pertpy 0.6.0__py3-none-any.whl → 0.7.0__py3-none-any.whl

{pertpy-0.6.0.dist-info → pertpy-0.7.0.dist-info}/METADATA

@@ -1,11 +1,11 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.3
 Name: pertpy
-Version: 0.6.0
+Version: 0.7.0
 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
+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
 Maintainer-email: Lukas Heumos <lukas.heumos@posteo.net>
 License: MIT License
         
@@ -29,18 +29,31 @@ 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: 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]
@@ -76,13 +89,13 @@ 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)
+[![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)
 [![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)
@@ -92,7 +105,7 @@ Description-Content-Type: text/markdown
 
 # pertpy
 
-![pertpy-wide1](https://user-images.githubusercontent.com/21954664/235677503-0c72f90d-3f6d-4a16-a1ff-ff8c11a540fb.png)
+![fig1](https://github.com/theislab/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
 
 ## Documentation
 
@@ -103,7 +116,13 @@ 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 please install it as:
+
+```console
+pip install pertpy[coda]
 ```
 
 [pip]: https://pip.pypa.io/

pertpy-0.7.0.dist-info/RECORD

@@ -0,0 +1,53 @@
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+pertpy/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pertpy/data/__init__.py,sha256=zj4jWyw_Dr6HJvdznQi9QUkZCoFN6vdFRhFF_tw4jts,1275
+pertpy/data/_dataloader.py,sha256=UTIFK2pofjO6HJjj1dJRbZiQ04_Sslg0d6ggBRkaTnk,2325
+pertpy/data/_datasets.py,sha256=78RQb4lGFhCDQdAwb8p_MYy4ZxFjRhhfAsKkuWMl5EQ,63179
+pertpy/metadata/__init__.py,sha256=9FC_FfcpGTsc3j5orjr3USkfsT63REnQBy4r7_VRjco,171
+pertpy/metadata/_cell_line.py,sha256=tA17gWp9uY0jn36S5bt5lfc9zU2HC2DxZ6x5jVRUosU,40644
+pertpy/metadata/_compound.py,sha256=Y1oaV_Nq4-wDVFPQhenJTjvOlY4HYi8bCxUUN3VNbMc,4861
+pertpy/metadata/_drug.py,sha256=q3snazwU_wTLC3Js-9pr_CvfBCRGuFBLlHSFVV-h3ko,9357
+pertpy/metadata/_look_up.py,sha256=Tb9BHZVc05aH4Kg2KLcfrgvra8gEV5aBqwAZ433krMc,29476
+pertpy/metadata/_metadata.py,sha256=h_m5bjn_DvCOuiie_q_DB6eM9ermJKXSnLJ0i84AGqI,3419
+pertpy/metadata/_moa.py,sha256=gLjM59ANqK5Ov-Y-v6COr5Bz4nI2O_LEBfJ2jRpR5U8,4941
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+pertpy/plot/_coda.py,sha256=qZfkfFT61pwf-rlOYPwJiYDkx_1DTkT4TfG9fObQWoc,26891
+pertpy/plot/_guide_rna.py,sha256=iIjkOus7tftIv01zaCTamSX2q8bHBI8O4dxv6QDRVM0,2702
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+pertpy/plot/_mixscape.py,sha256=wKsY1efBP9VtQptAq79w5-ODcgzomD3QgW8iOF-5LZY,14862
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+pertpy/preprocessing/_guide_rna.py,sha256=9FSu0QCxZujGPxhl-PcU4yRR7ZSGhgg99eJaLmf8hRA,7713
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+pertpy/tools/_augur.py,sha256=Lws7-oSjSFGRupoloj7yIA3YNvVt_dcjSnQ8_Ctt2u0,55797
+pertpy/tools/_cinemaot.py,sha256=EbnucYl-Q3sfPDL9RiA-cXjpGFJYvfF4CaDEkyr7Snc,39501
+pertpy/tools/_dialogue.py,sha256=u98h147h2PwhWxFQo8limNmt20e2r5La9-wZvS6tXjo,52143
