Differential regulation: T-test for two groups

Differential regulation: T-test for two groups#

This API example shows the functionality in the acore.differential_regulation module:

  • ANOVA (for two groups) is equivalent to a t-test between two groups

Then we can do the same for examples with three and more groups, where a omnibus analysis across groups is combined with posthoc anlysis for separate groups.

The functions are the same for both cases. The group1 and group2 columns give the posthoc comparison.

%pip install acore vuecore

Hide code cell output

 
Requirement already satisfied: acore in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (0.3.0)
Requirement already satisfied: vuecore in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (0.1.1)
Requirement already satisfied: numpy in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (2.4.6)
Requirement already satisfied: pandas in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (2.3.3)
Requirement already satisfied: dsp-pandas in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.0.5)
Requirement already satisfied: scipy in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (1.17.1)
Requirement already satisfied: scikit-learn>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (1.9.0)
Requirement already satisfied: gseapy!=1.1.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (1.2.1)
Requirement already satisfied: pingouin<0.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.5.5)
Requirement already satisfied: umap-learn in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.5.12)
Requirement already satisfied: statsmodels in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.14.6)
Requirement already satisfied: combat in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.3.3)
Requirement already satisfied: inmoose in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.9.1)
Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (2.34.2)
Requirement already satisfied: rarfile in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (4.2)
Requirement already satisfied: pandera in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from acore) (0.31.1)
Requirement already satisfied: matplotlib in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pingouin<0.6.0->acore) (3.11.0)
Requirement already satisfied: pandas-flavor in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pingouin<0.6.0->acore) (0.8.1)
Requirement already satisfied: seaborn in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pingouin<0.6.0->acore) (0.13.2)
Requirement already satisfied: tabulate in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pingouin<0.6.0->acore) (0.10.0)
Requirement already satisfied: plotly in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (6.8.0)
Requirement already satisfied: beautifulsoup4 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (4.15.0)
Requirement already satisfied: dash in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (4.2.0)
Requirement already satisfied: networkx in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (3.6.1)
Requirement already satisfied: kaleido in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (1.3.0)
Requirement already satisfied: pyvis in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (0.3.2)
Requirement already satisfied: wordcloud in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (1.9.6)
Requirement already satisfied: cyjupyter in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (0.2.0)
Requirement already satisfied: nltk in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (3.9.4)
Requirement already satisfied: webweb in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (0.0.37)
Requirement already satisfied: dash-cytoscape in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (1.0.2)
Requirement already satisfied: pydantic in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (2.13.4)
Requirement already satisfied: nbformat>=4.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from vuecore) (5.10.4)
Requirement already satisfied: contourpy>=1.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (1.3.3)
Requirement already satisfied: cycler>=0.10 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (0.12.1)
Requirement already satisfied: fonttools>=4.22.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (4.63.0)
Requirement already satisfied: kiwisolver>=1.3.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (1.5.0)
Requirement already satisfied: packaging>=20.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (26.2)
Requirement already satisfied: pillow>=9 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (12.2.0)
Requirement already satisfied: pyparsing>=3 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (3.3.2)
Requirement already satisfied: python-dateutil>=2.7 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from matplotlib->pingouin<0.6.0->acore) (2.9.0.post0)
Requirement already satisfied: fastjsonschema>=2.15 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from nbformat>=4.2.0->vuecore) (2.21.2)
Requirement already satisfied: jsonschema>=2.6 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from nbformat>=4.2.0->vuecore) (4.26.0)
Requirement already satisfied: jupyter-core!=5.0.*,>=4.12 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from nbformat>=4.2.0->vuecore) (5.9.1)
Requirement already satisfied: traitlets>=5.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from nbformat>=4.2.0->vuecore) (5.15.1)
Requirement already satisfied: attrs>=22.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0->vuecore) (26.1.0)
