pertpy 0.6.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

{pertpy-0.6.0.dist-info → pertpy-0.8.0.dist-info}/METADATA

@@ -1,11 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pertpy
-Version: 0.6.0
+Version: 0.8.0
 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
+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
         
@@ -29,18 +29,30 @@ License: MIT License
         OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
         SOFTWARE.
 License-File: LICENSE
-Requires-Python: >=3.9
+Classifier: Development Status :: 4 - Beta
+Classifier: Environment :: Console
+Classifier: Framework :: Jupyter
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS :: MacOS X
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Requires-Python: >=3.10
 Requires-Dist: adjusttext
-Requires-Dist: anndata
-Requires-Dist: arviz
+Requires-Dist: blitzgsea
 Requires-Dist: decoupler
-Requires-Dist: ipywidgets
+Requires-Dist: lamin-utils
 Requires-Dist: muon
-Requires-Dist: numba
-Requires-Dist: numpyro
 Requires-Dist: openpyxl
 Requires-Dist: ott-jax
-Requires-Dist: plotnine
+Requires-Dist: pubchempy
+Requires-Dist: pyarrow
 Requires-Dist: requests
 Requires-Dist: rich
 Requires-Dist: scanpy[leiden]
@@ -48,10 +60,14 @@ 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
@@ -76,23 +92,23 @@ Requires-Dist: sphinx>=4; extra == 'doc'
 Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
 Requires-Dist: sphinxext-opengraph; extra == 'doc'
 Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
 Requires-Dist: pytest; extra == 'test'
-Requires-Dist: pytest-cov; 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/branch/master/graph/badge.svg)](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
 
-![pertpy-wide1](https://user-images.githubusercontent.com/21954664/235677503-0c72f90d-3f6d-4a16-a1ff-ff8c11a540fb.png)
+![fig1](https://github.com/scverse/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
 
 ## Documentation
 
@@ -103,7 +119,19 @@ Please read the [documentation](https://pertpy.readthedocs.io/en/latest).
 You can install _pertpy_ via [pip] from [PyPI]:
 
 ```console
-$ pip install pertpy
+pip install pertpy
+```
+
+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]
 ```
 
