upsetplot-bombcell 0.10.0__tar.gz

upsetplot_bombcell-0.10.0/LICENSE

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+New BSD License
+
+Copyright (c) 2018-2024 Joel Nothman.
+All rights reserved.
+
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+  a. Redistributions of source code must retain the above copyright notice,
+     this list of conditions and the following disclaimer.
+  b. Redistributions in binary form must reproduce the above copyright
+     notice, this list of conditions and the following disclaimer in the
+     documentation and/or other materials provided with the distribution.
+  c. The names of the contributors may not be used to endorse or promote
+     products derived from this software without specific prior written
+     permission.
+
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
+LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
+OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
+DAMAGE.

upsetplot_bombcell-0.10.0/PKG-INFO

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+Metadata-Version: 2.2
+Name: upsetplot-bombcell
+Version: 0.10.0
+Summary: Draw UpSet plots with Pandas and Matplotlib (maintained fork for BombCell)
+Author-email: Joel Nothman <joel.nothman@gmail.com>
+Maintainer-email: Julie Fabre <julie.m.fabre@gmail.com>
+License: BSD-3-Clause
+Project-URL: Homepage, https://github.com/Julie-Fabre/UpSetPlot
+Project-URL: Repository, https://github.com/Julie-Fabre/UpSetPlot
+Project-URL: Issues, https://github.com/Julie-Fabre/UpSetPlot/issues
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.8
+Description-Content-Type: text/x-rst
+License-File: LICENSE
+Requires-Dist: pandas>=1.0
+Requires-Dist: matplotlib>=3.0
+Provides-Extra: testing
+Requires-Dist: pytest>=2.7; extra == "testing"
+Requires-Dist: pytest-cov; extra == "testing"
+
+UpSetPlot documentation
+============================
+
+|version| |licence| |py-versions|
+
+|issues| |build| |docs| |coverage|
+
+.. note::
+
+   This is a fork of the `original UpSetPlot repository <https://github.com/jnothman/UpSetPlot>`_,
+   which appears to be unmaintained (last updated 3+ years ago). This fork is maintained
+   to ensure compatibility with modern pandas versions and for use with
+   `BombCell <https://github.com/Julie-Fabre/bombcell>`_.
+
+This is another Python implementation of UpSet plots by Lex et al. [Lex2014]_.
+UpSet plots are used to visualise set overlaps; like Venn diagrams but
+more readable. Documentation is at https://upsetplot.readthedocs.io.
+
+This ``upsetplot`` library tries to provide a simple interface backed by an
+extensible, object-oriented design.
+
+There are many ways to represent the categorisation of data, as covered in
+our `Data Format Guide <https://upsetplot.readthedocs.io/en/stable/formats.html>`_.
+
+Our internal input format uses a `pandas.Series` containing counts
+corresponding to subset sizes, where each subset is an intersection of named
+categories.  The index of the Series indicates which rows pertain to which
+categories, by having multiple boolean indices, like ``example`` in the
+following::
+
+    >>> from upsetplot import generate_counts
+    >>> example = generate_counts()
+    >>> example
+    cat0   cat1   cat2
+    False  False  False      56
+                  True      283
+           True   False    1279
+                  True     5882
+    True   False  False      24
+                  True       90
+           True   False     429
+                  True     1957
+    Name: value, dtype: int64
+
+Then::
+
+    >>> from upsetplot import plot
+    >>> plot(example)  # doctest: +SKIP
+    >>> from matplotlib import pyplot
+    >>> pyplot.show()  # doctest: +SKIP
+
+makes:
+
+.. image:: http://upsetplot.readthedocs.io/en/latest/_images/sphx_glr_plot_generated_001.png
+   :target: ../auto_examples/plot_generated.html
+
+And you can save the image in various formats::
+
+    >>> pyplot.savefig("/path/to/myplot.pdf")  # doctest: +SKIP
+    >>> pyplot.savefig("/path/to/myplot.png")  # doctest: +SKIP
+
+This plot shows the cardinality of every category combination seen in our data.