Requirement already satisfied: jsonschema-specifications>=2023.03.6 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0->vuecore) (2025.9.1)
Requirement already satisfied: referencing>=0.28.4 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0->vuecore) (0.37.0)
Requirement already satisfied: rpds-py>=0.25.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from jsonschema>=2.6->nbformat>=4.2.0->vuecore) (2026.5.1)
Requirement already satisfied: platformdirs>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from jupyter-core!=5.0.*,>=4.12->nbformat>=4.2.0->vuecore) (4.10.0)
Requirement already satisfied: pytz>=2020.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandas->acore) (2026.2)
Requirement already satisfied: tzdata>=2022.7 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandas->acore) (2026.2)
Requirement already satisfied: six>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from python-dateutil>=2.7->matplotlib->pingouin<0.6.0->acore) (1.17.0)
Requirement already satisfied: typing-extensions>=4.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from referencing>=0.28.4->jsonschema>=2.6->nbformat>=4.2.0->vuecore) (4.15.0)
Requirement already satisfied: joblib>=1.4.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from scikit-learn>=1.5->acore) (1.5.3)
Requirement already satisfied: narwhals>=2.0.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from scikit-learn>=1.5->acore) (2.22.1)
Requirement already satisfied: threadpoolctl>=3.5.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from scikit-learn>=1.5->acore) (3.6.0)
Requirement already satisfied: soupsieve>=1.6.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from beautifulsoup4->vuecore) (2.8.4)
Requirement already satisfied: mpmath>=1.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from combat->acore) (1.4.1)
Requirement already satisfied: patsy>=0.5.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from combat->acore) (1.0.2)
Requirement already satisfied: ipywidgets>=7.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from cyjupyter->vuecore) (8.1.8)
Requirement already satisfied: comm>=0.1.3 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipywidgets>=7.0.0->cyjupyter->vuecore) (0.2.3)
Requirement already satisfied: ipython>=6.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipywidgets>=7.0.0->cyjupyter->vuecore) (9.14.1)
Requirement already satisfied: widgetsnbextension~=4.0.14 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipywidgets>=7.0.0->cyjupyter->vuecore) (4.0.15)
Requirement already satisfied: jupyterlab_widgets~=3.0.15 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipywidgets>=7.0.0->cyjupyter->vuecore) (3.0.16)
Requirement already satisfied: decorator>=5.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (5.3.1)
Requirement already satisfied: ipython-pygments-lexers>=1.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (1.1.1)
Requirement already satisfied: jedi>=0.18.2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (0.20.0)
Requirement already satisfied: matplotlib-inline>=0.1.6 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (0.2.2)
Requirement already satisfied: pexpect>4.6 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (4.9.0)
Requirement already satisfied: prompt_toolkit<3.1.0,>=3.0.41 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (3.0.52)
Requirement already satisfied: psutil>=7 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (7.2.2)
Requirement already satisfied: pygments>=2.14.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (2.20.0)
Requirement already satisfied: stack_data>=0.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (0.6.3)
Requirement already satisfied: wcwidth in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from prompt_toolkit<3.1.0,>=3.0.41->ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (0.8.1)
Requirement already satisfied: parso<0.9.0,>=0.8.6 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from jedi>=0.18.2->ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (0.8.7)
Requirement already satisfied: ptyprocess>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pexpect>4.6->ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (0.7.0)
Requirement already satisfied: executing>=1.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from stack_data>=0.6.0->ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (2.2.1)
Requirement already satisfied: asttokens>=2.1.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from stack_data>=0.6.0->ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (3.0.1)
Requirement already satisfied: pure-eval in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from stack_data>=0.6.0->ipython>=6.1.0->ipywidgets>=7.0.0->cyjupyter->vuecore) (0.2.3)
Requirement already satisfied: Flask<3.2,>=1.0.4 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from dash->vuecore) (3.1.3)
Requirement already satisfied: Werkzeug<3.2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from dash->vuecore) (3.1.8)
Requirement already satisfied: importlib-metadata in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from dash->vuecore) (9.0.0)
Requirement already satisfied: retrying in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from dash->vuecore) (1.4.2)
Requirement already satisfied: nest-asyncio in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from dash->vuecore) (1.6.0)
Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from dash->vuecore) (82.0.1)
Requirement already satisfied: janus>=1.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from dash->vuecore) (2.0.0)
Requirement already satisfied: blinker>=1.9.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from Flask<3.2,>=1.0.4->dash->vuecore) (1.9.0)
