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

pertpy/tools/_perturbation_space/_comparison.py

@@ -0,0 +1,112 @@
+from typing import TYPE_CHECKING
+
+import numpy as np
+import pynndescent
+from scipy.sparse import issparse
+from scipy.sparse import vstack as sp_vstack
+from sklearn.base import ClassifierMixin
+from sklearn.linear_model import LogisticRegression
+
+if TYPE_CHECKING:
+    from numpy.typing import NDArray
+
+
+class PerturbationComparison:
+    """Comparison between real and simulated perturbations."""
+
+    def compare_classification(
+        self,
+        real: np.ndarray,
+        simulated: np.ndarray,
+        control: np.ndarray,
+        clf: ClassifierMixin | None = None,
+    ) -> float:
+        """Compare classification accuracy between real and simulated perturbations.
+
+        Trains a classifier on the real perturbation data + the control data and reports a normalized
+        classification accuracy on the simulated perturbation.
+
+        Args:
+            real: Real perturbed data.
+            simulated: Simulated perturbed data.
+            control: Control data
+            clf: sklearn classifier to use, `sklearn.linear_model.LogisticRegression` if not provided.
+        """
+        assert real.shape[1] == simulated.shape[1] == control.shape[1]
+        if clf is None:
+            clf = LogisticRegression()
+        n_x = real.shape[0]
+        data = sp_vstack((real, control)) if issparse(real) else np.vstack((real, control))
+        labels = np.concatenate([np.full(real.shape[0], "comp"), np.full(control.shape[0], "ctrl")])
+
+        clf.fit(data, labels)
+        norm_score = clf.score(simulated, np.full(simulated.shape[0], "comp")) / clf.score(real, labels[:n_x])
+        norm_score = min(1.0, norm_score)
+
+        return norm_score
+
+    def compare_knn(
+        self,
+        real: np.ndarray,
+        simulated: np.ndarray,
+        control: np.ndarray | None = None,
+        use_simulated_for_knn: bool = False,
+        n_neighbors: int = 20,
+        random_state: int = 0,
+        n_jobs: int = 1,
+    ) -> dict[str, float]:
+        """Calculate proportions of real perturbed and control data points for simulated data.
+
+        Computes proportions of real perturbed, control and simulated (if `use_simulated_for_knn=True`)
+        data points for simulated data. If control (`C`) is not provided, builds the knn graph from
+        real perturbed + simulated perturbed.
+
+        Args:
+            real: Real perturbed data.
+            simulated: Simulated perturbed data.
+            control: Control data
+            use_simulated_for_knn: Include simulted perturbed data (`simulated`) into the knn graph. Only valid when
+                control (`control`) is provided.
+            n_neighbors: Number of neighbors to use in k-neighbor graph.
+            random_state: Random state used for k-neighbor graph construction.
+            n_jobs: Number of cores to use. Defaults to -1 (all).
+
+        """
+        assert real.shape[1] == simulated.shape[1]
+        if control is not None:
+            assert real.shape[1] == control.shape[1]
+
+        n_y = simulated.shape[0]
+
+        if control is None:
+            index_data = sp_vstack((simulated, real)) if issparse(real) else np.vstack((simulated, real))
+        else:
+            datas = (simulated, real, control) if use_simulated_for_knn else (real, control)
+            index_data = sp_vstack(datas) if issparse(real) else np.vstack(datas)
+
+        y_in_index = use_simulated_for_knn or control is None
+        c_in_index = control is not None
+        label_groups = ["comp"]
+        labels: NDArray[np.str_] = np.full(index_data.shape[0], "comp")
+        if y_in_index:
+            labels[:n_y] = "siml"
+            label_groups.append("siml")
+        if c_in_index:
+            labels[-control.shape[0] :] = "ctrl"
+            label_groups.append("ctrl")
+
+        index = pynndescent.NNDescent(
+            index_data,
+            n_neighbors=max(50, n_neighbors),
+            random_state=random_state,
+            n_jobs=n_jobs,
+        )
+        indices = index.query(simulated, k=n_neighbors)[0]
+
+        uq, uq_counts = np.unique(labels[indices], return_counts=True)
+        uq_counts_norm = uq_counts / uq_counts.sum()
+        counts = dict(zip(label_groups, [0.0] * len(label_groups), strict=False))
+        for group, count_norm in zip(uq, uq_counts_norm, strict=False):
+            counts[group] = count_norm
+
+        return counts

pertpy/tools/_perturbation_space/_discriminator_classifiers.py

@@ -1,7 +1,6 @@
 from __future__ import annotations
 
 import warnings
-from typing import TYPE_CHECKING, Literal
 
 import anndata
 import numpy as np
@@ -42,12 +41,12 @@ class LRClassifierSpace(PerturbationSpace):
 
