UpSetPlot documentation¶
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.
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)
>>> from matplotlib import pyplot
>>> pyplot.show()
makes:
And you can save the image in various formats:
>>> pyplot.savefig("/path/to/myplot.pdf")
>>> pyplot.savefig("/path/to/myplot.png")
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 are also supported!
Distributions¶
Providing a DataFrame rather than a Series as input allows us to expressively plot the distribution of variables in each subset.
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 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 |
- Examples
- Data Format Guide
- API Reference
- Changelog
- What’s new in version 0.9
- What’s new in version 0.8
- What’s new in version 0.7
- What’s new in version 0.6
- What’s new in version 0.5
- What’s new in version 0.4.4
- What’s new in version 0.4.3
- What’s new in version 0.4.2
- What’s new in version 0.4.1
- What’s new in version 0.4
- What’s new in version 0.3
- What’s new in version 0.2.1
- What’s new in version 0.2