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

pertpy/plot/_milopy.py

@@ -1,209 +0,0 @@
-from __future__ import annotations
-
-import warnings
-from typing import TYPE_CHECKING
-
-import matplotlib.pyplot as plt
-import numpy as np
-import pandas as pd
-import scanpy as sc
-import seaborn as sns
-
-if TYPE_CHECKING:
-    from collections.abc import Sequence
-
-    from mudata import MuData
-
-
-class MilopyPlot:
-    """Plotting functions for Milopy."""
-
-    @staticmethod
-    def nhood_graph(
-        mdata: MuData,
-        alpha: float = 0.1,
-        min_logFC: float = 0,
-        min_size: int = 10,
-        plot_edges: bool = False,
-        title: str = "DA log-Fold Change",
-        show: bool | None = None,
-        save: bool | str | None = None,
-        **kwargs,
-    ) -> None:
-        """Visualize DA results on abstracted graph (wrapper around sc.pl.embedding)
-
-        Args:
-            mdata: MuData object
-            alpha: Significance threshold. (default: 0.1)
-            min_logFC: Minimum absolute log-Fold Change to show results. If is 0, show all significant neighbourhoods. (default: 0)
-            min_size: Minimum size of nodes in visualization. (default: 10)
-            plot_edges: If edges for neighbourhood overlaps whould be plotted. Defaults to False.
-            title: Plot title. Defaults to "DA log-Fold Change".
-            show: Show the plot, do not return axis.
-            save: If `True` or a `str`, save the figure. A string is appended to the default filename.
-                  Infer the filetype if ending on {`'.pdf'`, `'.png'`, `'.svg'`}.
-            **kwargs: Additional arguments to `scanpy.pl.embedding`.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> adata = pt.dt.bhattacherjee()
-            >>> milo = pt.tl.Milo()
-            >>> mdata = milo.load(adata)
-            >>> sc.pp.neighbors(mdata["rna"])
-            >>> sc.tl.umap(mdata["rna"])
-            >>> milo.make_nhoods(mdata["rna"])
-            >>> mdata = milo.count_nhoods(mdata, sample_col="orig.ident")
-            >>> milo.da_nhoods(mdata,
-            >>>            design='~label',
-            >>>            model_contrasts='labelwithdraw_15d_Cocaine-labelwithdraw_48h_Cocaine')
-            >>> milo.build_nhood_graph(mdata)
-            >>> milo.plot_nhood_graph(mdata)
-        """
-        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 Milo
-
-        milo = Milo()
-
-        return milo.plot_nhood_graph(
-            madata=mdata,
-            alpha=alpha,
-            min_logFC=min_logFC,
-            min_size=min_size,
-            plot_edges=plot_edges,
-            title=title,
-            show=show,
-            save=save,
-            **kwargs,
-        )
-
-    @staticmethod
-    def nhood(
-        mdata: MuData,
-        ix: int,
-        feature_key: str | None = "rna",
-        basis="X_umap",
-        show: bool | None = None,
-        save: bool | str | None = None,
-        **kwargs,
-    ) -> None:
-        """Visualize cells in a neighbourhood.
-
-        Args:
-            mdata: MuData object with feature_key slot, storing neighbourhood assignments in `mdata[feature_key].obsm['nhoods']`
-            ix: index of neighbourhood to visualize
-            basis: Embedding to use for visualization. Defaults to "X_umap".
-            show: Show the plot, do not return axis.
-            save: If True or a str, save the figure. A string is appended to the default filename. Infer the filetype if ending on {'.pdf', '.png', '.svg'}.
