convert SpatialFeatureExperiment to XenSCE
sfe2xsce(sfe, BPPARAM = BiocParallel::SerialParam())example(cache_sfeLung)
#>
#> cch_sL> if (!requireNamespace("terra")) {
#> cch_sL+ message("install terra package to run this example")
#> cch_sL+ } else if (!requireNamespace("SpatialFeatureExperiment")) {
#> cch_sL+ message("install SpatialFeatureExperiment package to run this example")
#> cch_sL+ } else {
#> cch_sL+ zp = cache_sfeLung()
#> cch_sL+ td = tempdir()
#> cch_sL+ unzip(zp, exdir=td)
#> cch_sL+ ans = HDF5Array::loadHDF5SummarizedExperiment(file.path(td, "lungSFEtxg"))
#> cch_sL+ SpatialFeatureExperiment::show(ans)
#> cch_sL+ }
#> 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:
nx = sfe2xsce(ans, BPPARAM=BiocParallel::MulticoreParam(8))
nx
#> class: XenSCE
#> 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
#> Geometry elements:
#> nrow ncol
#> transcripts 10607572 4
#> cellbounds 4044931 3
#> nucbounds 3979037 3