Package index • monarchr

All functions
`ancestors()`	Expand ancestors transitively
`ancestors(<tbl_kgx>)`	Expand ancestors transitively
`base_engine()`	base_engine
`cypher_query()`	Execute a Cypher Query
`cypher_query_df()`	Execute a Cypher Query
`cytoscape()`	Send a graph to Cytoscape
`cytoscape(<tbl_kgx>)`	Send a graph to Cytoscape
`descendants()`	Expand descendants transitively
`descendants(<tbl_kgx>)`	Expand descendants transitively
`edges()`	Get graph edges table.
`example_graph()`	Return an example set of nodes from a KG engine.
`example_graph(<file_engine>)`	Return an example set of nodes from a KG engine.
`example_graph(<neo4j_engine>)`	Return an example set of nodes from a KG engine.
`expand()`	Fetch additional knowledge graph edges connected to a query graph
`expand_n()`	Iteratively fetch additional knowledge graph edges connected to a query graph
`explode()`	Explode a graph into a list of single-node graphs
`fetch_nodes()`	Fetch nodes from a graph using a set of IDs or conditions
`file_engine()`	Create a knowledge graph engine object from a KGX-based tsv file
`file_engine_check()`	Check availability of a file-based engine
`get_engine()`	Get most recent engine from a graph.
`get_engine(<tbl_kgx>)`	Get most recent engine from a graph.
`%in_list%`	Check if an element is contained in list sub-elements
`%~%`	Infix regular expression match.
`graph_centrality()`	Add centrality
`graph_semsim()`	Add semantic similarity
`graph_sparsity()`	Compute sparsity
`kg_edge_weights()`	Knowledge Graph edge weights
`kg_join()`	Join two KGX graphs by their nodes and edges.
`knit_print(<tbl_kgx>)`	Specialized print function for KGX graphs in knitted documents
`layout_umap()`	Layout UMAP
`load_kgx()`	Load a graph from a KGX-formatted .tar.gz file.
`merge_lists()`	Recursively Merge Two Named Lists
`monarch_edge_weight_encodings()`	Generate Default Edge Weight Encodings for Monarch Knowledge Graph
`monarch_engine()`	Create a knowledge graph engine object backed by the public Monarch Neo4j instance
`monarch_engine_check()`	Check availability of Monarch Initiative API
`monarch_palettes()`	Generate Default Color Palettes for Monarch Graph Visualization
`monarch_search()`	Search for KG nodes using the Monarch Initiative search API
`monarch_semsim()`	Semantic similarity mapping between two graphs
`neo2r_to_kgx()`	Process neo2R cypher to tbl_kgx
`neo4j_engine()`	Create a knowledge graph engine object for a neo4j database
`neo4j_engine_check()`	Check if a neo4j database is available and properly formatted
`nodes()`	Get graph nodes table.
`normalize_categories()`	Normalize Categories
`order_cols()`	Set edge/row data column order according to most recent engine preferences
`plot(<tbl_kgx>)`	Specialized `plot()` function for KGX graphs
`save_kgx()`	Save a graph as a KGX-formatted .tar.gz file.
`set_engine()`	Set the engine for a graph. See warning in details.
`stitch_vectors()`	Stitch Vectors
`summarize_neighborhood()`	Summarize neighborhood
`summary(<file_engine>)`	Summarize contents of a KGX-file-based KG engine
`summary(<neo4j_engine>)`	Summarize contents of a Neo4j KG engine
`tbl_kgx()`	Create a KGX graph object
`theme_monarch()`	Monarch Initiative plot theme
`unname_cols()`	Remove names from columns

Reference

All functions