Create a SpatialExperiment object

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)

Arguments

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.

Value

A SpatialExperiment object.