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Add spatial coordinates from SpatialData to Seurat object

Source: R/SpatialData.R
dot-add_spatialdata_coords.Rd

Add spatial coordinates from SpatialData to Seurat object

Usage

.add_spatialdata_coords(
  obj,
  coords,
  radius = 1,
  region_name = "spots",
  cell_names = NULL,
  instance_key = NULL,
  verbose = TRUE
)

Arguments

obj

Seurat object

coords

Coordinate matrix (n x 2) with x, y columns

radius

Spot radius

region_name

Name of the spatial region

cell_names

Cell names in the Seurat object

instance_key

Column in obs linking to shapes index

verbose

Show progress

Value

Modified Seurat object