Cluster SingleCellExperiment with monocle3::cluster_cells

Cluster SingleCellExperiment with monocle3::cluster_cells

cluster_sce(
  sce,
  cluster_method = "leiden",
  reduction_method = "UMAP_Liger",
  resolution = 1e-05,
  k = 50,
  louvain_iter = 1,
  verbose = T,
  ...
)

Arguments

sce

a SingleCellExperiment object

cluster_method

Available methods include leiden and louvain.

reduction_method

Input slot for clustering. Available options are PCA, UMAP_Liger, tSNE_Liger.

resolution

Clustering resolution. If NULL, clustering method will be set to louvain.

...

see monocle3::cluster_cells for more clustering options.

K

Integer number of nearest neighbors to use when creating the k nearest neighbor graph for Louvain/Leiden clustering. k is related to the resolution of the clustering result, a bigger k will result in lower resolution and vice versa. Default is 50.

Value

sce a SingleCellExperiment object annotated with reducedDims

See also

Other clustering and dimensionality reduction: .get_x_most_specific_genes(), .map_celltypes(), .map_celltypes_with_ewce(), map_custom_celltypes(), reduce_dims_sce()