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

pertpy/tools/_coda/_base_coda.py

@@ -1,17 +1,24 @@
 from __future__ import annotations
 
 from abc import ABC, abstractmethod
-from typing import TYPE_CHECKING
+from pathlib import Path
+from typing import TYPE_CHECKING, Literal, Optional, Union
 
 import arviz as az
-import ete3 as ete
 import jax.numpy as jnp
+import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import patsy as pt
+import scanpy as sc
+import seaborn as sns
+from adjustText import adjust_text
 from anndata import AnnData
-from jax import random
-from jax.config import config
+from jax import config, random
+from lamin_utils import logger
+from matplotlib import cm, rcParams
+from matplotlib import image as mpimg
+from matplotlib.colors import ListedColormap
 from mudata import MuData
 from numpyro.infer import HMC, MCMC, NUTS, initialization
 from rich import box, print
@@ -20,10 +27,15 @@ from rich.table import Table
 from scipy.cluster import hierarchy as sp_hierarchy
 
 if TYPE_CHECKING:
+    from collections.abc import Sequence
+
     import numpyro as npy
     import toytree as tt
-    from jax._src.prng import PRNGKeyArray
+    from ete3 import Tree
     from jax._src.typing import Array
+    from matplotlib.axes import Axes
+    from matplotlib.colors import Colormap
+    from matplotlib.figure import Figure
 
 config.update("jax_enable_x64", True)
 
@@ -99,9 +111,9 @@ class CompositionalModel2(ABC):
                 Categorical covariates are handled automatically, with the covariate value of the first sample being used as the reference category.
                 To set a different level as the base category for a categorical covariate, use "C(<CovariateName>, Treatment('<ReferenceLevelName>'))"
             reference_cell_type: Column name that sets the reference cell type.
-                Reference the name of a column. If "automatic", the cell type with the lowest dispersion in relative abundance that is present in at least 90% of samlpes will be chosen. Defaults to "automatic".
+                Reference the name of a column. If "automatic", the cell type with the lowest dispersion in relative abundance that is present in at least 90% of samlpes will be chosen.
             automatic_reference_absence_threshold: If using reference_cell_type = "automatic", determine the maximum fraction of zero entries for a cell type
-                to be considered as a possible reference cell type. Defaults to 0.05.
+                to be considered as a possible reference cell type.
 
         Returns:
             AnnData object that is ready for CODA models.
@@ -137,7 +149,7 @@ class CompositionalModel2(ABC):
             ref_index = np.where(cell_type_disp == min_var)[0][0]
 
             ref_cell_type = cell_types[ref_index]
-            print(f"[bold blue]Automatic reference selection! Reference cell type set to {ref_cell_type}")
+            logger.info(f"Automatic reference selection! Reference cell type set to {ref_cell_type}")
 
         # Column name as reference cell type
         elif reference_cell_type in cell_types:
@@ -149,7 +161,7 @@ class CompositionalModel2(ABC):
 
         # Add pseudocount if zeroes are present.
         if np.count_nonzero(sample_adata.X) != np.size(sample_adata.X):
-            print("Zero counts encountered in data! Added a pseudocount of 0.5.")
+            logger.info("Zero counts encountered in data! Added a pseudocount of 0.5.")
             sample_adata.X[sample_adata.X == 0] = 0.5
 
         sample_adata.obsm["sample_counts"] = np.sum(sample_adata.X, axis=1)
@@ -179,7 +191,7 @@ class CompositionalModel2(ABC):
         self,
         sample_adata: AnnData,
         kernel: npy.infer.mcmc.MCMCKernel,
-        rng_key: Array | PRNGKeyArray,
+        rng_key: Array,
         copy: bool = False,
         *args,
         **kwargs,
@@ -190,7 +202,7 @@ class CompositionalModel2(ABC):
             sample_adata: anndata object with cell counts as sample_adata.X and covariates saved in sample_adata.obs.
             kernel: A `numpyro.infer.mcmc.MCMCKernel` object
             rng_key: The rng state used. If None, a random state will be selected
-            copy: Return a copy instead of writing to adata. Defaults to False.
+            copy: Return a copy instead of writing to adata.
             args: Passed to `numpyro.infer.mcmc.MCMC`
             kwargs: Passed to `numpyro.infer.mcmc.MCMC`
 
@@ -226,13 +238,13 @@ class CompositionalModel2(ABC):
 
         acc_rate = np.array(self.mcmc.last_state.mean_accept_prob)
         if acc_rate < 0.6:
-            print(
-                f"[bold red]Acceptance rate unusually low ({acc_rate} < 0.5)! Results might be incorrect! "
+            logger.warning(
+                f"Acceptance rate unusually low ({acc_rate} < 0.5)! Results might be incorrect! "
                 f"Please check feasibility of results and re-run the sampling step with a different rng_key if necessary."
             )
         if acc_rate > 0.95:
-            print(
-                f"[bold red]Acceptance rate unusually high ({acc_rate} > 0.95)! Results might be incorrect! "
+            logger.warning(
+                f"Acceptance rate unusually high ({acc_rate} > 0.95)! Results might be incorrect! "
                 f"Please check feasibility of results and re-run the sampling step with a different rng_key if necessary."
             )
 
@@ -275,11 +287,11 @@ class CompositionalModel2(ABC):
 
         Args:
             data: AnnData object or MuData object.
-            modality_key: If data is a MuData object, specify which modality to use. Defaults to "coda".
-            num_samples: Number of sampled values after burn-in. Defaults to 10000.
-            num_warmup: Number of burn-in (warmup) samples. Defaults to 1000.
-            rng_key: The rng state used. Defaults to 0.
-            copy: Return a copy instead of writing to adata. Defaults to False.
+            modality_key: If data is a MuData object, specify which modality to use.
+            num_samples: Number of sampled values after burn-in.
+            num_warmup: Number of burn-in (warmup) samples.
+            rng_key: The rng state used.
+            copy: Return a copy instead of writing to adata.
 
         Returns:
             Calls `self.__run_mcmc`
@@ -288,14 +300,14 @@ class CompositionalModel2(ABC):
             try:
                 sample_adata = data[modality_key]
             except IndexError:
-                print("When data is a MuData object, modality_key must be specified!")
+                logger.error("When data is a MuData object, modality_key must be specified!")
                 raise
         if isinstance(data, AnnData):
             sample_adata = data
         if copy:
             sample_adata = sample_adata.copy()
 
-        rng_key_array = random.PRNGKey(rng_key)
+        rng_key_array = random.key(rng_key)
         sample_adata.uns["scCODA_params"]["mcmc"]["rng_key"] = np.array(rng_key_array)
 
         # Set up NUTS kernel
@@ -328,14 +340,13 @@ class CompositionalModel2(ABC):
 
         Args:
             data: AnnData object or MuData object.
-            modality_key: If data is a MuData object, specify which modality to use. Defaults to "coda".
-            num_samples: Number of sampled values after burn-in. Defaults to 20000.
-            num_warmup: Number of burn-in (warmup) samples. Defaults to 5000.
-            rng_key: The rng state used. If None, a random state will be selected. Defaults to None.
-            copy: Return a copy instead of writing to adata. Defaults to False.
+            modality_key: If data is a MuData object, specify which modality to use.
+            num_samples: Number of sampled values after burn-in.
+            num_warmup: Number of burn-in (warmup) samples.
+            rng_key: The rng state used. If None, a random state will be selected.
+            copy: Return a copy instead of writing to adata.
 
         Examples:
-            Example with scCODA:
             >>> import pertpy as pt
             >>> haber_cells = pt.dt.haber_2017_regions()
             >>> sccoda = pt.tl.Sccoda()
@@ -348,7 +359,7 @@ class CompositionalModel2(ABC):
             try:
                 sample_adata = data[modality_key]
             except IndexError:
-                print("When data is a MuData object, modality_key must be specified!")
+                logger.error("When data is a MuData object, modality_key must be specified!")
                 raise
         if isinstance(data, AnnData):
             sample_adata = data
@@ -358,10 +369,10 @@ class CompositionalModel2(ABC):
         # Set rng key if needed
         if rng_key is None:
             rng = np.random.default_rng()
-            rng_key = random.PRNGKey(rng.integers(0, 10000))
+            rng_key = random.key(rng.integers(0, 10000))
             sample_adata.uns["scCODA_params"]["mcmc"]["rng_key"] = rng_key
         else:
-            rng_key = random.PRNGKey(rng_key)
+            rng_key = random.key(rng_key)
 
         # Set up HMC kernel
         sample_adata = self.set_init_mcmc_states(
@@ -387,7 +398,7 @@ class CompositionalModel2(ABC):
 
         Args:
             sample_adata: Anndata object with cell counts as sample_adata.X and covariates saved in sample_adata.obs.
-            est_fdr: Desired FDR value. Defaults to 0.05.
+            est_fdr: Desired FDR value.
             args: Passed to ``az.summary``
             kwargs: Passed to ``az.summary``
 
@@ -423,7 +434,6 @@ class CompositionalModel2(ABC):
                 - Is credible: Boolean indicator whether effect is credible
 
