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‎README.md‎

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[![docs](https://readthedocs.org/projects/tda-mapper/badge/?version=main)](https://tda-mapper.readthedocs.io/en/main/?badge=main)
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[![codecov](https://codecov.io/github/lucasimi/tda-mapper-python/graph/badge.svg?token=FWSD8JUG6R)](https://codecov.io/github/lucasimi/tda-mapper-python)
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[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10642381.svg)](https://doi.org/10.5281/zenodo.10642381)
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[![Streamlit App](https://static.streamlit.io/badges/streamlit_badge_black_white.svg)](https://tda-mapper-app.streamlit.app/)
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# tda-mapper
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A simple and efficient Python implementation of Mapper algorithm for Topological Data Analysis
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**tda-mapper** is a simple and efficient Python implementation of Mapper algorithm for Topological Data Analysis
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* **Installation**: `pip install tda-mapper`
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For an in-depth coverage of Mapper you can read [the original paper](https://research.math.osu.edu/tgda/mapperPBG.pdf).
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| Step 1 | Step 2 | Step 3 | Step 4 |
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|--------|--------|--------|--------|
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| ------ | ------ | ------ | ------ |
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| ![Step 1](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_1.png) | ![Step 2](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_2.png) | ![Step 3](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_3.png) | ![Step 2](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_4.png) |
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| Chose lens | Cover image | Run clustering | Build graph |
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fig_std.show(config={'scrollZoom': True})
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```
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| Dataset | Mapper graph (average) | Mapper graph (deviation) |
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|--------------------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------|
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| Dataset | Mapper graph (average) | Mapper graph (deviation) |
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| ------- | ---------------------- | ------------------------ |
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| ![Dataset](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_dataset.png) | ![Mapper graph (average)](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_mean.png) | ![Mapper graph (standard deviation)](https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_std.png) |
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More examples can be found in the documentation https://tda-mapper.readthedocs.io/en/main/.

‎docs/source/citations.rst‎

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Citations
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=========
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If you want to use **tda-mapper** in your research please use one of the following citation.
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For the methodology you can use:
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Simi, L. (2024). A Scalable Implementation of Mapper for Topological Data Analysis via Vantage Point Trees. Zenodo. https://doi.org/10.5281/zenodo.10659652
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BibTeX entry:
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.. code:: RST
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@misc{simi_2024_10659652,
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author = {Simi, Luca},
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title = {A Scalable Implementation of Mapper for Topological Data Analysis via Vantage Point Trees},
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month = feb,
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year = 2024,
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publisher = {Zenodo},
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doi = {10.5281/zenodo.10659652},
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url = {https://doi.org/10.5281/zenodo.10659652}
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}
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If you want to refer to the actual library instead, you can reference the Zenodo
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archive `https://doi.org/10.5281/zenodo.10642381 <https://doi.org/10.5281/zenodo.10642381>`__.
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In the archive you can find a permanent reference to the exact version used in your work.

‎docs/source/conf.py‎

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html_theme = 'sphinx_rtd_theme'
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html_static_path = ['_static']
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html_logo = 'logos/tda-mapper-logo-horizontal.png'
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html_theme_options = {
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'sticky_navigation': True,

‎docs/source/examples.rst‎

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Examples
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========
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.. toctree::
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:maxdepth: 2
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notebooks/circles_online
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notebooks/digits_online
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.. |Dataset| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_dataset.png
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.. |Mapper graph (average)| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_mean.png
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.. |Mapper graph (standard deviation)| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_std.png

‎docs/source/index.rst‎

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You can adapt this file completely to your liking, but it should at least
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contain the root `toctree` directive.
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|PyPI version| |downloads| |test| |deploy| |docs| |codecov| |DOI|
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tda-mapper
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==========
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A simple and efficient implementation of Mapper algorithm for
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Topological Data Analysis.
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- **Installation**: ``pip install tda-mapper``
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########################
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tda-mapper documentation
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########################
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- **Documentation**: https://tda-mapper.readthedocs.io/en/main/
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The Mapper algorithm is a well-known technique in the field of
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topological data analysis that allows data to be represented as a graph.
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Mapper is used in various fields such as machine learning, data mining,
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and social sciences, due to its ability to preserve topological features
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of the underlying space, providing a visual representation that
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facilitates exploration and interpretation. For an in-depth coverage of
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Mapper you can read `the original
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paper <https://research.math.osu.edu/tgda/mapperPBG.pdf>`__.
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+-----------------+-----------------+-----------------+-----------------+
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| Step 1 | Step 2 | Step 3 | Step 4 |
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+=================+=================+=================+=================+
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| |Step 1| | |Step 2| | |Step 3| | |image1| |
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+-----------------+-----------------+-----------------+-----------------+
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.. toctree::
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:maxdepth: 2
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:caption: Examples
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|Logo|
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notebooks/circles_online
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notebooks/digits_online
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Citations
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^^^^^^^^^
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To cite **tda-mapper** in your work you can use the Zenodo archive
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`https://doi.org/10.5281/zenodo.10642381 <https://doi.org/10.5281/zenodo.10642381>`__.
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In the archive you can find a permanent reference to the exact version
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you used in your work. For example, to cite version ``v0.4.0`` you can use:
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::
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Simi, L. (2024). tda-mapper (v0.4.0). Zenodo. https://doi.org/10.5281/zenodo.10655755
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BibTeX entry:
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::
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|PyPI version| |downloads| |test| |deploy| |docs| |codecov| |DOI|
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@software{tda-mapper_v0.4.0,
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author = {Simi, Luca},
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title = {tda-mapper},
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month = feb,
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year = 2024,
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publisher = {Zenodo},
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version = {v0.4.0},
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doi = {10.5281/zenodo.10655755},
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url = {https://doi.org/10.5281/zenodo.10655755}
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}
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Contents
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========
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.. toctree::
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:maxdepth: 2
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:caption: API Reference
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:maxdepth: 1
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tdamapper
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overview
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examples
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citations
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modules
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.. |Logo| image:: logos/tda-mapper-logo-horizontal.png
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:alt: tda-mapper
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:target: https://github.com/lucasimi/tda-mapper-python
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.. |PyPI version| image:: https://badge.fury.io/py/tda-mapper.svg
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:target: https://badge.fury.io/py/tda-mapper
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.. |downloads| image:: https://img.shields.io/pypi/dm/tda-mapper
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.. |codecov| image:: https://codecov.io/github/lucasimi/tda-mapper-python/graph/badge.svg?token=FWSD8JUG6R
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:target: https://codecov.io/github/lucasimi/tda-mapper-python
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.. |DOI| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.10642381.svg
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:target: https://doi.org/10.5281/zenodo.10642381
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.. |Step 1| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_1.png
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.. |Step 2| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_2.png
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.. |Step 3| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_3.png
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.. |image1| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/mapper_4.png
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.. |Dataset| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_dataset.png
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.. |Mapper graph (average)| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_mean.png
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.. |Mapper graph (standard deviation)| image:: https://github.com/lucasimi/tda-mapper-python/raw/main/resources/circles_std.png
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:target: https://doi.org/10.5281/zenodo.10642381

‎docs/source/logos/tda-mapper-logo-horizontal.png‎

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‎docs/source/logos/tda-mapper-logo-icon.png‎

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‎docs/source/logos/tda-mapper-logo-vertical.png‎

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