         Args:
             adata: AnnData object of size cells x genes
-            target_col: .obs column that stores the perturbations. Defaults to "perturbations".
-            layer_key: Layer in adata to use. Defaults to None.
+            target_col: .obs column that stores the perturbations.
+            layer_key: Layer in adata to use.
             embedding_key: Key of the embedding in obsm to be used as data for the logistic regression classifier.
-                Can only be specified if layer_key is None. Defaults to None.
-            test_split_size: Fraction of data to put in the test set. Default to 0.2.
-            max_iter: Maximum number of iterations taken for the solvers to converge. Defaults to 1000.
+                Can only be specified if layer_key is None.
+            test_split_size: Fraction of data to put in the test set.
+            max_iter: Maximum number of iterations taken for the solvers to converge.
 
         Returns:
             AnnData object with the logistic regression coefficients as the embedding in X and the perturbations as .obs['perturbations'].
@@ -163,24 +162,23 @@ class MLPClassifierSpace(PerturbationSpace):
 
         Args:
             adata: AnnData object of size cells x genes
-            target_col: .obs column that stores the perturbations. Defaults to "perturbations".
-            layer_key: Layer in adata to use. Defaults to None.
+            target_col: .obs column that stores the perturbations.
+            layer_key: Layer in adata to use.
             hidden_dim: List of number of neurons in each hidden layers of the neural network. For instance, [512, 256]
                 will create a neural network with two hidden layers, the first with 512 neurons and the second with 256 neurons.
-                Defaults to [512].
-            dropout: Amount of dropout applied, constant for all layers. Defaults to 0.
-            batch_norm: Whether to apply batch normalization. Defaults to True.
-            batch_size: The batch size, i.e. the number of datapoints to use in one forward/backward pass. Defaults to 256.
+            dropout: Amount of dropout applied, constant for all layers.
+            batch_norm: Whether to apply batch normalization.
+            batch_size: The batch size, i.e. the number of datapoints to use in one forward/backward pass.
             test_split_size: Fraction of data to put in the test set. Default to 0.2.
             validation_split_size: Fraction of data to put in the validation set of the resultant train set.
                 E.g. a test_split_size of 0.2 and a validation_split_size of 0.25 means that 25% of 80% of the data
-                will be used for validation. Defaults to 0.25.
-            max_epochs: Maximum number of epochs for training. Defaults to 20.
+                will be used for validation.
+            max_epochs: Maximum number of epochs for training.
             val_epochs_check: Test performance on validation dataset after every val_epochs_check training epochs.
                 Note that this affects early stopping, as the model will be stopped if the validation performance does not
-                improve for patience epochs. Defaults to 2.
+                improve for patience epochs.
             patience: Number of validation performance checks without improvement, after which the early stopping flag
-                is activated and training is therefore stopped. Defaults to 2.
+                is activated and training is therefore stopped.
 
         Returns:
             AnnData whose `X` attribute is the perturbation embedding and whose .obs['perturbations'] are the names of the perturbations.
@@ -325,10 +323,10 @@ class MLP(torch.nn.Module):
         """
         Args:
             sizes: size of layers.
-            dropout: Dropout probability. Defaults to 0.0.
-            batch_norm: specifies if batch norm should be applied. Defaults to True.
-            layer_norm:  specifies if layer norm should be applied, as commonly used in Transformers. Defaults to False.
-            last_layer_act: activation function of last layer. Defaults to "linear".
+            dropout: Dropout probability.
+            batch_norm: specifies if batch norm should be applied.
+            layer_norm:  specifies if layer norm should be applied, as commonly used in Transformers.
+            last_layer_act: activation function of last layer.
         """
         super().__init__()
         layers = []
@@ -392,8 +390,8 @@ class PLDataset(Dataset):
         """
         Args:
             adata: AnnData object with observations and labels.
-            target_col: key with the perturbation labels numerically encoded. Defaults to 'perturbations'.
-            label_col: key with the perturbation labels. Defaults to 'perturbations'.
+            target_col: key with the perturbation labels numerically encoded.
+            label_col: key with the perturbation labels.
             layer_key: key of the layer to be used as data, otherwise .X
         """
 

pertpy/tools/_perturbation_space/_perturbation_space.py

@@ -5,7 +5,7 @@ from typing import TYPE_CHECKING
 import numpy as np
 import pandas as pd
 from anndata import AnnData
-from pynndescent import NNDescent
+from lamin_utils import logger
 from rich import print
 
