cache and/or retrieve path to an SFE of V1 lung demo data from 10x

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

Arguments

cache: defaults to BiocFileCache::BiocFileCache()
url: location where zip file can be retrieved

Note

We are explicitly avoiding declaring reliance on terra or SpatialFeatureExperiment, to keep package weight low. Thus the example will fail unless these are already present.

Examples

if (!requireNamespace("terra")) {
  message("install terra package to run this example")
  } else if (!requireNamespace("SpatialFeatureExperiment")) {
  message("install SpatialFeatureExperiment package to run this example")
  } else {
  zp = cache_sfeLung()
  td = tempdir()
  unzip(zp, exdir=td)
  ans = HDF5Array::loadHDF5SummarizedExperiment(file.path(td, "lungSFEtxg"))
  SpatialFeatureExperiment::show(ans)
  }
#> Loading required namespace: terra
#> Loading required namespace: SpatialFeatureExperiment
#> class: SpatialFeatureExperiment 
#> dim: 534 161894 
#> metadata(1): Samples
#> assays(1): counts
#> rownames(534): ABCC11 ACE2 ... UnassignedCodeword_0498
#>   UnassignedCodeword_0499
#> rowData names(3): ID Symbol Type
#> colnames(161894): aaaaficg-1 aaabbaka-1 ... ojacfhhg-1 ojacpeii-1
#> colData names(9): transcript_counts control_probe_counts ...
#>   nucleus_area sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : x_centroid y_centroid
#> imgData names(4): sample_id image_id data scaleFactor
#> 
#> unit: micron
#> Geometries:
#> colGeometries: centroids (POINT), cellSeg (MULTIPOLYGON), nucSeg (MULTIPOLYGON) 
#> rowGeometries: txSpots (MULTIPOINT) 
#> 
#> Graphs:
#> sample01: