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BodenmillerGroup / imcdatasets

ExperimentHub collection of imaging mass cytometry datasets
https://bodenmillergroup.github.io/imcdatasets/
GNU General Public License v3.0
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Make all datasets available as SpatialExperiment #13

Closed ndamond closed 2 years ago

ndamond commented 2 years ago

In addition to SingleCellExperiment, make all datasets available as SpatialExperiment class objects. https://bioconductor.org/packages/devel/bioc/html/SpatialExperiment.html

nilseling commented 2 years ago

I would not store the data twice but add an option (e.g. retrieve_as = c("sce", "spe")) to the load function. Internally, the SpatialExperiment object is constructed from the SingleCellExperiment object. What do you think?

ndamond commented 2 years ago

Done in v1.5.4 (Bioconductor >= 3.16). Note this only works for dataset versions >= v1.

Single cell data can be retrieved as SpatialExperiment by passing spe as data_type in the loading functions, e.g., spe <- JacksonFischer_2020_BreastCancer(data_type = "spe").

Data sets are stored in the SingleCellExperiment format and internally converted to SpatialExperiment objects.