          Examples:
-            Example with scCODA:
             >>> import pertpy as pt
             >>> haber_cells = pt.dt.haber_2017_regions()
             >>> sccoda = pt.tl.Sccoda()
@@ -433,7 +443,6 @@ class CompositionalModel2(ABC):
             >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
             >>> intercept_df, effect_df = sccoda.summary_prepare(mdata["coda"])
         """
-        # Get model and effect selection types
         select_type = sample_adata.uns["scCODA_params"]["select_type"]
         model_type = sample_adata.uns["scCODA_params"]["model_type"]
 
@@ -548,7 +557,11 @@ class CompositionalModel2(ABC):
         intercept_df = intercept_df.loc[:, ["final_parameter", hdis[0], hdis[1], "sd", "expected_sample"]].copy()
         intercept_df = intercept_df.rename(
             columns=dict(
-                zip(intercept_df.columns, ["Final Parameter", hdis_new[0], hdis_new[1], "SD", "Expected Sample"])
+                zip(
+                    intercept_df.columns,
+                    ["Final Parameter", hdis_new[0], hdis_new[1], "SD", "Expected Sample"],
+                    strict=False,
+                )
             )
         )
 
@@ -561,6 +574,7 @@ class CompositionalModel2(ABC):
                     zip(
                         effect_df.columns,
                         ["Effect", "Median", hdis_new[0], hdis_new[1], "SD", "Expected Sample", "log2-fold change"],
+                        strict=False,
                     )
                 )
             )
@@ -581,6 +595,7 @@ class CompositionalModel2(ABC):
                             "Expected Sample",
                             "log2-fold change",
                         ],
+                        strict=False,
                     )
                 )
             )
@@ -594,6 +609,7 @@ class CompositionalModel2(ABC):
                     zip(
                         node_df.columns,
                         ["Final Parameter", "Median", hdis_new[0], hdis_new[1], "SD", "Delta", "Is credible"],
+                        strict=False,
                     )
                 )  # type: ignore
             )  # type: ignore
@@ -622,8 +638,8 @@ class CompositionalModel2(ABC):
             effect_df: Effect summary, see ``summary_prepare``
             model_type: String indicating the model type ("classic" or "tree_agg")
             select_type:  String indicating the type of spike_and_slab selection ("spikeslab" or "sslasso")
-            target_fdr: Desired FDR value. Defaults to 0.05.
-            node_df: If using tree aggregation, the node-level effect DataFrame must be passed. Defaults to None.
+            target_fdr: Desired FDR value.
+            node_df: If using tree aggregation, the node-level effect DataFrame must be passed.
 
         Returns:
             pd.DataFrame:  effect DataFrame with inclusion probability, final parameters, expected sample.
@@ -775,13 +791,12 @@ class CompositionalModel2(ABC):
 
         Args:
             data: AnnData object or MuData object.
-            extended: If True, return the extended summary with additional statistics. Defaults to False.
-            modality_key: If data is a MuData object, specify which modality to use. Defaults to "coda".
+            extended: If True, return the extended summary with additional statistics.
+            modality_key: If data is a MuData object, specify which modality to use.
             args: Passed to az.summary
             kwargs: Passed to az.summary
 
         Examples:
-            Example with scCODA:
             >>> import pertpy as pt
             >>> haber_cells = pt.dt.haber_2017_regions()
             >>> sccoda = pt.tl.Sccoda()
@@ -795,11 +810,11 @@ class CompositionalModel2(ABC):
             try:
                 sample_adata = data[modality_key]
             except IndexError:
-                print("[bold red]When data is a MuData object, modality_key must be specified!")
+                logger.error("When data is a MuData object, modality_key must be specified!")
                 raise
         if isinstance(data, AnnData):
             sample_adata = data
-        # Get model and effect selection types
+
         select_type = sample_adata.uns["scCODA_params"]["select_type"]
         model_type = sample_adata.uns["scCODA_params"]["model_type"]
 
@@ -834,10 +849,10 @@ class CompositionalModel2(ABC):
         table.add_column("Name", justify="left", style="cyan")
         table.add_column("Value", justify="left")
         table.add_row("Data", "Data: %d samples, %d cell types" % data_dims)
-        table.add_row("Reference cell type", "%s" % str(sample_adata.uns["scCODA_params"]["reference_cell_type"]))
-        table.add_row("Formula", "%s" % sample_adata.uns["scCODA_params"]["formula"])
+        table.add_row("Reference cell type", "{}".format(str(sample_adata.uns["scCODA_params"]["reference_cell_type"])))
+        table.add_row("Formula", "{}".format(sample_adata.uns["scCODA_params"]["formula"]))
         if extended:
-            table.add_row("Reference index", "%s" % str(sample_adata.uns["scCODA_params"]["reference_index"]))
+            table.add_row("Reference index", "{}".format(str(sample_adata.uns["scCODA_params"]["reference_index"])))
             if select_type == "spikeslab":
                 table.add_row(
                     "Spike-and-slab threshold",
@@ -920,13 +935,12 @@ class CompositionalModel2(ABC):
 
         Args:
             data: AnnData object or MuData object.
-            modality_key: If data is a MuData object, specify which modality to use. Defaults to "coda".
+            modality_key: If data is a MuData object, specify which modality to use.
 
         Returns:
             pd.DataFrame: Intercept data frame.
 
         Examples:
-            Example with scCODA:
             >>> import pertpy as pt
             >>> haber_cells = pt.dt.haber_2017_regions()
             >>> sccoda = pt.tl.Sccoda()
@@ -936,12 +950,11 @@ class CompositionalModel2(ABC):
             >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
             >>> intercepts = sccoda.get_intercept_df(mdata)
         """
-
         if isinstance(data, MuData):
             try:
                 sample_adata = data[modality_key]
             except IndexError:
-                print("When data is a MuData object, modality_key must be specified!")
+                logger.error("When data is a MuData object, modality_key must be specified!")
                 raise
         if isinstance(data, AnnData):
             sample_adata = data
@@ -953,13 +966,12 @@ class CompositionalModel2(ABC):
 
         Args:
             data: AnnData object or MuData object.
-            modality_key: If data is a MuData object, specify which modality to use. Defaults to "coda".
+            modality_key: If data is a MuData object, specify which modality to use.
 
         Returns:
             pd.DataFrame: Effect data frame.
 
         Examples:
-            Example with scCODA:
             >>> import pertpy as pt
             >>> haber_cells = pt.dt.haber_2017_regions()
             >>> sccoda = pt.tl.Sccoda()
@@ -969,12 +981,11 @@ class CompositionalModel2(ABC):
             >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
             >>> effects = sccoda.get_effect_df(mdata)
         """
-
         if isinstance(data, MuData):
             try:
                 sample_adata = data[modality_key]
             except IndexError:
-                print("When data is a MuData object, modality_key must be specified!")
+                logger.error("When data is a MuData object, modality_key must be specified!")
                 raise
         if isinstance(data, AnnData):
             sample_adata = data
@@ -997,15 +1008,14 @@ class CompositionalModel2(ABC):
 
         Args:
             data: AnnData object or MuData object.
-            modality_key: If data is a MuData object, specify which modality to use. Defaults to "coda".
+            modality_key: If data is a MuData object, specify which modality to use.
 
         Returns:
             pd.DataFrame: Node effect data frame.
 
         Examples:
-            Example with tascCODA (works only for model of type tree_agg, i.e. a tascCODA model):
             >>> import pertpy as pt
-            >>> adata = pt.dt.smillie()
+            >>> adata = pt.dt.tasccoda_example()
             >>> tasccoda = pt.tl.Tasccoda()
             >>> mdata = tasccoda.load(
             >>>     adata, type="sample_level",
@@ -1023,7 +1033,7 @@ class CompositionalModel2(ABC):
             try:
                 sample_adata = data[modality_key]
             except IndexError:
-                print("When data is a MuData object, modality_key must be specified!")
+                logger.error("When data is a MuData object, modality_key must be specified!")
                 raise
         if isinstance(data, AnnData):
             sample_adata = data
@@ -1037,7 +1047,7 @@ class CompositionalModel2(ABC):
         Args:
             data: AnnData object or MuData object.
             est_fdr: Desired FDR value.
-            modality_key: If data is a MuData object, specify which modality to use. Defaults to "coda".
+            modality_key: If data is a MuData object, specify which modality to use.
             args: passed to self.summary_prepare
             kwargs: passed to self.summary_prepare
 
@@ -1048,7 +1058,7 @@ class CompositionalModel2(ABC):
             try:
                 sample_adata = data[modality_key]
             except IndexError:
-                print("When data is a MuData object, modality_key must be specified!")
+                logger.error("When data is a MuData object, modality_key must be specified!")
                 raise
         if isinstance(data, AnnData):
             sample_adata = data
@@ -1071,8 +1081,8 @@ class CompositionalModel2(ABC):
 
         Args:
             data: AnnData object or MuData object.
-            modality_key: If data is a MuData object, specify which modality to use. Defaults to "coda".
-            est_fdr: Estimated false discovery rate. Must be between 0 and 1. Defaults to None.
+            modality_key: If data is a MuData object, specify which modality to use.
+            est_fdr: Estimated false discovery rate. Must be between 0 and 1.
 
