gsMap 1.72.3__py3-none-any.whl → 1.73.1__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (20) hide show
  1. gsMap/GNN/train.py +1 -1
  2. gsMap/__init__.py +1 -1
  3. gsMap/cauchy_combination_test.py +5 -5
  4. gsMap/config.py +170 -37
  5. gsMap/create_slice_mean.py +33 -18
  6. gsMap/diagnosis.py +4 -14
  7. gsMap/find_latent_representation.py +19 -3
  8. gsMap/format_sumstats.py +6 -0
  9. gsMap/generate_ldscore.py +1071 -476
  10. gsMap/latent_to_gene.py +57 -19
  11. gsMap/run_all_mode.py +2 -0
  12. gsMap/utils/generate_r2_matrix.py +15 -294
  13. gsMap/utils/regression_read.py +0 -76
  14. gsmap-1.73.1.dist-info/METADATA +177 -0
  15. gsmap-1.73.1.dist-info/RECORD +31 -0
  16. {gsmap-1.72.3.dist-info → gsmap-1.73.1.dist-info}/WHEEL +1 -1
  17. {gsmap-1.72.3.dist-info → gsmap-1.73.1.dist-info/licenses}/LICENSE +6 -6
  18. gsmap-1.72.3.dist-info/METADATA +0 -120
  19. gsmap-1.72.3.dist-info/RECORD +0 -31
  20. {gsmap-1.72.3.dist-info → gsmap-1.73.1.dist-info}/entry_points.txt +0 -0
gsmap-1.73.1.dist-info/METADATA ADDED
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+ Metadata-Version: 2.4
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+ Name: gsMap
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+ Version: 1.73.1
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+ Summary: Genetics-informed pathogenic spatial mapping
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+ Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
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+ Requires-Python: >=3.10
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+ Description-Content-Type: text/markdown
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+ Classifier: Development Status :: 3 - Alpha
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+ Classifier: Intended Audience :: Developers
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Programming Language :: Python :: 3.10
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+ Classifier: Programming Language :: Python :: 3.11
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+ Classifier: Programming Language :: Python :: 3.12
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+ Classifier: Operating System :: POSIX :: Linux
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+ License-File: LICENSE
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+ Requires-Dist: numpy < 2.0.0
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+ Requires-Dist: pandas
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+ Requires-Dist: scipy
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+ Requires-Dist: scikit-learn
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+ Requires-Dist: matplotlib
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+ Requires-Dist: seaborn
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+ Requires-Dist: tqdm
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+ Requires-Dist: pyyaml
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+ Requires-Dist: torch
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+ Requires-Dist: torch-geometric
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+ Requires-Dist: pyranges
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+ Requires-Dist: pyfiglet
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+ Requires-Dist: plotly
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+ Requires-Dist: kaleido
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+ Requires-Dist: jinja2
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+ Requires-Dist: scanpy >=1.8.0
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+ Requires-Dist: zarr>=2,<3
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+ Requires-Dist: bitarray >=2.9.2, <3.0.0
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+ Requires-Dist: pyarrow
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+ Requires-Dist: scikit-misc
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+ Requires-Dist: sphinx ; extra == "doc"
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+ Requires-Dist: sphinx-argparse ; extra == "doc"
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+ Requires-Dist: sphinx-autobuild ; extra == "doc"
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+ Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
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+ Requires-Dist: sphinx-basic-ng ; extra == "doc"
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+ Requires-Dist: sphinx-charts ; extra == "doc"
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+ Requires-Dist: sphinx-copybutton ; extra == "doc"
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+ Requires-Dist: sphinx_inline_tabs ; extra == "doc"
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+ Requires-Dist: sphinx-markdown-tables ; extra == "doc"
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+ Requires-Dist: sphinx-rtd-theme ; extra == "doc"
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+ Requires-Dist: sphinxcontrib-applehelp ; extra == "doc"
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+ Requires-Dist: sphinxcontrib-devhelp ; extra == "doc"
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+ Requires-Dist: sphinxcontrib-htmlhelp ; extra == "doc"
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+ Requires-Dist: sphinxcontrib-jquery ; extra == "doc"
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+ Requires-Dist: sphinxcontrib-jsmath ; extra == "doc"
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+ Requires-Dist: sphinxcontrib-qthelp ; extra == "doc"
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+ Requires-Dist: sphinxcontrib-serializinghtml ; extra == "doc"
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+ Requires-Dist: furo ; extra == "doc"
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+ Requires-Dist: myst-parser ; extra == "doc"
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+ Requires-Dist: nbsphinx ; extra == "doc"
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+ Requires-Dist: pytest>=7.0.0 ; extra == "tests"
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+ Requires-Dist: pytest-cov>=4.0.0 ; extra == "tests"
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+ Requires-Dist: coverage ; extra == "tests"
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+ Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap/document/software
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+ Project-URL: Home, https://github.com/JianYang-Lab/gsMap
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+ Project-URL: Website, https://yanglab.westlake.edu.cn/gsmap/home