-            **kwargs: Additional arguments to `scanpy.pl.embedding`.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> import scanpy as sc
-            >>> adata = pt.dt.bhattacherjee()
-            >>> milo = pt.tl.Milo()
-            >>> mdata = milo.load(adata)
-            >>> sc.pp.neighbors(mdata["rna"])
-            >>> sc.tl.umap(mdata["rna"])
-            >>> milo.make_nhoods(mdata["rna"])
-            >>> pt.pl.milo.nhood(mdata, ix=0)
-        """
-        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 Milo
-
-        milo = Milo()
-
-        milo.plot_nhood(mdata=mdata, ix=ix, feature_key=feature_key, basis=basis, show=show, save=save, **kwargs)
-
-    @staticmethod
-    def da_beeswarm(
-        mdata: MuData,
-        feature_key: str | None = "rna",
-        anno_col: str = "nhood_annotation",
-        alpha: float = 0.1,
-        subset_nhoods: list[str] = None,
-        palette: str | Sequence[str] | dict[str, str] | None = None,
-    ):
-        """Plot beeswarm plot of logFC against nhood labels
-
-        Args:
-            mdata: MuData object
-            anno_col: Column in mdata['milo'].var to use as annotation. (default: 'nhood_annotation'.)
-            alpha: Significance threshold. (default: 0.1)
-            subset_nhoods: List of nhoods to plot. If None, plot all nhoods. (default: None)
-            palette: Name of Seaborn color palette for violinplots.
-                     Defaults to pre-defined category colors for violinplots.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> import scanpy as sc
-            >>> adata = pt.dt.bhattacherjee()
-            >>> milo = pt.tl.Milo()
-            >>> mdata = milo.load(adata)
-            >>> sc.pp.neighbors(mdata["rna"])
-            >>> milo.make_nhoods(mdata["rna"])
-            >>> mdata = milo.count_nhoods(mdata, sample_col="orig.ident")
-            >>> milo.da_nhoods(mdata, design="~label")
-            >>> milo.annotate_nhoods(mdata, anno_col="cell_type")
-            >>> milo.plot_da_beeswarm(mdata)
-        """
-        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 Milo
-
-        milo = Milo()
-
-        milo.plot_da_beeswarm(
-            mdata=mdata,
-            feature_key=feature_key,
-            anno_col=anno_col,
-            alpha=alpha,
-            subset_nhoods=subset_nhoods,
-            palette=palette,
-        )
-
-    @staticmethod
-    def nhood_counts_by_cond(
-        mdata: MuData,
-        test_var: str,
-        subset_nhoods: list = None,
-        log_counts: bool = False,
-    ):
-        """Plot boxplot of cell numbers vs condition of interest
-
-        Args:
-            mdata: MuData object storing cell level and nhood level information
-            test_var: Name of column in adata.obs storing condition of interest (y-axis for boxplot)
-            subset_nhoods: List of obs_names for neighbourhoods to include in plot. If None, plot all nhoods. (default: None)
-            log_counts: Whether to plot log1p of cell counts. (default: False)
-        """
-        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 Milo
-
-        milo = Milo()
-
-        milo.plot_nhood_counts_by_cond(
-            mdata=mdata, test_var=test_var, subset_nhoods=subset_nhoods, log_counts=log_counts
-        )

pertpy/plot/_mixscape.py

@@ -1,355 +0,0 @@
-from __future__ import annotations
-
-import warnings
-from typing import TYPE_CHECKING, Literal
-
-if TYPE_CHECKING:
-    from collections.abc import Sequence
-
-    from anndata import AnnData
-    from matplotlib.axes import Axes
-
-
-class MixscapePlot:
-    """Plotting functions for Mixscape."""
-
-    @staticmethod
-    def barplot(  # pragma: no cover
-        adata: AnnData,
-        guide_rna_column: str,
-        mixscape_class_global="mixscape_class_global",
-        axis_text_x_size: int = 8,
-        axis_text_y_size: int = 6,
-        axis_title_size: int = 8,
-        strip_text_size: int = 6,
-        panel_spacing_x: float = 0.3,
-        panel_spacing_y: float = 0.3,
-        legend_title_size: int = 18,
-        legend_text_size: int = 18,
-        show: bool | None = None,
-        save: bool | str | None = None,
-    ):
-        """Barplot to visualize perturbation scores calculated from RunMixscape function.
-
-        Args:
-            adata: The annotated data object.
-            guide_rna_column: The column of `.obs` with guide RNA labels. The target gene labels.