 [pip]: https://pip.pypa.io/

pertpy-0.8.0.dist-info/RECORD

@@ -0,0 +1,57 @@
+pertpy/__init__.py,sha256=GMFyfRErEysnlkYKMqQxtO7QbqjGki7SpvgtLxIuG6o,658
+pertpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pertpy/data/__init__.py,sha256=ah3yvoxkgbdMUNAWxS3SyqcUuVamBOSeuWkF2QRAEwM,2703
+pertpy/data/_dataloader.py,sha256=fl16n82nun01gGiP7qhr5sShfcDchp0szzZp7aXkfBI,2495
+pertpy/data/_datasets.py,sha256=I-keaJSTsRBySCPjiVonKmC9rRIM0AEgo0_0UlEX804,65616
+pertpy/metadata/__init__.py,sha256=zoE_VXNyuKa4nlXlUk2nTgsHRW3jSQSpDEulcCnzOT0,222
+pertpy/metadata/_cell_line.py,sha256=-8KSqmP5XjmLEmNX3TavxSM_MtIHwLWS_x3MVkk6JEw,38595
+pertpy/metadata/_compound.py,sha256=JEFwP_TOTyMzfd2qFMb2VkJJvPhCVIvu6gs9Bq_stgs,4756
+pertpy/metadata/_drug.py,sha256=8QDSyxiFl25JdS80EQJC_krg6fEe5LIQEE6BsV1r8nY,9006
+pertpy/metadata/_look_up.py,sha256=DoWp6OxIk_HyyyOhW1p8z5E68IZ31_nZDnqxk1rJqps,28778
+pertpy/metadata/_metadata.py,sha256=pvarnv3X5pblnvG8AQ8Omu5jQcC5ORzCxRk3FRhOLgs,3276
+pertpy/metadata/_moa.py,sha256=u_OcMonjOeeoW5P9xOltquVSoTH3Vs80ztHsXf-X1DY,4701
+pertpy/plot/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pertpy/preprocessing/__init__.py,sha256=VAPFaeq2_qCvdFkQTCj_Hm460HC4Tersu8Rig_tnp_Y,71
+pertpy/preprocessing/_guide_rna.py,sha256=Xrv0cN16Ub1U1z-3LDNTkm98zs9JOjc2h1N7IAt_FaE,7612
+pertpy/tools/__init__.py,sha256=yhDyv5J-nd3SDqc3T08Nzca8dzj3SpoVG2m9VU1rFUk,1481
+pertpy/tools/_augur.py,sha256=UWro1nIEZe_rWtjlQCBv4ucqeh3Vt1m8IRzKlux72Z8,55683
+pertpy/tools/_cinemaot.py,sha256=BD_oYC1TktbFMX7fpp0A57QAF6frLEgNQ_2wFUpxjyo,39509
+pertpy/tools/_dialogue.py,sha256=f2fbhKWdm4Co79ZzVgtVq9xYwjYWFLdGNDeGFOO_pfM,51990
+pertpy/tools/_enrichment.py,sha256=rjPHK9YBCJZfpa5Rvfxo3Ii7W5Mvm5dOdolAD7QazVg,21440
+pertpy/tools/_kernel_pca.py,sha256=_EJ9WlBLjHOafF34sZGdyBgZL6Fj0WiJ1elVT1XMmo4,1579
+pertpy/tools/_milo.py,sha256=kGnfx-CMOpYSl85fOW62J2X3utVjOsQFne7ixEptDmI,43691
+pertpy/tools/_mixscape.py,sha256=FtH3PKvbLTe03LPgN4O9sS70oj_6AHz4Mz5otzEwRl8,52406
+pertpy/tools/decoupler_LICENSE,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+pertpy/tools/transferlearning_MMD_LICENSE,sha256=MUvDA-o_j9htRpI8fStVdCRuyLdPkQUuIH0a_EIc57w,1069
+pertpy/tools/_coda/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pertpy/tools/_coda/_base_coda.py,sha256=jnoLPFfluxB0_CK8-T-qolPa7xPIEb6NpeEpGwHPiNg,113058
+pertpy/tools/_coda/_sccoda.py,sha256=gGmyd0MGpchulV9d4PxKSmGORyZ8fCDS9tQVPOuF_Og,22622
+pertpy/tools/_coda/_tasccoda.py,sha256=vNk43OQHn7pBLsez2rmSj0bMZKOf8jZTI7G8TfBByRg,30665
+pertpy/tools/_differential_gene_expression/__init__.py,sha256=sabAXym8mMLwp19ZjyBN7wp-oJh32iVj9plvJ-AbXlE,521
