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

pertpy/tools/_scgen/_jax_scgen.py

@@ -1,370 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Any
-
-import jax.numpy as jnp
-import numpy as np
-from anndata import AnnData
-from jax import Array
-from scvi import REGISTRY_KEYS
-from scvi.data import AnnDataManager
-from scvi.data.fields import CategoricalObsField, LayerField
-from scvi.model.base import BaseModelClass, JaxTrainingMixin
-from scvi.utils import setup_anndata_dsp
-
-from ._jax_scgenvae import JaxSCGENVAE
-from ._utils import balancer, extractor
-
-if TYPE_CHECKING:
-    from collections.abc import Sequence
-
-font = {"family": "Arial", "size": 14}
-
-
-class SCGEN(JaxTrainingMixin, BaseModelClass):
-    """Jax Implementation of scGen model for batch removal and perturbation prediction."""
-
-    def __init__(
-        self,
-        adata: AnnData,
-        n_hidden: int = 800,
-        n_latent: int = 100,
-        n_layers: int = 2,
-        dropout_rate: float = 0.2,
-        **model_kwargs,
-    ):
-        super().__init__(adata)
-
-        self.module = JaxSCGENVAE(
-            n_input=self.summary_stats.n_vars,
-            n_hidden=n_hidden,
-            n_latent=n_latent,
-            n_layers=n_layers,
-            dropout_rate=dropout_rate,
-            **model_kwargs,
-        )
-        self._model_summary_string = (
-            "SCGEN Model with the following params: \nn_hidden: {}, n_latent: {}, n_layers: {}, dropout_rate: " "{}"
-        ).format(
-            n_hidden,
-            n_latent,
-            n_layers,
-            dropout_rate,
-        )
-        self.init_params_ = self._get_init_params(locals())
-
-    def predict(
-        self,
-        ctrl_key=None,
-        stim_key=None,
-        adata_to_predict=None,
-        celltype_to_predict=None,
-        restrict_arithmetic_to="all",
-    ) -> tuple[AnnData, Any]:
-        """Predicts the cell type provided by the user in stimulated condition.
-
-        Args:
-            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`.
-            adata_to_predict: Adata for unperturbed cells you want to be predicted.
-            celltype_to_predict: The cell type you want to be predicted.
-            restrict_arithmetic_to: Dictionary of celltypes you want to be observed for prediction.
-
-        Returns:
-            `np nd-array` of predicted cells in primary space.
-        delta: float
-            Difference between stimulated and control cells in latent space
-
-        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)
-            >>> 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')
-        """
-        # use keys registered from `setup_anndata()`
-        cell_type_key = self.adata_manager.get_state_registry(REGISTRY_KEYS.LABELS_KEY).original_key
-        condition_key = self.adata_manager.get_state_registry(REGISTRY_KEYS.BATCH_KEY).original_key
-
-        if restrict_arithmetic_to == "all":
-            ctrl_x = self.adata[self.adata.obs[condition_key] == ctrl_key, :]
-            stim_x = self.adata[self.adata.obs[condition_key] == stim_key, :]
-            ctrl_x = balancer(ctrl_x, cell_type_key)
-            stim_x = balancer(stim_x, cell_type_key)
-        else:
-            key = list(restrict_arithmetic_to.keys())[0]
-            values = restrict_arithmetic_to[key]
-            subset = self.adata[self.adata.obs[key].isin(values)]
-            ctrl_x = subset[subset.obs[condition_key] == ctrl_key, :]
-            stim_x = subset[subset.obs[condition_key] == stim_key, :]
-            if len(values) > 1:
-                ctrl_x = balancer(ctrl_x, cell_type_key)
-                stim_x = balancer(stim_x, cell_type_key)
-        if celltype_to_predict is not None and adata_to_predict is not None:
-            raise Exception("Please provide either a cell type or adata not both!")
-        if celltype_to_predict is None and adata_to_predict is None:
-            raise Exception("Please provide a cell type name or adata for your unperturbed cells")
-        if celltype_to_predict is not None:
-            ctrl_pred = extractor(
-                self.adata,
-                celltype_to_predict,
-                condition_key,
-                cell_type_key,
-                ctrl_key,
-                stim_key,
-            )[1]
-        else:
-            ctrl_pred = adata_to_predict
-
-        eq = min(ctrl_x.X.shape[0], stim_x.X.shape[0])
-        rng = np.random.default_rng()
-        cd_ind = rng.choice(range(ctrl_x.shape[0]), size=eq, replace=False)
-        stim_ind = rng.choice(range(stim_x.shape[0]), size=eq, replace=False)
-        ctrl_adata = ctrl_x[cd_ind, :]
-        stim_adata = stim_x[stim_ind, :]
-
-        latent_ctrl = self._avg_vector(ctrl_adata)
-        latent_stim = self._avg_vector(stim_adata)
-
-        delta = latent_stim - latent_ctrl
-
-        latent_cd = self.get_latent_representation(ctrl_pred)
-
-        stim_pred = delta + latent_cd
-        predicted_cells = self.module.as_bound().generative(stim_pred)["px"]
-
-        predicted_adata = AnnData(
-            X=np.array(predicted_cells),
-            obs=ctrl_pred.obs.copy(),
-            var=ctrl_pred.var.copy(),
-            obsm=ctrl_pred.obsm.copy(),
-        )
-        return predicted_adata, delta
-
-    def _avg_vector(self, adata):
-        return np.mean(self.get_latent_representation(adata), axis=0)
-
-    def get_decoded_expression(
-        self,
-        adata: AnnData | None = None,
-        indices: Sequence[int] | None = None,
-        batch_size: int | None = None,
-    ) -> Array:
-        """Get decoded expression.
-
-        Args:
-            adata: AnnData object with equivalent structure to initial AnnData. If `None`, defaults to the
-                   AnnData object used to initialize the model.
-            indices: Indices of cells in adata to use. If `None`, all cells are used.
-            batch_size: Minibatch size for data loading into model. Defaults to `scvi.settings.batch_size`.
-
-        Returns:
-            Decoded expression for each cell
-
-        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)
-            >>> model.train(max_epochs=10, batch_size=64, early_stopping=True, early_stopping_patience=5)
-            >>> decoded_X = model.get_decoded_expression()
-        """
-        if self.is_trained_ is False:
-            raise RuntimeError("Please train the model first.")
-
-        adata = self._validate_anndata(adata)
-        scdl = self._make_data_loader(adata=adata, indices=indices, batch_size=batch_size)
-        decoded = []
-        for tensors in scdl:
-            _, generative_outputs = self.module.as_bound()(tensors, compute_loss=False)
-            px = generative_outputs["px"]
-            decoded.append(px)
-
-        return jnp.concatenate(decoded)
-
-    def batch_removal(self, adata: AnnData | None = None) -> AnnData:
-        """Removes batch effects.
-
-        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.
-
-        Returns:
-            corrected: `~anndata.AnnData`
-            AnnData of corrected gene expression in adata.X and corrected latent space in adata.obsm["latent"].
-            A reference to the original AnnData is in `corrected.raw` if the input adata had no `raw` attribute.
-
-        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)
-            >>> model.train(max_epochs=10, batch_size=64, early_stopping=True, early_stopping_patience=5)
-            >>> corrected_adata = model.batch_removal()
-        """
-        adata = self._validate_anndata(adata)
-        latent_all = self.get_latent_representation(adata)
-        # use keys registered from `setup_anndata()`
-        cell_label_key = self.adata_manager.get_state_registry(REGISTRY_KEYS.LABELS_KEY).original_key
-        batch_key = self.adata_manager.get_state_registry(REGISTRY_KEYS.BATCH_KEY).original_key
-
-        adata_latent = AnnData(latent_all)
-        adata_latent.obs = adata.obs.copy(deep=True)
-        unique_cell_types = np.unique(adata_latent.obs[cell_label_key])
-        shared_ct = []
-        not_shared_ct = []
-        for cell_type in unique_cell_types:
-            temp_cell = adata_latent[adata_latent.obs[cell_label_key] == cell_type].copy()
-            if len(np.unique(temp_cell.obs[batch_key])) < 2:
-                cell_type_ann = adata_latent[adata_latent.obs[cell_label_key] == cell_type]
-                not_shared_ct.append(cell_type_ann)
-                continue
-            temp_cell = adata_latent[adata_latent.obs[cell_label_key] == cell_type].copy()
-            batch_list = {}
-            batch_ind = {}
-            max_batch = 0
-            max_batch_ind = ""
-            batches = np.unique(temp_cell.obs[batch_key])
-            for i in batches:
-                temp = temp_cell[temp_cell.obs[batch_key] == i]
-                temp_ind = temp_cell.obs[batch_key] == i
-                if max_batch < len(temp):
-                    max_batch = len(temp)
-                    max_batch_ind = i
-                batch_list[i] = temp
-                batch_ind[i] = temp_ind
-            max_batch_ann = batch_list[max_batch_ind]
-            for study in batch_list:
-                delta = np.average(max_batch_ann.X, axis=0) - np.average(batch_list[study].X, axis=0)
-                batch_list[study].X = delta + batch_list[study].X
-                temp_cell[batch_ind[study]].X = batch_list[study].X
-            shared_ct.append(temp_cell)
-
-        all_shared_ann = AnnData.concatenate(*shared_ct, batch_key="concat_batch", index_unique=None)
-        if "concat_batch" in all_shared_ann.obs.columns:
-            del all_shared_ann.obs["concat_batch"]
-        if len(not_shared_ct) < 1:
-            corrected = AnnData(
-                np.array(self.module.as_bound().generative(all_shared_ann.X)["px"]),
-                obs=all_shared_ann.obs,
-            )
-            corrected.var_names = adata.var_names.tolist()
-            corrected = corrected[adata.obs_names]
-            if adata.raw is not None:
-                adata_raw = AnnData(X=adata.raw.X, var=adata.raw.var)
-                adata_raw.obs_names = adata.obs_names
