cache and/or retrieve path to xenium human primary melanoma, 5k genes

cache and/or retrieve path to xenium human primary melanoma, 5k genes

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

Arguments

cache

defaults to BiocFileCache::BiocFileCache()

url

location where tiff file can be retrieved

Note

Retrieves path to a 1.05GB zip file. The zip file 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_sk()
 dir.create(xpw <- file.path(td, "xen_sk_work"))
 unzip(pzip_path, exdir=xpw)
 mel = HDF5Array::loadHDF5SummarizedExperiment(file.path(xpw, "xen_sk"))
 mel = reset_parq_paths(mel, xpw)
 mel = loadGeometry(mel)
 print(slot(mel, "cbtab") |> head() |> dplyr::collect())
 print(slot(mel, "txtab") |> dplyr::count() |> dplyr::collect())
 plot(SpatialExperiment::spatialCoords(mel), pch=".",
   main="10x FFPE Human dermal melanoma sample")
}