Add ClustoCell cluster annotations to a Seurat or SingleCellExperiment object

Adds major cluster and/or sub-cluster labels stored in a ClustoCell object to the cell-level metadata of a Seurat or SingleCellExperiment object.

Usage

addClustoData(
  obj,
  clustoCell,
  add_major_clusters = TRUE,
  add_sub_clusters = TRUE,
  major_cluster_name = "ClustoCell_Clusters",
  sub_cluster_name = "ClustoCell_SubClusters"
)

Arguments

obj

An object of class Seurat or SingleCellExperiment.

clustoCell

An object of class ClustoCell, generated via clustoCell() or markoClust().

add_major_clusters

Logical; whether to add major cluster labels to the metadata of obj.

add_sub_clusters

Logical; whether to add sub-cluster labels to the metadata of obj.

major_cluster_name

Character; name of the metadata column to store major cluster labels.

sub_cluster_name

Character; name of the metadata column to store sub-cluster labels.

Value

The input object obj with additional metadata columns containing ClustoCell cluster annotations.

Details

This function transfers clustering results obtained using clustoCell() or markoClust() into an existing single-cell object by appending cluster labels as metadata columns. Major clusters and sub-clusters can be added independently and assigned custom column names.

See also

clustoCell, markoClust

Examples

utils::data("pbmc_small", package = "SeuratObject")

pbmc_small_cc <- clustoCell(
  data = pbmc_small,
  identify_subclusters = TRUE,
  num_threads = 1,
  verbose = FALSE
)
#> Loading required namespace: SeuratObject

pbmc_small <- addClustoData(
  obj = pbmc_small,
  clustoCell = pbmc_small_cc,
  add_major_clusters = TRUE,
  add_sub_clusters = TRUE
)