Add cell type annotation results to a Seurat object

Writes the record returned by RunCellTypeAnnotation() into the object's metadata, so that the annotation can be used by the downstream steps. The per-cell labels the tool produced (record$cells for cluster-level tools that also predict per cell, record$mapping for cell-level tools) are added as metadata columns, and the annotation itself is stored in anno_col.

Usage

EmbedSeuratCellTypeAnnotation(
  object,
  record,
  case = NULL,
  ident = NULL,
  anno_col = "CellType",
  add_prefix = TRUE,
  set_ident = TRUE,
  merge = FALSE,
  subset = NULL,
  log = NULL
)

Arguments

object

Seurat object

record

A record returned by RunCellTypeAnnotation()

case

Name of the case the record came from, used as the prefix of the new column names unless add_prefix is FALSE. NULL (default) adds no prefix.

ident

The metadata column the record$mapping is keyed on, ie. the ident the tool was run with. Only used for record$type = "cluster", where it defaults to the identity column (GetIdentityColumn()).

anno_col

Name of the metadata column to store the annotation in.

add_prefix

Whether to prefix the new column names with case.

set_ident

Whether to set the identity of the object to the annotation column.

merge

Whether to merge the clusters annotated with the same cell type. Otherwise a suffix (.1, .2, ...) is added to the cell types.

subset

A character vector of cell names the record covers. When given, the new columns are filled with NA for the cells not in subset. For cluster-level records the mapping is restricted to the subset cells even when the other cells share their clusters. NULL (default) applies the record to every cell.

log

Logger.

Value

The Seurat object with the annotation added to the metadata

Details

Unlike RunCellTypeAnnotation(), no tool is run here: the caller runs the tool and passes the record in, so the same record can be applied to different objects or under different column names. Calling this once per record with a different case reproduces the per-case columns of biopipen's CellTypeAnnotation process.

Examples

# \donttest{
obj <- SeuratObject::pbmc_small
rec <- RunCellTypeAnnotation(
    obj, "direct",
    args = list(cell_types = list(g1 = "T", g2 = "B")),
    ident = "groups"
)
#> INFO    [2026-11-04 17:41:55] Running cell type annotation tool 'direct' ...
obj <- EmbedSeuratCellTypeAnnotation(obj, rec, ident = "groups")
#> INFO    [2026-11-04 17:41:55] Adding annotation as new column: CellType
table(obj$CellType)
#> 
#>  T  B 
#> 44 36 
# }