+The leftmost column counts items absent from any category. The next three
+columns count items only in ``cat1``, ``cat2`` and ``cat3`` respectively, with
+following columns showing cardinalities for items in each combination of
+exactly two named sets. The rightmost column counts items in all three sets.
+
+Rotation
+........
+
+We call the above plot style "horizontal" because the category intersections
+are presented from left to right.  `Vertical plots
+<http://upsetplot.readthedocs.io/en/latest/auto_examples/plot_vertical.html>`__
+are also supported!
+
+.. image:: http://upsetplot.readthedocs.io/en/latest/_images/sphx_glr_plot_vertical_001.png
+   :target: http://upsetplot.readthedocs.io/en/latest/auto_examples/plot_vertical.html
+
+Distributions
+.............
+
+Providing a DataFrame rather than a Series as input allows us to expressively
+`plot the distribution of variables
+<http://upsetplot.readthedocs.io/en/latest/auto_examples/plot_diabetes.html>`__
+in each subset.
+
+.. image:: http://upsetplot.readthedocs.io/en/latest/_images/sphx_glr_plot_diabetes_001.png
+   :target: http://upsetplot.readthedocs.io/en/latest/auto_examples/plot_diabetes.html
+
+Loading datasets
+................
+
+While the dataset above is randomly generated, you can prepare your own dataset
+for input to upsetplot.  A helpful tool is `from_memberships`, which allows
+us to reconstruct the example above by indicating each data point's category
+membership::
+
+    >>> from upsetplot import from_memberships
+    >>> example = from_memberships(
+    ...     [[],
+    ...      ['cat2'],
+    ...      ['cat1'],
+    ...      ['cat1', 'cat2'],
+    ...      ['cat0'],
+    ...      ['cat0', 'cat2'],
+    ...      ['cat0', 'cat1'],
+    ...      ['cat0', 'cat1', 'cat2'],
+    ...      ],
+    ...      data=[56, 283, 1279, 5882, 24, 90, 429, 1957]
+    ... )
+    >>> example
+    cat0   cat1   cat2
+    False  False  False      56
+                  True      283
+           True   False    1279
+                  True     5882
+    True   False  False      24
+                  True       90
+           True   False     429
+                  True     1957
+    dtype: int64
+
+See also `from_contents`, another way to describe categorised data, and
+`from_indicators` which allows each category to be indicated by a column in
+the data frame (or a function of the column's data such as whether it is a
+missing value).
+
+Installation
+------------
+
+To install the library, you can use `pip`::
+
+    $ pip install upsetplot
+
+Installation requires:
+
+* pandas
+* matplotlib >= 2.0
+* seaborn to use `UpSet.add_catplot`
+
+It should then be possible to::
+
+    >>> import upsetplot
+
+in Python.
+
+Why an alternative to py-upset?
+-------------------------------
+
+Probably for petty reasons. It appeared `py-upset
+<https://github.com/ImSoErgodic/py-upset>`_ was not being maintained.  Its
+input format was undocumented, inefficient and, IMO, inappropriate.  It did not
+facilitate showing plots of each subset's distribution as in Lex et al's work
+introducing UpSet plots. Nor did it include the horizontal bar plots
+illustrated there. It did not support Python 2. I decided it would be easier to
+construct a cleaner version than to fix it.
+
+References
+----------
+
+.. [Lex2014] Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister,
+   *UpSet: Visualization of Intersecting Sets*,
+   IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), vol. 20, no. 12, pp. 1983–1992, 2014.