 if TYPE_CHECKING:
@@ -40,13 +40,13 @@ 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. Defaults to 'perturbations'.
-            group_col: .obs column name that stores the label of the group of eah cell. If None, ignore groups. Defaults to 'perturbations'.
-            reference_key: The key of the control values. Defaults to 'control'.
-            layer_key: Key of the AnnData layer to use for computation. Defaults to the `X` matrix otherwise.
-            new_layer_key: the results are stored in the given layer. Defaults to 'control_diff'.
-            embedding_key: `obsm` key of the AnnData embedding to use for computation. Defaults to the 'X' matrix otherwise.
-            new_embedding_key: Results are stored in a new embedding in `obsm` with this key. Defaults to 'control_diff'.
+            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.
+            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.
+            embedding_key: `obsm` key of the AnnData embedding to use for computation.
+            new_embedding_key: Results are stored in a new embedding in `obsm` with this key.
             all_data: if True, do the computation in all data representations (X, all layers and all embeddings)
             copy: If True returns a new Anndata of same size with the new column; otherwise it updates the initial AnnData object.
 
@@ -150,14 +150,14 @@ class PerturbationSpace:
         ensure_consistency: bool = False,
         target_col: str = "perturbation",
     ) -> tuple[AnnData, AnnData] | AnnData:
-        """Add perturbations linearly. Assumes input of size n_perts x dimensionality
+        """Add perturbations linearly. Assumes input of size n_perts x dimensionality.
 
         Args:
             adata: Anndata object of size n_perts x dim.
             perturbations: Perturbations to add.
-            reference_key: perturbation source from which the perturbation summation starts. Defaults to 'control'.
+            reference_key: perturbation source from which the perturbation summation starts.
             ensure_consistency: If True, runs differential expression on all data matrices to ensure consistency of linear space.
-            target_col: .obs column name that stores the label of the perturbation applied to each cell. Defaults to 'perturbation'.
+            target_col: .obs column name that stores the label of the perturbation applied to each cell.
 
         Returns:
             Anndata object of size (n_perts+1) x dim, where the last row is the addition of the specified perturbations.
@@ -182,8 +182,8 @@ class PerturbationSpace:
             new_pert_name += perturbation + "+"
 
         if not ensure_consistency:
-            print(
-                "[bold yellow]Operation might be done in non-consistent space (perturbation - perturbation != control). \n"
+            logger.warning(
+                "Operation might be done in non-consistent space (perturbation - perturbation != control). \n"
                 "Subtract control perturbation needed for consistency of space in all data representations. \n"
                 "Run with ensure_consistency=True"
             )
@@ -264,9 +264,9 @@ class PerturbationSpace:
         Args:
             adata: Anndata object of size n_perts x dim.
             perturbations: Perturbations to subtract.
-            reference_key: Perturbation source from which the perturbation subtraction starts. Defaults to 'control'.
+            reference_key: Perturbation source from which the perturbation subtraction starts.
             ensure_consistency: If True, runs differential expression on all data matrices to ensure consistency of linear space.
-            target_col: .obs column name that stores the label of the perturbation applied to each cell. Defaults to 'perturbations'.
+            target_col: .obs column name that stores the label of the perturbation applied to each cell.
 
         Returns:
             Anndata object of size (n_perts+1) x dim, where the last row is the subtraction of the specified perturbations.
@@ -291,8 +291,8 @@ class PerturbationSpace:
             new_pert_name += perturbation + "-"
 
         if not ensure_consistency:
-            print(
-                "[bold yellow]Operation might be done in non-consistent space (perturbation - perturbation != control).\n"
+            logger.warning(
+                "Operation might be done in non-consistent space (perturbation - perturbation != control).\n"
                 "Subtract control perturbation needed for consistency of space in all data representations.\n"
                 "Run with ensure_consistency=True"
             )
@@ -372,10 +372,10 @@ class PerturbationSpace:
 
         Args:
             adata: The AnnData object containing single-cell data.
-            column: The column name in AnnData object to perform imputation on. Defaults to "perturbation".
-            target_val: The target value to impute. Defaults to "unknown".
-            n_neighbors: Number of neighbors to use for imputation. Defaults to 5.
-            use_rep: The key in `adata.obsm` where the embedding (UMAP, PCA, etc.) is stored. Defaults to 'X_umap'.
+            column: The column name in AnnData object to perform imputation on.
+            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.
 
