Create sf geometry object from CosMx Seurat data

Source: R/06_Utils.R

Create a sf data frame object (package sf) using CosMx cell coordinates

smi2sf(seurat = NULL, poly_file = NULL, id = "cell_ID", return.seurat = F)

Arguments

seurat

a Seurat object containing CosMx data

poly_file

character string indicating the path for the polygon coordinates file. This parameter is ignored if Seurat object has been created using the function prepare_cosmx_seurat()

id

name of the variable to use as single cell identifier

return.seurat

boolean, whether returning the input Seurat file with the sf object stored in the Kandinsky sf slot or Seurat misc slot (TRUE) or the nb object alone (FALSE). Default value is TRUE

Value

Seurat object with the new sf object stored in the misc slot, or in the Kandinsky sf slot, or the sf object alone, depending on the return.seurat parameter

Details

This function will use CosMx cell boundary coordinates to create cell polygon geometries using the R package sf