pertpy 0.9.4__py3-none-any.whl → 0.10.0__py3-none-any.whl

pertpy/tools/_perturbation_space/_perturbation_space.py

@@ -7,6 +7,7 @@ import pandas as pd
 from anndata import AnnData
 from lamin_utils import logger
 from rich import print
+from scipy.stats import entropy
 
 if TYPE_CHECKING:
     from collections.abc import Iterable
@@ -41,7 +42,7 @@ class PerturbationSpace:
         Args:
             adata: Anndata object of size cells x genes.
             target_col: .obs column name that stores the label of the perturbation applied to each cell.
-            group_col: .obs column name that stores the label of the group of eah cell. If None, ignore groups.
+            group_col: .obs column name that stores the label of the group of each cell. If None, ignore groups.
             reference_key: The key of the control values.
             layer_key: Key of the AnnData layer to use for computation.
             new_layer_key: the results are stored in the given layer.
@@ -364,50 +365,58 @@ class PerturbationSpace:
         self,
         adata: AnnData,
         column: str = "perturbation",
+        column_uncertainty_score_key: str = "perturbation_transfer_uncertainty",
         target_val: str = "unknown",
-        n_neighbors: int = 5,
-        use_rep: str = "X_umap",
+        neighbors_key: str = "neighbors",
     ) -> None:
         """Impute missing values in the specified column using KNN imputation in the space defined by `use_rep`.
 
+        Uncertainty is calculated as the entropy of the label distribution in the neighborhood of the target cell.
+        In other words, a cell where all neighbors have the same set of labels will have an uncertainty of 0, whereas a cell
+        where all neighbors have many different labels will have high uncertainty.
+
         Args:
             adata: The AnnData object containing single-cell data.
-            column: The column name in AnnData object to perform imputation on.
+            column: The column name in adata.obs to perform imputation on.
+            column_uncertainty_score_key: The column name in adata.obs to store the uncertainty score of the label transfer.
             target_val: The target value to impute.
-            n_neighbors: Number of neighbors to use for imputation.
-            use_rep: The key in `adata.obsm` where the embedding (UMAP, PCA, etc.) is stored.
+            neighbors_key: The key in adata.uns where the neighbors are stored.
 
         Examples:
             >>> import pertpy as pt
             >>> import scanpy as sc
             >>> import numpy as np
             >>> adata = sc.datasets.pbmc68k_reduced()
-            >>> rng = np.random.default_rng()
-            >>> adata.obs["perturbation"] = rng.choice(
-            ...     ["A", "B", "C", "unknown"], size=adata.n_obs, p=[0.33, 0.33, 0.33, 0.01]
-            ... )
+            >>> # randomly dropout 10% of the data annotations
+            >>> adata.obs["perturbation"] = adata.obs["louvain"].astype(str).copy()
+            >>> random_cells = np.random.choice(adata.obs.index, int(adata.obs.shape[0] * 0.1), replace=False)
+            >>> adata.obs.loc[random_cells, "perturbation"] = "unknown"
             >>> sc.pp.neighbors(adata)
             >>> sc.tl.umap(adata)
             >>> ps = pt.tl.PseudobulkSpace()
-            >>> ps.label_transfer(adata, n_neighbors=5, use_rep="X_umap")
+            >>> ps.label_transfer(adata)
         """
-        if use_rep not in adata.obsm:
-            raise ValueError(f"Representation {use_rep} not found in the AnnData object.")
-
-        embedding = adata.obsm[use_rep]
-
-        from pynndescent import NNDescent
-
-        nnd = NNDescent(embedding, n_neighbors=n_neighbors)
-        indices, _ = nnd.query(embedding, k=n_neighbors)
-
-        perturbations = np.array(adata.obs[column])
-        missing_mask = perturbations == target_val
-
-        for idx in np.where(missing_mask)[0]:
-            neighbor_indices = indices[idx]
-            neighbor_categories = perturbations[neighbor_indices]
-            most_common = pd.Series(neighbor_categories).mode()[0]
-            perturbations[idx] = most_common
-
-        adata.obs[column] = perturbations
+        if neighbors_key not in adata.uns:
+            raise ValueError(f"Key {neighbors_key} not found in adata.uns. Please run `sc.pp.neighbors` first.")
+
+        labels = adata.obs[column].astype(str)
+        target_cells = labels == target_val
+
+        connectivities = adata.obsp[adata.uns[neighbors_key]["connectivities_key"]]
+        # convert labels to an incidence matrix
+        one_hot_encoded_labels = adata.obs[column].astype(str).str.get_dummies()
+        # convert to distance-weighted neighborhood incidence matrix
+        weighted_label_occurence = pd.DataFrame(
+            (one_hot_encoded_labels.values.T * connectivities).T,
+            index=adata.obs_names,
+            columns=one_hot_encoded_labels.columns,
+        )
+        # choose best label for each target cell
+        best_labels = weighted_label_occurence.drop(target_val, axis=1)[target_cells].idxmax(axis=1)
+        adata.obs[column] = labels
+        adata.obs.loc[target_cells, column] = best_labels
+
+        # calculate uncertainty
+        uncertainty = np.zeros(adata.n_obs)
+        uncertainty[target_cells] = entropy(weighted_label_occurence.drop(target_val, axis=1)[target_cells], axis=1)
+        adata.obs[column_uncertainty_score_key] = uncertainty

pertpy/tools/_perturbation_space/_simple.py

@@ -1,13 +1,20 @@
 from __future__ import annotations
 
+from typing import TYPE_CHECKING
+
 import decoupler as dc
+import matplotlib.pyplot as plt
 import numpy as np
 from anndata import AnnData
 from sklearn.cluster import DBSCAN, KMeans
 