         Examples:
             >>> import pertpy as pt
@@ -396,6 +396,8 @@ class PerturbationSpace:
 
         embedding = adata.obsm[use_rep]
 
+        from pynndescent import NNDescent
+
         nnd = NNDescent(embedding, n_neighbors=n_neighbors)
         indices, _ = nnd.query(embedding, k=n_neighbors)
 

pertpy/tools/_perturbation_space/_simple.py

@@ -28,7 +28,7 @@ class CentroidSpace(PerturbationSpace):
             layer_key: If specified pseudobulk computation is done by using the specified layer. Otherwise, computation is done with .X
             embedding_key: `obsm` key of the AnnData embedding to use for computation. Defaults to the 'X' matrix otherwise.
             keep_obs: Whether .obs columns in the input AnnData should be kept in the output pseudobulk AnnData. Only .obs columns with the same value for
-                each cell of one perturbation are kept. Defaults to True.
+                each cell of one perturbation are kept.
 
         Returns:
             AnnData object with one observation per perturbation, storing the embedding data of the
@@ -129,7 +129,7 @@ class PseudobulkSpace(PerturbationSpace):
             adata: Anndata object of size cells x genes
             target_col: .obs column that stores the label of the perturbation applied to each cell.
             groups_col: Optional .obs column that stores a grouping label to consider for pseudobulk computation.
-                The summarized expression per perturbation (target_col) and group (groups_col) is computed. Defaults to None.
+                The summarized expression per perturbation (target_col) and group (groups_col) is computed.
             layer_key: If specified pseudobulk computation is done by using the specified layer. Otherwise, computation is done with .X
             embedding_key: `obsm` key of the AnnData embedding to use for computation. Defaults to the 'X' matrix otherwise.
             **kwargs: Are passed to decoupler's get_pseuobulk.
@@ -254,7 +254,7 @@ class DBSCANSpace(ClusteringSpace):
             adata: Anndata object of size cells x genes
             layer_key: If specified and exists in the adata, the clustering is done by using it. Otherwise, clustering is done with .X
             embedding_key: if specified and exists in the adata, the clustering is done with that embedding. Otherwise, clustering is done with .X
-            cluster_key: name of the .obs column to store the cluster labels. Defaults to 'dbscan'
+            cluster_key: name of the .obs column to store the cluster labels.
             copy: if True returns a new Anndata of same size with the new column; otherwise it updates the initial adata
             return_object: if True returns the clustering object
             **kwargs: Are passed to sklearn's DBSCAN.

pertpy/tools/_scgen/__init__.py

@@ -1 +1 @@
-from pertpy.tools._scgen._scgen import SCGEN
+from pertpy.tools._scgen._scgen import Scgen

pertpy/tools/_scgen/_base_components.py

@@ -28,7 +28,7 @@ class FlaxEncoder(nn.Module):
 
         Args:
             x: The input data matrix.
-            training: Whether
+            training: Whether to use running training average.
 
         Returns:
             Mean and variance.
@@ -69,12 +69,11 @@ class FlaxDecoder(nn.Module):
 
         Args:
             x: Input data.
-            training:
+            training: Whether to use running training average.
 
         Returns:
             Decoded data.
         """
-
         training = nn.merge_param("training", self.training, training)
 
         for _ in range(self.n_layers):

pertpy/tools/_scgen/_scgen.py

@@ -10,6 +10,7 @@ import scanpy as sc
 from adjustText import adjust_text
 from anndata import AnnData
 from jax import Array
+from lamin_utils import logger
 from scipy import stats
 from scvi import REGISTRY_KEYS
 from scvi.data import AnnDataManager
@@ -26,7 +27,7 @@ if TYPE_CHECKING:
 font = {"family": "Arial", "size": 14}
 
 
-class SCGEN(JaxTrainingMixin, BaseModelClass):
+class Scgen(JaxTrainingMixin, BaseModelClass):
     """Jax Implementation of scGen model for batch removal and perturbation prediction."""
 
