Resolve parent: declarations in a population specification — resolve_population

WHY. A cut on the whole CD45+ parent sits wherever the lineages that dominate that mixture put a valley, which is not where a subset is defined. Regulatory T cells are CD25+ CD127lo WITHIN CD4+ T cells (Santegoets et al. 2015), and the CD25 valley across all leukocytes is not the one that separates them from activated conventional CD4 T cells (Seddiki et al. 2006); monocyte subsets are split by CD14 and CD16 within monocytes (Abeles et al. 2012). Gating templates express this as a hierarchy, each gate derived on its parent's events (openCyto; Finak et al. 2014).

Usage

resolve_population_parents(spec)

Arguments

spec: population specification as read from YAML.

Value

the specification with every parent: resolved, carrying attributes cut_scope and parents; unchanged when no population names a parent.

Details

WHAT. A population may name another in its parent: key:

Tregs:
  parent: CD4 T cells
  CD25: above
  CD127: below

Its own markers' cuts are then derived on the parent's events (see derive_scoped_cuts()), and it is scored within the parent. The parent's conditions are merged into the child here, so the definition every other part of the package reads is the complete one; attribute cut_scope records, per population and marker, which parent's events that marker's cut comes from (NA for the CD45+ cut), and parents the declared parent of each population.

A child may not re-declare a marker its parent requires in a different direction, and parent and child cannot both carry an any_of group: both would leave the child's relation to its parent undefined.