pertpy 0.7.0__py3-none-any.whl → 0.9.1__py3-none-any.whl

{pertpy-0.7.0.dist-info → pertpy-0.9.1.dist-info}/METADATA

@@ -1,11 +1,11 @@
 Metadata-Version: 2.3
 Name: pertpy
-Version: 0.7.0
+Version: 0.9.1
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
-Project-URL: Source, https://github.com/theislab/pertpy
-Project-URL: Home-page, https://github.com/theislab/pertpy
-Author: Lukas Heumos, Yuge Ji, Alejandro Tejada, Johannes Köster, Emma Dann, Xinyue Zhang, Xichen Wu, Amir Moinfar, Sergei Rybakov, Tessa Green, Stefan Peidli, Antonia Schumacher, Lilly May
+Project-URL: Source, https://github.com/scverse/pertpy
+Project-URL: Home-page, https://github.com/scverse/pertpy
+Author: Lukas Heumos, Yuge Ji, Lilly May, Alejandro Tejada, Johannes Köster, Emma Dann, Xinyue Zhang, Xichen Wu, Tessa Green, Stefan Peidli, Antonia Schumacher, Gregor Sturm
 Maintainer-email: Lukas Heumos <lukas.heumos@posteo.net>
 License: MIT License
         
@@ -41,15 +41,15 @@ Classifier: Operating System :: POSIX :: Linux
 Classifier: Programming Language :: Python :: 3
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Visualization
 Requires-Python: >=3.10
 Requires-Dist: adjusttext
-Requires-Dist: arviz
 Requires-Dist: blitzgsea
 Requires-Dist: decoupler
+Requires-Dist: lamin-utils
 Requires-Dist: muon
-Requires-Dist: numpyro
 Requires-Dist: openpyxl
 Requires-Dist: ott-jax
 Requires-Dist: pubchempy
@@ -61,10 +61,14 @@ Requires-Dist: scikit-misc
 Requires-Dist: scipy
 Requires-Dist: scvi-tools
 Requires-Dist: sparsecca
-Requires-Dist: toytree
 Provides-Extra: coda
+Requires-Dist: arviz; extra == 'coda'
 Requires-Dist: ete3; extra == 'coda'
 Requires-Dist: pyqt5; extra == 'coda'
+Requires-Dist: toytree; extra == 'coda'
+Provides-Extra: de
+Requires-Dist: formulaic; extra == 'de'
+Requires-Dist: pydeseq2; extra == 'de'
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Provides-Extra: doc
@@ -94,18 +98,18 @@ Requires-Dist: pytest; extra == 'test'
 Description-Content-Type: text/markdown
 
 [![Black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
-[![Build](https://github.com/theislab/pertpy/actions/workflows/build.yml/badge.svg)](https://github.com/theislab/pertpy/actions/workflows/build.yml)
-[![codecov](https://codecov.io/gh/theislab/pertpy/graph/badge.svg?token=1dTpIPBShv)](https://codecov.io/gh/theislab/pertpy)
-[![License](https://img.shields.io/github/license/theislab/pertpy)](https://opensource.org/licenses/Apache2.0)
+[![Build](https://github.com/scverse/pertpy/actions/workflows/build.yml/badge.svg)](https://github.com/scverse/pertpy/actions/workflows/build.yml)
+[![codecov](https://codecov.io/gh/scverse/pertpy/graph/badge.svg?token=1dTpIPBShv)](https://codecov.io/gh/scverse/pertpy)
+[![License](https://img.shields.io/github/license/scverse/pertpy)](https://opensource.org/licenses/Apache2.0)
 [![PyPI](https://img.shields.io/pypi/v/pertpy.svg)](https://pypi.org/project/pertpy/)
 [![Python Version](https://img.shields.io/pypi/pyversions/pertpy)](https://pypi.org/project/pertpy)
 [![Read the Docs](https://img.shields.io/readthedocs/pertpy/latest.svg?label=Read%20the%20Docs)](https://pertpy.readthedocs.io/)
-[![Test](https://github.com/theislab/pertpy/actions/workflows/test.yml/badge.svg)](https://github.com/theislab/pertpy/actions/workflows/test.yml)
+[![Test](https://github.com/scverse/pertpy/actions/workflows/test.yml/badge.svg)](https://github.com/scverse/pertpy/actions/workflows/test.yml)
 [![PyPI](https://img.shields.io/badge/pre--commit-enabled-brightgreen?logo=pre-commit&logoColor=white)](https://github.com/pre-commit/pre-commit)
 
