dolomite-sce 0.1.1

Save and load single-cell experiments in the dolomite framework!

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']