| check_ontology_translate | make sure ontology names are all translated to ontology ids while warning, consider manual reannotation |
| fill_query | Get a names list of ontology and id by id |
| getOntologyId | Get a names list of ontology and id by name |
| getOntologyName | Get a names list of ontology and id by id |
| getOntoMapping | match ontology terms by direct mapping and mapping descendants to ancestors |
| getOntoMinimal | match descendant terms to ancestor terms within a dataset |
| getOntoMultiMapping | Match descendants to ancestors in multiple ontology id lists |
| getSeuratRds | read in seurat object .rds files as a named list of seurat object |
| ontoMinimal | get the minimal ontology tree of a dataset by reducing descendant terms to ancestor terms return obj meta.data[["cell_ontology_base"]] storing the reduced ontology annotation |
| ontoMultiMatch | Core function of scOntoMatch Match the ontology annotation of multiple seurat objects |
| ontoMultiMinimal | get the minimal ontology tree of a list of seurat objects by reducing descendant terms to ancestor terms return a named list of seurat objects with meta.data[["cell_ontology_base"]] storing the reduced ontology annotation |
| ontoTranslate | translate named list of obj_list to named list of cell ontology ids per obj |
| plotMatchedOntoTree | Plot a ontology tree with matched ontology from ontoMatch |
| plotOntoTree | Plot a tree representation of ontology terms |