produce a pre-loaded XenSPEP (SpatialExperiment with parquet references)

ingest_xen(folder)

Arguments

folder: character(1) 'standard' Xenium output folder

Value

instance of XenSPEP

Examples

chkns = function(pkstring) {
if (!requireNamespace(pkstring)) {
  message(sprintf("install %s to use this feature; returning NULL", pkstring))
  return(NULL)
  }
}
chkns("SFEData")
#> Loading required namespace: SFEData
chkns("HDF5Array")
chkns("SingleCellExperiment")
if (requireNamespace("SFEData")) {
td = tempdir()
z = SFEData::XeniumOutput("v2", td)
ii = ingest_xen(file.path(td, "xenium2"))
print(validObject(ii))
plot(SpatialExperiment::spatialCoords(ii), pch=".")
}
#> see ?SFEData and browseVignettes('SFEData') for documentation
#> loading from cache
#> The downloaded files are in /home/vincent/TEMP/RtmpJJXExZ/xenium2 
#> [1] TRUE