         Returns:
             pd.Series: Credible effect decision series which includes boolean values indicate whether effects are credible under inc_prob_threshold.
@@ -1081,7 +1091,7 @@ class CompositionalModel2(ABC):
             try:
                 sample_adata = data[modality_key]
             except IndexError:
-                print("When data is a MuData object, modality_key must be specified!")
+                logger.error("When data is a MuData object, modality_key must be specified!")
                 raise
         if isinstance(data, AnnData):
             sample_adata = data
@@ -1113,9 +1123,1120 @@ class CompositionalModel2(ABC):
 
         return out
 
+    def _stackbar(  # pragma: no cover
+        self,
+        y: np.ndarray,
+        type_names: list[str],
+        title: str,
+        level_names: list[str],
+        figsize: tuple[float, float] | None = None,
+        dpi: int | None = 100,
+        palette: ListedColormap | None = cm.tab20,
+        show_legend: bool | None = True,
+    ) -> plt.Axes:
+        """Plots a stacked barplot for one (discrete) covariate.
+
+        Typical use (only inside stacked_barplot): plot_one_stackbar(data.X, data.var.index, "xyz", data.obs.index)
+
+        Args:
+            y: The count data, collapsed onto the level of interest. i.e. a binary covariate has two rows,
+               one for each group, containing the count mean of each cell type
+            type_names: The names of all cell types
+            title: Plot title, usually the covariate's name
+            level_names: Names of the covariate's levels
+            figsize: Figure size (matplotlib).
+            dpi: Resolution in DPI (matplotlib).
+            palette: The color map for the barplot.
+            show_legend: If True, adds a legend.
+
+        Returns:
+            A :class:`~matplotlib.axes.Axes` object
+        """
+        n_bars, n_types = y.shape
+
+        figsize = rcParams["figure.figsize"] if figsize is None else figsize
+
+        _, ax = plt.subplots(figsize=figsize, dpi=dpi)
+        r = np.array(range(n_bars))
+        sample_sums = np.sum(y, axis=1)
+
+        barwidth = 0.85
+        cum_bars = np.zeros(n_bars)
+
+        for n in range(n_types):
+            bars = [i / j * 100 for i, j in zip([y[k][n] for k in range(n_bars)], sample_sums, strict=False)]
+            plt.bar(
+                r,
+                bars,
+                bottom=cum_bars,
+                color=palette(n % palette.N),
+                width=barwidth,
+                label=type_names[n],
+                linewidth=0,
+            )
+            cum_bars += bars
+
+        ax.set_title(title)
+        if show_legend:
+            ax.legend(loc="upper left", bbox_to_anchor=(1, 1), ncol=1)
+        ax.set_xticks(r)
+        ax.set_xticklabels(level_names, rotation=45, ha="right")
+        ax.set_ylabel("Proportion")
+
+        return ax
+
+    def plot_stacked_barplot(  # pragma: no cover
+        self,
+        data: AnnData | MuData,
+        feature_name: str,
+        modality_key: str = "coda",
+        palette: ListedColormap | None = cm.tab20,
+        show_legend: bool | None = True,
+        level_order: list[str] = None,
+        figsize: tuple[float, float] | None = None,
+        dpi: int | None = 100,
+        return_fig: bool | None = None,
+        ax: plt.Axes | None = None,
+        show: bool | None = None,
+        save: str | bool | None = None,
+        **kwargs,
+    ) -> plt.Axes | plt.Figure | None:
+        """Plots a stacked barplot for all levels of a covariate or all samples (if feature_name=="samples").
+
+        Args:
+            data: AnnData object or MuData object.
+            feature_name: The name of the covariate to plot. If feature_name=="samples", one bar for every sample will be plotted
+            modality_key: If data is a MuData object, specify which modality to use.
+            figsize: Figure size.
+            dpi: Dpi setting.
+            palette: The matplotlib color map for the barplot.
+            show_legend: If True, adds a legend.
+            level_order: Custom ordering of bars on the x-axis.
+
+        Returns:
+            A :class:`~matplotlib.axes.Axes` object
+
+        Examples:
+            >>> import pertpy as pt
+            >>> haber_cells = pt.dt.haber_2017_regions()
+            >>> sccoda = pt.tl.Sccoda()
+            >>> mdata = sccoda.load(haber_cells, type="cell_level", generate_sample_level=True, cell_type_identifier="cell_label", \
+                sample_identifier="batch", covariate_obs=["condition"])
+            >>> sccoda.plot_stacked_barplot(mdata, feature_name="samples")
+
+        Preview:
+            .. image:: /_static/docstring_previews/sccoda_stacked_barplot.png
+        """
+        if isinstance(data, MuData):
+            data = data[modality_key]
+        if isinstance(data, AnnData):
+            data = data
+
+        ct_names = data.var.index
+
+        # option to plot one stacked barplot per sample
+        if feature_name == "samples":
+            if level_order:
+                assert set(level_order) == set(data.obs.index), "level order is inconsistent with levels"
+                data = data[level_order]
+            ax = self._stackbar(
+                data.X,
+                type_names=data.var.index,
+                title="samples",
+                level_names=data.obs.index,
+                figsize=figsize,
+                dpi=dpi,
+                palette=palette,
+                show_legend=show_legend,
+            )
+        else:
+            # Order levels
+            if level_order:
+                assert set(level_order) == set(data.obs[feature_name]), "level order is inconsistent with levels"
+                levels = level_order
+            elif hasattr(data.obs[feature_name], "cat"):
+                levels = data.obs[feature_name].cat.categories.to_list()
+            else:
+                levels = pd.unique(data.obs[feature_name])
+            n_levels = len(levels)
+            feature_totals = np.zeros([n_levels, data.X.shape[1]])
+
+            for level in range(n_levels):
+                l_indices = np.where(data.obs[feature_name] == levels[level])
+                feature_totals[level] = np.sum(data.X[l_indices], axis=0)
+
+            ax = self._stackbar(
+                feature_totals,
+                type_names=ct_names,
+                title=feature_name,
+                level_names=levels,
+                figsize=figsize,
+                dpi=dpi,
+                palette=palette,
+                show_legend=show_legend,
+            )
+
+        if save:
+            plt.savefig(save, bbox_inches="tight")
+        if show:
+            plt.show()
+        if return_fig:
+            return plt.gcf()
+        if not (show or save):
+            return ax
+        return None
+
+    def plot_effects_barplot(  # pragma: no cover
+        self,
+        data: AnnData | MuData,
+        modality_key: str = "coda",
+        covariates: str | list | None = None,
+        parameter: Literal["log2-fold change", "Final Parameter", "Expected Sample"] = "log2-fold change",
+        plot_facets: bool = True,
+        plot_zero_covariate: bool = True,
+        plot_zero_cell_type: bool = False,
+        palette: str | ListedColormap | None = cm.tab20,
+        level_order: list[str] = None,
+        args_barplot: dict | None = None,
+        figsize: tuple[float, float] | None = None,
+        dpi: int | None = 100,
+        return_fig: bool | None = None,
+        ax: plt.Axes | None = None,
+        show: bool | None = None,
+        save: str | bool | None = None,
+    ) -> plt.Axes | plt.Figure | sns.axisgrid.FacetGrid | None:
+        """Barplot visualization for effects.
+
+        The effect results for each covariate are shown as a group of barplots, with intra--group separation by cell types.
+        The covariates groups can either be ordered along the x-axis of a single plot (plot_facets=False) or as plot facets (plot_facets=True).
+
+        Args:
+            data: AnnData object or MuData object.
+            modality_key: If data is a MuData object, specify which modality to use.
+            covariates: The name of the covariates in data.obs to plot.
+            parameter: The parameter in effect summary to plot.
+            plot_facets: If False, plot cell types on the x-axis. If True, plot as facets.
+            plot_zero_covariate: If True, plot covariate that have all zero effects. If False, do not plot.
+            plot_zero_cell_type: If True, plot cell type that have zero effect. If False, do not plot.
+            figsize: Figure size.
+            dpi: Figure size.
+            palette: The seaborn color map for the barplot.
+            level_order: Custom ordering of bars on the x-axis.
+            args_barplot: Arguments passed to sns.barplot.
+
+        Returns:
+            Depending on `plot_facets`, returns a :class:`~matplotlib.axes.Axes` (`plot_facets = False`)
+            or :class:`~sns.axisgrid.FacetGrid` (`plot_facets = True`) object
+
+        Examples:
+            >>> import pertpy as pt
+            >>> haber_cells = pt.dt.haber_2017_regions()
+            >>> sccoda = pt.tl.Sccoda()
+            >>> mdata = sccoda.load(haber_cells, type="cell_level", generate_sample_level=True, cell_type_identifier="cell_label", \
+                sample_identifier="batch", covariate_obs=["condition"])
+            >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
+            >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
+            >>> sccoda.plot_effects_barplot(mdata)
+
+        Preview:
+            .. image:: /_static/docstring_previews/sccoda_effects_barplot.png
+        """
+        if args_barplot is None:
+            args_barplot = {}
+        if isinstance(data, MuData):
+            data = data[modality_key]
+        if isinstance(data, AnnData):
+            data = data
+        # Get covariate names from adata, partition into those with nonzero effects for min. one cell type/no cell types
+        covariate_names = data.uns["scCODA_params"]["covariate_names"]
+        if covariates is not None:
+            if isinstance(covariates, str):
+                covariates = [covariates]
+            partial_covariate_names = [
+                covariate_name
+                for covariate_name in covariate_names
+                if any(covariate in covariate_name for covariate in covariates)
+            ]
+            covariate_names = partial_covariate_names
+        covariate_names_non_zero = [
+            covariate_name
+            for covariate_name in covariate_names
+            if data.varm[f"effect_df_{covariate_name}"][parameter].any()
+        ]
+        covariate_names_zero = list(set(covariate_names) - set(covariate_names_non_zero))
+        if not plot_zero_covariate:
+            covariate_names = covariate_names_non_zero
+
+        # set up df for plotting
+        plot_df = pd.concat(
+            [data.varm[f"effect_df_{covariate_name}"][parameter] for covariate_name in covariate_names],
+            axis=1,
+        )
+        plot_df.columns = covariate_names
+        plot_df = pd.melt(plot_df, ignore_index=False, var_name="Covariate")
+
+        plot_df = plot_df.reset_index()
+
+        if len(covariate_names_zero) != 0:
+            if plot_facets:
+                if plot_zero_covariate and not plot_zero_cell_type:
+                    plot_df = plot_df[plot_df["value"] != 0]
+                    for covariate_name_zero in covariate_names_zero:
+                        new_row = {
+                            "Covariate": covariate_name_zero,
+                            "Cell Type": "zero",
+                            "value": 0,
+                        }
+                        plot_df = pd.concat([plot_df, pd.DataFrame([new_row])], ignore_index=True)
+                    plot_df["covariate_"] = pd.Categorical(plot_df["Covariate"], covariate_names)