+pertpy/tools/_differential_gene_expression/_base.py,sha256=qnQkK_hyIcViHBSkgJcAazC26JQ72bEyafKiytZikCY,23624
+pertpy/tools/_differential_gene_expression/_checks.py,sha256=SxNHJDsCYZ6rWLTMEymEBpigs_B9cnXyw0kkAe1l6e0,1675
+pertpy/tools/_differential_gene_expression/_dge_comparison.py,sha256=9HjmWkrqZhj_ZJeR-ymyEDzpRJNx7JiYJoStvCfKuCU,4188
+pertpy/tools/_differential_gene_expression/_edger.py,sha256=JziiW5rkXuQBJISAD_LvB2HOZUgJ1_qoqiR5Q4hEoP0,4321
+pertpy/tools/_differential_gene_expression/_formulaic.py,sha256=X4rPv4j8SDu5VJnf6_AIYJCCquUQka7G2LGtDLa8FhE,8715
+pertpy/tools/_differential_gene_expression/_pydeseq2.py,sha256=JK7H7u4va0q_TLE_sqi4JEzoPBd_xNRycYGu1507HS4,4117
+pertpy/tools/_differential_gene_expression/_simple_tests.py,sha256=tTSr0Z2Qbpxdy9bcO8Gi_up6R616IcoK_e4_rlanyx4,6621
+pertpy/tools/_differential_gene_expression/_statsmodels.py,sha256=zSOwJYDJyrl3hsEhMI5Q9Pyw2XLuEuj7T0zSAVcP6tQ,2585
+pertpy/tools/_distances/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pertpy/tools/_distances/_distance_tests.py,sha256=mNmNu5cX0Wj5IegR6x5K-CbBSid8EhrH2jZPQxuvK4U,13521
+pertpy/tools/_distances/_distances.py,sha256=iuHpBtWZbJhMZNSEjQkZUu6KPJXCjs_fX6YjopIWvwY,50343
+pertpy/tools/_perturbation_space/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pertpy/tools/_perturbation_space/_clustering.py,sha256=m52-J8c8OnIXRCf3NoFabIO2yMHIuy1X0m0amtsK2vE,3556
+pertpy/tools/_perturbation_space/_comparison.py,sha256=rLO-EGU0I7t5MnLw4k1gYU-ypRu-JsDPLat1t4h2U2M,4329
+pertpy/tools/_perturbation_space/_discriminator_classifiers.py,sha256=BNMP-2g4X_9jhs3Vf2rwlIjSCAcADkxBAFYGlsQ5Irw,21609
+pertpy/tools/_perturbation_space/_metrics.py,sha256=y8-baP8WRdB1iDgvP3uuQxSCDxA2lcxvEHHM2C_vWHY,3248
+pertpy/tools/_perturbation_space/_perturbation_space.py,sha256=cZPPzzK4_UZV7ktcD5BQVXEy6ITHrfkg1CLFov3TzsY,18497
+pertpy/tools/_perturbation_space/_simple.py,sha256=LH5EYvcAbzFMvgd9bH7AUPKFmdioPiy2xG8xGaXzmq0,12624
+pertpy/tools/_scgen/__init__.py,sha256=uERFlFyF88TH0uLiwmsUGEfHfLVCiZMFuk8gO5f7164,45
+pertpy/tools/_scgen/_base_components.py,sha256=Qq8myRUm43q9XBrZ9gBggfa2cSV2wbz_KYoLgH7iF1A,3009
+pertpy/tools/_scgen/_scgen.py,sha256=HPvFVjY9SS9bGqgTkCDuPYjmA4QHW7rKgHnI2yuI_Q4,30608
+pertpy/tools/_scgen/_scgenvae.py,sha256=v_6tZ4wY-JjdMH1QVd_wG4_N0PoaqB-FM8zC2JsDu1o,3935
+pertpy/tools/_scgen/_utils.py,sha256=1upgOt1FpadfvNG05YpMjYYG-IAlxrC3l_ZxczmIczo,2841
+pertpy-0.8.0.dist-info/METADATA,sha256=cLAhPubizJ7vgCThHv-kHsAAvepUyRTnTHTKRKX9kYQ,6054
+pertpy-0.8.0.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+pertpy-0.8.0.dist-info/licenses/LICENSE,sha256=OZ-ZkXM5CmExJiEMM90b_7dGNNvRpj7kdE-49AnrLuI,1070
+pertpy-0.8.0.dist-info/RECORD,,

