Compute transitive reduction over a predicate.

Computes the transitive reduction of a graph, treating the specified predicate as transitive.

transitive_reduction(g, predicate = "biolink:subclass_of")

Arguments

g

The tbl_kgx graph to compute on.

predicate

The edge predicate to reduce over.

Value

Graph with transitive edges added.

See also

transitive_closure(), roll_up(), transfer(), descendants(), ancestors()

Examples

library(dplyr)
library(tidygraph)
data(eds_marfan_kg)

g <- eds_marfan_kg |>
    fetch_nodes(name == "Tall stature") |>
    expand_n(predicates = "biolink:subclass_of", direction = "out", n = 3) |>
    bind_edges(data.frame(
        from = 2,
        to = 9,
        predicate = "biolink_subclass_of",
        primary_knowledge_source = "hand_annotated"
    ))
#> Initial graph size:1nodes ||0edges
#> Expanding graph: iteration 1/3
#> Graph size:3nodes ||2edges
#> Expanding graph: iteration 2/3
#> Graph size:7nodes ||7edges
#> Expanding graph: iteration 3/3
#> Graph size:13nodes ||15edges

plot(g, edge_color = primary_knowledge_source)
#> Using "sugiyama" as default layout


g_closed <- g |>
    transitive_closure(predicate = "biolink:subclass_of")

plot(g_closed, edge_color = primary_knowledge_source)
#> Using "sugiyama" as default layout


g_reduced <- g_closed |>
    transitive_reduction()

plot(g_reduced, edge_color = primary_knowledge_source)
#> Using "sugiyama" as default layout