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Cellular decomposition of intrinsic and neighborhood-induced omic effects
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MintFlow (**M**icroenvironment-induced and **IN**trinsic **T**ranscriptomic **FLOW**s) is a package to decompose spatial transcriptomics data into microenvironment-induced and intrinsic gene expression components. It interoperates with the [scverse](https://scverse.org/) ecosystem to enable seamless analysis workflows of spatial transcriptomics data to identify spatial biomarkers.
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## Installing the Python Environment
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**SANGER INTERNAL**: The environment is already available on farm.
The recommended way of accessing inflow predictions is by `adata_inflowOutput_norm.h5ad` and `adata_inflowOutput_unnorm.h5ad` created in the provided `--path_output`and `adata.obsm` and `adata.uns` in these files.
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In the former file `..._norm.h5ad` the readcount matrix `adata.X` as well as inflow predictions Xint and Xspl are row normalised, while in the latter file `_unnorm.h5ad` they are not.
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The recommended way of accessing MintFlow predictions is by `adata_mintflowOutput_norm.h5ad` and `adata_mintflowOutput_unnorm.h5ad` created in the provided `--path_output`and `adata.obsm` and `adata.uns` in these files.
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In the former file `..._norm.h5ad` the readcount matrix `adata.X` as well as MintFlow predictions Xint and Xspl are row normalised, while in the latter file `_unnorm.h5ad` they are not.
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Inflow dumps a README file in the provided `--path_output`, as well as each subfolder therein.
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MintFlow dumps a README file in the provided `--path_output`, as well as each subfolder therein.
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## Common Issues
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- Use absolute paths (and not relative paths like `../../some/path/`) in the config files, as well as when running `python inflow_cli.py ...`.
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- Use absolute paths (and not relative paths like `../../some/path/`) in the config files, as well as when running `python mintflow_cli.py ...`.
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- TODO: intro to the script for tune window width.
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- It's common to face out of memory issue in the very last step where the big anndata objects `adata_inflowOutput_norm.h5ad` and `adata_inflowOutput_unnorm.h5ad` are created and dumped.
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- It's common to face out of memory issue in the very last step where the big anndata objects `adata_mintflowOutput_norm.h5ad` and `adata_mintflowOutput_unnorm.h5ad` are created and dumped.
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If that step fails, the results are still accesible in the output path the subfolder `CheckpointAndPredictions/`.
Before making a release, you need to update the version number in the `pyproject.toml` file. Please adhere to [Semantic Versioning][semver], in brief
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> Given a version number MAJOR.MINOR.PATCH, increment the:
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>
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> 1. MAJOR version when you make incompatible API changes,
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> 2. MINOR version when you add functionality in a backwards compatible manner, and
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> 3. PATCH version when you make backwards compatible bug fixes.
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>
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> Additional labels for pre-release and build metadata are available as extensions to the MAJOR.MINOR.PATCH format.
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Once you are done, commit and push your changes and navigate to the "Releases" page of this project on GitHub.
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Specify `vX.X.X` as a tag name and create a release. For more information, see [managing GitHub releases][]. This will automatically create a git tag and trigger a Github workflow that creates a release on PyPI.
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## Writing documentation
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Please write documentation for new or changed features and use-cases. This project uses [sphinx][] with the following features:
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- the [myst][] extension allows to write documentation in markdown/Markedly Structured Text
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-[Numpy-style docstrings][numpydoc] (through the [napoloen][numpydoc-napoleon] extension).
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- Jupyter notebooks as tutorials through [myst-nb][] (See [Tutorials with myst-nb](#tutorials-with-myst-nb-and-jupyter-notebooks))
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-[Sphinx autodoc typehints][], to automatically reference annotated input and output types
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- Citations (like {cite:p}`Virshup_2023`) can be included with [sphinxcontrib-bibtex](https://sphinxcontrib-bibtex.readthedocs.io/)
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See the [scanpy developer docs](https://scanpy.readthedocs.io/en/latest/dev/documentation.html) for more information
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on how to write documentation.
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### Tutorials with myst-nb and jupyter notebooks
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The documentation is set-up to render jupyter notebooks stored in the `docs/notebooks` directory using [myst-nb][].
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Currently, only notebooks in `.ipynb` format are supported that will be included with both their input and output cells.
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It is your responsibility to update and re-run the notebook whenever necessary.
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If you are interested in automatically running notebooks as part of the continuous integration, please check
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out [this feature request](https://github.com/scverse/cookiecutter-scverse/issues/40) in the `cookiecutter-scverse`
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repository.
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#### Hints
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- If you refer to objects from other packages, please add an entry to `intersphinx_mapping` in `docs/conf.py`. Only
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if you do so can sphinx automatically create a link to the external documentation.
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- If building the documentation fails because of a missing link that is outside your control, you can add an entry to
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