+                    plot_df = plot_df.sort_values(["covariate_"])
+        if not plot_zero_cell_type:
+            cell_type_names_zero = [
+                name
+                for name in plot_df["Cell Type"].unique()
+                if (plot_df[plot_df["Cell Type"] == name]["value"] == 0).all()
+            ]
+            plot_df = plot_df[~plot_df["Cell Type"].isin(cell_type_names_zero)]
+
+        # If plot as facets, create a FacetGrid and map barplot to it.
+        if plot_facets:
+            if isinstance(palette, ListedColormap):
+                palette = np.array([palette(i % palette.N) for i in range(len(plot_df["Cell Type"].unique()))]).tolist()
+            if figsize is not None:
+                height = figsize[0]
+                aspect = np.round(figsize[1] / figsize[0], 2)
+            else:
+                height = 3
+                aspect = 2
+
+            g = sns.FacetGrid(
+                plot_df,
+                col="Covariate",
+                sharey=True,
+                sharex=False,
+                height=height,
+                aspect=aspect,
+            )
+
+            g.map(
+                sns.barplot,
+                "Cell Type",
+                "value",
+                palette=palette,
+                order=level_order,
+                **args_barplot,
+            )
+            g.set_xticklabels(rotation=90)
+            g.set(ylabel=parameter)
+            axes = g.axes.flatten()
+            for i, ax in enumerate(axes):
+                ax.set_title(covariate_names[i])
+                if len(ax.get_xticklabels()) < 5:
+                    ax.set_aspect(10 / len(ax.get_xticklabels()))
+                    if len(ax.get_xticklabels()) == 1:
+                        if ax.get_xticklabels()[0]._text == "zero":
+                            ax.set_xticks([])
+
+            if save:
+                plt.savefig(save, bbox_inches="tight")
+            if show:
+                plt.show()
+            if return_fig:
+                return plt.gcf()
+            if not (show or save):
+                return g
+            return None
+
+        # If not plot as facets, call barplot to plot cell types on the x-axis.
+        else:
+            _, ax = plt.subplots(figsize=figsize, dpi=dpi)
+            if len(covariate_names) == 1:
+                if isinstance(palette, ListedColormap):
+                    palette = np.array(
+                        [palette(i % palette.N) for i in range(len(plot_df["Cell Type"].unique()))]
+                    ).tolist()
+                sns.barplot(
+                    data=plot_df,
+                    x="Cell Type",
+                    y="value",
+                    hue="x",
+                    palette=palette,
+                    ax=ax,
+                )
+                ax.set_title(covariate_names[0])
+            else:
+                if isinstance(palette, ListedColormap):
+                    palette = np.array([palette(i % palette.N) for i in range(len(covariate_names))]).tolist()
+                sns.barplot(
+                    data=plot_df,
+                    x="Cell Type",
+                    y="value",
+                    hue="Covariate",
+                    palette=palette,
+                    ax=ax,
+                )
+            cell_types = pd.unique(plot_df["Cell Type"])
+            ax.set_xticklabels(cell_types, rotation=90)
+
+            if save:
+                plt.savefig(save, bbox_inches="tight")
+            if show:
+                plt.show()
+            if return_fig:
+                return plt.gcf()
+            if not (show or save):
+                return ax
+            return None
+
+    def plot_boxplots(  # pragma: no cover
+        self,
+        data: AnnData | MuData,
+        feature_name: str,
+        modality_key: str = "coda",
+        y_scale: Literal["relative", "log", "log10", "count"] = "relative",
+        plot_facets: bool = False,
+        add_dots: bool = False,
+        cell_types: list | None = None,
+        args_boxplot: dict | None = None,
+        args_swarmplot: dict | None = None,
+        palette: str | None = "Blues",
+        show_legend: bool | None = True,
+        level_order: list[str] = None,
+        figsize: tuple[float, float] | None = None,
+        dpi: int | None = 100,
+        return_fig: bool | None = None,
+        ax: plt.Axes | None = None,
+        show: bool | None = None,
+        save: str | bool | None = None,
+    ) -> plt.Axes | plt.Figure | sns.axisgrid.FacetGrid | None:
+        """Grouped boxplot visualization.
+
+         The cell counts for each cell type are shown as a group of boxplots
+         with intra--group separation by a covariate from data.obs.
+
+        Args:
+            data: AnnData object or MuData object
+            feature_name: The name of the feature in data.obs to plot
+            modality_key: If data is a MuData object, specify which modality to use.
+            y_scale: Transformation to of cell counts. Options: "relative" - Relative abundance, "log" - log(count),
+                     "log10" - log10(count), "count" - absolute abundance (cell counts).
+            plot_facets: If False, plot cell types on the x-axis. If True, plot as facets.
+            add_dots: If True, overlay a scatterplot with one dot for each data point.
+            cell_types: Subset of cell types that should be plotted.
+            args_boxplot: Arguments passed to sns.boxplot.
+            args_swarmplot: Arguments passed to sns.swarmplot.
+            figsize: Figure size.
+            dpi: Dpi setting.
+            palette: The seaborn color map for the barplot.
+            show_legend: If True, adds a legend.
+            level_order: Custom ordering of bars on the x-axis.
+
+        Returns:
+            Depending on `plot_facets`, returns a :class:`~matplotlib.axes.Axes` (`plot_facets = False`)
+            or :class:`~sns.axisgrid.FacetGrid` (`plot_facets = True`) object
+
+        Examples:
+            >>> import pertpy as pt
+            >>> haber_cells = pt.dt.haber_2017_regions()
+            >>> sccoda = pt.tl.Sccoda()
+            >>> mdata = sccoda.load(haber_cells, type="cell_level", generate_sample_level=True, cell_type_identifier="cell_label", \
+                sample_identifier="batch", covariate_obs=["condition"])
+            >>> sccoda.plot_boxplots(mdata, feature_name="condition", add_dots=True)
+
+        Preview:
+            .. image:: /_static/docstring_previews/sccoda_boxplots.png
+        """
+        if args_boxplot is None:
+            args_boxplot = {}
+        if args_swarmplot is None:
+            args_swarmplot = {}
+        if isinstance(data, MuData):
+            data = data[modality_key]
+        if isinstance(data, AnnData):
+            data = data
+        # y scale transformations
+        if y_scale == "relative":
+            sample_sums = np.sum(data.X, axis=1, keepdims=True)
+            X = data.X / sample_sums
+            value_name = "Proportion"
+        # add pseudocount 0.5 if using log scale
+        elif y_scale == "log":
+            X = data.X.copy()
+            X[X == 0] = 0.5
+            X = np.log(X)
+            value_name = "log(count)"
+        elif y_scale == "log10":
+            X = data.X.copy()
+            X[X == 0] = 0.5
+            X = np.log(X)
+            value_name = "log10(count)"
+        elif y_scale == "count":
+            X = data.X
+            value_name = "count"
+        else:
+            raise ValueError("Invalid y_scale transformation")
+
+        count_df = pd.DataFrame(X, columns=data.var.index, index=data.obs.index).merge(
+            data.obs[feature_name], left_index=True, right_index=True
+        )
+        plot_df = pd.melt(count_df, id_vars=feature_name, var_name="Cell type", value_name=value_name)
+        if cell_types is not None:
+            plot_df = plot_df[plot_df["Cell type"].isin(cell_types)]
+
+        # Currently disabled because the latest statsannotations does not support the latest seaborn.
+        # We had to drop the dependency.
+        # Get credible effects results from model
+        # if draw_effects:
+        #     if model is not None:
+        #         credible_effects_df = model.credible_effects(data, modality_key).to_frame().reset_index()
+        #     else:
+        #         print("[bold yellow]Specify a tasCODA model to draw effects")
+        #     credible_effects_df[feature_name] = credible_effects_df["Covariate"].str.removeprefix(f"{feature_name}[T.")
+        #     credible_effects_df[feature_name] = credible_effects_df[feature_name].str.removesuffix("]")
+        #     credible_effects_df = credible_effects_df[credible_effects_df["Final Parameter"]]
+
+        # If plot as facets, create a FacetGrid and map boxplot to it.
+        if plot_facets:
+            if level_order is None:
+                level_order = pd.unique(plot_df[feature_name])
+
+            K = X.shape[1]
+
+            if figsize is not None:
+                height = figsize[0]
+                aspect = np.round(figsize[1] / figsize[0], 2)
+            else:
+                height = 3
+                aspect = 2
+
+            g = sns.FacetGrid(
+                plot_df,
+                col="Cell type",
+                sharey=False,
+                col_wrap=int(np.floor(np.sqrt(K))),
+                height=height,
+                aspect=aspect,
+            )
+            g.map(
+                sns.boxplot,
+                feature_name,
+                value_name,
+                palette=palette,
+                order=level_order,
+                **args_boxplot,
+            )
+
+            if add_dots:
+                if "hue" in args_swarmplot:
+                    hue = args_swarmplot.pop("hue")
+                else:
+                    hue = None
+
+                if hue is None:
+                    g.map(
+                        sns.swarmplot,
+                        feature_name,
+                        value_name,
+                        color="black",
+                        order=level_order,
+                        **args_swarmplot,
+                    ).set_titles("{col_name}")
+                else:
+                    g.map(
+                        sns.swarmplot,
+                        feature_name,
+                        value_name,
+                        hue,
+                        order=level_order,
+                        **args_swarmplot,
+                    ).set_titles("{col_name}")
+
+            if save:
+                plt.savefig(save, bbox_inches="tight")
+            if show:
+                plt.show()
+            if return_fig:
+                return plt.gcf()
+            if not (show or save):
+                return g
+            return None
+
+        # If not plot as facets, call boxplot to plot cell types on the x-axis.
+        else:
+            if level_order:
+                args_boxplot["hue_order"] = level_order
+                args_swarmplot["hue_order"] = level_order
+
+            _, ax = plt.subplots(figsize=figsize, dpi=dpi)
+
+            ax = sns.boxplot(
+                x="Cell type",
+                y=value_name,
+                hue=feature_name,
+                data=plot_df,
+                fliersize=1,
+                palette=palette,
+                ax=ax,
+                **args_boxplot,
+            )
+
+            # Currently disabled because the latest statsannotations does not support the latest seaborn.
+            # We had to drop the dependency.
+            # if draw_effects:
+            #     pairs = [
+            #         [(row["Cell Type"], row[feature_name]), (row["Cell Type"], "Control")]
+            #         for _, row in credible_effects_df.iterrows()
+            #     ]
+            #     annot = Annotator(ax, pairs, data=plot_df, x="Cell type", y=value_name, hue=feature_name)
