retrieve a specified zipped takane-formatted SpatialFeatureExperiment from cache, downloading to cache if necessary

Usage

path_to_zipped_mcm(
  experiment = "m62.1.sfe.zip",
  local = FALSE,
  cache = BiocFileCache::BiocFileCache()
)

Arguments

experiment: character(1)
local: logical(1), if TRUE, assume available at Sys.getenv("MCM_LOCAL")
cache: like BiocFileCache() value

Note

alabaster.sfe's saveObject was used before zipping these results of `process_mcmicro` for datasets supplied by Jeremy Goecks.

Examples

pa = path_to_zipped_mcm()
tf = tempfile()
unzip(pa, exdir=tf)
requireNamespace("alabaster.sfe")
#> Loading required namespace: alabaster.sfe
dem = alabaster.base::readObject(file.path(tf, "m62.1.sfe"))
#> >>> Reading SpatialExperiment
#> >>> Reading colgeometries
#> >>> Reading spatial graphs
#> >>> Reading localResults
dem
#> class: SpatialFeatureExperiment 
#> dim: 30 8577 
#> metadata(1): all_markers
#> assays(1): X
#> rownames(30): AF488 AF555 ... CD1B CD8A
#> rowData names(0):
#> colnames(8577): 1 2 ... 8576 8577
#> colData names(12): X_centroid Y_centroid ... phenotype 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: 
#> Geometries:
#> colGeometries: centroids (POINT) 
#> 
#> Graphs:
#> sample01: col: spatNeigh
table(dem$phenotype)
#> 
#>     CD8 T cells     Endothelial      Epithelial          Immune Myeloid Lineage 
#>            2826             146             438             127             856 
#>          Stroma  T Helper cells         T cells         Unknown 
#>            1164            2320             207             493