+from pertpy._doc import _doc_params, doc_common_plot_args
 from pertpy.tools._perturbation_space._clustering import ClusteringSpace
 from pertpy.tools._perturbation_space._perturbation_space import PerturbationSpace
 
+if TYPE_CHECKING:
+    from matplotlib.pyplot import Figure
+
 
 class CentroidSpace(PerturbationSpace):
     """Computes the centroids per perturbation of a pre-computed embedding."""
@@ -168,6 +175,47 @@ class PseudobulkSpace(PerturbationSpace):
 
         return ps_adata
 
+    @_doc_params(common_plot_args=doc_common_plot_args)
+    def plot_psbulk_samples(
+        self,
+        adata: AnnData,
+        groupby: str,
+        *,
+        return_fig: bool = False,
+        **kwargs,
+    ) -> Figure | None:
+        """Plot the pseudobulk samples of an AnnData object.
+
+        Plot the count number vs. the number of cells per pseudobulk sample.
+
+        Args:
+            adata: Anndata containing pseudobulk samples.
+            groupby: `.obs` column to color the samples by.
+            {common_plot_args}
+            **kwargs: Are passed to decoupler's plot_psbulk_samples.
+
+        Returns:
+            If `return_fig` is `True`, returns the figure, otherwise `None`.
+
+        Examples:
+            >>> import pertpy as pt
+            >>> adata = pt.dt.zhang_2021()
+            >>> ps = pt.tl.PseudobulkSpace()
+            >>> pdata = ps.compute(
+            ...     adata, target_col="Patient", groups_col="Cluster", mode="sum", min_cells=10, min_counts=1000
+            ... )
+            >>> ps.plot_psbulk_samples(pdata, groupby=["Patient", "Major celltype"], figsize=(12, 4))
+
+        Preview:
+            .. image:: /_static/docstring_previews/pseudobulk_samples.png
+        """
+        fig = dc.plot_psbulk_samples(adata, groupby, return_fig=True, **kwargs)
+
+        if return_fig:
+            return fig
+        plt.show()
+        return None
+
 
 class KMeansSpace(ClusteringSpace):
     """Computes K-Means clustering of the expression values."""

pertpy/tools/_scgen/_scgen.py

@@ -18,12 +18,16 @@ from scvi.data.fields import CategoricalObsField, LayerField
 from scvi.model.base import BaseModelClass, JaxTrainingMixin
 from scvi.utils import setup_anndata_dsp
 
+from pertpy._doc import _doc_params, doc_common_plot_args
+
 from ._scgenvae import JaxSCGENVAE
 from ._utils import balancer, extractor
 
 if TYPE_CHECKING:
     from collections.abc import Sequence
 
+    from matplotlib.pyplot import Figure
+
 font = {"family": "Arial", "size": 14}
 
 
@@ -377,9 +381,8 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
         condition_key: str,
         axis_keys: dict[str, str],
         labels: dict[str, str],
-        save: str | bool | None = None,
+        *,
         gene_list: list[str] = None,
-        show: bool = False,
         top_100_genes: list[str] = None,
         verbose: bool = False,
         legend: bool = True,
@@ -387,6 +390,8 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
         x_coeff: float = 0.30,
         y_coeff: float = 0.8,
         fontsize: float = 14,
+        show: bool = False,
+        save: str | bool | None = None,
         **kwargs,
     ) -> tuple[float, float] | float:
         """Plots mean matching for a set of specified genes.
@@ -397,21 +402,23 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
                     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.
+                       {`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`}.
             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.,
+            verbose: Specify if you want information to be printed while creating the plot.
             legend: Whether to plot a legend.
             title: Set if you want the plot to display a title.
             x_coeff: Offset to print the R^2 value in x-direction.
             y_coeff: Offset to print the R^2 value in y-direction.
             fontsize: Fontsize used for text in the plot.
+            show: if `True`, will show to the plot after saving it.
+            save: Specify if the plot should be saved or not.
             **kwargs:
 