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+ Provides-Extra: doc
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+ Provides-Extra: tests
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+
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+ # gsMap
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+
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+ | | | | |
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+ | ------------- | ---------------------------------------------------------------------------------------------------- | -------------- | -------------------------------------------------------------------------------------------------- |
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+ | __Version__ | [![PyPI version][pypi-badge]][pypi-url] [![Python][python-badge]][python-url] | __Status__ | [![Project Status][status-badge]][status-url] [![Maintenance][maintenance-badge]][maintenance-url] |
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+ | __Activity__ | [![GitHub commits][commits-badge]][commits-url] [![Last Commit][last-commit-badge]][last-commit-url] | __Quality__ | [![codecov][codecov-badge]][codecov-url] [![Ruff][ruff-badge]][ruff-url] |
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+ | __CI/CD__ | [![Docs][docs-badge]][docs-url] [![test][test-badge]][test-url] | __Community__ | [![GitHub stars][stars-badge]][stars-url] [![GitHub forks][forks-badge]][forks-url] |
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+ | __Downloads__ | [![Downloads][downloads-badge]][downloads-url] | __License__ | [![License: MIT][license-badge]][license-url] [![DOI][doi-badge]][doi-url] |
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+ | __Platform__ | [![Linux][linux-badge]][linux-url] | __Contribute__ | [![Issues][issues-badge]][issues-url] [![PRs Welcome][pr-badge]][pr-url] |
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+
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+ ## Introduction
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+
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+ `gsMap` (genetically informed spatial mapping of cells for complex traits)
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+ integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS)
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+ summary statistics to map cells to human complex traits, including diseases,
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+ in a spatially resolved manner.
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+
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+ ## Key Features
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+
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+ - __Spatially-aware High-Resolution Trait Mapping__
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+ - __Spatial Region Identification__
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+ - __Putative Causal Genes Identification__
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+
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+ ![Model Architecture](schematic.png)
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+
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+ ## Installation
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+
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+ Install using pip:
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+
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+ ```bash
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+ conda create -n gsMap python>=3.10
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+ conda activate gsMap
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+ pip install gsMap
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+ ```
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+
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+ Install using conda:
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+
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+ ```bash
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+ conda create -n gsMap python>=3.10
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+ conda activate gsMap
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+ conda install bioconda::gsmap
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+ ```
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+
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+ Install from source:
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+
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+ ```bash
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+ git clone https://github.com/JianYang-Lab/gsMap
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+ cd gsMap
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+ pip install -e .
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+ ```
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+
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+ Verify the installation by running the following command:
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+
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+ ```bash
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+ gsmap --help
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+ ```
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+
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+ ## Usage
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+
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+ Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
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+
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+ ## Online Visualization
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+
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+ To visualize the traits-cell association spatial maps,
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+ please refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
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+
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+ ## Citation
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+
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+ Song, L., Chen, W., Hou, J., Guo, M. & Yang, J.
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+ [Spatially resolved mapping of cells associated with human complex traits.](https://doi.org/10.1038/s41586-025-08757-x)
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+ Nature (2025).
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+
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+ Please cite the paper and give us a STAR if you find gsMap useful for your research.