+pertpy/tools/_differential_gene_expression.py,sha256=eqit0SJ_fIpSYRS5grYZxEln_JkpXyng-q3LUw9ArY8,14360
+pertpy/tools/_enrichment.py,sha256=U2WY7t--FCQFZsXXBLZYBwF4WO9t5WToWjCGn_-tP6I,21922
+pertpy/tools/_kernel_pca.py,sha256=3S1D_wrp4vlHUPiRbCAoRbUyY-rVs112Qh-BZHSmTxE,1578
+pertpy/tools/_milo.py,sha256=SxpEjhvn2FOYQcQ56tG9ts8fS2vpp4DsB3V7lr8QHbc,43388
+pertpy/tools/_mixscape.py,sha256=5s0BrLsv1uv1tbZkZnNXN2qUzWjxvIuGe2iu9czBIxA,52500
+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=L6OEz7PHDve_geS6JdyjMC5fSMNitZ4pYQOyMjSW04E,115262
+pertpy/tools/_coda/_sccoda.py,sha256=K_zsU8z_YP1hwJV1Urug4fd7kS-q23eLkcSsX_hxqYg,22849
+pertpy/tools/_coda/_tasccoda.py,sha256=xTe89TMtbUkw7WAEAvWzOQsMotdekP3Vs5zhMtB2t6c,31033
+pertpy/tools/_distances/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pertpy/tools/_distances/_distance_tests.py,sha256=aC4zspn4nJ2JRk56c76xTgSxl9znY7QI7zLktwsQ8SY,13604
+pertpy/tools/_distances/_distances.py,sha256=_dB9dyqWvg_yJBMJTuruFw5w-CLtQWqol-28KVifPBM,35619
+pertpy/tools/_perturbation_space/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+pertpy/tools/_perturbation_space/_clustering.py,sha256=a1p0vzjN9nsmtWXWaKIeR3To3mL-7mzqD3HTTiHCpRk,3470
+pertpy/tools/_perturbation_space/_discriminator_classifiers.py,sha256=JYDPJlyqxeFbBqWqXk0el6ClXIwrUIYTye5ehmQvmao,22080
+pertpy/tools/_perturbation_space/_metrics.py,sha256=y8-baP8WRdB1iDgvP3uuQxSCDxA2lcxvEHHM2C_vWHY,3248
+pertpy/tools/_perturbation_space/_perturbation_space.py,sha256=VwwYjQ8-VfRHp8_97Id320xd3tnvv-wea6iLFkRE0RY,18868
+pertpy/tools/_perturbation_space/_simple.py,sha256=37zZweW-50Oa8pTQyC53KyNZQH157HurSc8qXZZt7JA,12681
+pertpy/tools/_scgen/__init__.py,sha256=neOj3JEcXxnIvgSMrSuPaUSGl1upo7yQ7K_NXHb8Rb8,45
+pertpy/tools/_scgen/_base_components.py,sha256=dIw-_7Z8iCietPF4tnpM7bFHtDksjnaHXwUjp9GoCIQ,2936
+pertpy/tools/_scgen/_scgen.py,sha256=qPu_zWCdLvcuOqSDNb2FLzxE5Y1uH0uSbpPGu7kOKks,30705
+pertpy/tools/_scgen/_scgenvae.py,sha256=v_6tZ4wY-JjdMH1QVd_wG4_N0PoaqB-FM8zC2JsDu1o,3935
+pertpy/tools/_scgen/_utils.py,sha256=y0LGS1OLmIVUBq2ZYySM2Up51o3c08-yjTvUkFb3E0U,2841
+pertpy-0.7.0.dist-info/METADATA,sha256=tSfWThb8uxC4jwbO5VfOIikt8DRBpO4UdHdFde0al3w,5782
+pertpy-0.7.0.dist-info/WHEEL,sha256=as-1oFTWSeWBgyzh0O_qF439xqBe6AbBgt4MfYe5zwY,87
+pertpy-0.7.0.dist-info/licenses/LICENSE,sha256=OZ-ZkXM5CmExJiEMM90b_7dGNNvRpj7kdE-49AnrLuI,1070
+pertpy-0.7.0.dist-info/RECORD,,

{pertpy-0.6.0.dist-info → pertpy-0.7.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.18.0
+Generator: hatchling 1.22.5
 Root-Is-Purelib: true
 Tag: py3-none-any

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

pertpy/plot/_dialogue.py

@@ -1,91 +0,0 @@
-import matplotlib.pyplot as plt
-import pandas as pd
-import scanpy as sc
-import seaborn as sns
-from anndata import AnnData
-from seaborn import PairGrid
-
-
-class DialoguePlot:
-    @staticmethod
-    def split_violins(
-        adata: AnnData,
-        split_key: str,
-        celltype_key=str,
-        split_which: tuple[str, str] = None,
-        mcp: str = "mcp_0",
-    ) -> plt.Axes:
-        """Plots split violin plots for a given MCP and split variable.
-
-        Any cells with a value for split_key not in split_which are removed from the plot.
-
-        Args:
-            adata: Annotated data object.
-            split_key: Variable in adata.obs used to split the data.
-            celltype_key: Key for cell type annotations.
-            split_which: Which values of split_key to plot. Required if more than 2 values in split_key.
-            mcp: Key for MCP data. Defaults to "mcp_0".
-
-        Returns:
-            A :class:`~matplotlib.axes.Axes` object
-
-        Examples:
-            >>> import pertpy as pt
-            >>> import scanpy as sc
-            >>> adata = pt.dt.dialogue_example()
-            >>> sc.pp.pca(adata)
-            >>> dl = pt.tl.Dialogue(sample_id = "clinical.status", celltype_key = "cell.subtypes", \
-                n_counts_key = "nCount_RNA", n_mpcs = 3)
-            >>> adata, mcps, ws, ct_subs = dl.calculate_multifactor_PMD(adata, normalize=True)
-            >>> pt.pl.dl.split_violins(adata, split_key='gender', celltype_key='cell.subtypes')
-        """
-        df = sc.get.obs_df(adata, [celltype_key, mcp, split_key])
-        if split_which is None:
-            split_which = df[split_key].unique()
-        df = df[df[split_key].isin(split_which)]
-        df[split_key] = df[split_key].cat.remove_unused_categories()
-
-        ax = sns.violinplot(data=df, x=celltype_key, y=mcp, hue=split_key, split=True)
-
-        ax.set_xticklabels(ax.get_xticklabels(), rotation=90)
-
-        return ax
-
-    @staticmethod
-    def pairplot(adata: AnnData, celltype_key: str, color: str, sample_id: str, mcp: str = "mcp_0") -> PairGrid:
-        """Generate a pairplot visualization for multi-cell perturbation (MCP) data.
-
-        Computes the mean of a specified MCP feature (mcp) for each combination of sample and cell type,
-        then creates a pairplot to visualize the relationships between these mean MCP values.
-
-        Args:
-            adata: Annotated data object.
-            celltype_key: Key in adata.obs containing cell type annotations.
-            color: Key in adata.obs for color annotations. This parameter is used as the hue
-            sample_id: Key in adata.obs for the sample annotations.
-            mcp: Key in adata.obs for MCP feature values. Defaults to "mcp_0".
-
-        Returns:
-            Seaborn Pairgrid object.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> import scanpy as sc
-            >>> adata = pt.dt.dialogue_example()
-            >>> sc.pp.pca(adata)
-            >>> dl = pt.tl.Dialogue(sample_id = "clinical.status", celltype_key = "cell.subtypes", \
-                n_counts_key = "nCount_RNA", n_mpcs = 3)
-            >>> adata, mcps, ws, ct_subs = dl.calculate_multifactor_PMD(adata, normalize=True)
-            >>> pt.pl.dl.pairplot(adata, celltype_key="cell.subtypes", color="gender", sample_id="clinical.status")
-        """
-        mean_mcps = adata.obs.groupby([sample_id, celltype_key])[mcp].mean()
-        mean_mcps = mean_mcps.reset_index()
-        mcp_pivot = pd.pivot(mean_mcps[[sample_id, celltype_key, mcp]], index=sample_id, columns=celltype_key)[mcp]
-
-        aggstats = adata.obs.groupby([sample_id])[color].describe()
-        aggstats = aggstats.loc[list(mcp_pivot.index), :]
-        aggstats[color] = aggstats["top"]
-        mcp_pivot = pd.concat([mcp_pivot, aggstats[color]], axis=1)
-        ax = sns.pairplot(mcp_pivot, hue=color, corner=True)
-
-        return ax

pertpy/plot/_scgen.py

@@ -1,337 +0,0 @@
-import numpy as np
-import pandas as pd
-import scanpy as sc
-from adjustText import adjust_text
-from matplotlib import pyplot
-from scipy import stats
-from scvi import REGISTRY_KEYS
-
-
-class JaxscgenPlot:
-    """Plotting functions for Jaxscgen."""
