Import multiple cell-level annotation columns as landmark-level celltyping solutions

Scans a cell-level metadata data.frame for categorical columns and imports each as a named landmark-level celltyping solution via celltyping Mode B. After importing, users can switch between solutions with set_active_celltyping.

Usage

import_cell_annotations(x, ...)

# S3 method for class 'TDRObj'
import_cell_annotations(
  x,
  .cell.meta,
  .sample.var,
  .celltype.vec = NULL,
  .verbose = TRUE,
  ...
)

Arguments

x: A TDRObj, Seurat, or SingleCellExperiment object.
...: Additional arguments passed to methods.
.cell.meta: A data.frame with rownames set to cell IDs (original IDs before the tinydenseR sample prefix). Must contain at least the .sample.var column.
.sample.var: Character(1). Column name in .cell.meta identifying sample membership.
.celltype.vec: Character(1) or NULL. If non-NULL, the name of a column in .cell.meta that should be set as the active $ids after import.
.verbose: Logical (default TRUE). If TRUE, prints a message listing the imported columns.

Value

The updated object with imported celltyping solutions stored in @landmark.annot$celltyping$<column_name>.

Details

This function is designed to be called after get.graph and before get.map in the pipeline. Because get.map() has not yet run, .refresh_celltyping() inside each celltyping() call is a no-op, making the loop efficient.

Column selection criteria

A column in .cell.meta is imported if it is:

character or factor type (not numeric, logical, integer, etc.)
Not the .sample.var column
Has more than 1 unique non-NA value
Has fewer unique non-NA values than total cells (excludes ID-like columns)
Column name is not "ids" (reserved by the multi-solution system)

Examples

if (FALSE) { # \dontrun{
tdr.obj <- setup.tdr.obj(.cells, .meta) |>
  get.landmarks() |>
  get.graph()

# Import all categorical cell-level columns
tdr.obj <- import_cell_annotations(tdr.obj,
  .cell.meta = cell_metadata,
  .sample.var = "sample_id",
  .celltype.vec = "cell_type_l1"
)

# Check what was imported
list_celltyping_solutions(tdr.obj)

# Switch to a different annotation
tdr.obj <- set_active_celltyping(tdr.obj, "cell_type_l2")
} # }