Requirement already satisfied: click>=8.1.3 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from Flask<3.2,>=1.0.4->dash->vuecore) (8.4.1)
Requirement already satisfied: itsdangerous>=2.2.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from Flask<3.2,>=1.0.4->dash->vuecore) (2.2.0)
Requirement already satisfied: jinja2>=3.1.2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from Flask<3.2,>=1.0.4->dash->vuecore) (3.1.6)
Requirement already satisfied: markupsafe>=2.1.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from Flask<3.2,>=1.0.4->dash->vuecore) (3.0.3)
Requirement already satisfied: openpyxl in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from dsp-pandas->acore) (3.1.5)
Requirement already satisfied: zipp>=3.20 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from importlib-metadata->dash->vuecore) (4.1.0)
Requirement already satisfied: anndata in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from inmoose->acore) (0.12.17)
Requirement already satisfied: fastcluster in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from inmoose->acore) (1.3.0)
Requirement already satisfied: array-api-compat>=1.7.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (1.15.0)
Requirement already satisfied: h5py>=3.8 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (3.16.0)
Requirement already satisfied: legacy-api-wrap in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (1.5)
Requirement already satisfied: natsort in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (8.4.0)
Requirement already satisfied: scverse-misc>=0.0.3 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (0.0.3)
Requirement already satisfied: zarr!=3.0.*,>=2.18.7 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from anndata->inmoose->acore) (3.1.6)
Requirement already satisfied: session-info2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from scverse-misc>=0.0.3->anndata->inmoose->acore) (0.4.1)
Requirement already satisfied: donfig>=0.8 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from zarr!=3.0.*,>=2.18.7->anndata->inmoose->acore) (0.8.1.post1)
Requirement already satisfied: google-crc32c>=1.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from zarr!=3.0.*,>=2.18.7->anndata->inmoose->acore) (1.8.0)
Requirement already satisfied: numcodecs>=0.14 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from zarr!=3.0.*,>=2.18.7->anndata->inmoose->acore) (0.16.5)
Requirement already satisfied: pyyaml in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from donfig>=0.8->zarr!=3.0.*,>=2.18.7->anndata->inmoose->acore) (6.0.3)
Requirement already satisfied: choreographer>=1.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from kaleido->vuecore) (1.3.0)
Requirement already satisfied: logistro>=1.0.8 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from kaleido->vuecore) (2.0.1)
Requirement already satisfied: orjson>=3.10.15 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from kaleido->vuecore) (3.11.9)
Requirement already satisfied: simplejson>=3.19.3 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from choreographer>=1.3.0->kaleido->vuecore) (4.1.1)
Requirement already satisfied: regex>=2021.8.3 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from nltk->vuecore) (2026.5.9)
Requirement already satisfied: tqdm in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from nltk->vuecore) (4.68.2)
Requirement already satisfied: et-xmlfile in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from openpyxl->dsp-pandas->acore) (2.0.0)
Requirement already satisfied: xarray in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandas-flavor->pingouin<0.6.0->acore) (2026.4.0)
Requirement already satisfied: typeguard in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandera->acore) (4.5.2)
Requirement already satisfied: typing_inspect>=0.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pandera->acore) (0.9.0)
Requirement already satisfied: mypy-extensions>=0.3.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from typing_inspect>=0.6.0->pandera->acore) (1.1.0)
Requirement already satisfied: annotated-types>=0.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pydantic->vuecore) (0.7.0)
Requirement already satisfied: pydantic-core==2.46.4 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pydantic->vuecore) (2.46.4)
Requirement already satisfied: typing-inspection>=0.4.2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pydantic->vuecore) (0.4.2)
Requirement already satisfied: jsonpickle>=1.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from pyvis->vuecore) (4.1.2)
Requirement already satisfied: charset_normalizer<4,>=2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from requests->acore) (3.4.7)
Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from requests->acore) (3.18)
Requirement already satisfied: urllib3<3,>=1.26 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from requests->acore) (2.7.0)
Requirement already satisfied: certifi>=2023.5.7 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from requests->acore) (2026.5.20)
Requirement already satisfied: numba>=0.51.2 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from umap-learn->acore) (0.65.1)
Requirement already satisfied: pynndescent>=0.5 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from umap-learn->acore) (0.6.0)
Requirement already satisfied: llvmlite<0.48,>=0.47.0dev0 in /home/docs/checkouts/readthedocs.org/user_builds/analytics-core/envs/stable/lib/python3.11/site-packages (from numba>=0.51.2->umap-learn->acore) (0.47.0)
Note: you may need to restart the kernel to use updated packages.

