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keviny2 merged 4 commits into from
May 16, 2025
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Add details to to_anndata() docstring #55

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5cdf896
Add details to docstring
keviny2 May 16, 2025
635e3e9
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] May 16, 2025
ff19cf0
Import Tuple type
keviny2 May 16, 2025
92c7c46
Update CHANGELOG
keviny2 May 16, 2025
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
# Changelog

## Version 0.0.11-0.0.12
## Version 0.0.11-0.0.13
- BUGFIX: `to_anndata()` only populates `obsm` with spatial coordinates if the original `SpatialExperiment` has spatial coordinates (PR #53, #54)
- Enhance docstring for `to_anndata()` to describe the structure of returned AnnData object (PR #55)


## Version 0.0.10
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28 changes: 25 additions & 3 deletions src/spatialexperiment/spatialexperiment.py
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from pathlib import Path
from typing import Any, Dict, List, Optional, Sequence, Union
from typing import Any, Dict, List, Optional, Sequence, Union, Tuple
from urllib.parse import urlparse
from warnings import warn

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######>> AnnData interop <<#####
################################

def to_anndata(self, include_alternative_experiments: bool = False) -> "anndata.AnnData":
def to_anndata(
self, include_alternative_experiments: bool = False
) -> Tuple["anndata.AnnData", Dict[str, "anndata.AnnData"]]:
"""Transform :py:class:`~SpatialExperiment`-like into a :py:class:`~anndata.AnnData` representation.

This method converts the main experiment data, spatial coordinates,
and image data into an AnnData structure. Image data, including the
image arrays and their scale factors, are stored within the ``obj.uns["spatial"]``
dictionary, adhering to a common convention for spatial single-cell data.

The ``obj.uns["spatial"]`` dictionary is structured as follows:
- It is a dictionary where each key is a unique ``library_id``.
The ``library_id`` is generated by combining ``sample_id`` and ``image_id``
from the input image data (e.g., "sample1-image01").
- Each ``library_id`` entry is itself a dictionary containing:
- ``"images"``: A dictionary to store image arrays.
Currently, images are stored under the key ``"hires"`` by default
(e.g., ``obj.uns["spatial"][library_id]["images"]["hires"] = image_numpy_array``).
- ``"scalefactors"``: A dictionary to store scale factors associated
with the images. Currently, scale factors are stored under the key
``"tissue_hires_scalef"`` by default (e.g.,
``obj.uns["spatial"][library_id]["scalefactors"]["tissue_hires_scalef"] = scale_factor_value``).

Spatial coordinates are stored in ``obj.obsm["spatial"]``.

Args:
include_alternative_experiments:
Whether to transform alternative experiments.

Returns:
An ``AnnData`` representation of the experiment.
A tuple containing an ``AnnData`` object with spatial information and a list of alternative experiments.
"""
obj, alt_exps = super().to_anndata(include_alternative_experiments=include_alternative_experiments)

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