{pertpy-0.6.0.dist-info → pertpy-0.8.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.18.0
+Generator: hatchling 1.25.0
 Root-Is-Purelib: true
 Tag: py3-none-any

pertpy/plot/_augur.py

@@ -1,234 +0,0 @@
-from __future__ import annotations
-
-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, return_figure: bool = False) -> 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)
-            >>> pt.pl.ag.dp_scatter(pvals)
-        """
-        x = results["mean_augur_score1"]
-        y = results["mean_augur_score2"]
-
-        if ax is None:
-            fig, ax = plt.subplots()
-        scatter = ax.scatter(x, y, c=results.z, cmap="Greens")
-
-        # adding optional labels
-        top_n_index = results.sort_values(by="pval").index[:top_n]
-        for idx in top_n_index:
-            ax.annotate(
-                results.loc[idx, "cell_type"],
-                (results.loc[idx, "mean_augur_score1"], results.loc[idx, "mean_augur_score2"]),
-            )
-
-        # add diagonal
-        limits = max(ax.get_xlim(), ax.get_ylim())
-        (diag_line,) = ax.plot(limits, limits, ls="--", c=".3")
-
-        # formatting and details
-        plt.xlabel("Augur scores 1")
-        plt.ylabel("Augur scores 2")
-        legend1 = ax.legend(*scatter.legend_elements(), loc="center left", title="z-scores", bbox_to_anchor=(1, 0.5))
-        ax.add_artist(legend1)
-
-        return fig if return_figure else ax
-
-    @staticmethod
-    def important_features(
-        data: dict[str, Any], key: str = "augurpy_results", top_n=10, ax: Axes = None, return_figure: bool = False
-    ) -> 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)
-            >>> pt.pl.ag.important_features(v_results)
-        """
-        if isinstance(data, AnnData):
-            results = data.uns[key]
-        else:
-            results = data
-        # top_n features to plot
-        n_features = (
-            results["feature_importances"]
-            .groupby("genes", as_index=False)
-            .feature_importances.mean()
-            .sort_values(by="feature_importances")[-top_n:]
-        )
-
-        if ax is None:
-            fig, ax = plt.subplots()
-        y_axes_range = range(1, top_n + 1)
-        ax.hlines(
-            y_axes_range,
-            xmin=0,
-            xmax=n_features["feature_importances"],
-        )
-
-        # drawing the markers (circle)
-        ax.plot(n_features["feature_importances"], y_axes_range, "o")
-
-        # formatting and details
-        plt.xlabel("Mean Feature Importance")
-        plt.ylabel("Gene")
-        plt.yticks(y_axes_range, n_features["genes"])
-
-        return fig if return_figure else ax
-
-    @staticmethod
-    def lollipop(
-        data: dict[str, Any], key: str = "augurpy_results", ax: Axes = None, return_figure: bool = False
-    ) -> Figure | Axes:
-        """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)
-            >>> pt.pl.ag.lollipop(v_results)
-        """
-        if isinstance(data, AnnData):
-            results = data.uns[key]
-        else:
-            results = data
-        if ax is None:
-            fig, ax = plt.subplots()
-        y_axes_range = range(1, len(results["summary_metrics"].columns) + 1)
-        ax.hlines(
-            y_axes_range,
-            xmin=0,
-            xmax=results["summary_metrics"].sort_values("mean_augur_score", axis=1).loc["mean_augur_score"],
-        )
-
-        # drawing the markers (circle)
-        ax.plot(
-            results["summary_metrics"].sort_values("mean_augur_score", axis=1).loc["mean_augur_score"],
-            y_axes_range,
-            "o",
-        )
-
-        # formatting and details
-        plt.xlabel("Mean Augur Score")
-        plt.ylabel("Cell Type")
-        plt.yticks(y_axes_range, results["summary_metrics"].sort_values("mean_augur_score", axis=1).columns)
-
-        return fig if return_figure else ax
-
-    @staticmethod
-    def scatterplot(
-        results1: dict[str, Any], results2: dict[str, Any], top_n=None, return_figure: bool = False
-    ) -> 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)
-            >>> pt.pl.ag.scatterplot(v_results, h_results)
-        """
-        cell_types = results1["summary_metrics"].columns
-
-        fig, ax = plt.subplots()
-        ax.scatter(
-            results1["summary_metrics"].loc["mean_augur_score", cell_types],
-            results2["summary_metrics"].loc["mean_augur_score", cell_types],
-        )
-
-        # adding optional labels
-        top_n_cell_types = (
-            (results1["summary_metrics"].loc["mean_augur_score"] - results2["summary_metrics"].loc["mean_augur_score"])
-            .sort_values(ascending=False)
-            .index[:top_n]
-        )
-        for txt in top_n_cell_types:
-            ax.annotate(
-                txt,
-                (
-                    results1["summary_metrics"].loc["mean_augur_score", txt],
-                    results2["summary_metrics"].loc["mean_augur_score", txt],
-                ),
-            )
-
-        # adding diagonal
-        limits = max(ax.get_xlim(), ax.get_ylim())
-        (diag_line,) = ax.plot(limits, limits, ls="--", c=".3")
-
-        # formatting and details
-        plt.xlabel("Augur scores 1")
-        plt.ylabel("Augur scores 2")
-
-        return fig if return_figure else ax