+            #     annot.configure(test=None, loc="outside", color="red", line_height=0, verbose=False)
+            #     annot.set_custom_annotations([row[feature_name] for _, row in credible_effects_df.iterrows()])
+            #     annot.annotate()
+
+            if add_dots:
+                sns.swarmplot(
+                    x="Cell type",
+                    y=value_name,
+                    data=plot_df,
+                    hue=feature_name,
+                    ax=ax,
+                    dodge=True,
+                    palette="dark:black",
+                    **args_swarmplot,
+                )
+
+            cell_types = pd.unique(plot_df["Cell type"])
+            ax.set_xticklabels(cell_types, rotation=90)
+
+            if show_legend:
+                handles, labels = ax.get_legend_handles_labels()
+                handout = []
+                labelout = []
+                for h, l in zip(handles, labels, strict=False):
+                    if l not in labelout:
+                        labelout.append(l)
+                        handout.append(h)
+                ax.legend(
+                    handout,
+                    labelout,
+                    loc="upper left",
+                    bbox_to_anchor=(1, 1),
+                    ncol=1,
+                    title=feature_name,
+                )
+
+            if save:
+                plt.savefig(save, bbox_inches="tight")
+            if show:
+                plt.show()
+            if return_fig:
+                return plt.gcf()
+            if not (show or save):
+                return ax
+            return None
+
+    def plot_rel_abundance_dispersion_plot(  # pragma: no cover
+        self,
+        data: AnnData | MuData,
+        modality_key: str = "coda",
+        abundant_threshold: float | None = 0.9,
+        default_color: str | None = "Grey",
+        abundant_color: str | None = "Red",
+        label_cell_types: bool = True,
+        figsize: tuple[float, float] | None = None,
+        dpi: int | None = 100,
+        return_fig: bool | None = None,
+        ax: plt.Axes | None = None,
+        show: bool | None = None,
+        save: str | bool | None = None,
+    ) -> plt.Axes | plt.Figure | None:
+        """Plots total variance of relative abundance versus minimum relative abundance of all cell types for determination of a reference cell type.
+
+        If the count of the cell type is larger than 0 in more than abundant_threshold percent of all samples, the cell type will be marked in a different color.
+
+        Args:
+            data: AnnData or MuData object.
+            modality_key: If data is a MuData object, specify which modality to use.
+            abundant_threshold: Presence threshold for abundant cell types.
+            default_color: Bar color for all non-minimal cell types.
+            abundant_color: Bar color for cell types with abundant percentage larger than abundant_threshold.
+            label_cell_types: Label dots with cell type names.
+            figsize: Figure size.
+            dpi: Dpi setting.
+            ax: A matplotlib axes object. Only works if plotting a single component.
+
+        Returns:
+            A :class:`~matplotlib.axes.Axes` object
+
+        Examples:
+            >>> import pertpy as pt
+            >>> haber_cells = pt.dt.haber_2017_regions()
+            >>> sccoda = pt.tl.Sccoda()
+            >>> mdata = sccoda.load(haber_cells, type="cell_level", generate_sample_level=True, cell_type_identifier="cell_label", \
+                sample_identifier="batch", covariate_obs=["condition"])
+            >>> mdata = sccoda.prepare(mdata, formula="condition", reference_cell_type="Endocrine")
+            >>> sccoda.run_nuts(mdata, num_warmup=100, num_samples=1000, rng_key=42)
+            >>> sccoda.plot_rel_abundance_dispersion_plot(mdata)
+
+        Preview:
+            .. image:: /_static/docstring_previews/sccoda_rel_abundance_dispersion_plot.png
+        """
+        if isinstance(data, MuData):
+            data = data[modality_key]
+        if isinstance(data, AnnData):
+            data = data
+        if ax is None:
+            _, ax = plt.subplots(figsize=figsize, dpi=dpi)
+
+        rel_abun = data.X / np.sum(data.X, axis=1, keepdims=True)
+
+        percent_zero = np.sum(data.X == 0, axis=0) / data.X.shape[0]
+        nonrare_ct = np.where(percent_zero < 1 - abundant_threshold)[0]
+
+        # select reference
+        cell_type_disp = np.var(rel_abun, axis=0) / np.mean(rel_abun, axis=0)
+
+        is_abundant = [x in nonrare_ct for x in range(data.X.shape[1])]
+
+        # Scatterplot
+        plot_df = pd.DataFrame(
+            {
+                "Total dispersion": cell_type_disp,
+                "Cell type": data.var.index,
+                "Presence": 1 - percent_zero,
+                "Is abundant": is_abundant,
+            }
+        )
+
+        if len(np.unique(plot_df["Is abundant"])) > 1:
+            palette = [default_color, abundant_color]
+        elif np.unique(plot_df["Is abundant"]) == [False]:
+            palette = [default_color]
+        else:
+            palette = [abundant_color]
+
+        ax = sns.scatterplot(
+            data=plot_df,
+            x="Presence",
+            y="Total dispersion",
+            hue="Is abundant",
+            palette=palette,
+            ax=ax,
+        )
+
+        # Text labels for abundant cell types
+
+        abundant_df = plot_df.loc[plot_df["Is abundant"], :]
+
+        def label_point(x, y, val, ax):
+            a = pd.concat({"x": x, "y": y, "val": val}, axis=1)
+            texts = [
+                ax.text(
+                    point["x"],
+                    point["y"],
+                    str(point["val"]),
+                )
+                for i, point in a.iterrows()
+            ]
+            adjust_text(texts)
+
+        if label_cell_types:
+            label_point(
+                abundant_df["Presence"],
+                abundant_df["Total dispersion"],
+                abundant_df["Cell type"],
+                plt.gca(),
+            )
+
+        ax.legend(loc="upper left", bbox_to_anchor=(1, 1), ncol=1, title="Is abundant")
+
+        if save:
+            plt.savefig(save, bbox_inches="tight")
+        if show:
+            plt.show()
+        if return_fig:
+            return plt.gcf()
+        if not (show or save):
+            return ax
+        return None
+
+    def plot_draw_tree(  # pragma: no cover
+        self,
+        data: AnnData | MuData,
+        modality_key: str = "coda",
+        tree: str = "tree",  # Also type ete3.Tree. Omitted due to import errors
+        tight_text: bool | None = False,
+        show_scale: bool | None = False,
+        units: Literal["px", "mm", "in"] | None = "px",
+        figsize: tuple[float, float] | None = (None, None),
+        dpi: int | None = 100,
+        show: bool | None = True,
+        save: str | bool | None = None,
+    ) -> Tree | None:
+        """Plot a tree using input ete3 tree object.
+
+        Args:
+            data: AnnData object or MuData object.
+            modality_key: If data is a MuData object, specify which modality to use.
+            tree: A ete3 tree object or a str to indicate the tree stored in `.uns`.
+            tight_text: When False, boundaries of the text are approximated according to general font metrics,
+                        producing slightly worse aligned text faces but improving the performance of tree visualization in scenes with a lot of text faces.
+            show_scale: Include the scale legend in the tree image or not.
+            show: If True, plot the tree inline. If false, return tree and tree_style objects.
+            file_name: Path to the output image file. Valid extensions are .SVG, .PDF, .PNG.
+                       Output image can be saved whether show is True or not.
+            units: Unit of image sizes. “px”: pixels, “mm”: millimeters, “in”: inches.
+            figsize: Figure size.
+            dpi: Dots per inches.
+
+        Returns:
+            Depending on `show`, returns :class:`ete3.TreeNode` and :class:`ete3.TreeStyle` (`show = False`) or plot the tree inline (`show = False`)
+
+        Examples:
+            >>> import pertpy as pt
+            >>> adata = pt.dt.tasccoda_example()
+            >>> tasccoda = pt.tl.Tasccoda()
+            >>> mdata = tasccoda.load(
+            >>>     adata, type="sample_level",
+            >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
+            >>>     key_added="lineage", add_level_name=True
+            >>> )
+            >>> mdata = tasccoda.prepare(
+            >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
+            >>> )
+            >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
+            >>> tasccoda.plot_draw_tree(mdata, tree="lineage")
+
+        Preview:
+            .. image:: /_static/docstring_previews/tasccoda_draw_tree.png
+        """
+        try:
+            from ete3 import CircleFace, NodeStyle, TextFace, Tree, TreeStyle, faces
+        except ImportError:
+            raise ImportError(
+                "To use tasccoda please install additional dependencies with `pip install pertpy[coda]`"
+            ) from None
+
+        if isinstance(data, MuData):
+            data = data[modality_key]
+        if isinstance(data, AnnData):
+            data = data
+        if isinstance(tree, str):
+            tree = data.uns[tree]
+
+        def my_layout(node):
+            text_face = TextFace(node.name, tight_text=tight_text)
+            faces.add_face_to_node(text_face, node, column=0, position="branch-right")
+
+        tree_style = TreeStyle()
+        tree_style.show_leaf_name = False
+        tree_style.layout_fn = my_layout
+        tree_style.show_scale = show_scale
+
+        if save is not None:
+            tree.render(save, tree_style=tree_style, units=units, w=figsize[0], h=figsize[1], dpi=dpi)  # type: ignore
+        if show:
+            return tree.render("%%inline", tree_style=tree_style, units=units, w=figsize[0], h=figsize[1], dpi=dpi)  # type: ignore
+        else:
+            return tree, tree_style
+
+    def plot_draw_effects(  # pragma: no cover
+        self,
+        data: AnnData | MuData,
+        covariate: str,
+        modality_key: str = "coda",
+        tree: str = "tree",  # Also type ete3.Tree. Omitted due to import errors
+        show_legend: bool | None = None,
+        show_leaf_effects: bool | None = False,
+        tight_text: bool | None = False,
+        show_scale: bool | None = False,
+        units: Literal["px", "mm", "in"] | None = "px",
+        figsize: tuple[float, float] | None = (None, None),
+        dpi: int | None = 100,
+        show: bool | None = True,
+        save: str | None = None,
+    ) -> Tree | None:
+        """Plot a tree with colored circles on the nodes indicating significant effects with bar plots which indicate leave-level significant effects.
+
+        Args:
+            data: AnnData object or MuData object.
+            covariate: The covariate, whose effects should be plotted.
+            modality_key: If data is a MuData object, specify which modality to use.
+            tree: A ete3 tree object or a str to indicate the tree stored in `.uns`.
+            show_legend: If show legend of nodes significant effects or not.
+                         Defaults to False if show_leaf_effects is True.
+            show_leaf_effects: If True, plot bar plots which indicate leave-level significant effects.
+            tight_text: When False, boundaries of the text are approximated according to general font metrics,
+                        producing slightly worse aligned text faces but improving the performance of tree visualization in scenes with a lot of text faces.
+            show_scale: Include the scale legend in the tree image or not.
+            show: If True, plot the tree inline. If false, return tree and tree_style objects.