-
-    @staticmethod
-    def reg_mean_plot(
-        adata,
-        condition_key,
-        axis_keys,
-        labels,
-        path_to_save="./reg_mean.pdf",
-        save=True,
-        gene_list=None,
-        show=False,
-        top_100_genes=None,
-        verbose=False,
-        legend=True,
-        title=None,
-        x_coeff=0.30,
-        y_coeff=0.8,
-        fontsize=14,
-        **kwargs,
-    ):
-        """Plots mean matching figure for a set of specific genes.
-
-        Args:
-            adata:  AnnData object with equivalent structure to initial AnnData. If `None`, defaults to the
-                    AnnData object used to initialize the model. Must have been setup with `batch_key` and `labels_key`,
-                    corresponding to batch and cell type metadata, respectively.
-            condition_key: The key for the condition
-            axis_keys: Dictionary of `adata.obs` keys that are used by the axes of the plot. Has to be in the following form:
-                       `{"x": "Key for x-axis", "y": "Key for y-axis"}`.
-            labels: Dictionary of axes labels of the form `{"x": "x-axis-name", "y": "y-axis name"}`.
-            path_to_save: path to save the plot.
-            save: Specify if the plot should be saved or not.
-            gene_list: list of gene names to be plotted.
-            show: if `True`: will show to the plot after saving it.
-            top_100_genes: List of the top 100 differentially expressed genes. Specify if you want the top 100 DEGs to be assessed extra.
-            verbose: Specify if you want information to be printed while creating the plot, defaults to `False`.
-            legend: if `True`: plots a legend, defaults to `True`.
-            title: Set if you want the plot to display a title.
-            x_coeff: Offset to print the R^2 value in x-direction, defaults to 0.3.
-            y_coeff: Offset to print the R^2 value in y-direction, defaults to 0.8.
-            fontsize: Fontsize used for text in the plot, defaults to 14.
-            **kwargs:
-
-        Examples:
-            >>> import pertpy at pt
-            >>> data = pt.dt.kang_2018()
-            >>> pt.tl.SCGEN.setup_anndata(data, batch_key="label", labels_key="cell_type")
-            >>> model = pt.tl.SCGEN(data)
-            >>> model.train(max_epochs=10, batch_size=64, early_stopping=True, early_stopping_patience=5)
-            >>> pred, delta = model.predict(ctrl_key='ctrl', stim_key='stim', celltype_to_predict='CD4 T cells')
-            >>> pred.obs['label'] = 'pred'
-            >>> eval_adata = data[data.obs['cell_type'] == 'CD4 T cells'].copy().concatenate(pred)
-            >>> r2_value = pt.pl.scg.reg_mean_plot(eval_adata, condition_key='label', axis_keys={"x": "pred", "y": "stim"}, \
-                labels={"x": "predicted", "y": "ground truth"}, save=False, show=True)
-        """
-        import seaborn as sns
-
-        sns.set()
-        sns.set(color_codes=True)
-
-        diff_genes = top_100_genes
-        stim = adata[adata.obs[condition_key] == axis_keys["y"]]
-        ctrl = adata[adata.obs[condition_key] == axis_keys["x"]]
-        if diff_genes is not None:
-            if hasattr(diff_genes, "tolist"):
-                diff_genes = diff_genes.tolist()
-            adata_diff = adata[:, diff_genes]
-            stim_diff = adata_diff[adata_diff.obs[condition_key] == axis_keys["y"]]
-            ctrl_diff = adata_diff[adata_diff.obs[condition_key] == axis_keys["x"]]
-            x_diff = np.asarray(np.mean(ctrl_diff.X, axis=0)).ravel()
-            y_diff = np.asarray(np.mean(stim_diff.X, axis=0)).ravel()