     def __init__(
@@ -49,7 +50,7 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
             **model_kwargs,
         )
         self._model_summary_string = (
-            f"SCGEN Model with the following params: \nn_hidden: {n_hidden}, n_latent: {n_latent}, n_layers: {n_layers}, dropout_rate: "
+            f"Scgen Model with the following params: \nn_hidden: {n_hidden}, n_latent: {n_latent}, n_layers: {n_layers}, dropout_rate: "
             f"{dropout_rate}"
         )
         self.init_params_ = self._get_init_params(locals())
@@ -79,8 +80,8 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
         Examples:
             >>> import pertpy as pt
             >>> data = pt.dt.kang_2018()
-            >>> pt.tl.SCGEN.setup_anndata(data, batch_key="label", labels_key="cell_type")
-            >>> model = pt.tl.SCGEN(data)
+            >>> 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")
         """
@@ -166,8 +167,8 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
         Examples:
             >>> import pertpy as pt
             >>> data = pt.dt.kang_2018()
-            >>> pt.tl.SCGEN.setup_anndata(data, batch_key="label", labels_key="cell_type")
-            >>> model = pt.tl.SCGEN(data)
+            >>> 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)
             >>> decoded_X = model.get_decoded_expression()
         """
@@ -200,8 +201,8 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
         Examples:
             >>> import pertpy as pt
             >>> data = pt.dt.kang_2018()
-            >>> pt.tl.SCGEN.setup_anndata(data, batch_key="label", labels_key="cell_type")
-            >>> model = pt.tl.SCGEN(data)
+            >>> 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)
             >>> corrected_adata = model.batch_removal()
         """
@@ -304,7 +305,7 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
         Examples:
             >>> import pertpy as pt
             >>> data = pt.dt.kang_2018()
-            >>> pt.tl.SCGEN.setup_anndata(data, batch_key="label", labels_key="cell_type")
+            >>> pt.tl.Scgen.setup_anndata(data, batch_key="label", labels_key="cell_type")
         """
         setup_method_args = cls._get_setup_method_args(**locals())
         anndata_fields = [
@@ -345,8 +346,8 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
         Examples:
             >>> import pertpy as pt
             >>> data = pt.dt.kang_2018()
-            >>> pt.tl.SCGEN.setup_anndata(data, batch_key="label", labels_key="cell_type")
-            >>> model = pt.tl.SCGEN(data)
+            >>> 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)
             >>> latent_X = model.get_latent_representation()
         """
@@ -403,19 +404,19 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
             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`.
+            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, 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.
+            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.
             **kwargs:
 
         Examples:
             >>> import pertpy as pt
             >>> data = pt.dt.kang_2018()
-            >>> pt.tl.SCGEN.setup_anndata(data, batch_key="label", labels_key="cell_type")
-            >>> scg = pt.tl.SCGEN(data)
+            >>> pt.tl.Scgen.setup_anndata(data, batch_key="label", labels_key="cell_type")
+            >>> scg = pt.tl.Scgen(data)
             >>> scg.train(max_epochs=10, batch_size=64, early_stopping=True, early_stopping_patience=5)
             >>> pred, delta = scg.predict(ctrl_key='ctrl', stim_key='stim', celltype_to_predict='CD4 T cells')
             >>> pred.obs['label'] = 'pred'
@@ -444,12 +445,12 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
             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)
+                logger.info("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)
+            logger.info("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)
@@ -540,12 +541,12 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
             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`.
+            legend: Whether to plot a elgend
             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.
+            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.
         """
         import seaborn as sns
 
@@ -566,14 +567,14 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
             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)
+                logger.info("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)
+            logger.info("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)
@@ -637,7 +638,7 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
 
     def plot_binary_classifier(
         self,
-        scgen: SCGEN,
+        scgen: Scgen,
         adata: AnnData | None,
         delta: np.ndarray,
         ctrl_key: str,
@@ -699,3 +700,7 @@ class SCGEN(JaxTrainingMixin, BaseModelClass):
         if not (show or save):
             return ax
         return None
+
+
+# compatibility
+SCGEN = Scgen

pertpy/tools/_scgen/_utils.py

@@ -27,7 +27,7 @@ def extractor(
     Example:
         .. code-block:: python
 
-            import SCGEN
+            import Scgen
             import anndata
 
             train_data = anndata.read("./data/train.h5ad")
@@ -58,7 +58,7 @@ def balancer(
     Example:
         .. code-block:: python
 
-            import SCGEN
+            import Scgen
             import anndata
 
             train_data = anndata.read("./train_kang.h5ad")

{pertpy-0.7.0.dist-info → pertpy-0.8.0.dist-info}/METADATA

@@ -1,11 +1,11 @@
 Metadata-Version: 2.3
 Name: pertpy
-Version: 0.7.0
+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, 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
         
@@ -45,11 +45,10 @@ 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 +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
@@ -94,18 +97,18 @@ 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/scverse/pertpy/assets/99650244/182fa9c3-6d23-4002-b86a-82bf2a243377)
 
 ## Documentation
 
@@ -119,12 +122,18 @@ You can install _pertpy_ via [pip] from [PyPI]:
 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]
+```
+
 [pip]: https://pip.pypa.io/
 [pypi]: https://pypi.org/
 [usage]: https://pertpy.readthedocs.io/en/latest/usage/usage.html