+            file_name: Path to the output image file. valid extensions are .SVG, .PDF, .PNG. Output image can be saved whether show is True or not.
+            units: Unit of image sizes. “px”: pixels, “mm”: millimeters, “in”: inches.
+            figsize: Figure size.
+            dpi: Dots per inches.
+
+        Returns:
+            Depending on `show`, returns :class:`ete3.TreeNode` and :class:`ete3.TreeStyle` (`show = False`)
+            or  plot the tree inline (`show = False`)
+
+        Examples:
+            >>> import pertpy as pt
+            >>> adata = pt.dt.tasccoda_example()
+            >>> tasccoda = pt.tl.Tasccoda()
+            >>> mdata = tasccoda.load(
+            >>>     adata, type="sample_level",
+            >>>     levels_agg=["Major_l1", "Major_l2", "Major_l3", "Major_l4", "Cluster"],
+            >>>     key_added="lineage", add_level_name=True
+            >>> )
+            >>> mdata = tasccoda.prepare(
+            >>>     mdata, formula="Health", reference_cell_type="automatic", tree_key="lineage", pen_args={"phi": 0}
+            >>> )
+            >>> tasccoda.run_nuts(mdata, num_samples=1000, num_warmup=100, rng_key=42)
+            >>> tasccoda.plot_draw_effects(mdata, covariate="Health[T.Inflamed]", tree="lineage")
+
+        Preview:
+            .. image:: /_static/docstring_previews/tasccoda_draw_effects.png
+        """
+        try:
+            from ete3 import CircleFace, NodeStyle, TextFace, Tree, TreeStyle, faces
+        except ImportError:
+            raise ImportError(
+                "To use tasccoda please install additional dependencies as `pip install pertpy[coda]`"
+            ) from None
+
+        if isinstance(data, MuData):
+            data = data[modality_key]
+        if isinstance(data, AnnData):
+            data = data
+        if show_legend is None:
+            show_legend = not show_leaf_effects
+        elif show_legend:
+            logger.info("Tree leaves and leaf effect bars won't be aligned when legend is shown!")
+
+        if isinstance(tree, str):
+            tree = data.uns[tree]
+        # Collapse tree singularities
+        tree2 = collapse_singularities_2(tree)
+
+        node_effs = data.uns["scCODA_params"]["node_df"].loc[(covariate + "_node",),].copy()
+        node_effs.index = node_effs.index.get_level_values("Node")
+
+        covariates = data.uns["scCODA_params"]["covariate_names"]
+        effect_dfs = [data.varm[f"effect_df_{cov}"] for cov in covariates]
+        eff_df = pd.concat(effect_dfs)
+        eff_df.index = pd.MultiIndex.from_product(
+            (covariates, data.var.index.tolist()),
+            names=["Covariate", "Cell Type"],
+        )
+        leaf_effs = eff_df.loc[(covariate,),].copy()
+        leaf_effs.index = leaf_effs.index.get_level_values("Cell Type")
+
+        # Add effect values
+        for n in tree2.traverse():
+            nstyle = NodeStyle()
+            nstyle["size"] = 0
+            n.set_style(nstyle)
+            if n.name in node_effs.index:
+                e = node_effs.loc[n.name, "Final Parameter"]
+                n.add_feature("node_effect", e)
+            else:
+                n.add_feature("node_effect", 0)
+            if n.name in leaf_effs.index:
+                e = leaf_effs.loc[n.name, "Effect"]
+                n.add_feature("leaf_effect", e)
+            else:
+                n.add_feature("leaf_effect", 0)
+
+        # Scale effect values to get nice node sizes
+        eff_max = np.max([np.abs(n.node_effect) for n in tree2.traverse()])
+        leaf_eff_max = np.max([np.abs(n.leaf_effect) for n in tree2.traverse()])
+
+        def my_layout(node):
+            text_face = TextFace(node.name, tight_text=tight_text)
+            text_face.margin_left = 10
+            faces.add_face_to_node(text_face, node, column=0, aligned=True)
+
+            # if node.is_leaf():
+            size = (np.abs(node.node_effect) * 10 / eff_max) if node.node_effect != 0 else 0
+            if np.sign(node.node_effect) == 1:
+                color = "blue"
+            elif np.sign(node.node_effect) == -1:
+                color = "red"
+            else:
+                color = "cyan"
+            if size != 0:
+                faces.add_face_to_node(CircleFace(radius=size, color=color), node, column=0)
+
+        tree_style = TreeStyle()
+        tree_style.show_leaf_name = False
+        tree_style.layout_fn = my_layout
+        tree_style.show_scale = show_scale
+        tree_style.draw_guiding_lines = True
+        tree_style.legend_position = 1
+
+        if show_legend:
+            tree_style.legend.add_face(TextFace("Effects"), column=0)
+            tree_style.legend.add_face(TextFace("       "), column=1)
+            for i in range(4, 0, -1):
+                tree_style.legend.add_face(
+                    CircleFace(
+                        float(f"{np.abs(eff_max) * 10 * i / (eff_max * 4):.2f}"),
+                        "red",
+                    ),
+                    column=0,
+                )
+                tree_style.legend.add_face(TextFace(f"{-eff_max * i / 4:.2f} "), column=0)
+                tree_style.legend.add_face(
+                    CircleFace(
+                        float(f"{np.abs(eff_max) * 10 * i / (eff_max * 4):.2f}"),
+                        "blue",
+                    ),
+                    column=1,
+                )
+                tree_style.legend.add_face(TextFace(f" {eff_max * i / 4:.2f}"), column=1)
+
+        if show_leaf_effects:
+            leaf_name = [node.name for node in tree2.traverse("postorder") if node.is_leaf()]
+            leaf_effs = leaf_effs.loc[leaf_name].reset_index()
+            palette = ["blue" if Effect > 0 else "red" for Effect in leaf_effs["Effect"].tolist()]
+
+            dir_path = Path.cwd()
+            dir_path = Path(dir_path / "tree_effect.png")
+            tree2.render(dir_path, tree_style=tree_style, units="in")
+            _, ax = plt.subplots(1, 2, figsize=(10, 10))
+            sns.barplot(data=leaf_effs, x="Effect", y="Cell Type", palette=palette, ax=ax[1])
+            img = mpimg.imread(dir_path)
+            ax[0].imshow(img)
+            ax[0].get_xaxis().set_visible(False)
+            ax[0].get_yaxis().set_visible(False)
+            ax[0].set_frame_on(False)
+
+            ax[1].get_yaxis().set_visible(False)
+            ax[1].spines["left"].set_visible(False)
+            ax[1].spines["right"].set_visible(False)
+            ax[1].spines["top"].set_visible(False)
+            plt.xlim(-leaf_eff_max, leaf_eff_max)
+            plt.subplots_adjust(wspace=0)
+
+            if save is not None:
+                plt.savefig(save)
+
+        if save is not None and not show_leaf_effects:
+            tree2.render(save, tree_style=tree_style, units=units)
+        if show:
+            if not show_leaf_effects:
+                return tree2.render("%%inline", tree_style=tree_style, units=units, w=figsize[0], h=figsize[1], dpi=dpi)
+        else:
+            if not show_leaf_effects:
+                return tree2, tree_style
+        return None
+
+    def plot_effects_umap(  # pragma: no cover
+        self,
+        mdata: MuData,
+        effect_name: str | list | None,
+        cluster_key: str,
+        modality_key_1: str = "rna",
+        modality_key_2: str = "coda",
+        color_map: Colormap | str | None = None,
+        palette: str | Sequence[str] | None = None,
+        return_fig: bool | None = None,
+        ax: Axes = None,
+        show: bool = None,
+        save: str | bool | None = None,
+        **kwargs,
+    ) -> plt.Axes | plt.Figure | None:
+        """Plot a UMAP visualization colored by effect strength.
+
+        Effect results in .varm of aggregated sample-level AnnData (default is data['coda']) are assigned to cell-level AnnData
+        (default is data['rna']) depending on the cluster they were assigned to.
+
+        Args:
+            mudata: MuData object.
+            effect_name: The name of the effect results in .varm of aggregated sample-level AnnData to plot
+            cluster_key: The cluster information in .obs of cell-level AnnData (default is data['rna']).
+                         To assign cell types' effects to original cells.
+            modality_key_1: Key to the cell-level AnnData in the MuData object.
+            modality_key_2: Key to the aggregated sample-level AnnData object in the MuData object.
+            show: Whether to display the figure or return axis.
+            ax: A matplotlib axes object. Only works if plotting a single component.
+            **kwargs: All other keyword arguments are passed to `scanpy.plot.umap()`
+
+        Returns:
+            If `show==False` a :class:`~matplotlib.axes.Axes` or a list of it.
+
+        Examples:
+            >>> import pertpy as pt
+            >>> import scanpy as sc
+            >>> import schist
+            >>> adata = pt.dt.haber_2017_regions()
+            >>> sc.pp.neighbors(adata)
+            >>> schist.inference.nested_model(adata, n_init=100, random_seed=5678)
+            >>> tasccoda_model = pt.tl.Tasccoda()
+            >>> tasccoda_data = tasccoda_model.load(adata, type="cell_level",
+            >>>                 cell_type_identifier="nsbm_level_1",
+            >>>                 sample_identifier="batch", covariate_obs=["condition"],
+            >>>                 levels_orig=["nsbm_level_4", "nsbm_level_3", "nsbm_level_2", "nsbm_level_1"],
+            >>>                 add_level_name=True)
+            >>> tasccoda_model.prepare(
+            >>>     tasccoda_data,
+            >>>     modality_key="coda",
+            >>>     reference_cell_type="18",
+            >>>     formula="condition",
+            >>>     pen_args={"phi": 0, "lambda_1": 3.5},
+            >>>     tree_key="tree"
+            >>> )
+            >>> tasccoda_model.run_nuts(
+            ...     tasccoda_data, modality_key="coda", rng_key=1234, num_samples=10000, num_warmup=1000
+            ... )
+            >>> tasccoda_model.run_nuts(
+            ...     tasccoda_data, modality_key="coda", rng_key=1234, num_samples=10000, num_warmup=1000
+            ... )
+            >>> sc.tl.umap(tasccoda_data["rna"])
+            >>> tasccoda_model.plot_effects_umap(tasccoda_data,
+            >>>                         effect_name=["effect_df_condition[T.Salmonella]",
+            >>>                                      "effect_df_condition[T.Hpoly.Day3]",
+            >>>                                      "effect_df_condition[T.Hpoly.Day10]"],
+            >>>                                       cluster_key="nsbm_level_1",
+            >>>                         )
+
+        Preview:
+            .. image:: /_static/docstring_previews/tasccoda_effects_umap.png
+        """
+        # TODO: Add effect_name parameter and cluster_key and test the example
+        data_rna = mdata[modality_key_1]
+        data_coda = mdata[modality_key_2]
+        if isinstance(effect_name, str):
+            effect_name = [effect_name]
+        for _, effect in enumerate(effect_name):
+            data_rna.obs[effect] = [data_coda.varm[effect].loc[f"{c}", "Effect"] for c in data_rna.obs[cluster_key]]
+        if kwargs.get("vmin"):
+            vmin = kwargs["vmin"]
+            kwargs.pop("vmin")
+        else:
+            vmin = min(data_rna.obs[effect].min() for _, effect in enumerate(effect_name))
+        if kwargs.get("vmax"):
+            vmax = kwargs["vmax"]
+            kwargs.pop("vmax")
+        else:
+            vmax = max(data_rna.obs[effect].max() for _, effect in enumerate(effect_name))
+
+        return sc.pl.umap(
+            data_rna,
+            color=effect_name,
+            vmax=vmax,
+            vmin=vmin,
+            palette=palette,
+            color_map=color_map,
+            return_fig=return_fig,
+            ax=ax,
+            show=show,
+            save=save,
+            **kwargs,
+        )
+
 