-            m, b, r_value_diff, p_value_diff, std_err_diff = stats.linregress(x_diff, y_diff)
-            if verbose:
-                print("top_100 DEGs mean: ", r_value_diff**2)
-        x = np.asarray(np.mean(ctrl.X, axis=0)).ravel()
-        y = np.asarray(np.mean(stim.X, axis=0)).ravel()
-        m, b, r_value, p_value, std_err = stats.linregress(x, y)
-        if verbose:
-            print("All genes mean: ", r_value**2)
-        df = pd.DataFrame({axis_keys["x"]: x, axis_keys["y"]: y})
-        ax = sns.regplot(x=axis_keys["x"], y=axis_keys["y"], data=df)
-        ax.tick_params(labelsize=fontsize)
-        if "range" in kwargs:
-            start, stop, step = kwargs.get("range")
-            ax.set_xticks(np.arange(start, stop, step))
-            ax.set_yticks(np.arange(start, stop, step))
-        ax.set_xlabel(labels["x"], fontsize=fontsize)
-        ax.set_ylabel(labels["y"], fontsize=fontsize)
-        if gene_list is not None:
-            texts = []
-            for i in gene_list:
-                j = adata.var_names.tolist().index(i)
-                x_bar = x[j]
-                y_bar = y[j]
-                texts.append(pyplot.text(x_bar, y_bar, i, fontsize=11, color="black"))
-                pyplot.plot(x_bar, y_bar, "o", color="red", markersize=5)
-                # if "y1" in axis_keys.keys():
-                # y1_bar = y1[j]
-                # pyplot.text(x_bar, y1_bar, i, fontsize=11, color="black")
-        if gene_list is not None:
-            adjust_text(
-                texts,
-                x=x,
-                y=y,
-                arrowprops={"arrowstyle": "->", "color": "grey", "lw": 0.5},
-                force_points=(0.0, 0.0),
-            )
-        if legend:
-            pyplot.legend(loc="center left", bbox_to_anchor=(1, 0.5))
-        if title is None:
-            pyplot.title("", fontsize=fontsize)
-        else:
-            pyplot.title(title, fontsize=fontsize)
-        ax.text(
-            max(x) - max(x) * x_coeff,
-            max(y) - y_coeff * max(y),
-            r"$\mathrm{R^2_{\mathrm{\mathsf{all\ genes}}}}$= " + f"{r_value ** 2:.2f}",
-            fontsize=kwargs.get("textsize", fontsize),
-        )
-        if diff_genes is not None:
-            ax.text(
-                max(x) - max(x) * x_coeff,
-                max(y) - (y_coeff + 0.15) * max(y),
-                r"$\mathrm{R^2_{\mathrm{\mathsf{top\ 100\ DEGs}}}}$= " + f"{r_value_diff ** 2:.2f}",
-                fontsize=kwargs.get("textsize", fontsize),
-            )
-        if save:
-            pyplot.savefig(f"{path_to_save}", bbox_inches="tight", dpi=100)
-        if show:
-            pyplot.show()
-        pyplot.close()
-        if diff_genes is not None:
-            return r_value**2, r_value_diff**2
-        else:
-            return r_value**2
-
-    @staticmethod
-    def reg_var_plot(
-        adata,
-        condition_key,
-        axis_keys,
-        labels,
-        path_to_save="./reg_var.pdf",
-        save=True,
-        gene_list=None,
-        top_100_genes=None,
-        show=False,
-        legend=True,
-        title=None,
-        verbose=False,
-        x_coeff=0.30,
-        y_coeff=0.8,
-        fontsize=14,
-        **kwargs,
-    ):
-        """Plots variance matching figure for a set of specific genes.
-
-        Args:
-            adata: AnnData object with equivalent structure to initial AnnData. If `None`, defaults to the
-                   AnnData object used to initialize the model. Must have been setup with `batch_key` and `labels_key`,
-                   corresponding to batch and cell type metadata, respectively.
-            condition_key: Key of the condition.
