Neighborhoods analysis

Use hoodscanR package to do the neighborhoods analysis.

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

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

spatialCoordsNames

The column names for spatial coordinates in the metadata of the Seurat object.

...

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