Package index • genewalkR

Node2Vec

Run Node2Vec

node2vec(): Node2Vec

GeneWalk workflow

Main classes and methods to run GeneWalk

GeneWalk(): GeneWalk
GeneWalkGenerator: Gene Walk Network Generator
check_degree_distribution(): Check the degree across different node types
generate_initial_emb(): Generate the initial graph embedding
generate_permuted_emb(): Generate the random, permuted embedding
calculate_genewalk_stats(): Calculate the pathway and gene statistics
plot_gw_results(): Plot the gene walk results
plot_similarities(): Plot similarity distributions

Gene / Embedding drift

Main classes and methods to run a gene/embedding drift

EmbedDrift(): EmbedDrift
generate_initial_embeddings(): Generate initial node embeddings for both graphs
calculate_drift(): Calculate embedding drift between two graphs

Helpers and getters

Various getters and helper classes

get_stats(): Get the statistical results
get_graph_dt(): Get the edge data.table
get_graph_dts(): Get graph edge tables
get_gw_data(): Get the full GW data stored in the class
get_gw_data_filtered(): Get the filtered GW data for a list of genes
get_gene_pathway_dt(): Get the gene to pathway data.table
get_embedding(): Get the list of embeddings
get_embeddings(): Get node embeddings
get_aligned_embd(): Get the aligned embedding
get_gene_info(): Get the gene main information
n_nodes(): Number of nodes represented
new_data_builder(): Generate a new DataBuilder helper class

Data sources

How to download and interact with the internal DB.

reload_db(): Clean the cache and download the DB again
download_database(): Download database from GitHub release
get_db_connection(): Internal connector to the DB
get_interactions_combined(): Get the Combined network
get_interactions_intact(): Get the Intact network
get_interactions_reactome(): Get the Reactome network
get_interactions_signor(): Get the SIGNOR network
get_interactions_string(): Get the STRING network
get_interactions_pc(): Get the pathway commons network
get_gene_ontology_info(): Get the Gene Ontology main information
get_gene_ontology_hierarchy(): Get the Gene Ontology
get_reactome_info(): Get the Reactome main information
get_reactome_hierarchy(): Get the Reactome pathway hierarchy
get_gene_to_go(): Get the Gene Ontology to gene connections
get_gene_to_reactome(): Get the Reactome to gene connections

(Synthetic) Data & testing

differential_graph_test_data(): Generate Synthetic Differential Graph Data
synthetic_genewalk_data(): Generate synthetic GeneWalk data
node2vec_test_data(): Generate Simple Node2Vec Test Data
evaluate_node2vec_test(): Evaluate node2vec test results
myc_genes: MYC target genes

Params

Wrapper functions around core parameters

params_genewalk(): Wrapper function for the GeneWalk-specific node2vec parameters
params_node2vec(): Wrapper function for the node2vec parameters
params_genewalk_data(): GeneWalk synthetic data params

Rust wrappers

Everything rusty - only use this if you know what you are doing…

rs_node2vec(): Generate a node2vec embeddings
rs_cosine_sim(): Cosine similarity between two vectors
rs_gene_walk(): Generate GeneWalk node embeddings (multiple reps)
rs_gene_walk_perm(): Generate null distributions from degree-matched random networks
rs_gene_walk_test(): Calculate GeneWalk test statistics
rs_procrustes_align(): Orthogonal Procrustes alignment and cosine similarity scoring
rs_build_synthetic_genewalk(): Generate synthetic GeneWalk data with controlled signal structure
rs_node2vec_synthetic_data(): Generate synthetic data for node2vec
rs_differential_graph_data(): Generate a synthetic differential graph pair for testing context-aware node embeddings