-                corrected.raw = adata_raw
-            corrected.obsm["latent"] = all_shared_ann.X
-            corrected.obsm["corrected_latent"] = self.get_latent_representation(corrected)
-            return corrected
-        else:
-            all_not_shared_ann = AnnData.concatenate(*not_shared_ct, batch_key="concat_batch", index_unique=None)
-            all_corrected_data = AnnData.concatenate(
-                all_shared_ann,
-                all_not_shared_ann,
-                batch_key="concat_batch",
-                index_unique=None,
-            )
-            if "concat_batch" in all_shared_ann.obs.columns:
-                del all_corrected_data.obs["concat_batch"]
-            corrected = AnnData(
-                np.array(self.module.as_bound().generative(all_corrected_data.X)["px"]),
-                obs=all_corrected_data.obs,
-            )
-            corrected.var_names = adata.var_names.tolist()
-            corrected = corrected[adata.obs_names]
-            if adata.raw is not None:
-                adata_raw = AnnData(X=adata.raw.X, var=adata.raw.var)
-                adata_raw.obs_names = adata.obs_names
-                corrected.raw = adata_raw
-            corrected.obsm["latent"] = all_corrected_data.X
-            corrected.obsm["corrected_latent"] = self.get_latent_representation(corrected)
-
-            return corrected
-
-    @classmethod
-    @setup_anndata_dsp.dedent
-    def setup_anndata(
-        cls,
-        adata: AnnData,
-        batch_key: str | None = None,
-        labels_key: str | None = None,
-        **kwargs,
-    ):
-        """%(summary)s.
-
-        scGen expects the expression data to come from `adata.X`
-
-        %(param_batch_key)s
-        %(param_labels_key)s
-
-        Examples:
-            >>> import pertpy as pt
-            >>> data = pt.dt.kang_2018()
-            >>> pt.tl.SCGEN.setup_anndata(data, batch_key="label", labels_key="cell_type")
-        """
-        setup_method_args = cls._get_setup_method_args(**locals())
-        anndata_fields = [
-            LayerField(REGISTRY_KEYS.X_KEY, None, is_count_data=False),
-            CategoricalObsField(REGISTRY_KEYS.BATCH_KEY, batch_key),
-            CategoricalObsField(REGISTRY_KEYS.LABELS_KEY, labels_key),
-        ]
-        adata_manager = AnnDataManager(fields=anndata_fields, setup_method_args=setup_method_args)
-        adata_manager.register_fields(adata, **kwargs)
-        cls.register_manager(adata_manager)
-
-    def to_device(self, device):
-        pass
-
-    @property
-    def device(self):
-        return self.module.device
-
-    def get_latent_representation(
-        self,
-        adata: AnnData | None = None,
-        indices: Sequence[int] | None = None,
-        give_mean: bool = True,
-        n_samples: int = 1,
-        batch_size: int | None = None,
-    ) -> np.ndarray:
-        """Return the latent representation for each cell.
-
-        Args:
-            adata: AnnData object with equivalent structure to initial AnnData. If `None`, defaults to the
-                   AnnData object used to initialize the model.
-            indices: Indices of cells in adata to use. If `None`, all cells are used.
-            batch_size: Minibatch size for data loading into model. Defaults to `scvi.settings.batch_size`.
-
-        Returns:
-            Low-dimensional representation for each cell
-
-        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)
-            >>> model.train(max_epochs=10, batch_size=64, early_stopping=True, early_stopping_patience=5)
-            >>> latent_X = model.get_latent_representation()
-        """
-        self._check_if_trained(warn=False)
-
-        adata = self._validate_anndata(adata)
-        scdl = self._make_data_loader(adata=adata, indices=indices, batch_size=batch_size, iter_ndarray=True)
-
-        jit_inference_fn = self.module.get_jit_inference_fn(inference_kwargs={"n_samples": n_samples})
-
-        latent = []
-        for array_dict in scdl:
-            out = jit_inference_fn(self.module.rngs, array_dict)
-            if give_mean:
-                z = out["qz"].mean
-            else:
-                z = out["z"]
-            latent.append(z)
-        concat_axis = 0 if ((n_samples == 1) or give_mean) else 1
-        latent = jnp.concatenate(latent, axis=concat_axis)  # type: ignore
-
-        return self.module.as_numpy_array(latent)

pertpy-0.6.0.dist-info/RECORD

@@ -1,50 +0,0 @@
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