Save and load single-cell experiments in the dolomite framework!
Project description
Save and write SingleCellExperiments
in Python
Introduction
The dolomite-sce package is the Python counterpart to the alabaster.sce R package,
providing methods for saving/reading SingleCellExperiment
objects within the dolomite framework.
Quick start
Let's mock up a SingleCellExperiment
that contains reduced dimensions and alternative experiments,
from singlecellexperiment import SingleCellExperiment
import biocframe
import numpy
sce = SingleCellExperiment(
assays={"counts": numpy.random.rand(1000, 200)},
row_data=biocframe.BiocFrame(
{"foo": numpy.random.rand(1000), "bar": numpy.random.rand(1000)}
),
column_data=biocframe.BiocFrame(
{"whee": numpy.random.rand(200), "stuff": numpy.random.rand(200)}
),
reduced_dims={"tsnooch": numpy.random.rand(200, 4)},
alternative_experiments={
"very_useful_modality": SummarizedExperiment(
{"counts": numpy.random.rand(100, 200)}
)
},
)
Now we can save it:
from dolomite_base import save_object
import dolomite_sce
import os
from tempfile import mkdtemp
path = os.path.join(mkdtemp(), "test")
save_object(se, path)
And load it again, e,g., in a new session:
from dolomite_base import read_object
roundtrip = read_object(path)
## Class SingleCellExperiment with 1000 features and 200 cells
## assays: ['counts']
## row_data: ['foo']
## column_data: ['whee']
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