+   doi: `doi.org/10.1109/TVCG.2014.2346248 <https://doi.org/10.1109/TVCG.2014.2346248>`_
+
+
+.. |py-versions| image:: https://img.shields.io/pypi/pyversions/upsetplot.svg
+    :alt: Python versions supported
+
+.. |version| image:: https://badge.fury.io/py/UpSetPlot.svg
+    :alt: Latest version on PyPi
+    :target: https://badge.fury.io/py/UpSetPlot
+
+.. |build| image:: https://github.com/jnothman/upsetplot/actions/workflows/test.yml/badge.svg
+    :alt: Github Workflows CI build status
+    :target: https://github.com/jnothman/UpSetPlot/actions/workflows/test.yml
+
+.. |issues| image:: https://img.shields.io/github/issues/jnothman/UpSetPlot.svg
+    :alt: Issue tracker
+    :target: https://github.com/jnothman/UpSetPlot
+
+.. |coverage| image:: https://coveralls.io/repos/github/jnothman/UpSetPlot/badge.svg
+    :alt: Test coverage
+    :target: https://coveralls.io/github/jnothman/UpSetPlot
+
+.. |docs| image:: https://readthedocs.org/projects/upsetplot/badge/?version=latest
+     :alt: Documentation Status
+     :target: https://upsetplot.readthedocs.io/en/latest/?badge=latest
+
+.. |licence| image:: https://img.shields.io/badge/Licence-BSD-blue.svg
+     :target: https://opensource.org/licenses/BSD-3-Clause

upsetplot_bombcell-0.10.0/README.rst

@@ -0,0 +1,191 @@
+UpSetPlot documentation
+============================
+
+|version| |licence| |py-versions|
+
+|issues| |build| |docs| |coverage|
+
+.. note::
+
+   This is a fork of the `original UpSetPlot repository <https://github.com/jnothman/UpSetPlot>`_,
+   which appears to be unmaintained (last updated 3+ years ago). This fork is maintained
+   to ensure compatibility with modern pandas versions and for use with
+   `BombCell <https://github.com/Julie-Fabre/bombcell>`_.
+
+This is another Python implementation of UpSet plots by Lex et al. [Lex2014]_.
+UpSet plots are used to visualise set overlaps; like Venn diagrams but
+more readable. Documentation is at https://upsetplot.readthedocs.io.
+
+This ``upsetplot`` library tries to provide a simple interface backed by an
+extensible, object-oriented design.
+
+There are many ways to represent the categorisation of data, as covered in
+our `Data Format Guide <https://upsetplot.readthedocs.io/en/stable/formats.html>`_.
+
+Our internal input format uses a `pandas.Series` containing counts
+corresponding to subset sizes, where each subset is an intersection of named
+categories.  The index of the Series indicates which rows pertain to which
+categories, by having multiple boolean indices, like ``example`` in the
+following::
+
+    >>> from upsetplot import generate_counts
+    >>> example = generate_counts()
+    >>> example
+    cat0   cat1   cat2
+    False  False  False      56
+                  True      283
+           True   False    1279
+                  True     5882
+    True   False  False      24
+                  True       90
+           True   False     429
+                  True     1957
+    Name: value, dtype: int64
+
+Then::
+
+    >>> from upsetplot import plot
+    >>> plot(example)  # doctest: +SKIP
+    >>> from matplotlib import pyplot
+    >>> pyplot.show()  # doctest: +SKIP
+
+makes:
+
+.. image:: http://upsetplot.readthedocs.io/en/latest/_images/sphx_glr_plot_generated_001.png
+   :target: ../auto_examples/plot_generated.html
+
+And you can save the image in various formats::
+
+    >>> pyplot.savefig("/path/to/myplot.pdf")  # doctest: +SKIP
+    >>> pyplot.savefig("/path/to/myplot.png")  # doctest: +SKIP
+
+This plot shows the cardinality of every category combination seen in our data.
+The leftmost column counts items absent from any category. The next three
+columns count items only in ``cat1``, ``cat2`` and ``cat3`` respectively, with
+following columns showing cardinalities for items in each combination of
+exactly two named sets. The rightmost column counts items in all three sets.
+
+Rotation
+........
+
+We call the above plot style "horizontal" because the category intersections
+are presented from left to right.  `Vertical plots
+<http://upsetplot.readthedocs.io/en/latest/auto_examples/plot_vertical.html>`__
+are also supported!
+
+.. image:: http://upsetplot.readthedocs.io/en/latest/_images/sphx_glr_plot_vertical_001.png
+   :target: http://upsetplot.readthedocs.io/en/latest/auto_examples/plot_vertical.html
+
+Distributions
+.............
+
+Providing a DataFrame rather than a Series as input allows us to expressively
+`plot the distribution of variables
+<http://upsetplot.readthedocs.io/en/latest/auto_examples/plot_diabetes.html>`__
+in each subset.
