First computes of each node in a graph. Then adds the centrality score as an node attribute.
graph_centrality(
graph,
fun = igraph::harmonic_centrality,
col = "centrality",
...
)A graph object
The centrality function to use. Default is harmonic_centrality.
Name of the new node attribute to store the centrality score.
Additional arguments passed to the centrality function
(sim_fun).
Graph object with centrality added as a new node attribute.
filename <- system.file("extdata", "eds_marfan_kg.tar.gz", package = "monarchr")
g <- file_engine(filename) |>
fetch_nodes(query_ids = "MONDO:0007525") |>
expand(predicates = "biolink:has_phenotype",
categories = "biolink:PhenotypicFeature")|>
expand(categories = "biolink:Gene")
g <- graph_centrality(g)
#> Computing node centrality.
nodes(g)$centrality
#> Ehlers-Danlos syndrome, arthrochalasia type
#> 48
#> Hyperextensible skin
#> 0
#> Joint hypermobility
#> 0
#> Inguinal hernia
#> 0
#> Thin skin
#> 0
#> Bruising susceptibility
#> 0
#> Soft, doughy skin
#> 0
#> Poor wound healing
#> 0
#> Atrophic scars
#> 0
#> Joint dislocation
#> 0
#> Pes planus
#> 0
#> Hallux valgus
#> 0
#> Scoliosis
#> 0
#> Generalized hypotonia
#> 1
#> Delayed gross motor development
#> 0
#> Joint subluxation
#> 1
#> Kyphosis
#> 0
#> Hip dislocation
#> 0
#> Breech presentation
#> 0
#> Hypotonia
#> 0
#> Micrognathia
#> 0
#> Congenital bilateral hip dislocation
#> 1
#> Retrognathia
#> 0
#> Premature osteoarthritis
#> 0
#> Malar flattening
#> 0
#> Osteopenia
#> 0
#> Epicanthus
#> 0
#> Depressed nasal bridge
#> 0
#> Delayed closure of the anterior fontanelle
#> 0
#> Mutism
#> 0
#> Aphasia
#> 0
#> Coxa valga
#> 0
#> Coxa vara
#> 0
#> Severe short stature
#> 0
#> Avascular necrosis of the capital femoral epiphysis
#> 0
#> Echolalia
#> 0
#> Scarring
#> 0
#> Femoral hernia
#> 0
#> Abnormality of subcutaneous fat tissue
#> 0
#> Hip dysplasia
#> 0
#> Joint stiffness
#> 0
#> Hypertelorism
#> 0
#> Midface retrusion
#> 0
#> Increased susceptibility to fractures
#> 0
#> Congenital knee dislocation
#> 0
#> Contracture of the proximal interphalangeal joint of the 2nd finger
#> 0
#> Mild short stature
#> 0
#> Contracture of the proximal interphalangeal joint of the 3rd finger
#> 0
#> Muscle flaccidity
#> 0
#> COL1A1
#> 25
#> COL1A2
#> 25