Create scMetaLink from Seurat Spatial Object — createScMetaLinkFromSeuratSpatial • scMetaLink

Initialize a scMetaLink object from a Seurat object with spatial data

createScMetaLinkFromSeuratSpatial(
  seurat_obj,
  cell_type_column = "cell_type",
  assay = "Spatial",
  slot = "data",
  image = NULL,
  min_cells = 5
)

Arguments

seurat_obj: A Seurat object with spatial assay and coordinates
cell_type_column: Character. Column name in meta.data for cell type
assay: Character. Assay to use (default: "Spatial")
slot: Character. Slot to use (default: "data" for normalized data)
image: Character. Name of the spatial image to use (default: first available)
min_cells: Integer. Minimum spots per cell type

Value

A scMetaLink object with spatial information