trevismd / statannotations

add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.
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annotations plotting seaborn statistics

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Python Documentation Status DOI

What is it

Python package to optionally compute statistical test and add statistical annotations on plots generated with seaborn.

Derived work

This repository is based on webermarcolivier/statannot (commit 1835078 of Feb 21, 2020, tagged "v0.2.3").

Additions/modifications since that version are below represented in bold (previous fixes are not listed).

! From version 0.4.0 onwards (introduction of Annotator), statannot's API is no longer usable in statannotations. Please use the latest v0.3.2 release if you must keep statannot's API in your code, but are looking for bug fixes we have covered.

statannot's interface, at least until its version 0.2.3, is usable in statannotations until v.0.3.x, which already provides additional features (see corresponding branch).

Features

Installation

From version 0.3.0 on, the package is distributed on PyPi. The latest stable release (v0.6.0) can be downloaded and installed with:

pip install statannotations

or, with conda Conda (channel only)

conda install -c conda-forge statannotations

or, after cloning the repository,

pip install .

# OR, to have optional dependencies too (multiple comparisons & testing)
pip install -r requirements.txt .

Important note

! Seaborn ≥ v0.12 and pandas 2 are not officially supported, we know there are at least some bugs. Issues can still be reported (and upvoted) in order to plan further development to support these versions. Also see discussion.

Usage

Here is a minimal example:

import seaborn as sns

from statannotations.Annotator import Annotator

df = sns.load_dataset("tips")
x = "day"
y = "total_bill"
order = ['Sun', 'Thur', 'Fri', 'Sat']

ax = sns.boxplot(data=df, x=x, y=y, order=order)

pairs=[("Thur", "Fri"), ("Thur", "Sat"), ("Fri", "Sun")]

annotator = Annotator(ax, pairs, data=df, x=x, y=y, order=order)
annotator.configure(test='Mann-Whitney', text_format='star', loc='outside')
annotator.apply_and_annotate()

Examples

Example 2

Example 3

Example 4

Example 5

Documentation

Requirements

Citation

If you are using this work, please use the following information to cite it.

Bibtex

@software{florian_charlier_2022_7213391,
  author       = {Florian Charlier and
                  Marc Weber and
                  Dariusz Izak and
                  Emerson Harkin and
                  Marcin Magnus and
                  Joseph Lalli and
                  Louison Fresnais and
                  Matt Chan and
                  Nikolay Markov and
                  Oren Amsalem and
                  Sebastian Proost and
                  Agamemnon Krasoulis and
                  getzze and
                  Stefan Repplinger},
  title        = {Statannotations},
  month        = oct,
  year         = 2022,
  publisher    = {Zenodo},
  version      = {v0.6},
  doi          = {10.5281/zenodo.7213391},
  url          = {https://doi.org/10.5281/zenodo.7213391}
}

Example

Florian Charlier, Marc Weber, Dariusz Izak, Emerson Harkin, Marcin Magnus, 
Joseph Lalli, Louison Fresnais, Matt Chan, Nikolay Markov, Oren Amsalem, 
Sebastian Proost, Agamemnon Krasoulis, getzze, & Stefan Repplinger. (2022). 
Statannotations (v0.6). Zenodo. https://doi.org/10.5281/zenodo.7213391

Contributing

Opening issues and PRs are very much welcome! (preferably in that order).
In addition to git's history, contributions to statannotations are logged in the changelog.
If you don't know where to start, there may be a few ideas in opened issues or discussion, or something to work for the documentation. NB: More on CONTRIBUTING.md