Hide code cell source

 
import dsp_pandas
import pandas as pd
import vuecore.plots.basic.scatter

import acore.differential_regulation as ad

dsp_pandas.format.set_pandas_options(
    max_columns=9,
    max_colwidth=20,
)

BASE = (
    "https://raw.githubusercontent.com/Multiomics-Analytics-Group/acore/"
    "main/example_data/alzheimer_proteomics/"
)
# data is already preprocessed: log2, filtered
fname: str = "alzheimer_example_omics_and_clinic.csv"  # combined omics and meta data
covariates: list[str] = ["age", "male"]
group: str = "AD"
subject_col: str = "Sample ID"
drop_cols: list[str] = ["collection_site"]
factor_and_covars: list[str] = [group, *covariates]

Alternatively you can use the metabolomics dataset MTBLS13311, which is also preprocessed and combined.

Hide code cell source

 
# BASE = (
#     "https://raw.githubusercontent.com/Multiomics-Analytics-Group/acore/"
#     "main/example_data/MTBLS13311/"
# )
# fname: str = "MTBLS13411_omics_and_meta.csv"  # combined omics and meta data
# covariates: list[str] = []
# group: str = "Factor Value[Strain type]"
# drop_cols: list[str] = ["group"]
# subject_col: str | int = 0
# factor_and_covars: list[str] = [group, *covariates]

ANOVA analysis for two groups#

Use combined dataset for ANOVA analysis. Drop unnecessary columns, if there are any specified in drop_cols.

Hide code cell source

 
omics_and_meta = (
    pd.read_csv(f"{BASE}/{fname}", index_col=subject_col)
    .convert_dtypes()
    .dropna(subset=factor_and_covars)
    .drop(columns=drop_cols)
)
omics_and_meta
AD age male Q6UX72 ... Q9Y5I4 P55283 A1L4H1 Q7Z4T9
Sample ID
Sample_000 0 71 0 16.047 ... 17.187 17.422 15.542 19.331
Sample_001 1 77 1 14.457 ... 17.447 17.097 15.734 18.980
Sample_002 1 75 1 15.631 ... 17.410 17.752 15.824 19.326
Sample_003 1 72 0 16.204 ... 17.545 17.483 15.515 18.953
Sample_004 1 63 0 15.968 ... 17.297 17.172 15.334 18.651
... ... ... ... ... ... ... ... ... ...
Sample_205 1 69 0 15.262 ... 17.104 16.952 15.705 18.844
Sample_206 0 73 1 <NA> ... 17.109 18.056 15.282 18.686
Sample_207 0 71 0 15.463 ... 16.938 17.248 14.874 19.146
Sample_208 0 83 1 15.786 ... 17.155 16.353 15.471 16.853
Sample_209 0 63 0 15.691 ... 16.776 16.597 14.699 18.087

197 rows × 103 columns

Check data types of the columns. Metadata can be numeric, but also strings.