-                              The format must be <gene_target>g<#>. For example, 'STAT2g1' and 'ATF2g1'.
-            mixscape_class_global: The column of `.obs` with mixscape global classification result (perturbed, NP or NT).
-            show: Show the plot, do not return axis.
-            save: If True or a str, save the figure. A string is appended to the default filename.
-                  Infer the filetype if ending on {'.pdf', '.png', '.svg'}.
-
-        Returns:
-            If show is False, return ggplot object used to draw the plot.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> mdata = pt.dt.papalexi_2021()
-            >>> ms = pt.tl.Mixscape()
-            >>> ms.perturbation_signature(mdata["rna"], "perturbation", "NT", "replicate")
-            >>> ms.mixscape(adata=mdata["rna"], control="NT", labels="gene_target", layer="X_pert")
-            >>> ms.plot_barplot(mdata["rna"], guide_rna_column="NT")
-        """
-        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 Mixscape
-
-        ms = Mixscape()
-        return ms.plot_barplot(
-            adata=adata,
-            guide_rna_column=guide_rna_column,
-            mixscape_class_global=mixscape_class_global,
-            axis_text_x_size=axis_text_x_size,
-            axis_text_y_size=axis_text_y_size,
-            axis_title_size=axis_title_size,
-            legend_title_size=legend_title_size,
-            legend_text_size=legend_text_size,
-            show=show,
-            save=save,
-        )
-
-    @staticmethod
-    def heatmap(  # pragma: no cover
-        adata: AnnData,
-        labels: str,
-        target_gene: str,
-        control: str,
-        layer: str | None = None,
-        method: str | None = "wilcoxon",
-        subsample_number: int | None = 900,
-        vmin: float | None = -2,
-        vmax: float | None = 2,
-        show: bool | None = None,
-        save: bool | str | None = None,
-        **kwargs,
-    ):
-        """Heatmap plot using mixscape results. Requires `pt.tl.mixscape()` to be run first.
-
-        Args:
-            adata: The annotated data object.
-            labels: The column of `.obs` with target gene labels.
-            target_gene: Target gene name to visualize heatmap for.
-            control: Control category from the `pert_key` column.
-            layer: Key from `adata.layers` whose value will be used to perform tests on.
-            method: The default method is 'wilcoxon', see `method` parameter in `scanpy.tl.rank_genes_groups` for more options.
-            subsample_number: Subsample to this number of observations.
-            vmin: The value representing the lower limit of the color scale. Values smaller than vmin are plotted with the same color as vmin.
-            vmax: The value representing the upper limit of the color scale. Values larger than vmax are plotted with the same color as vmax.
-            show: Show the plot, do not return axis.
-            save: If `True` or a `str`, save the figure. A string is appended to the default filename. Infer the filetype if ending on {`'.pdf'`, `'.png'`, `'.svg'`}.
-            **kwds: Additional arguments to `scanpy.pl.rank_genes_groups_heatmap`.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> mdata = pt.dt.papalexi_2021()
-            >>> ms = pt.tl.Mixscape()
-            >>> ms.perturbation_signature(mdata["rna"], "perturbation", "NT", "replicate")
-            >>> ms.mixscape(adata=mdata["rna"], control="NT", labels="gene_target", layer="X_pert")
-            >>> ms.plot_heatmap(
-            ...     adata=mdata["rna"], labels="gene_target", target_gene="IFNGR2", layer="X_pert", control="NT"
-            ... )
-        """
-        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 Mixscape
-
-        ms = Mixscape()
-        return ms.plot_heatmap(
-            adata=adata,
-            labels=labels,
-            target_gene=target_gene,
-            control=control,
-            layer=layer,
-            method=method,
-            subsample_number=subsample_number,
-            vmin=vmin,
-            vmax=vmax,
-            show=show,
-            save=save,
-            **kwargs,
-        )
-
-    @staticmethod
-    def perturbscore(  # pragma: no cover
-        adata: AnnData,
-        labels: str,
-        target_gene: str,
-        mixscape_class="mixscape_class",
-        color="orange",
-        split_by: str = None,
-        before_mixscape=False,
-        perturbation_type: str = "KO",
-    ):
-        """Density plots to visualize perturbation scores calculated by the `pt.tl.mixscape` function. Requires `pt.tl.mixscape` to be run first.
