Use hoodscanR package to do the neighborhoods analysis.

neighborhoodsAna(seu, k = 25, anno_col = "celltype_first", clusterK = 12, ...)

Arguments

seu

A Seurat object

k

The maximum number of nearest cells to compute. See findNearCells.

anno_col

Character vector. The name of annotation column to use. See findNearCells.

clusterK

The number of clusters for clustByHood

...

Other parameters used by clustByHood except 'object', 'pm_cols' and 'k'.