 # pertpy
 
-![fig1](https://github.com/theislab/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
+![fig1](https://github.com/user-attachments/assets/d2e32d69-b767-4be3-a938-77a9dce45d3f)
 
 ## Documentation
 
@@ -113,18 +117,32 @@ Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
 
 ## Installation
 
-You can install _pertpy_ via [pip] from [PyPI]:
+We recommend installing and running pertpy on a recent version of Linux (e.g. Ubuntu 24.04 LTS).
+No particular hardware beyond a standard laptop is required.
+
+You can install _pertpy_ in less than a minute via [pip] from [PyPI]:
 
 ```console
 pip install pertpy
 ```
 
-if you want to use scCODA please install it as:
+if you want to use scCODA or tascCODA, please install pertpy as follows:
 
 ```console
 pip install pertpy[coda]
 ```
 
+If you want to use the differential gene expression interface, please install pertpy by running:
+
+```console
+pip install pertpy[de]
+```
+
+## Citation
+
+[Lukas Heumos, Yuge Ji, Lilly May, Tessa Green, Xinyue Zhang, Xichen Wu, Johannes Ostner, Stefan Peidli, Antonia Schumacher, Karin Hrovatin, Michaela Mueller, Faye Chong, Gregor Sturm, Alejandro Tejada, Emma Dann, Mingze Dong, Mojtaba Bahrami, Ilan Gold, Sergei Rybakov, Altana Namsaraeva, Amir Ali Moinfar, Zihe Zheng, Eljas Roellin, Isra Mekki, Chris Sander, Mohammad Lotfollahi, Herbert B. Schiller, Fabian J. Theis
+bioRxiv 2024.08.04.606516; doi: https://doi.org/10.1101/2024.08.04.606516](https://www.biorxiv.org/content/10.1101/2024.08.04.606516v1)
+
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
 [usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html

pertpy-0.9.1.dist-info/RECORD

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{pertpy-0.7.0.dist-info → pertpy-0.9.1.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.22.5
+Generator: hatchling 1.25.0
 Root-Is-Purelib: true
 Tag: py3-none-any

