Create a SpatialExperiment object — create

This function creates a SpatialExperiment object from a SingleCellExperiment object and a spatial barcode file.

Usage

create_spe(
  sce,
  spatial_barcode_file,
  mannual_align_json,
  image,
  tissue_positions_file
)

sce: The SingleCellExperiment object obtained from running the sc_long_pipeline function.
spatial_barcode_file: The path to the spatial barcode file, e.g. "spaceranger-2.1.1/lib/python/cellranger/barcodes/visium-v2_coordinates.txt".
mannual_align_json: The path to the mannual alignment json file.
image: 'DataFrame' containing the image data. See ?SpatialExperiment::readImgData and ?SpatialExperiment::SpatialExperiment.
tissue_positions_file: The path to Visium positions file, e.g. "spaceranger-2.1.1/lib/python/cellranger/barcodes/visium-v2_tissue_positions_list.csv".

A SpatialExperiment object.