 def get_a(
-    tree: tt.tree,
+    tree: tt.core.ToyTree,
 ) -> tuple[np.ndarray, int]:
     """Calculate ancestor matrix from a toytree tree
 
@@ -1154,7 +2275,7 @@ def get_a(
     return A, n_nodes - 1
 
 
-def collapse_singularities(tree: tt.tree) -> tt.tree:
+def collapse_singularities(tree: tt.core.ToyTree) -> tt.core.ToyTree:
     """Collapses (deletes) nodes in a toytree tree that are singularities (have only one child).
 
     Args:
@@ -1242,7 +2363,7 @@ def df2newick(df: pd.DataFrame, levels: list[str], inner_label: bool = True) ->
 
 
 def get_a_2(
-    tree: ete.Tree,
+    tree: Tree,
     leaf_order: list[str] = None,
     node_order: list[str] = None,
 ) -> tuple[np.ndarray, int]:
@@ -1263,6 +2384,13 @@ def get_a_2(
         T
             number of nodes in the tree, excluding the root node
     """
+    try:
+        import ete3 as ete
+    except ImportError:
+        raise ImportError(
+            "To use tasccoda please install additional dependencies as `pip install pertpy[coda]`"
+        ) from None
+
     n_tips = len(tree.get_leaves())
     n_nodes = len(tree.get_descendants())
 
@@ -1292,7 +2420,7 @@ def get_a_2(
     return A_, n_nodes
 
 
-def collapse_singularities_2(tree: ete.Tree) -> ete.Tree:
+def collapse_singularities_2(tree: Tree) -> Tree:
     """Collapses (deletes) nodes in a ete3 tree that are singularities (have only one child).
 