-            axis_keys: Dictionary of `adata.obs` keys that are used by the axes of the plot. Has to be in the following form:
-                       `{"x": "Key for x-axis", "y": "Key for y-axis"}`.
-            labels: Dictionary of axes labels of the form `{"x": "x-axis-name", "y": "y-axis name"}`.
-            path_to_save: path to save the plot.
-            save: Specify if the plot should be saved or not.
-            gene_list: list of gene names to be plotted.
-            show: if `True`: will show to the plot after saving it.
-            top_100_genes: List of the top 100 differentially expressed genes. Specify if you want the top 100 DEGs to be assessed extra.
-            legend: if `True`: plots a legend, defaults to `True`.
-            title: Set if you want the plot to display a title.
-            verbose: Specify if you want information to be printed while creating the plot, defaults to `False`.
-            x_coeff: Offset to print the R^2 value in x-direction, defaults to 0.3.
-            y_coeff: Offset to print the R^2 value in y-direction, defaults to 0.8.
-            fontsize: Fontsize used for text in the plot, defaults to 14.
-        """
-        import seaborn as sns
-
-        sns.set()
-        sns.set(color_codes=True)
-
-        sc.tl.rank_genes_groups(adata, groupby=condition_key, n_genes=100, method="wilcoxon")
-        diff_genes = top_100_genes
-        stim = adata[adata.obs[condition_key] == axis_keys["y"]]
-        ctrl = adata[adata.obs[condition_key] == axis_keys["x"]]
-        if diff_genes is not None:
-            if hasattr(diff_genes, "tolist"):
-                diff_genes = diff_genes.tolist()
-            adata_diff = adata[:, diff_genes]
-            stim_diff = adata_diff[adata_diff.obs[condition_key] == axis_keys["y"]]
-            ctrl_diff = adata_diff[adata_diff.obs[condition_key] == axis_keys["x"]]
-            x_diff = np.asarray(np.var(ctrl_diff.X, axis=0)).ravel()
-            y_diff = np.asarray(np.var(stim_diff.X, axis=0)).ravel()
-            m, b, r_value_diff, p_value_diff, std_err_diff = stats.linregress(x_diff, y_diff)
-            if verbose:
-                print("Top 100 DEGs var: ", r_value_diff**2)
-        if "y1" in axis_keys.keys():
-            real_stim = adata[adata.obs[condition_key] == axis_keys["y1"]]
-        x = np.asarray(np.var(ctrl.X, axis=0)).ravel()
-        y = np.asarray(np.var(stim.X, axis=0)).ravel()
-        m, b, r_value, p_value, std_err = stats.linregress(x, y)
-        if verbose:
-            print("All genes var: ", r_value**2)
-        df = pd.DataFrame({axis_keys["x"]: x, axis_keys["y"]: y})
-        ax = sns.regplot(x=axis_keys["x"], y=axis_keys["y"], data=df)
-        ax.tick_params(labelsize=fontsize)
-        if "range" in kwargs:
-            start, stop, step = kwargs.get("range")
-            ax.set_xticks(np.arange(start, stop, step))
-            ax.set_yticks(np.arange(start, stop, step))
-        # _p1 = pyplot.scatter(x, y, marker=".", label=f"{axis_keys['x']}-{axis_keys['y']}")
-        # pyplot.plot(x, m * x + b, "-", color="green")
-        ax.set_xlabel(labels["x"], fontsize=fontsize)
-        ax.set_ylabel(labels["y"], fontsize=fontsize)
-        if "y1" in axis_keys.keys():
-            y1 = np.asarray(np.var(real_stim.X, axis=0)).ravel()
-            _ = pyplot.scatter(
-                x,
-                y1,
-                marker="*",
-                c="grey",
-                alpha=0.5,
-                label=f"{axis_keys['x']}-{axis_keys['y1']}",
-            )
-        if gene_list is not None:
-            for i in gene_list:
-                j = adata.var_names.tolist().index(i)
-                x_bar = x[j]
-                y_bar = y[j]
-                pyplot.text(x_bar, y_bar, i, fontsize=11, color="black")
-                pyplot.plot(x_bar, y_bar, "o", color="red", markersize=5)
-                if "y1" in axis_keys.keys():
