Convert SpatialExperiment to Seurat — spe_to_srt • scop

Create a Seurat object from a SpatialExperiment, preserving colData and spatial coordinates as metadata columns.

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.