cache and/or retrieve path to xenium human prostate adenocarcinoma, 5k genes

cache and/or retrieve path to xenium human prostate adenocarcinoma, 5k genes

cache_xen_prost(
  cache = BiocFileCache::BiocFileCache(),
  url = "https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenData/xen_prost.zip"
)

Arguments

cache

defaults to BiocFileCache::BiocFileCache()

url

location where tiff file can be retrieved

Note

Retrieves path to a 912MB zip file. This includes a 'saved' HDF5-backed SpatialExperiment and parquet files for cell, nucleus, and transcript coordinates. The example shows how these can be assembled into a XenSPEP instance.

Examples

if (interactive()) {
 td = tempdir()
 pzip_path = cache_xen_prost()
 dir.create(xpw <- file.path(td, "xen_prost_work"))
 unzip(pzip_path, exdir=xpw)
 prost = HDF5Array::loadHDF5SummarizedExperiment(file.path(xpw, "xen_prost"))
 prost
 prost = reset_parq_paths(prost, xpw)
 prost = loadGeometry(prost)
 print(slot(prost, "cbtab") |> head() |> dplyr::collect())
 print(slot(prost, "txtab") |> dplyr::count() |> dplyr::collect())
 plot(SpatialExperiment::spatialCoords(prost), pch=".",
   main="10x FFPE Human prostate adenocarcinoma sample")
}