Choose the markers that define the embedding space — select_umap

WHAT: returns the subset of available markers to use as UMAP input features. WHY: the embedding must be driven by lineage/phenotype identity, not by (a) scatter channels, which encode size/granularity and are already used for gating, (b) the viability dye, whose variation is technical, (c) height/width channels, which are redundant duplicates of area and would double-weight every marker, or (d) time. The original template selected features by channel-name regex and so retained 26 redundant height channels – the single largest cause of its uninformative UMAP.

Usage

select_umap_features(
  marker_cols,
  prefer = NULL,
  exclude = NULL,
  lineage_only = TRUE
)

Arguments

marker_cols: named integer vector: marker symbol -> column index (AREA channels only, as produced by the reading module).
prefer: character vector of preferred lineage markers; those present are used. If none of them are present, falls back to all eligible markers.
exclude: character vector of marker symbols to drop unconditionally (e.g. the detected viability marker).
lineage_only: logical; if FALSE, every eligible marker is used.

Value

character vector of marker symbols, in stable sorted order.