Transfer labels from a reference Seurat object — transfer

Reference-based annotation wrapping Seurat's reference-mapping workflow (Seurat::FindTransferAnchors() + Seurat::TransferData()) to annotate query with labels (cell type, or any other categorical metadata) from an already integrated and annotated reference object. Optionally also projects query onto the reference's UMAP via Seurat::MapQuery().

Usage

transfer_labels(
  query,
  ref,
  query_label_col,
  ref_label_col,
  query_assay,
  ref_assay,
  normalization,
  ref_reduction = "pca",
  num_dim,
  anchor_reduction = "pcaproject",
  ref_umap = FALSE,
  verbose = TRUE
)

Arguments

query: Query Seurat object.
ref: Reference Seurat object - already integrated and annotated.
query_label_col: Metadata column name added to query for the transferred labels.
ref_label_col: Metadata column in ref holding the labels to transfer (cell type, or any other category).
query_assay: Assay in query to use for anchor finding. "RNA" (log-normalized) or "SCT", depending on how query was built. No default, like the params below: this and ref_assay/normalization/ num_dim all describe how a specific object was built.
ref_assay: Assay in ref to use for anchor finding.
normalization: Normalization method shared by ref and query ("log"/"LogNormalize" or "sct"/"SCT"). Seurat::FindTransferAnchors() takes one value for both objects, so ref and query must actually share a method.
ref_reduction: Reduction in ref to project query onto.
num_dim: Number of dimensions to use for anchor finding and label transfer.
anchor_reduction: Dimensional reduction workflow Seurat::FindTransferAnchors() uses to find anchors.
ref_umap: If TRUE, also runs Seurat::MapQuery() and adds a "ref.umap" reduction to query, projecting it onto ref's UMAP. ref needs a UMAP built with return.model = TRUE, which this function does not check for - MapQuery() errors on its own if it is missing.
verbose: Print progress messages.

Value

query with query_label_col (a factor) added to its metadata, and a "ref.umap" reduction added if ref_umap = TRUE. Also writes the predictions table (cell/predicted.id/prediction.score.max) to annotation/annotation-transfer-label-<query_label_col>.csv.gz, and a dr-<reduction>-<query_label_col>.png UMAP colored by the transferred labels for each of "umap"/"ref.umap" already present on query.