Save and load multi-assay experiments in the dolomite framework!
Project description
Save and load MultiAssayExperiments
in Python
Introduction
The dolomite-mae package is the Python counterpart to the alabaster.mae R package,
providing methods for saving/reading MultiAssayExperiment
objects within the dolomite framework.
All components of the MultiAssayExperiment
- column_data, sample map and experiments - are saved to their respective file representations,
which can be loaded in a new R/Python environment for cross-language analyses.
Quick start
Let's mock up a MultiAssayExperiment
:
from multiassayexperiment import MultiAssayExperiment
from singlecellexperiment import SingleCellExperiment
from summarizedexperiment import SummarizedExperiment
import biocframe
import numpy
x = numpy.random.rand(1000, 200)
x2 = (numpy.random.rand(1000, 200) * 10).astype(numpy.int32)
sce = SingleCellExperiment(
{"logcounts": x, "counts": x2},
main_experiment_name="aaron's secret modality",
row_data=biocframe.BiocFrame(
{"foo": numpy.random.rand(1000), "bar": numpy.random.rand(1000)},
row_names=["gene_sce_" + str(i) for i in range(1000)],
),
column_data=biocframe.BiocFrame(
{"whee": numpy.random.rand(200), "stuff": numpy.random.rand(200)},
row_names=["cell_sce" + str(i) for i in range(200)],
),
)
se = SummarizedExperiment(
{"counts": numpy.random.rand(100, 200)},
row_data=biocframe.BiocFrame(
{"foo": numpy.random.rand(100), "bar": numpy.random.rand(100)},
row_names=["gene_se_" + str(i) for i in range(100)],
),
column_data=biocframe.BiocFrame(
{"whee": numpy.random.rand(200), "stuff": numpy.random.rand(200)},
row_names=["cell_se" + str(i) for i in range(200)],
),
)
mae = MultiAssayExperiment(experiments={"jay_expt": sce, "aarons_expt": se})
Now we can save it:
from dolomite_base import save_object
import dolomite_se
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)
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