pertpy 0.7.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

pertpy-0.8.0.dist-info/RECORD

@@ -0,0 +1,57 @@
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+pertpy/tools/_scgen/_base_components.py,sha256=Qq8myRUm43q9XBrZ9gBggfa2cSV2wbz_KYoLgH7iF1A,3009
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+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-0.7.0.dist-info → pertpy-0.8.0.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)