Hide code cell source

 
omics_and_meta.dtypes.value_counts()

Float64   100
Int64       3
Name: count, dtype: int64

Hide code cell source

 
omics_and_meta[[group, *covariates]]
AD age male
Sample ID
Sample_000 0 71 0
Sample_001 1 77 1
Sample_002 1 75 1
Sample_003 1 72 0
Sample_004 1 63 0
... ... ... ...
Sample_205 1 69 0
Sample_206 0 73 1
Sample_207 0 71 0
Sample_208 0 83 1
Sample_209 0 63 0

197 rows × 3 columns

ANOVA analysis for two groups#

  • is not controlling for covariates

if not isinstance(subject_col, str):
    subject_col = omics_and_meta.index.name or "index"
    omics_and_meta.rename_axis(subject_col, axis=0, inplace=True)
anova = (
    ad.run_anova(
        omics_and_meta,
        subject=None,
        drop_cols=covariates,
        group=group,
    )
    .set_index("identifier")
    .sort_values(by="padj")
)
anova
T-Statistics pvalue mean(group1) mean(group2) ... group2 FC -log10 pvalue Method
identifier
P14174 -5.915 0.000 18.069 18.648 ... 1 0.669 7.829 Unpaired t-test
P17174 -5.666 0.000 19.100 19.492 ... 1 0.762 7.180 Unpaired t-test
P08294 5.548 0.000 21.490 21.205 ... 1 1.219 7.020 Unpaired t-test
P01834 5.483 0.000 24.322 23.712 ... 1 1.526 6.886 Unpaired t-test
P36222 -5.217 0.000 20.205 20.627 ... 1 0.746 6.333 Unpaired t-test
... ... ... ... ... ... ... ... ... ...
Q13433 -0.214 0.830 14.130 14.154 ... 1 0.984 0.081 Unpaired t-test
A1L4H1 -0.186 0.852 15.496 15.510 ... 1 0.990 0.069 Unpaired t-test
O75874 -0.172 0.863 13.815 13.831 ... 1 0.989 0.064 Unpaired t-test
Q13508 -0.154 0.878 17.946 17.956 ... 1 0.993 0.057 Unpaired t-test
H3BMA1 0.120 0.905 15.261 15.247 ... 1 1.009 0.044 Unpaired t-test

100 rows × 16 columns

See summary statistics for numeric values in ANOVA results, such as for

  • pvalue (unadjusted)

  • padj (adjusted p-value, FDR corrected)

  • fold change (FC) of the mean of group1 vs group2 (group1/group2)

Hide code cell source

 
anova.describe().T
count mean std min 25% 50% 75% max
T-Statistics 100.000 -0.178 2.268 -5.915 -1.821 -0.246 1.292 5.548
pvalue 100.000 0.231 0.269 0.000 0.017 0.098 0.389 0.905
mean(group1) 100.000 17.402 2.915 12.665 15.482 16.788 18.836 28.587
mean(group2) 100.000 17.404 2.860 12.780 15.478 16.703 18.682 28.523
std(group1) 100.000 0.680 0.392 0.265 0.460 0.596 0.747 3.108
std(group2) 100.000 0.644 0.360 0.253 0.417 0.563 0.731 2.721
log2FC 100.000 -0.002 0.209 -0.579 -0.144 -0.021 0.133 0.610
padj 100.000 0.303 0.281 0.000 0.065 0.194 0.507 0.905
FC 100.000 1.009 0.149 0.669 0.905 0.985 1.097 1.526
-log10 pvalue 100.000 1.472 1.629 0.044 0.410 1.010 1.781 7.829

Inspect ANOVA results#

  • summary statistics for each group

  • test results

  • t-test statistic, FDR correction method, etc.

