Simplify the combined cell count table

This function is designed to offer flexible simplification of mapped cells counts. This can be applied after running combine_norm_cell_counts(). However, if mapping is being conducted using the SMARTR package, we recommend simplifying mapped counts earlier, at the level of mouse objects using normalize_cell_counts() because the options offered for simplification are more flexible. The benefit of this function is that it can operate on experiment objects with externally imported combined cell counts tables that are formatted for compatibility. This allows for simplification using other ontologies. See the available atlas options under the ontology parameter.

Usage

simplify_cell_count(
  e,
  ontology = "allen",
  simplify_keywords = c("layer", "part", "stratum", "division", "leaflet",
    "Subgeniculate", "island", "Islands", "Fields of Forel", "Cajal", "Darkschewitsch",
    "Precommissural"),
  dont_fold = c("Dorsal part of the lateral geniculate complex",
    "Ventral posterolateral nucleus of the thalamus, parvicellular part",
    "Ventral posteromedial nucleus of the thalamus, parvicellular part",
    "Ventral posterolateral nucleus of the thalamus, parvicellular part",
    "Ventral posteromedial nucleus of the thalamus, parvicellular part",
    "Substantia nigra")
)

Arguments

e

experiment object

ontology

(str, default = "allen") Region ontology to use. options = "allen" or "unified"

simplify_keywords

(str vec, default = c("layer","part","stratum","division", "leaflet", "Subgeniculate", "island", "Islands", "Fields of Forel", "Cajal", "Darkschewitsch", "Precommissural")). Keywords to search through region names and simplify to parent structure. This means the parent structure is also excluded if the list of excluded right and left

dont_fold

(vec) vector of regions to not fold in. regions can be further

Value

e experiment object with simplified keywords