-
-        https://satijalab.org/seurat/reference/plotperturbscore
-
-        Args:
-            adata: The annotated data object.
-            labels: The column of `.obs` with target gene labels.
-            target_gene: Target gene name to visualize perturbation scores for.
-            mixscape_class: The column of `.obs` with mixscape classifications.
-            color: Specify color of target gene class or knockout cell class. For control non-targeting and non-perturbed cells, colors are set to different shades of grey.
-            split_by: Provide the column `.obs` if multiple biological replicates exist to calculate
-                the perturbation signature for every replicate separately.
-            before_mixscape: Option to split densities based on mixscape classification (default) or original target gene classification. Default is set to NULL and plots cells by original class ID.
-            perturbation_type: specify type of CRISPR perturbation expected for labeling mixscape classifications. Default is KO.
-
-        Returns:
-            The ggplot object used for drawn.
-
-        Examples:
-            Visualizing the perturbation scores for the cells in a dataset:
-
-            >>> import pertpy as pt
-            >>> mdata = pt.dt.papalexi_2021()
-            >>> mixscape_identifier = pt.tl.Mixscape()
-            >>> mixscape_identifier.perturbation_signature(mdata["rna"], "perturbation", "NT", "replicate")
-            >>> mixscape_identifier.mixscape(adata=mdata["rna"], control="NT", labels="gene_target", layer="X_pert")
-            >>> mixscape_identifier.perturbscore(
-            ...     adata=mdata["rna"], labels="gene_target", target_gene="IFNGR2", color="orange"
-            ... )
-        """
-        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 Mixscape
-
-        ms = Mixscape()
-        return ms.plot_perturbscore(
-            adata=adata,
-            labels=labels,
-            target_gene=target_gene,
-            mixscape_class=mixscape_class,
-            color=color,
-            split_by=split_by,
-            before_mixscape=before_mixscape,
-            perturbation_type=perturbation_type,
-        )
-
-    @staticmethod
-    def violin(  # pragma: no cover
-        adata: AnnData,
-        target_gene_idents: str | list[str],
-        keys: str | Sequence[str] = "mixscape_class_p_ko",
-        groupby: str | None = "mixscape_class",
-        log: bool = False,
-        use_raw: bool | None = None,
-        stripplot: bool = True,
-        hue: str | None = None,
-        jitter: float | bool = True,
-        size: int = 1,
-        layer: str | None = None,
-        scale: Literal["area", "count", "width"] = "width",
-        order: Sequence[str] | None = None,
-        multi_panel: bool | None = None,
-        xlabel: str = "",
-        ylabel: str | Sequence[str] | None = None,
-        rotation: float | None = None,
-        show: bool | None = None,
-        save: bool | str | None = None,
-        ax: Axes | None = None,
-        **kwargs,
-    ):
-        """Violin plot using mixscape results. Requires `pt.tl.mixscape` to be run first.
-
-        Args:
-            adata: The annotated data object.
-            target_gene: Target gene name to plot.
-            keys: Keys for accessing variables of `.var_names` or fields of `.obs`. Default is 'mixscape_class_p_ko'.
-            groupby: The key of the observation grouping to consider. Default is 'mixscape_class'.
-            log: Plot on logarithmic axis.
-            use_raw: Whether to use `raw` attribute of `adata`. Defaults to `True` if `.raw` is present.
-            stripplot: Add a stripplot on top of the violin plot.
-            order: Order in which to show the categories.
-            xlabel: Label of the x axis. Defaults to `groupby` if `rotation` is `None`, otherwise, no label is shown.
-            ylabel: Label of the y axis. If `None` and `groupby` is `None`, defaults to `'value'`. If `None` and `groubpy` is not `None`, defaults to `keys`.
-            show: Show the plot, do not return axis.
