pertpy 0.6.0__py3-none-any.whl → 0.8.0__py3-none-any.whl

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()

pertpy/tools/_differential_gene_expression.py

@@ -1,99 +0,0 @@
-from __future__ import annotations
-
-from typing import TYPE_CHECKING, Literal
-
-import decoupler as dc
-import numpy as np
-import numpy.typing as npt
-
-if TYPE_CHECKING:
-    import pandas as pd
-    from anndata import AnnData
-
-
-class DifferentialGeneExpression:
-    """Support for differential gene expression for scverse."""
-
-    def pseudobulk(
-        self,
-        adata: AnnData,
-        sample_col: str,
-        groups_col: str,
-        obs: pd.DataFrame = None,
-        layer: str = None,
-        use_raw: bool = False,
-        min_prop: float = 0.2,
-        min_counts: int = 1000,
-        min_samples: int = 2,
-        dtype: npt.DTypeLike = np.float32,
-    ) -> AnnData:
-        """Generate Pseudobulk for DE analysis.
-
-        Wraps decoupler's get_pseudobulk function.
-        See: https://decoupler-py.readthedocs.io/en/latest/generated/decoupler.get_pseudobulk.html#decoupler.get_pseudobulk
-        for more details
-
-        Args:
-            adata: Input AnnData object.
-            sample_col: Column of obs where to extract the samples names.
-            groups_col: Column of obs where to extract the groups names.
-            obs: If provided, metadata dataframe.
-            layer: If provided, which layer to use.
-            use_raw: Use raw attribute of adata if present.
-            min_prop: Minimum proportion of cells with non-zero values.
-            min_counts: Minimum number of cells per sample.
-            min_samples: Minimum number of samples per feature.
-            dtype: Type of float used.
-
-        Returns:
-            Returns new AnnData object with unormalized pseudobulk profiles per sample and group.
-        """
-        pseudobulk_adata = dc.get_pseudobulk(
-            adata,
-            sample_col=sample_col,
-            groups_col=groups_col,
-            obs=obs,
-            layer=layer,
-            use_raw=use_raw,
-            min_prop=min_prop,
-            min_counts=min_counts,
-            min_smpls=min_samples,
-            dtype=dtype,
-        )
-
-        return pseudobulk_adata
-
-    def de_analysis(
-        self,
-        adata: AnnData,
-        groupby: str,
-        method: Literal["t-test", "wilcoxon", "pydeseq2", "deseq2", "edger"],
-        *formula: str | None,
-        contrast: str | None,
-        inplace: bool = True,
-        key_added: str | None,
-    ) -> pd.DataFrame:
-        """Perform differential expression analysis.
-
-        Args:
-            adata: single-cell or pseudobulk AnnData object
-            groupby: Column in adata.obs that contains the factor to test, e.g. `treatment`.
-                     For simple statistical tests (t-test, wilcoxon), it is sufficient to specify groupby.
-                     Linear models require to specify a formula.
-                     In that case, the `groupby` column is used to compute the contrast.
-            method: Which method to use to perform the DE test.
-            formula: model specification for linear models. E.g. `~ treatment + sex + age`.
-                     MUST contain the factor specified in `groupby`.
-            contrast: See e.g. https://www.statsmodels.org/devel/contrasts.html for more information.
-            inplace: if True, save the result in `adata.varm[key_added]`
-            key_added: Key under which the result is saved in `adata.varm` if inplace is True.
-                       If set to None this defaults to `de_{method}_{groupby}`.
-        Returns:
-            Depending on the method a Pandas DataFrame containing at least:
-            * gene_id
-            * log2 fold change
-            * mean expression
-            * unadjusted p-value
-            * adjusted p-value
-        """
-        raise NotImplementedError