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+
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+ <!-- Badge links -->
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+
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+ [codecov-badge]: https://codecov.io/gh/JianYang-Lab/gsMap/graph/badge.svg?token=NFZFXZIEUU
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+ [codecov-url]: https://codecov.io/gh/JianYang-Lab/gsMap
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+ [commits-badge]: https://img.shields.io/github/commit-activity/m/JianYang-Lab/gsMap
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+ [commits-url]: https://github.com/JianYang-Lab/gsMap/commits/main
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+ [docs-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml/badge.svg
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+ [docs-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/docs.yml
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+ [doi-badge]: https://img.shields.io/badge/DOI-10.1038%2Fs41586--025--08757--x-blue
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+ [doi-url]: https://doi.org/10.1038/s41586-025-08757-x
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+ [downloads-badge]: https://static.pepy.tech/badge/gsMap
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+ [downloads-url]: https://pepy.tech/project/gsMap
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+ [forks-badge]: https://img.shields.io/github/forks/JianYang-Lab/gsMap
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+ [forks-url]: https://github.com/JianYang-Lab/gsMap/network/members
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+ [issues-badge]: https://img.shields.io/github/issues/JianYang-Lab/gsMap
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+ [issues-url]: https://github.com/JianYang-Lab/gsMap/issues
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+ [last-commit-badge]: https://img.shields.io/github/last-commit/JianYang-Lab/gsMap
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+ [last-commit-url]: https://github.com/JianYang-Lab/gsMap/commits/main
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+ [license-badge]: https://img.shields.io/badge/License-MIT-yellow.svg
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+ [license-url]: https://opensource.org/licenses/MIT
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+ [linux-badge]: https://img.shields.io/badge/Linux-%E2%9C%93-success
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+ [linux-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml
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+ [maintenance-badge]: https://img.shields.io/badge/Maintained%3F-yes-green.svg
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+ [maintenance-url]: https://github.com/JianYang-Lab/gsMap/graphs/commit-activity
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+ [pr-badge]: https://img.shields.io/badge/PRs-welcome-brightgreen.svg
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+ [pr-url]: https://github.com/JianYang-Lab/gsMap/pulls
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+ [pypi-badge]: https://img.shields.io/pypi/v/gsMap
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+ [pypi-url]: https://pypi.org/project/gsMap/
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+ [python-badge]: https://img.shields.io/pypi/pyversions/gsMap
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+ [python-url]: https://www.python.org
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+ [ruff-badge]: https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json
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+ [ruff-url]: https://github.com/astral-sh/ruff
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+ [stars-badge]: https://img.shields.io/github/stars/JianYang-Lab/gsMap
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+ [stars-url]: https://github.com/JianYang-Lab/gsMap/stargazers
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+ [status-badge]: https://www.repostatus.org/badges/latest/active.svg
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+ [status-url]: https://www.repostatus.org/#active
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+ [test-badge]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml/badge.svg
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+ [test-url]: https://github.com/JianYang-Lab/gsMap/actions/workflows/test_linux.yml
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+
gsmap-1.73.1.dist-info/RECORD ADDED
@@ -0,0 +1,31 @@
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+ gsMap/__init__.py,sha256=JH9MEzz0OCzOzCkWe26fsjrbx9Bstvsy68Pjx82trOA,77
2
+ gsMap/__main__.py,sha256=Vdhw8YA1K3wPMlbJQYL5WqvRzAKVeZ16mZQFO9VRmCo,62
3
+ gsMap/cauchy_combination_test.py,sha256=SiUyqJKr4ATFtRgsCEJ43joGcSagCOnnurkB1FlQiB4,5105
4
