Convert SpatialExperiment to Seurat — spe_to

Create a Seurat object from a SpatialExperiment, preserving colData and spatial coordinates as metadata columns. SCOP display exports are inverted to raw coordinates using their saved transform. External SpatialExperiment coordinates without SCOP provenance are treated as raw coordinates in their supplied units. Original import provenance is retained in object@misc$spatial_coordinate_import.

Usage

spe_to_srt(
  spe,
  assay = "Spatial",
  layer = NULL,
  coord.cols = c("x", "y"),
  project = "SpatialExperiment"
)

Arguments

spe: A SpatialExperiment or SummarizedExperiment.
assay: Assay name for the created Seurat assay.
layer: Assay from spe to use as counts. If NULL, the first assay is used.
coord.cols: Metadata names used for spatial coordinates in Seurat.
project: Project name passed to Seurat::CreateSeuratObject().

Value

A Seurat object.