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Documentation updates #12

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Nov 29, 2023
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Documentation updates #12

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765392d
Update README.md
tdrose Nov 29, 2023
bb1fb9c
Added anndata_to_image_array to examples.rst
tdrose Nov 29, 2023
75452e4
Added badges and installation instructions to docs index.
tdrose Nov 29, 2023
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Updated authors
tdrose Nov 29, 2023
b1cc83e
Testcode fix.
tdrose Nov 29, 2023
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Update index.rst
tdrose Nov 29, 2023
114d68b
Update examples.rst
tdrose Nov 29, 2023
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10 changes: 9 additions & 1 deletion README.md
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Expand Up @@ -27,8 +27,9 @@ If you encounter any bugs or have suggestions for new features, please open an i

Our package requires `python >= 3.9`.

You can install the package directly from [PyPI](https://pypi.org/project/metaspace-converter/):
```bash
pip install -U git+https://github.com/metaspace2020/metaspace-converter@master
pip install metaspace-converter
```

### Import package
Expand All @@ -39,6 +40,8 @@ import metaspace_converter

## Short tutorial

The full documentation for the package can be found here: [https://metaspace2020.github.io/metaspace-converter/](https://metaspace2020.github.io/metaspace-converter/)

The METASPACE-converter package is using the
[python client](https://github.com/metaspace2020/metaspace/tree/master/metaspace/python-client)
download datasets from METASPACE.
Expand Down Expand Up @@ -160,6 +163,11 @@ sdata.points["maldi_points"] = sdata.transform_element_to_coordinate_system(

![Image](docs/_static/img/example_img_sd.png)

## License

Unless specified otherwise in file headers or LICENSE files present in subdirectories, all files are licensed under the [Apache 2.0 license](https://github.com/metaspace2020/metaspace/blob/master/LICENSE).


[badge-docs]: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/docs.yml?label=documentation
[badge-pypi]: https://img.shields.io/pypi/v/metaspace-converter
[badge-tests]: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/tests.yml?branch=master&label=tests
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4 changes: 2 additions & 2 deletions docs/conf.py
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Expand Up @@ -18,8 +18,8 @@
# -- Project information -----------------------------------------------------

project = "METASPACE Converter"
copyright = "2023, Tim Daniel Rose"
author = "Tim Daniel Rose"
copyright = "2023; Tim Daniel Rose, Andreas Eisenbarth, Theodore Alexandrov"
author = "Tim Daniel Rose, Andreas Eisenbarth"


# -- General configuration ---------------------------------------------------
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20 changes: 20 additions & 0 deletions docs/examples.rst
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Expand Up @@ -51,6 +51,26 @@ SquidPy
.. image:: ./_static/img/example_img_sq.png
:alt: Visualization with SquidPy

Convert AnnData objects to ion image arrays
-------------------------------------------

If you want to work with the ion images as numpy arrays, the function `anndata_to_image_array` can
convert previously downloaded AnnData objects to numpy arrays.

.. testcode::

from metaspace_converter import metaspace_to_anndata, anndata_to_image_array

# Download data
adata2 = metaspace_to_anndata(dataset_id="2023-11-14_21h58m39s", fdr=0.1)

ion_images = anndata_to_image_array(adata2)

# 6 ion images of shape 61x78
print(ion_images.shape)
# > (6, 61, 78)
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Great you found testoutput!
# > (6, 61, 78) is now not needed anymore.



SpatialData
-----------

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21 changes: 21 additions & 0 deletions docs/index.rst
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Expand Up @@ -6,10 +6,23 @@
Welcome to METASPACE Converter's documentation!
===============================================

|Tests badge|
|Docs badge|
|PyPI badge|

Functions to convert `METASPACE`_ datasets to `AnnData`_ objects.

This makes it easy to work with the `ScanPy`_, `SquidPy`_ and `SpatialData`_ ecosystem with METASPACE data.

Installation
------------
You can install the package via pip:

.. testcode::
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The directive testcode is from the Sphinx extension doctest, as configured here. It is derived from the code directive and runs the Python code with pytest. Because of this, the doctests fail. It should be ignored if you replace it by just code.


pip install metaspace-converter


.. toctree::
:maxdepth: 2
:caption: Contents:
Expand All @@ -22,3 +35,11 @@ This makes it easy to work with the `ScanPy`_, `SquidPy`_ and `SpatialData`_ eco
.. _ScanPy: https://scanpy.readthedocs.io/en/stable/
.. _SquidPy: https://squidpy.readthedocs.io/en/stable/
.. _SpatialData: https://spatialdata.scverse.org/en/latest/


.. |Tests badge| image:: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/tests.yml?branch=master&label=tests
:target: https://github.com/metaspace2020/metaspace-converter/actions/workflows/tests.yml
.. |Docs badge| image:: https://img.shields.io/github/actions/workflow/status/metaspace2020/metaspace-converter/docs.yml?label=documentation
:target: https://metaspace2020.github.io/metaspace-converter/
.. |PyPI badge| image:: https://img.shields.io/pypi/v/metaspace-converter
:target: https://pypi.org/project/metaspace-converter/
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