+
+.. image:: http://upsetplot.readthedocs.io/en/latest/_images/sphx_glr_plot_diabetes_001.png
+   :target: http://upsetplot.readthedocs.io/en/latest/auto_examples/plot_diabetes.html
+
+Loading datasets
+................
+
+While the dataset above is randomly generated, you can prepare your own dataset
+for input to upsetplot.  A helpful tool is `from_memberships`, which allows
+us to reconstruct the example above by indicating each data point's category
+membership::
+
+    >>> from upsetplot import from_memberships
+    >>> example = from_memberships(
+    ...     [[],
+    ...      ['cat2'],
+    ...      ['cat1'],
+    ...      ['cat1', 'cat2'],
+    ...      ['cat0'],
+    ...      ['cat0', 'cat2'],
+    ...      ['cat0', 'cat1'],
+    ...      ['cat0', 'cat1', 'cat2'],
+    ...      ],
+    ...      data=[56, 283, 1279, 5882, 24, 90, 429, 1957]
+    ... )
+    >>> example
+    cat0   cat1   cat2
+    False  False  False      56
+                  True      283
+           True   False    1279
+                  True     5882
+    True   False  False      24
+                  True       90
+           True   False     429
+                  True     1957
+    dtype: int64
+
+See also `from_contents`, another way to describe categorised data, and
+`from_indicators` which allows each category to be indicated by a column in
+the data frame (or a function of the column's data such as whether it is a
+missing value).
+
+Installation
+------------
+
+To install the library, you can use `pip`::
+
+    $ pip install upsetplot
+
+Installation requires:
+
+* pandas
+* matplotlib >= 2.0
+* seaborn to use `UpSet.add_catplot`
+
+It should then be possible to::
+
+    >>> import upsetplot
+
+in Python.
+
+Why an alternative to py-upset?
+-------------------------------
+
+Probably for petty reasons. It appeared `py-upset
+<https://github.com/ImSoErgodic/py-upset>`_ was not being maintained.  Its
+input format was undocumented, inefficient and, IMO, inappropriate.  It did not
+facilitate showing plots of each subset's distribution as in Lex et al's work
+introducing UpSet plots. Nor did it include the horizontal bar plots
+illustrated there. It did not support Python 2. I decided it would be easier to
+construct a cleaner version than to fix it.
+
+References
+----------
+
+.. [Lex2014] Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister,
+   *UpSet: Visualization of Intersecting Sets*,
+   IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), vol. 20, no. 12, pp. 1983–1992, 2014.
+   doi: `doi.org/10.1109/TVCG.2014.2346248 <https://doi.org/10.1109/TVCG.2014.2346248>`_
+
+
+.. |py-versions| image:: https://img.shields.io/pypi/pyversions/upsetplot.svg
+    :alt: Python versions supported
+
+.. |version| image:: https://badge.fury.io/py/UpSetPlot.svg
+    :alt: Latest version on PyPi
+    :target: https://badge.fury.io/py/UpSetPlot
+
+.. |build| image:: https://github.com/jnothman/upsetplot/actions/workflows/test.yml/badge.svg
+    :alt: Github Workflows CI build status
+    :target: https://github.com/jnothman/UpSetPlot/actions/workflows/test.yml
+
+.. |issues| image:: https://img.shields.io/github/issues/jnothman/UpSetPlot.svg
+    :alt: Issue tracker
+    :target: https://github.com/jnothman/UpSetPlot
+
+.. |coverage| image:: https://coveralls.io/repos/github/jnothman/UpSetPlot/badge.svg
+    :alt: Test coverage
+    :target: https://coveralls.io/github/jnothman/UpSetPlot
+
+.. |docs| image:: https://readthedocs.org/projects/upsetplot/badge/?version=latest
+     :alt: Documentation Status
+     :target: https://upsetplot.readthedocs.io/en/latest/?badge=latest
+
+.. |licence| image:: https://img.shields.io/badge/Licence-BSD-blue.svg
+     :target: https://opensource.org/licenses/BSD-3-Clause