Read Xenium output into spe

Usage

readXenium(
  dir,
  sample_id = "sample01",
  count = file.path(dir, "cell_feature_matrix.h5"),
  coord = file.path(dir, "cells.parquet"),
  image = file.path(dir, "morphology.ome.tif"),
  image_reso = 6,
  image_layer = NULL
)

Arguments

dir: directory containing the Xenium files
sample_id: Name of the sample.
count: Name of the h5 file with the count assay.
coord: Name of the parquet file with the tissue coordinates
image: Names of the ome.tif image files.
image_reso: resolution of the image to use. From 1-8 (lower = better resolution). See https://kb.10xgenomics.com/hc/articles/11636252598925. Default to 6
image_layer: Which layer of the tiff image to use. Default is the middle-most layer