Map cell type — map_tissue • MSTExplorer

Map cell types to cell ontology terms.

map_tissue(
  results = NULL,
  map = KGExplorer::get_data_package(package = "MSTExplorer", name = "tissue_maps"),
  lvl = 10,
  uberon = KGExplorer::get_ontology(name = "uberon", lvl = lvl),
  return_agg = FALSE
)

Arguments

results: The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
map: Many:many mapping between tissue ontology terms and cell type ontology terms.
lvl: Depth of the ancestor terms to add. Will get the closest ancestor to this level if none have this exact level.
uberon: UBERON ontology object of class ontology_DAG.
return_agg: Return the aggregated results instead of merging with a table of association results.

Examples

results <- load_example_results()
results2 <- map_tissue(results = results)
#> Mapping cell types to cell ontology terms.
#> Adding stage information.
#> Mapping cell types to UBERON tissue ontology terms.
#> Loading cached ontology: /github/home/.cache/R/KGExplorer/uberon.rds