-            save: If `True` or a `str`, save the figure. A string is appended to the default filename. Infer the filetype if ending on {`'.pdf'`, `'.png'`, `'.svg'`}.
-            ax: A matplotlib axes object. Only works if plotting a single component.
-            **kwargs: Additional arguments to `seaborn.violinplot`.
-
-        Returns:
-            A :class:`~matplotlib.axes.Axes` object if `ax` is `None` else `None`.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> mdata = pt.dt.papalexi_2021()
-            >>> ms = pt.tl.Mixscape()
-            >>> ms.perturbation_signature(mdata["rna"], "perturbation", "NT", "replicate")
-            >>> ms.mixscape(adata=mdata["rna"], control="NT", labels="gene_target", layer="X_pert")
-            >>> ms.plot_violin(
-            ...     adata=mdata["rna"], target_gene_idents=["NT", "IFNGR2 NP", "IFNGR2 KO"], groupby="mixscape_class"
-            ... )
-        """
-        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 Mixscape
-
-        ms = Mixscape()
-        return ms.plot_violin(
-            adata=adata,
-            target_gene_idents=target_gene_idents,
-            keys=keys,
-            groupby=groupby,
-            log=log,
-            use_raw=use_raw,
-            stripplot=stripplot,
-            hue=hue,
-            jitter=jitter,
-            size=size,
-            layer=layer,
-            scale=scale,
-            order=order,
-            multi_panel=multi_panel,
-            xlabel=xlabel,
-            ylabel=ylabel,
-            rotation=rotation,
-            show=show,
-            save=save,
-            ax=ax,
-            **kwargs,
-        )
-
-    @staticmethod
-    def lda(  # pragma: no cover
-        adata: AnnData,
-        control: str,
-        mixscape_class="mixscape_class",
-        mixscape_class_global="mixscape_class_global",
-        perturbation_type: str | None = "KO",
-        lda_key: str | None = "mixscape_lda",
-        n_components: int | None = None,
-        show: bool | None = None,
-        save: bool | str | None = None,
-        **kwargs,
-    ):
-        """Visualizing perturbation responses with Linear Discriminant Analysis. Requires `pt.tl.mixscape()` to be run first.
-
-        Args:
-            adata: The annotated data object.
-            control: Control category from the `pert_key` column.
-            labels: The column of `.obs` with target gene labels.
-            mixscape_class: The column of `.obs` with the mixscape classification result.
-            mixscape_class_global: The column of `.obs` with mixscape global classification result (perturbed, NP or NT).
-            perturbation_type: Specify type of CRISPR perturbation expected for labeling mixscape classifications.
-                               Defaults to 'KO'.
-            lda_key: If not speficied, lda looks .uns["mixscape_lda"] for the LDA results.
-            n_components: The number of dimensions of the embedding.
-            show: Show the plot, do not return axis.
-            save: If `True` or a `str`, save the figure. A string is appended to the default filename.
-                  Infer the filetype if ending on {`'.pdf'`, `'.png'`, `'.svg'`}.
-            **kwargs: Additional arguments to `scanpy.pl.umap`.
-
-        Examples:
-            >>> import pertpy as pt
-            >>> mdata = pt.dt.papalexi_2021()
-            >>> ms = pt.tl.Mixscape()
-            >>> ms.perturbation_signature(mdata["rna"], "perturbation", "NT", "replicate")
-            >>> ms.mixscape(adata=mdata["rna"], control="NT", labels="gene_target", layer="X_pert")
-            >>> ms.lda(adata=mdata["rna"], control="NT", labels="gene_target", layer="X_pert")
-            >>> ms.plot_lda(adata=mdata["rna"], control="NT")
-        """
-        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 Mixscape
-
-        ms = Mixscape()
-
-        return ms.plot_lda(
-            adata=adata,
-            control=control,
-            mixscape_class=mixscape_class,
-            mixscape_class_global=mixscape_class_global,
-            perturbation_type=perturbation_type,
-            lda_key=lda_key,
-            n_components=n_components,
-            show=show,
-            save=save,
-            **kwargs,
-        )