UpSetPlot 0.2.0

Draw Lex et al.'s UpSet plots with Pandas and Matplotlib

UpSetPlot documentation
============================

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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.

The basic input format is a `pandas.Series` containing counts
corresponding to set intersection sizes. The index indicates which rows
pertain to which sets, by having multiple boolean indices, like ``example``
in the following::

>>> from upsetplot import generate_data
>>> example = generate_data(aggregated=True)
>>> example # doctest: +NORMALIZE_WHITESPACE
set0 set1 set2
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

This plot shows the cardinality of every set combination seen in our data. The
leftmost column counts items absent from any set. The next three columns count
items only in ``set1``, ``set2`` and ``set3``` 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 set 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_boston.html>`__
in each subset.

.. image:: http://upsetplot.readthedocs.io/en/latest/_images/sphx_glr_plot_boston_001.png
:target: http://upsetplot.readthedocs.io/en/latest/auto_examples/plot_boston.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 set
membership::

>>> from upsetplot import from_memberships
>>> example = from_memberships(
... [[],
... ['set2'],
... ['set1'],
... ['set1', 'set2'],
... ['set0'],
... ['set0', 'set2'],
... ['set0', 'set1'],
... ['set0', 'set1', 'set2'],
... ],
... data=[56, 283, 1279, 5882, 24, 90, 429, 1957]
... )
>>> example # doctest: +NORMALIZE_WHITESPACE
0
set0 set1 set2
False False False 56
True 283
True False 1279
True 5882
True False False 24
True 90
True False 429
True 1957

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 set intersection 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>`_


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