This function creates a new tbl_kgx object which inherits from tidygraph::tbl_graph, from node and edge dataframes, ensuring they conform to the KGX specification described at https://github.com/biolink/kgx/blob/master/specification/kgx-format.md. Specifically, nodes must have an 'id' and 'category' column, and edges, if provided, must have 'subject', 'predicate', and 'object' columns. The function allows graphs with no edges. The function sets 'from' and 'to' columns in the edges from 'subject' and 'object' respectively, and sets the node key to 'id'. Additional columns are allowed.
tbl_kgx(nodes = NULL, edges = NULL, attach_engine = NULL, ...)A data frame containing the nodes of the graph. Must have 'id' and 'category' columns.
A data frame containing the edges of the graph. Must have 'subject', 'predicate', and 'object' columns. Can be NULL.
An engine to attach to the newly created graph for use in future queries based on the graph.
Additional arguments passed to the function.
A KGX graph object.
This function will generally be called internally.
nodes <- data.frame(id = c("A", "B"), category = c("gene", "disease"))
edges <- data.frame(subject = c("A"), predicate = c("associated_with"), object = c("B"))
g <- tbl_kgx(nodes, edges)