View averages per protein group#

Hide code cell source

 
view = anova.filter(regex="group")
viewed_cols = view.columns.to_list()
view
mean(group1) mean(group2) std(group1) std(group2) group1 group2
identifier
P14174 18.069 18.648 0.729 0.645 0 1
P17174 19.100 19.492 0.411 0.534 0 1
P08294 21.490 21.205 0.426 0.293 0 1
P01834 24.322 23.712 0.823 0.736 0 1
P36222 20.205 20.627 0.641 0.493 0 1
... ... ... ... ... ... ...
Q13433 14.130 14.154 0.704 0.753 0 1
A1L4H1 15.496 15.510 0.510 0.533 0 1
O75874 13.815 13.831 0.503 0.591 0 1
Q13508 17.946 17.956 0.533 0.337 0 1
H3BMA1 15.261 15.247 0.628 0.740 0 1

100 rows × 6 columns

Test results#

Hide code cell source

 
regex_filter = "pval|padj|reject|stat|FC"
view = anova.filter(regex=regex_filter)
viewed_cols.extend(view.columns)
view
pvalue log2FC padj rejected FC -log10 pvalue
identifier
P14174 0.000 -0.579 0.000 True 0.669 7.829
P17174 0.000 -0.392 0.000 True 0.762 7.180
P08294 0.000 0.285 0.000 True 1.219 7.020
P01834 0.000 0.610 0.000 True 1.526 6.886
P36222 0.000 -0.422 0.000 True 0.746 6.333
... ... ... ... ... ... ...
Q13433 0.830 -0.024 0.865 False 0.984 0.081
A1L4H1 0.852 -0.014 0.879 False 0.990 0.069
O75874 0.863 -0.016 0.881 False 0.989 0.064
Q13508 0.878 -0.010 0.887 False 0.993 0.057
H3BMA1 0.905 0.014 0.905 False 1.009 0.044

100 rows × 6 columns

Other information#

on test statistic and FDR correction method.

Hide code cell source

 
anova.drop(columns=viewed_cols)
T-Statistics test correction Method
identifier
P14174 -5.915 t-Test FDR correction BH Unpaired t-test
P17174 -5.666 t-Test FDR correction BH Unpaired t-test
P08294 5.548 t-Test FDR correction BH Unpaired t-test
P01834 5.483 t-Test FDR correction BH Unpaired t-test
P36222 -5.217 t-Test FDR correction BH Unpaired t-test
... ... ... ... ...
Q13433 -0.214 t-Test FDR correction BH Unpaired t-test
A1L4H1 -0.186 t-Test FDR correction BH Unpaired t-test
O75874 -0.172 t-Test FDR correction BH Unpaired t-test
Q13508 -0.154 t-Test FDR correction BH Unpaired t-test
H3BMA1 0.120 t-Test FDR correction BH Unpaired t-test

100 rows × 4 columns

View Volcano plot for the ANOVA results#

  • p-value (unadjusted) using the -log10 transformation on the y-axis, using -log10 pvalue

  • fold change (FC) in the log2 space on the x-axis (2 means a fold change of 4, 1 a doubeling and -1 means a fold change of 0.5 and -2 of 0.25), using log2FC

  • significant features are colored in red using the reject column, which is True for significant features and False for non-significant features, and is calculated based on the padj column and a significance threshold (default 0.05)

scatter_plot_adv = vuecore.plots.basic.scatter.create_scatter_plot(
    data=anova.reset_index(),
    x="log2FC",
    y="-log10 pvalue",
    color="rejected",
    title="Simple Volcano Plot",
    subtitle="Visualizing ANOVA results",
    labels={
        "log2FC": "Log2 Fold Change",
        "-log10 pvalue": "-log10(p-value)",
        "rejected": "FDR corrected Significant",
        "identifier": "Protein Identifier",
    },
    hover_data=["identifier"],
    # currently does not work:
    # color_discrete_map={False: "#2166AC", True: "#B2182B"},  # Blue  # Red
    color_discrete_sequence=["red", "blue"],
    opacity=1,
    marker_line_width=1,
    marker_line_color="darkgray",
    width=800,
    height=600,
)
scatter_plot_adv

Done.