pertpy/plot/_augur.py

@@ -1,171 +0,0 @@
-from __future__ import annotations
-
-import warnings
-from typing import TYPE_CHECKING, Any
-
-from anndata import AnnData
-from matplotlib import pyplot as plt
-
-if TYPE_CHECKING:
-    import pandas as pd
-    from matplotlib.axes import Axes
-    from matplotlib.figure import Figure
-
-
-class AugurpyPlot:
-    """Plotting functions for Augurpy."""
-
-    @staticmethod
-    def dp_scatter(results: pd.DataFrame, top_n=None, ax: Axes = None) -> Figure | Axes:
-        """Plot result of differential prioritization.
-
-        Args:
-            results: Results after running differential prioritization.
-            top_n: optionally, the number of top prioritized cell types to label in the plot
-            ax: optionally, axes used to draw plot
-            return_figure: if `True` returns figure of the plot
-
-        Returns:
-            Axes of the plot.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> adata = pt.dt.bhattacherjee()
-            >>> ag_rfc = pt.tl.Augur("random_forest_classifier")
-
-            >>> data_15 = ag_rfc.load(adata, condition_label="Maintenance_Cocaine", treatment_label="withdraw_15d_Cocaine")
-            >>> adata_15, results_15 = ag_rfc.predict(data_15, random_state=None, n_threads=4)
-            >>> adata_15_permute, results_15_permute = ag_rfc.predict(data_15, augur_mode="permute", n_subsamples=100, random_state=None, n_threads=4)
-
-            >>> data_48 = ag_rfc.load(adata, condition_label="Maintenance_Cocaine", treatment_label="withdraw_48h_Cocaine")
-            >>> adata_48, results_48 = ag_rfc.predict(data_48, random_state=None, n_threads=4)
-            >>> adata_48_permute, results_48_permute = ag_rfc.predict(data_48, augur_mode="permute", n_subsamples=100, random_state=None, n_threads=4)
-
-            >>> pvals = ag_rfc.predict_differential_prioritization(augur_results1=results_15, augur_results2=results_48, \
-                permuted_results1=results_15_permute, permuted_results2=results_48_permute)
-            >>> ag_rfc.plot_dp_scatter(pvals)
-        """
-        warnings.warn(
-            "This function is deprecated and will be removed in pertpy 0.8.0!"
-            " Please use the corresponding 'pt.tl' object",
-            FutureWarning,
-            stacklevel=2,
-        )
-
-        from pertpy.tools import Augur
-
-        ag = Augur("random_forest_classifier")
-
-        return ag.plot_dp_scatter(results=results, top_n=top_n, ax=ax)
-
-    @staticmethod
-    def important_features(
-        data: dict[str, Any], key: str = "augurpy_results", top_n=10, ax: Axes = None
-    ) -> Figure | Axes:
-        """Plot a lollipop plot of the n features with largest feature importances.
-
-        Args:
-            results: results after running `predict()` as dictionary or the AnnData object.
-            key: Key in the AnnData object of the results
-            top_n: n number feature importance values to plot. Default is 10.
-            ax: optionally, axes used to draw plot
-            return_figure: if `True` returns figure of the plot, default is `False`
-
-        Returns:
-            Axes of the plot.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> adata = pt.dt.sc_sim_augur()
-            >>> ag_rfc = pt.tl.Augur("random_forest_classifier")
-            >>> loaded_data = ag_rfc.load(adata)
-            >>> v_adata, v_results = ag_rfc.predict(
-            ...     loaded_data, subsample_size=20, select_variance_features=True, n_threads=4
-            ... )
-            >>> ag_rfc.plot_important_features(v_results)
-        """
-        warnings.warn(
-            "This function is deprecated and will be removed in pertpy 0.8.0!"
-            " Please use the corresponding 'pt.tl' object",
-            FutureWarning,
-            stacklevel=2,
-        )
-
-        from pertpy.tools import Augur
-
-        ag = Augur("random_forest_classifier")
-
-        return ag.plot_important_features(data=data, key=key, top_n=top_n, ax=ax)
-
-    @staticmethod
-    def lollipop(data: dict[str, Any], key: str = "augurpy_results", ax: Axes = None) -> Figure | Axes | None:
-        """Plot a lollipop plot of the mean augur values.
-
-        Args:
-            results: results after running `predict()` as dictionary or the AnnData object.
-            key: Key in the AnnData object of the results
-            ax: optionally, axes used to draw plot
-            return_figure: if `True` returns figure of the plot
-
-        Returns:
-            Axes of the plot.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> adata = pt.dt.sc_sim_augur()
-            >>> ag_rfc = pt.tl.Augur("random_forest_classifier")
-            >>> loaded_data = ag_rfc.load(adata)
-            >>> v_adata, v_results = ag_rfc.predict(
-            ...     loaded_data, subsample_size=20, select_variance_features=True, n_threads=4
-            ... )
-            >>> ag_rfc.plot_lollipop(v_results)
-        """
-        warnings.warn(
-            "This function is deprecated and will be removed in pertpy 0.8.0!"
-            " Please use the corresponding 'pt.tl' object",
-            FutureWarning,
-            stacklevel=2,
-        )
-
-        from pertpy.tools import Augur
-
-        ag = Augur("random_forest_classifier")
-
-        return ag.plot_lollipop(data=data, key=key, ax=ax)
-
-    @staticmethod
-    def scatterplot(results1: dict[str, Any], results2: dict[str, Any], top_n=None) -> Figure | Axes:
-        """Create scatterplot with two augur results.
-
-        Args:
-            results1: results after running `predict()`
-            results2: results after running `predict()`
-            top_n: optionally, the number of top prioritized cell types to label in the plot
-            return_figure: if `True` returns figure of the plot
-
-        Returns:
-            Axes of the plot.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> adata = pt.dt.sc_sim_augur()
-            >>> ag_rfc = pt.tl.Augur("random_forest_classifier")
-            >>> loaded_data = ag_rfc.load(adata)
-            >>> h_adata, h_results = ag_rfc.predict(loaded_data, subsample_size=20, n_threads=4)
-            >>> v_adata, v_results = ag_rfc.predict(
-            ...     loaded_data, subsample_size=20, select_variance_features=True, n_threads=4
-            ... )
-            >>> ag_rfc.plot_scatterplot(v_results, h_results)
-        """
-        warnings.warn(
-            "This function is deprecated and will be removed in pertpy 0.8.0!"
-            " Please use the corresponding 'pt.tl' object",
-            FutureWarning,
-            stacklevel=2,
-        )
-
-        from pertpy.tools import Augur
-
-        ag = Augur("random_forest_classifier")
-
-        return ag.plot_scatterplot(results1=results1, results2=results2, top_n=top_n)