     Args:
@@ -1327,10 +2455,10 @@ def linkage_to_newick(
 
     def build_newick(node, newick, parentdist, leaf_names):
         if node.is_leaf():
-            return f"{leaf_names[node.id]}:{(parentdist - node.dist)/2}{newick}"
+            return f"{leaf_names[node.id]}:{(parentdist - node.dist) / 2}{newick}"
         else:
             if len(newick) > 0:
-                newick = f"):{(parentdist - node.dist)/2}{newick}"
+                newick = f"):{(parentdist - node.dist) / 2}{newick}"
             else:
                 newick = ");"
             newick = build_newick(node.get_left(), newick, node.dist, leaf_names)
@@ -1363,14 +2491,14 @@ def import_tree(
 
     Args:
         data: A tascCODA-compatible data object.
-        modality_1: If `data` is MuData, specifiy the modality name to the original cell level anndata object. Defaults to None.
-        modality_2: If `data` is MuData, specifiy the modality name to the aggregated level anndata object. Defaults to None.
-        dendrogram_key: Key to the scanpy.tl.dendrogram result in `.uns` of original cell level anndata object. Defaults to None.
-        levels_orig: List that indicates which columns in `.obs` of the original data correspond to tree levels. The list must begin with the root level, and end with the leaf level. Defaults to None.
-        levels_agg: List that indicates which columns in `.var` of the aggregated data correspond to tree levels. The list must begin with the root level, and end with the leaf level. Defaults to None.
-        add_level_name: If True, internal nodes in the tree will be named as "{level_name}_{node_name}" instead of just {level_name}. Defaults to True.
-        key_added: If not specified, the tree is stored in .uns[‘tree’]. If `data` is AnnData, save tree in `data`. If `data` is MuData, save tree in data[modality_2]. Defaults to "tree".
-        copy: Return a copy instead of writing to `data`. Defaults to False.
+        modality_1: If `data` is MuData, specify the modality name to the original cell level anndata object.
+        modality_2: If `data` is MuData, specify the modality name to the aggregated level anndata object.
+        dendrogram_key: Key to the scanpy.tl.dendrogram result in `.uns` of original cell level anndata object.
+        levels_orig: List that indicates which columns in `.obs` of the original data correspond to tree levels. The list must begin with the root level, and end with the leaf level.
+        levels_agg: List that indicates which columns in `.var` of the aggregated data correspond to tree levels. The list must begin with the root level, and end with the leaf level.
+        add_level_name: If True, internal nodes in the tree will be named as "{level_name}_{node_name}" instead of just {level_name}.
+        key_added: If not specified, the tree is stored in .uns[‘tree’]. If `data` is AnnData, save tree in `data`.
+                   If `data` is MuData, save tree in data[modality_2].
 
     Returns:
         Updates data with the following:
@@ -1379,15 +2507,22 @@ def import_tree(
 
         tree: A ete3 tree object.
     """
+    try:
+        import ete3 as ete
+    except ImportError:
+        raise ImportError(
+            "To use tasccoda please install additional dependencies as `pip install pertpy[coda]`"
+        ) from None
+
     if isinstance(data, MuData):
         try:
             data_1 = data[modality_1]
             data_2 = data[modality_2]
         except KeyError as name:
-            print(f"No {name} slot in MuData")
+            logger.error(f"No {name} slot in MuData")
             raise
         except IndexError:
-            print("Please specify modality_1 and modality_2 to indicate modalities in MuData")
+            logger.error("Please specify modality_1 and modality_2 to indicate modalities in MuData")
             raise
     else:
         data_1 = data
@@ -1443,68 +2578,54 @@ def from_scanpy(
 
     The anndata object needs to have a column in adata.obs that contains the cell type assignment.
     Further, it must contain one column or a set of columns (e.g. subject id, treatment, disease status) that uniquely identify each (statistical) sample.
-    Further covariates (e.g. subject age) can either be specified via addidional column names in adata.obs, a key in adata.uns, or as a separate DataFrame.
+    Further covariates (e.g. subject age) can either be specified via additional column names in adata.obs, a key in adata.uns, or as a separate DataFrame.
 
-    NOTE: The order of samples in the returned dataset is determined by the first occurence of cells from each sample in `adata`
+    NOTE: The order of samples in the returned dataset is determined by the first occurrence of cells from each sample in `adata`
 
     Args:
         adata: An anndata object from scanpy
         cell_type_identifier: column name in adata.obs that specifies the cell types
         sample_identifier: column name or list of column names in adata.obs that uniquely identify each sample
         covariate_uns: key for adata.uns, where covariate values are stored
-        covariate_obs: list of column names in adata.obs, where covariate values are stored. Note: If covariate values are not unique for a value of sample_identifier, this covaariate will be skipped.
+        covariate_obs: list of column names in adata.obs, where covariate values are stored.
+                       Note: If covariate values are not unique for a value of sample_identifier, this covariate will be skipped.
         covariate_df: DataFrame with covariates
 
     Returns:
         AnnData: A data set with cells aggregated to the (sample x cell type) level
     """
-    if isinstance(sample_identifier, str):
-        sample_identifier = [sample_identifier]
-
-    if covariate_obs:
-        covariate_obs += [i for i in sample_identifier if i not in covariate_obs]
-    else:
-        covariate_obs = sample_identifier  # type: ignore
+    sample_identifier = [sample_identifier] if isinstance(sample_identifier, str) else sample_identifier
+    covariate_obs = list(set(covariate_obs or []) | set(sample_identifier))
 
-    # join sample identifiers
     if isinstance(sample_identifier, list):
         adata.obs["scCODA_sample_id"] = adata.obs[sample_identifier].agg("-".join, axis=1)
         sample_identifier = "scCODA_sample_id"
 
-    # get cell type counts
     groups = adata.obs.value_counts([sample_identifier, cell_type_identifier])
-    count_data = groups.unstack(level=cell_type_identifier)
-    count_data = count_data.fillna(0)
-
-    # get covariates from different sources
-    covariate_df_ = pd.DataFrame(index=count_data.index)
-
-    if covariate_df is None and covariate_obs is None and covariate_uns is None:
-        print("No covariate information specified!")
+    ct_count_data = groups.unstack(level=cell_type_identifier).fillna(0)
+    covariate_df_ = pd.DataFrame(index=ct_count_data.index)
 
     if covariate_uns is not None:
-        covariate_df_uns = pd.DataFrame(adata.uns[covariate_uns])
-        covariate_df_ = pd.concat((covariate_df_, covariate_df_uns), axis=1)
+        covariate_df_uns = pd.DataFrame(adata.uns[covariate_uns], index=ct_count_data.index)
+        covariate_df_ = pd.concat([covariate_df_, covariate_df_uns], axis=1)
 
-    if covariate_obs is not None:
-        for c in covariate_obs:
-            if any(adata.obs.groupby(sample_identifier).nunique()[c] != 1):
-                print(f"Covariate {c} has non-unique values! Skipping...")
+    if covariate_obs:
+        unique_check = adata.obs.groupby(sample_identifier).nunique()
+        for c in covariate_obs.copy():
+            if unique_check[c].max() != 1:
+                logger.warning(f"Covariate {c} has non-unique values for batch! Skipping...")
                 covariate_obs.remove(c)
-
-        covariate_df_obs = adata.obs.groupby(sample_identifier).first()[covariate_obs]
-        covariate_df_ = pd.concat((covariate_df_, covariate_df_obs), axis=1)
+        if covariate_obs:
+            covariate_df_obs = adata.obs.groupby(sample_identifier).first()[covariate_obs]
+            covariate_df_ = pd.concat([covariate_df_, covariate_df_obs], axis=1)
 
     if covariate_df is not None:
-        if set(covariate_df.index) != set(count_data.index):
-            raise ValueError("anndata sample names and covariate_df index do not have the same elements!")
-        covs_ord = covariate_df.reindex(count_data.index)
-        covariate_df_ = pd.concat((covariate_df_, covs_ord), axis=1)
+        if set(covariate_df.index) != set(ct_count_data.index):
+            raise ValueError("Mismatch between sample names in anndata and covariate_df!")
+        covariate_df_ = pd.concat([covariate_df_, covariate_df.reindex(ct_count_data.index)], axis=1)
 
-    covariate_df_.index = covariate_df_.index.astype(str)
-
-    # create var (number of cells for each type as only column)
-    var_dat = count_data.sum(axis=0).rename("n_cells").to_frame()
+    var_dat = ct_count_data.sum().rename("n_cells").to_frame()
     var_dat.index = var_dat.index.astype(str)
+    covariate_df_.index = covariate_df_.index.astype(str)
 
-    return AnnData(X=count_data.values, var=var_dat, obs=covariate_df_)
+    return AnnData(X=ct_count_data.values, var=var_dat, obs=covariate_df_)