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

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Latest version on PyPi licence Python versions supported

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This is another Python implementation of UpSet plots by Lex et al. [Lex2014].

It 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


>>> from upsetplot import plot
>>> plot(example)  # doctest: +SKIP


Why an alternative to py-upset?

Probably for petty reasons. It appeared 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.



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:

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