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Pipeline step: graph-based clustering

step_clusters_sc.Rd

Wraps find_clusters_sc() as an ScStep.

Usage

step_clusters_sc(
  cluster_algorithm = c("leiden", "louvain"),
  res = 1,
  name = "leiden_clustering",
  modality = c("rna", "adt", "wnn"),
  seed = 42L
)

Arguments

cluster_algorithm

String. One of c("leiden", "louvain").

res

Numeric. The resolution parameter for igraph::cluster_leiden() or igraph::cluster_louvain().

name

String. The name to add to the obs table in the DuckDB.

modality

String. On which modality to run the UMAP. One of c("rna", "adt", "wnn"). The two latter options are only available for multi-modal versions with the added data.

seed

Integer. For reproducibility.

Value

An ScStep.

Examples

# Leiden over the graph the neighbours step wrote
step_neighbours_sc() %>>% step_clusters_sc(res = 0.5)
#> <ScPipeline> 2 steps
#>   1. neighbours  embd_to_use = "pca", no_embd_to_use = NULL, modality = c("rna", "adt"), neighbours_params = <list>, seed = 42L, .verbose = TRUE
#>   2. clusters    cluster_algorithm = c("leiden", "louvain"), res = 0.5, name = "leiden_clustering", modality = c("rna", "adt", "wnn"), seed = 42L