+        Returns:
+            Returns R^2 value for all genes and R^2 value for top 100 DEGs if `top_100_genes` is not `None`.
+
         Examples:
             >>> import pertpy as pt
             >>> data = pt.dt.kang_2018()
@@ -498,6 +505,7 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
                 r"$\mathrm{R^2_{\mathrm{\mathsf{top\ 100\ DEGs}}}}$= " + f"{r_value_diff ** 2:.2f}",
                 fontsize=kwargs.get("textsize", fontsize),
             )
+
         if save:
             plt.savefig(save, bbox_inches="tight")
         if show:
@@ -514,16 +522,17 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
         condition_key: str,
         axis_keys: dict[str, str],
         labels: dict[str, str],
-        save: str | bool | None = None,
+        *,
         gene_list: list[str] = None,
         top_100_genes: list[str] = None,
-        show: bool = False,
         legend: bool = True,
         title: str = None,
         verbose: bool = False,
         x_coeff: float = 0.3,
         y_coeff: float = 0.8,
         fontsize: float = 14,
+        show: bool = True,
+        save: str | bool | None = None,
         **kwargs,
     ) -> tuple[float, float] | float:
         """Plots variance matching for a set of specified genes.
@@ -534,19 +543,18 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
                    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.
+                       {"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"}.
             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: Whether to plot a elgend
+            legend: Whether to plot a legend.
             title: Set if you want the plot to display a title.
             verbose: Specify if you want information to be printed while creating the plot.
             x_coeff: Offset to print the R^2 value in x-direction.
             y_coeff: Offset to print the R^2 value in y-direction.
             fontsize: Fontsize used for text in the plot.
+            show: if `True`, will show to the plot after saving it.
+            save: Specify if the plot should be saved or not.
         """
         import seaborn as sns
 
@@ -636,6 +644,7 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
         else:
             return r_value**2
 
+    @_doc_params(common_plot_args=doc_common_plot_args)
     def plot_binary_classifier(
         self,
         scgen: Scgen,
@@ -643,10 +652,10 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
         delta: np.ndarray,
         ctrl_key: str,
         stim_key: str,
-        show: bool = False,
-        save: str | bool | None = None,
+        *,
         fontsize: float = 14,
-    ) -> plt.Axes | None:
+        return_fig: bool = False,
+    ) -> Figure | None:
         """Plots the dot product between delta and latent representation of a linear classifier.
 
         Builds a linear classifier based on the dot product between
@@ -661,9 +670,11 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
             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.
+            {common_plot_args}
+
+        Returns:
+            If `return_fig` is `True`, returns the figure, otherwise `None`.
         """
         plt.close("all")
         adata = scgen._validate_anndata(adata)
@@ -693,12 +704,9 @@ class Scgen(JaxTrainingMixin, BaseModelClass):
         ax = plt.gca()
         ax.grid(False)
 
-        if save:
-            plt.savefig(save, bbox_inches="tight")
-        if show:
-            plt.show()
-        if not (show or save):
-            return ax
+        if return_fig:
+            return plt.gcf()
+        plt.show()
         return None
 
 

{pertpy-0.9.4.dist-info → pertpy-0.10.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
-Metadata-Version: 2.3
+Metadata-Version: 2.4
 Name: pertpy
-Version: 0.9.4
+Version: 0.10.0
 Summary: Perturbation Analysis in the scverse ecosystem.
 Project-URL: Documentation, https://pertpy.readthedocs.io
 Project-URL: Source, https://github.com/scverse/pertpy
@@ -44,9 +44,8 @@ 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-Python: <3.13,>=3.10
 Requires-Dist: adjusttext
-Requires-Dist: anndata<0.10.9
 Requires-Dist: blitzgsea
 Requires-Dist: decoupler
 Requires-Dist: lamin-utils
@@ -58,8 +57,8 @@ Requires-Dist: pyarrow
 Requires-Dist: requests
 Requires-Dist: rich
 Requires-Dist: scanpy[leiden]
+Requires-Dist: scikit-learn>=1.4
 Requires-Dist: scikit-misc
-Requires-Dist: scipy
 Requires-Dist: scvi-tools
 Requires-Dist: sparsecca
 Provides-Extra: coda
@@ -69,7 +68,8 @@ Requires-Dist: pyqt5; extra == 'coda'
 Requires-Dist: toytree; extra == 'coda'
 Provides-Extra: de
 Requires-Dist: formulaic; extra == 'de'
-Requires-Dist: pydeseq2; extra == 'de'
+Requires-Dist: formulaic-contrasts>=0.2.0; extra == 'de'
+Requires-Dist: pydeseq2>=v0.5.0pre1; extra == 'de'
 Provides-Extra: dev
 Requires-Dist: pre-commit; extra == 'dev'
 Provides-Extra: doc

{pertpy-0.9.4.dist-info → pertpy-0.10.0.dist-info}/RECORD

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 pertpy/tools/_perturbation_space/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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 pertpy/tools/_scgen/__init__.py,sha256=uERFlFyF88TH0uLiwmsUGEfHfLVCiZMFuk8gO5f7164,45
 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
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-pertpy-0.9.4.dist-info/RECORD,,
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{pertpy-0.9.4.dist-info → pertpy-0.10.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.25.0
+Generator: hatchling 1.27.0
 Root-Is-Purelib: true
 Tag: py3-none-any