# Generated by roxygen2: do not edit by hand

S3method(print,ontology_tree)
export(CA_terms)
export(LCA_depth)
export(LCA_term)
export(MICA_IC)
export(MICA_term)
export(NCA_term)
export(add_annotation)
export(all_group_sim_methods)
export(all_term_IC_methods)
export(all_term_sim_methods)
export(alternative_GO_terms)
export(annotated_terms)
export(avg_children)
export(avg_parents)
export(create_ontology_DAG)
export(create_ontology_DAG_from_GO_db)
export(create_ontology_DAG_from_igraph)
export(dag_add_random_children)
export(dag_all_terms)
export(dag_ancestors)
export(dag_as_DOT)
export(dag_as_dendrogram)
export(dag_as_igraph)
export(dag_children)
export(dag_circular_viz)
export(dag_depth)
export(dag_distinct_ancestors)
export(dag_enrich_on_genes)
export(dag_enrich_on_items)
export(dag_enrich_on_offsprings)
export(dag_filter)
export(dag_graphviz)
export(dag_has_terms)
export(dag_height)
export(dag_is_leaf)
export(dag_leaves)
export(dag_longest_dist_from_ancestors)
export(dag_longest_dist_to_offspring)
export(dag_n_leaves)
export(dag_n_relations)
export(dag_n_terms)
export(dag_offspring)
export(dag_parents)
export(dag_permutate_children)
export(dag_random)
export(dag_random_tree)
export(dag_reorder)
export(dag_root)
export(dag_shiny)
export(dag_shortest_dist_from_ancestors)
export(dag_shortest_dist_from_root)
export(dag_shortest_dist_to_leaves)
export(dag_shortest_dist_to_offspring)
export(dag_siblings)
export(dag_treelize)
export(group_sim)
export(import_obo)
export(import_ontology)
export(import_owl)
export(import_ttl)
export(longest_distances_directed)
export(longest_distances_via_LCA)
export(max_ancestor_id)
export(max_ancestor_path_sum)
export(max_ancestor_v)
export(method_param)
export(n_ancestors)
export(n_annotations)
export(n_children)
export(n_connected_leaves)
export(n_offspring)
export(n_parents)
export(ontology_DAG)
export(ontology_chebi)
export(ontology_go)
export(ontology_hp)
export(ontology_kw)
export(ontology_pw)
export(ontology_rdo)
export(ontology_vt)
export(partition_by_level)
export(partition_by_size)
export(random_items)
export(random_terms)
export(shortest_distances_directed)
export(shortest_distances_via_NCA)
export(simona_opt)
export(term_IC)
export(term_annotations)
export(term_sim)
exportClasses(ontology_DAG)
exportMethods("[")
exportMethods("[[")
exportMethods('mcols<-')
exportMethods(mcols)
exportMethods(show)
import(ComplexHeatmap)
import(GlobalOptions)
import(Rcpp)
import(grid)
import(igraph)
import(shiny)
importFrom(GetoptLong,qq)
importFrom(Polychrome,alphabet.colors)
importFrom(circlize,rand_color)
importFrom(grDevices,col2rgb)
importFrom(grDevices,dev.off)
importFrom(grDevices,dev.size)
importFrom(grDevices,png)
importFrom(grDevices,rgb)
importFrom(graphics,barplot)
importFrom(graphics,par)
importFrom(matrixStats,colMaxs)
importFrom(matrixStats,rowMaxs)
importFrom(methods,as)
importFrom(methods,new)
importFrom(stats,dendrapply)
importFrom(stats,p.adjust)
importFrom(stats,phyper)
importFrom(stats,quantile)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(utils,data)
importFrom(utils,download.file)
importFrom(utils,getFromNamespace)
importFrom(utils,packageDescription)
importFrom(utils,read.csv)
importFrom(utils,read.table)
importFrom(xml2,read_xml)
importFrom(xml2,xml_attr)
importFrom(xml2,xml_find_all)
importFrom(xml2,xml_ns)
importFrom(xml2,xml_text)
importMethodsFrom(S4Vectors,'mcols<-')
importMethodsFrom(S4Vectors,mcols)
useDynLib(simona, .registration = TRUE)