app to review molecular properties of cell types via cell ontology

Usage

ctmarks(cl, pr, go)

Arguments

cl: an import of a Cell Ontology (or extended Cell Ontology) in ontology_index form
pr: an import of a Protein Ontology in ontology_index form
go: an import of a Gene Ontology in ontology_index form

Value

a data.frame with features for selected cell types

Note

Prototype of harvesting of cell ontology by searching has_part, has_plasma_membrane_part, intersection_of and allied ontology relationships. Uses shiny. Can perform better if getPROnto() and getGeneOnto() values are in .GlobalEnv as pr and go respectively.

Examples

if (interactive()) {
   co = getOnto("cellOnto", year_added="2023")  # has plasma membrane relations
   go = getOnto("goOnto", "2023")
   pr = getOnto("Pronto", "2021") # peculiar tag used in legacy, would be PROnto with 2022
   ctmarks(co, go, pr)
}