gistfile1.txt

>>> tiledbsoma.show_package_versions()
tiledbsoma.__version__        1.5.0rc3.post11.dev1922351648
TileDB-Py tiledb.version()    (0, 23, 4)
TileDB core version           2.17.4
libtiledbsoma version()       libtiledb=2.17.4
python version                3.9.0.final.0
OS version                    Darwin 23.0.0

>>> exp = soma.Experiment.open('s3://tiledb-johnkerl/s/v/pbmc3k')

>>> exp.obs.schema
soma_joinid: int64
obs_id: large_string
n_genes: int64
percent_mito: float
n_counts: float
louvain: dictionary<values=string, indices=int8, ordered=0>

>>> exp.obs.read(value_filter='n_genes > 500').concat()
pyarrow.Table
soma_joinid: int64
obs_id: large_string
n_genes: int64
percent_mito: float
n_counts: float
louvain: dictionary<values=string, indices=int8, ordered=0>
----
soma_joinid: [[0,1,2,3,4,...,2632,2633,2634,2635,2637]]
obs_id: [["AAACATACAACCAC-1","AAACATTGAGCTAC-1","AAACATTGATCAGC-1","AAACCGTGCTTCCG-1","AAACCGTGTATGCG-1",...,"TTTCGAACACCTGA-1","TTTCGAACTCTCAT-1","TTTCTACTGAGGCA-1","TTTCTACTTCCTCG-1","TTTGCATGCCTCAC-1"]]
n_genes: [[781,1352,1131,960,522,...,1544,1155,1227,622,724]]
percent_mito: [[0.030177759,0.037935957,0.008897362,0.017430846,0.012244898,...,0.013019079,0.021104366,0.00929422,0.021971496,0.008064516]]
n_counts: [[2419,4903,3147,2639,980,...,4455,3459,3443,1684,1984]]
louvain: [  -- dictionary:
["CD4 T cells","CD14+ Monocytes","B cells","CD8 T cells","NK cells","FCGR3A+ Monocytes","Dendritic cells","Megakaryocytes"]  -- indices:
[0,2,0,1,4,...,6,1,2,2,0]]

>>> exp.obs.read(value_filter='louvain == "B cells"').concat()
pyarrow.Table
soma_joinid: int64
obs_id: large_string
n_genes: int64
percent_mito: float
n_counts: float
louvain: dictionary<values=string, indices=int8, ordered=0>
----
soma_joinid: [[1,10,18,19,20,...,2628,2630,2634,2635,2636]]
obs_id: [["AAACATTGAGCTAC-1","AAACTTGAAAAACG-1","AAAGGCCTGTCTAG-1","AAAGTTTGATCACG-1","AAAGTTTGGGGTGA-1",...,"TTTCAGTGTCACGA-1","TTTCAGTGTGCAGT-1","TTTCTACTGAGGCA-1","TTTCTACTTCCTCG-1","TTTGCATGAGAGGC-1"]]
n_genes: [[1352,1116,1446,446,1020,...,700,637,1227,622,454]]
percent_mito: [[0.037935957,0.02631579,0.015282526,0.034700315,0.025906736,...,0.034313727,0.018925056,0.00929422,0.021971496,0.020547945]]
n_counts: [[4903,3914,4973,1268,3281,...,1632,1321,3443,1684,1022]]
louvain: [  -- dictionary:
["CD4 T cells","CD14+ Monocytes","B cells","CD8 T cells","NK cells","FCGR3A+ Monocytes","Dendritic cells","Megakaryocytes"]  -- indices:
[2,2,2,2,2,...,2,2,2,2,2]]