+ gsMap/config.py,sha256=LmBVMb0eda6bfrKkQuh7eZnZdvgecjCnozRd_clqvlY,51584
5
+ gsMap/create_slice_mean.py,sha256=Nnmb7ACtS-9TurW5xQ4TqCinejPsYcvuT5Oxqa5Uges,5723
6
+ gsMap/diagnosis.py,sha256=rQIjtM5inqrLlNULC88JVEO1XA64XOQWEgaKLx2oA_g,12553
7
+ gsMap/find_latent_representation.py,sha256=aZ5fFY2RhAsNaDeoehd5lN28556d6GGHK9xEUTvo6G4,5365
8
+ gsMap/format_sumstats.py,sha256=1c9OgbqDQWOgXeSrbAhbJfChv_2IwXIgLE6Pbw2sx0s,13778
9
+ gsMap/generate_ldscore.py,sha256=xxzbaANl638bRvRAowrTPmFA4dEC0zDBv6i8KQTJvJ8,45094
10
+ gsMap/latent_to_gene.py,sha256=sDPvOU4iF-HkfQY0nnkIVXpjyTQ9-PjQflwEFWrPg-A,12869
11
+ gsMap/main.py,sha256=SzfAXhrlr4LXnSD4gkvAtUUPYXyra6a_MzVCxDBZjr0,1170
12
+ gsMap/report.py,sha256=_1FYkzGhVGMnvHgEQ8z51iMrVEVlh48a31jLqbV2o9w,6953
13
+ gsMap/run_all_mode.py,sha256=LhMTT85B6yoDG9MvKmclQWYdQyNIP0FFdHpYVGTCJTs,9381
14
+ gsMap/setup.py,sha256=lsIQCChHwR0ojWZs7xay8rukRaLlueuLkc83bp-B2ZE,103
15
+ gsMap/spatial_ldsc_multiple_sumstats.py,sha256=-mawOBjn8-Y5Irl8mv8ye83hfiEJ1mkLrRIQiI-XaMM,17973
16
+ gsMap/visualize.py,sha256=N55s-xmzSd_DtIesrGewfDeoytYUcMd2acDsjEpChCA,7242
17
+ gsMap/GNN/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
18
+ gsMap/GNN/adjacency_matrix.py,sha256=MfkhgpAHJcC-3l_iZDQQYD30w4bpe29-8s6kkGxiwQw,3231
19
+ gsMap/GNN/model.py,sha256=75In9sxBkaqqpCQSrQEUO-zsQQVQnkXVbKsAgyAZjiQ,2918
20
+ gsMap/GNN/train.py,sha256=4qipaxaz3rQOtlRpTYCfl1Oz4kz_A6vNB1aw8_gGK_k,3076
21
+ gsMap/templates/report_template.html,sha256=QODZEbVxpW1xsLz7lDrD_DyUfzYoi9E17o2tLJlf8OQ,8016
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+ gsMap/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+ gsMap/utils/generate_r2_matrix.py,sha256=0zyoJDWUVavlQtR6_XXb7Ah9UhPyT3n0t6XCqlI1HXQ,17354
24
+ gsMap/utils/jackknife.py,sha256=w_qMj9GlqViouHuOw1U80N6doWuCTXuPoAVU4P-5mm8,17673
25
+ gsMap/utils/manhattan_plot.py,sha256=N7jd0Cn-7JMsTBgv41k1w0174rqnPT-v7xLIV2cfY5U,25241
26
+ gsMap/utils/regression_read.py,sha256=rKA0nkUpTJf6WuGddhKrsBCExchDNEyojOWu_qddZNw,5474
27
+ gsmap-1.73.1.dist-info/entry_points.txt,sha256=s_P2Za22O077tc1FPLKMinbdRVXaN_HTcDBgWMYpqA4,41
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+ gsmap-1.73.1.dist-info/licenses/LICENSE,sha256=fb5WP6qQytSKO5rM0ZSqQXg_92Fdt0aAeFNwSi3Lpmc,1069
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+ gsmap-1.73.1.dist-info/WHEEL,sha256=G2gURzTEtmeR8nrdXUJfNiB3VYVxigPQ-bEQujpNiNs,82
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+ gsmap-1.73.1.dist-info/METADATA,sha256=34Y4_egICgzOwwCJ2L3u8j9OvKsUBPPlLJfi-t-gm98,8196
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+ gsmap-1.73.1.dist-info/RECORD,,
{gsmap-1.72.3.dist-info → gsmap-1.73.1.dist-info}/WHEEL RENAMED
@@ -1,4 +1,4 @@
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  Wheel-Version: 1.0
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- Generator: flit 3.10.1
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+ Generator: flit 3.12.0
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  Root-Is-Purelib: true
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  Tag: py3-none-any
{gsmap-1.72.3.dist-info → gsmap-1.73.1.dist-info/licenses}/LICENSE RENAMED
@@ -1,6 +1,6 @@
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- The MIT License (MIT)
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+ MIT License
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- Copyright (c) 2023 liyang
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+ Copyright (c) 2025 JianYang-Lab
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  Permission is hereby granted, free of charge, to any person obtaining a copy
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  of this software and associated documentation files (the "Software"), to deal
@@ -9,13 +9,13 @@ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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  copies of the Software, and to permit persons to whom the Software is
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  furnished to do so, subject to the following conditions:
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- The above copyright notice and this permission notice shall be included in
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- all copies or substantial portions of the Software.
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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  IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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  FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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  AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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- OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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- THE SOFTWARE.
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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+ SOFTWARE.