-                    y1_bar = y1[j]
-                    pyplot.text(x_bar, y1_bar, "*", color="black", alpha=0.5)
-        if legend:
-            pyplot.legend(loc="center left", bbox_to_anchor=(1, 0.5))
-        if title is None:
-            pyplot.title("", fontsize=12)
-        else:
-            pyplot.title(title, fontsize=12)
-        ax.text(
-            max(x) - max(x) * x_coeff,
-            max(y) - y_coeff * max(y),
-            r"$\mathrm{R^2_{\mathrm{\mathsf{all\ genes}}}}$= " + f"{r_value ** 2:.2f}",
-            fontsize=kwargs.get("textsize", fontsize),
-        )
-        if diff_genes is not None:
-            ax.text(
-                max(x) - max(x) * x_coeff,
-                max(y) - (y_coeff + 0.15) * max(y),
-                r"$\mathrm{R^2_{\mathrm{\mathsf{top\ 100\ DEGs}}}}$= " + f"{r_value_diff ** 2:.2f}",
-                fontsize=kwargs.get("textsize", fontsize),
-            )
-
-        if save:
-            pyplot.savefig(f"{path_to_save}", bbox_inches="tight", dpi=100)
-        if show:
-            pyplot.show()
-        pyplot.close()
-        if diff_genes is not None:
-            return r_value**2, r_value_diff**2
-        else:
-            return r_value**2
-
-    @staticmethod
-    def binary_classifier(
-        scgen,
-        adata,
-        delta,
-        ctrl_key,
-        stim_key,
-        path_to_save,
-        save=True,
-        fontsize=14,
-    ):
-        """Latent space classifier.
-
-        Builds a linear classifier based on the dot product between
-        the difference vector and the latent representation of each
-        cell and plots the dot product results between delta and latent representation.
-
-        Args:
-            scgen: ScGen object that was trained.
-            adata: AnnData object with equivalent structure to initial AnnData. If `None`, defaults to the
-                   AnnData object used to initialize the model. Must have been setup with `batch_key` and `labels_key`,
-                   corresponding to batch and cell type metadata, respectively.
-            delta: Difference between stimulated and control cells in latent space
-            ctrl_key: Key for `control` part of the `data` found in `condition_key`.
-            stim_key: Key for `stimulated` part of the `data` found in `condition_key`.
-            path_to_save: Path to save the plot.
-            save: Specify if the plot should be saved or not.
-            fontsize: Set the font size of the plot.
-        """
-        # matplotlib.rcParams.update(matplotlib.rcParamsDefault)
-        pyplot.close("all")
-        adata = scgen._validate_anndata(adata)
-        condition_key = scgen.adata_manager.get_state_registry(REGISTRY_KEYS.BATCH_KEY).original_key
-        cd = adata[adata.obs[condition_key] == ctrl_key, :]
-        stim = adata[adata.obs[condition_key] == stim_key, :]
-        all_latent_cd = scgen.get_latent_representation(cd.X)
-        all_latent_stim = scgen.get_latent_representation(stim.X)
-        dot_cd = np.zeros(len(all_latent_cd))
-        dot_sal = np.zeros(len(all_latent_stim))
-        for ind, vec in enumerate(all_latent_cd):
-            dot_cd[ind] = np.dot(delta, vec)
-        for ind, vec in enumerate(all_latent_stim):
-            dot_sal[ind] = np.dot(delta, vec)
-        pyplot.hist(
-            dot_cd,
-            label=ctrl_key,
-            bins=50,
-        )
-        pyplot.hist(dot_sal, label=stim_key, bins=50)
-        pyplot.axvline(0, color="k", linestyle="dashed", linewidth=1)
-        pyplot.title("  ", fontsize=fontsize)
-        pyplot.xlabel("  ", fontsize=fontsize)
-        pyplot.ylabel("  ", fontsize=fontsize)
-        pyplot.xticks(fontsize=fontsize)
-        pyplot.yticks(fontsize=fontsize)
-        ax = pyplot.gca()
-        ax.grid(False)
-
-        if save:
-            pyplot.savefig(f"{path_to_save}", bbox_inches="tight", dpi=100)
-        pyplot.show()