pertpy/plot/_cinemaot.py

@@ -1,81 +0,0 @@
-from typing import Optional
-
-import matplotlib.pyplot as plt
-import pandas as pd
-import scanpy as sc
-import seaborn as sns
-from anndata import AnnData
-from matplotlib.axes import Axes
-from scanpy.plotting import _utils
-
-
-class CinemaotPlot:
-    """Plotting functions for CINEMA-OT. Only includes new functions beyond the scanpy.pl.embedding family."""
-
-    @staticmethod
-    def vis_matching(
-        adata: AnnData,
-        de: AnnData,
-        pert_key: str,
-        control: str,
-        de_label: str,
-        source_label: str,
-        matching_rep: str = "ot",
-        resolution: float = 0.5,
-        normalize: str = "col",
-        title: str = "CINEMA-OT matching matrix",
-        min_val: float = 0.01,
-        show: bool = True,
-        save: Optional[str] = None,
-        ax: Optional[Axes] = None,
-        **kwargs,
-    ) -> None:
-        """Visualize the CINEMA-OT matching matrix.
-
-        Args:
-            adata: the original anndata after running cinemaot.causaleffect or cinemaot.causaleffect_weighted.
-            de: The anndata output from Cinemaot.causaleffect() or Cinemaot.causaleffect_weighted().
-            pert_key: The column  of `.obs` with perturbation categories, should also contain `control`.
-            control: Control category from the `pert_key` column.
-            de_label: the label for differential response. If none, use leiden cluster labels at resolution 1.0.
-            source_label: the confounder / cell type label.
-            matching_rep: the place that stores the matching matrix. default de.obsm['ot'].
-            normalize: normalize the coarse-grained matching matrix by row / column.
-            title: the title for the figure.
-            min_val: The min value to truncate the matching matrix.
-            show: Show the plot, do not return axis.
-            save: If `True` or a `str`, save the figure. A string is appended to the default filename.
-                Infer the filetype if ending on {`'.pdf'`, `'.png'`, `'.svg'`}.
-            **kwargs: Other parameters to input for seaborn.heatmap.
-        """
-        adata_ = adata[adata.obs[pert_key] == control]
-
-        df = pd.DataFrame(de.obsm[matching_rep])
-        if de_label is None:
-            de_label = "leiden"
-            sc.pp.neighbors(de, use_rep="X_embedding")
-            sc.tl.leiden(de, resolution=resolution)
-        df["de_label"] = de.obs[de_label].astype(str).values
-        df["de_label"] = "Response " + df["de_label"]
-        df = df.groupby("de_label").sum().T
-        df["source_label"] = adata_.obs[source_label].astype(str).values
-        df = df.groupby("source_label").sum()
-
-        if normalize == "col":
-            df = df / df.sum(axis=0)
-        else:
-            df = (df.T / df.sum(axis=1)).T
-        df = df.clip(lower=min_val) - min_val
-        if normalize == "col":
-            df = df / df.sum(axis=0)
-        else:
-            df = (df.T / df.sum(axis=1)).T
-
-        g = sns.heatmap(df, annot=True, ax=ax, **kwargs)
-        plt.title(title)
-        _utils.savefig_or_show("matching_heatmap", show=show, save=save)
-        if not show:
-            if ax is not None:
-                return ax
-            else:
-                return g