gsmap-1.72.3.dist-info/METADATA DELETED
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- Metadata-Version: 2.3
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- Name: gsMap
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- Version: 1.72.3
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- Summary: Genetics-informed pathogenic spatial mapping
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- Author-email: liyang <songliyang@westlake.edu.cn>, wenhao <chenwenhao@westlake.edu.cn>
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- Requires-Python: >=3.8
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- Description-Content-Type: text/markdown
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- Classifier: Development Status :: 3 - Alpha
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- Classifier: Intended Audience :: Developers
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- Classifier: License :: OSI Approved :: MIT License
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- Classifier: Programming Language :: Python :: 3.8
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- Classifier: Programming Language :: Python :: 3.9
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- Classifier: Operating System :: POSIX :: Linux
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- Requires-Dist: numpy < 2.0.0
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- Requires-Dist: pandas
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- Requires-Dist: scipy
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- Requires-Dist: scikit-learn
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- Requires-Dist: matplotlib
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- Requires-Dist: seaborn
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- Requires-Dist: tqdm
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- Requires-Dist: pyyaml
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- Requires-Dist: torch
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- Requires-Dist: torch-geometric
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- Requires-Dist: pyranges
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- Requires-Dist: pyfiglet
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- Requires-Dist: plotly
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- Requires-Dist: kaleido
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- Requires-Dist: jinja2
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- Requires-Dist: scanpy >=1.8.0
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- Requires-Dist: zarr
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- Requires-Dist: bitarray >=2.9.2, <3.0.0
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- Requires-Dist: pyarrow
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- Requires-Dist: scikit-misc
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- Requires-Dist: sphinx ; extra == "doc"
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- Requires-Dist: sphinx-argparse ; extra == "doc"
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- Requires-Dist: sphinx-autobuild ; extra == "doc"
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- Requires-Dist: sphinx-autodoc-typehints ; extra == "doc"
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- Requires-Dist: sphinx-basic-ng ; extra == "doc"
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- Requires-Dist: sphinx-charts ; extra == "doc"
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- Requires-Dist: sphinx-copybutton ; extra == "doc"
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- Requires-Dist: sphinx_inline_tabs ; extra == "doc"
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- Requires-Dist: sphinx-markdown-tables ; extra == "doc"
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- Requires-Dist: sphinx-rtd-theme ; extra == "doc"
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- Requires-Dist: sphinxcontrib-applehelp ; extra == "doc"
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- Requires-Dist: sphinxcontrib-devhelp ; extra == "doc"
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- Requires-Dist: sphinxcontrib-htmlhelp ; extra == "doc"
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- Requires-Dist: sphinxcontrib-jquery ; extra == "doc"
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- Requires-Dist: sphinxcontrib-jsmath ; extra == "doc"
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- Requires-Dist: sphinxcontrib-qthelp ; extra == "doc"
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- Requires-Dist: sphinxcontrib-serializinghtml ; extra == "doc"
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- Requires-Dist: furo ; extra == "doc"
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- Requires-Dist: myst-parser ; extra == "doc"
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- Requires-Dist: nbsphinx ; extra == "doc"
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- Project-URL: Documentation, https://yanglab.westlake.edu.cn/gsmap/document/software
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- Project-URL: Home, https://github.com/LeonSong1995/gsMap
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- Project-URL: Website, https://yanglab.westlake.edu.cn/gsmap/home
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- Provides-Extra: doc
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-
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- [![GitHub Stars](https://img.shields.io/github/stars/JianYang-Lab/gsMap?logo=GitHub&color=yellow)](https://github.com/LeonSong1995/gsMap/stargazers)
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- [![PyPI Version](https://img.shields.io/pypi/v/gsMap)](https://pypi.org/project/gsMap)
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- [![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
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-
63
- # gsMap
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-
65
- ## Introduction
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-
67
- `gsMap` (genetically informed spatial mapping of cells for complex traits)
68
- integrates spatial transcriptomics (ST) data with genome-wide association study (GWAS)
69
- summary statistics to map cells to human complex traits, including diseases,
70
- in a spatially resolved manner.
71
-
72
- ## Key Features
73
-
74
- - **Spatially-aware High-Resolution Trait Mapping**
75
- - **Spatial Region Identification**
76
- - **Putative Causal Genes Identification**
77
-
78
- ![Model Architecture](schematic.png)
79
-
80
- ## Installation
81
-
82
- Install using pip:
83
-
84
- ```bash
85
- conda create -n gsMap python>=3.10
86
- conda activate gsMap
87
- pip install gsMap
88
- ```
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-
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- Install from source:
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-
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- ```bash
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- git clone https://github.com/LeonSong1995/gsMap.git
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- cd gsMap
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- pip install -e .
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- ```
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-
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- Verify the installation by running the following command:
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-
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- ```bash
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- gsmap --help
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- ```
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-
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- ## Usage
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-
106
- Please check out the documentation and tutorials at [gsMap Documentation](https://yanglab.westlake.edu.cn/gsmap/document/software).
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-
108
- ## Online Visualization
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-
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- To visualize the traits-cell association spatial maps,
111
- please refer to [gsMap Visualization](https://yanglab.westlake.edu.cn/gsmap/visualize).
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-
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- ## Citation
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-
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- Song, L., Chen, W., Hou, J., Guo, M. & Yang, J.
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- [Spatially reso lved mapping of cells associated with human complex traits.](https://www.medrxiv.org/content/10.1101/2024.10.31.24316538v1)
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- medRxiv, 2024.2010.2031.24316538 (2024) (Nature in press).
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-
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- Please cite the paper and give us a STAR if you find gsMap useful for your research.
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-
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