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Convert KEGG pathway to graph

Source: R/exported_functions.R
kegg_to_graph.Rd

Convert KEGG pathway to graph

Usage

kegg_to_graph(
  pathway_id,
  kgml_file = NULL,
  scaling_factor = 3,
  verbose = FALSE
)

Arguments

pathway_id

KEGG pathway ID (e.g., "hsa04110").

kgml_file

Optional local path to a KGML file. If provided, the function will use this file instead of downloading it.

scaling_factor

Numeric scaling factor for node sizes (default: 2).

verbose

Logical, if TRUE, print additional messages.

Value

An igraph object representing the KEGG pathway graph.

Details

This function downloads the KGML file for a given KEGG pathway ID, parses it and constructs an igraph object.

Examples

pathway_graph <- kegg_to_graph(
  pathway_id = "hsa04110"
)
#> adding rname 'https://rest.kegg.jp/get/hsa04110/kgml'
#> 
#> adding rname 'https://rest.kegg.jp/list/compound'
#> 
#> adding rname 'https://rest.kegg.jp/list/glycan'
#> 
#> adding rname 'https://rest.kegg.jp/list/ko'
#> 
#> adding rname 'https://rest.kegg.jp/list/enzyme'
#> 
#> adding rname 'https://rest.kegg.jp/list/reaction'
#>