-> uniref90 -(ChocoPhlAn)-> ec
#> 
#> Path 5:
#> ko -(ChocoPhlAn)-> uniref50 -(ChocoPhlAn)-> ec
#> 

# Search first path including uniref90
searchPath(graph, taxname ~ ko, include = "uniref90")
#> Path 1:
#> taxname -(UniProt)-> uniref90 -(ChocoPhlAn)-> ko
#> 

# Search first 5 paths excluding uniref50 and uniref100
searchPath(graph, taxname ~ ko, k = 5, exclude = "uniref50")
#> Path 1:
#> taxname -(UniProt)-> uniref90 -(ChocoPhlAn)-> ko
#> 
#> Path 2:
#> taxname -(UniProt)-> uniref90 -(UniProt)-> kegg_genes -(KEGG)-> ko
#> 
#> Path 3:
#> taxname -(UniProt)-> taxid -(UniProt)-> uniref90 -(ChocoPhlAn)-> ko
#> 
#> Path 4:
#> taxname -(UniProt)-> uniref90 -(UniProt)-> ec -(KEGG)-> ko
#> 
#> Path 5:
#> taxname -(OTT)-> taxid -(UniProt)-> uniref90 -(ChocoPhlAn)-> ko
#> 

# Search path for a subset of resources
searchPath(graph, uniref90 ~ eggnog, k = 3, res.name = "ChocoPhlAn")
#> Path 1:
#> uniref90 -(ChocoPhlAn)-> eggnog
#> 
#> Path 2:
#> uniref90 -(ChocoPhlAn)-> uniref50 -(ChocoPhlAn)-> eggnog
#> 
#> Path 3:
#> uniref90 -(ChocoPhlAn)-> pfam -(ChocoPhlAn)-> uniref50 -(ChocoPhlAn)-> eggnog
#>