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Transfer ClustoCell cluster labels to a full-resolution dataset

Source: R/clustoCell_TransferLabel.R
clustoCell_TransferLabel.Rd

Transfers major and sub-cluster labels from a ClustoCell object generated on a sketched (subsampled) dataset to a full-resolution dataset using EWCSR-based correlation or Seurat-based projection and anchor transfer strategies.

Usage

clustoCell_TransferLabel(
  clustoCell,
  query_ewcsr_mat = NULL,
  query_expr_mat = NULL,
  assay = "RNA",
  layer = "counts",
  method = c("ewcsr-cor", "seurat-project", "ewcsr-red-cor", "seurat-knn"),
  dims = 30,
  num_threads = -1,
  inherit_major_clusters = TRUE,
  seed = 121,
  verbose = TRUE
)

Arguments

clustoCell

An object of class ClustoCell obtained by running clustoCell() on a sketched dataset.

query_ewcsr_mat

A sparse matrix (dgCMatrix) containing EWCSR values for the full dataset. Required for EWCSR-based methods and ignored when method = "seurat-knn" or method = "seurat-project".

query_expr_mat

Either a Seurat object or a sparse count matrix (dgCMatrix) for the full dataset. Required for method = "seurat-knn" or method = "seurat-project" and optional otherwise.

assay

Character string specifying the assay used in query_expr_mat when a Seurat object is provided.

layer

Character string specifying the layer of assay to use (e.g., "counts").

method

Character string specifying the label transfer strategy. Options include:

  • "ewcsr-cor": Transfers labels by computing correlations between EWCSR profiles of query cells and EWCSR centroids of sketched clusters in the full feature space.

  • "seurat-project": Uses Seurat's ProjectData() workflow to transfer labels by projecting the full expression dataset (raw counts, log-normalized, or SCT-normalized) onto the low-dimensional embedding learned from the sketched dataset.

  • "ewcsr-red-cor": Similar to "ewcsr-cor", but correlations are computed in a reduced dimensional space (PCA embedding).

  • "seurat-knn": Uses Seurat's FindTransferAnchors() and TransferData() workflow to transfer labels from the sketched dataset to the full dataset using nearest-neighbor matching. Supports standard Seurat normalization workflows (e.g., LogNormalize and SCTransform).

dims

Integer; number of dimensions used during sketching or PCA-based label transfer.

num_threads

Integer; number of CPU threads to use. Default -1 uses all available cores.

inherit_major_clusters

Logical; whether to restrict sub-cluster label transfer within inherited major clusters when such labels are available.

seed

Integer; random seed for reproducibility.

verbose

Logical; whether to print progress messages.

Value

An updated object of class ClustoCell containing transferred major and sub-cluster labels for the full dataset.

Details

The "seurat-project" and "seurat-knn" methods operate on the original expression matrix (`query_expr_mat`) rather than the EWCSR representation. The supplied expression data may consist of raw counts, log-normalized expression values, or SCTransform-normalized data, provided that the sketched and full datasets were processed using the same normalization strategy. These methods leverage Seurat's native label transfer workflows (ProjectData, FindTransferAnchors, and TransferData) and do not require integer count matrices.

Examples

if (FALSE) { # \dontrun{
cc_full <- clustoCell_TransferLabel(
  clustoCell = cc_sketched,
  query_expr_mat = expr_mat_full,
  method = "seurat-knn"
)
} # }