Identify single cell/spot clusters on the basis of their neighbourhood composition

Use model based clustering on single-cell neighbour composition to define cellular clusters

nbCluster(seurat = NULL, n_clust = 3:12, seed = 347548)

Arguments

seurat

a Seurat object containing Kandinsky data (KanData())

n_clust

numeric vector indicating the possible niche numbers to be tested to find the optimal number

seed

numeric, random seed for reproducibility. Default is set to 347548

Value

Seurat object with new nbClust_ variable column stored in the Seurat meta.data

See also

cellcharter_clust(), mesa_clust(), spatialleiden_clust(), spatopic_clust(), kmeans_clust(), giotto_clust(), hoodscanR_clust() for alternative clustering methods