modelbase2 0.1.78__py3-none-any.whl → 0.2.0__py3-none-any.whl

modelbase2/plot.py

@@ -0,0 +1,829 @@
+"""Plotting Utilities Module.
+
+This module provides functions and classes for creating various plots and visualizations
+for metabolic models. It includes functionality for plotting heatmaps, time courses,
+and parameter scans.
+
+Functions:
+    plot_heatmap: Plot a heatmap of the given data.
+    plot_time_course: Plot a time course of the given data.
+    plot_parameter_scan: Plot a parameter scan of the given data.
+    plot_3d_surface: Plot a 3D surface of the given data.
+    plot_3d_scatter: Plot a 3D scatter plot of the given data.
+    plot_label_distribution: Plot the distribution of labels in the given data.
+    plot_linear_label_distribution: Plot the distribution of linear labels in the given
+        data.
+    plot_label_correlation: Plot the correlation between labels in the given data.
+"""
+
+from __future__ import annotations
+
+__all__ = [
+    "FigAx",
+    "FigAxs",
+    "add_grid",
+    "bars",
+    "grid_layout",
+    "heatmap",
+    "heatmap_from_2d_idx",
+    "heatmaps_from_2d_idx",
+    "line_autogrouped",
+    "line_mean_std",
+    "lines",
+    "lines_grouped",
+    "lines_mean_std_from_2d_idx",
+    "relative_label_distribution",
+    "rotate_xlabels",
+    "shade_protocol",
+    "trajectories_2d",
+    "two_axes",
+    "violins",
+    "violins_from_2d_idx",
+]
+
+import itertools as it
+import math
+from typing import TYPE_CHECKING, Literal, cast
+
+import numpy as np
+import pandas as pd
+import seaborn as sns
+from matplotlib import pyplot as plt
+from matplotlib.axes import Axes
+from matplotlib.colors import (
+    LogNorm,
+    Normalize,
+    SymLogNorm,
+    colorConverter,  # type: ignore
+)
+from matplotlib.figure import Figure
+from mpl_toolkits.mplot3d import Axes3D
+
+from modelbase2.label_map import LabelMapper
+
+if TYPE_CHECKING:
+    from matplotlib.collections import QuadMesh
+
+    from modelbase2.linear_label_map import LinearLabelMapper
+    from modelbase2.model import Model
+    from modelbase2.types import Array, ArrayLike
+
+type FigAx = tuple[Figure, Axes]
+type FigAxs = tuple[Figure, list[Axes]]
+
+
+##########################################################################
+# Helpers
+##########################################################################
+
+
+def _relative_luminance(color: Array) -> float:
+    """Calculate the relative luminance of a color."""
+    rgb = colorConverter.to_rgba_array(color)[:, :3]
+
+    # If RsRGB <= 0.03928 then R = RsRGB/12.92 else R = ((RsRGB+0.055)/1.055) ^ 2.4
+    rsrgb = np.where(
+        rgb <= 0.03928,  # noqa: PLR2004
+        rgb / 12.92,
+        ((rgb + 0.055) / 1.055) ** 2.4,
+    )
+
+    # L = 0.2126 * R + 0.7152 * G + 0.0722 * B
+    return np.matmul(rsrgb, [0.2126, 0.7152, 0.0722])[0]
+
+
+def _get_norm(vmin: float, vmax: float) -> Normalize:
+    """Get a suitable normalization object for the given data.
+
+    Uses a logarithmic scale for values greater than 1000 or less than -1000,
+    a symmetrical logarithmic scale for values less than or equal to 0,
+    and a linear scale for all other values.
+
+    Args:
+        vmin: Minimum value of the data.
+        vmax: Maximum value of the data.
+
+    Returns:
+        Normalize: A normalization object for the given data.
+
+    """
+    if vmax < 1000 and vmin > -1000:  # noqa: PLR2004
+        norm = Normalize(vmin=vmin, vmax=vmax)
+    elif vmin <= 0:
+        norm = SymLogNorm(linthresh=1, vmin=vmin, vmax=vmax, base=10)
+    else:
+        norm = LogNorm(vmin=vmin, vmax=vmax)
+    return norm
+
+
+def _norm_with_zero_center(df: pd.DataFrame) -> Normalize:
+    """Get a normalization object with zero-centered values for the given data."""
+    v = max(abs(df.min().min()), abs(df.max().max()))
+    return _get_norm(vmin=-v, vmax=v)
+
+
+def _partition_by_order_of_magnitude(s: pd.Series) -> list[list[str]]:
+    """Partition a series into groups based on the order of magnitude of the values."""
+    return [
+        i.to_list()
+        for i in np.floor(np.log10(s)).to_frame(name=0).groupby(0)[0].groups.values()  # type: ignore
+    ]
+
+
+def _split_large_groups[T](groups: list[list[T]], max_size: int) -> list[list[T]]:
+    """Split groups larger than the given size into smaller groups."""
+    return list(
+        it.chain(
+            *(
+                (
+                    [group]
+                    if len(group) < max_size
+                    else [  # type: ignore
+                        list(i)
+                        for i in np.array_split(group, math.ceil(len(group) / max_size))  # type: ignore
+                    ]
+                )
+                for group in groups
+            )
+        )
+    )  # type: ignore
+
+
+def _default_color(ax: Axes, color: str | None) -> str:
+    """Get a default color for the given axis."""
+    return f"C{len(ax.lines)}" if color is None else color
+
+
+def _default_labels(
+    ax: Axes,
+    xlabel: str | None = None,
+    ylabel: str | None = None,
+    zlabel: str | None = None,
+) -> None:
+    """Set default labels for the given axis.
+
+    Args:
+        ax: matplotlib Axes
+        xlabel: Label for the x-axis.
+        ylabel: Label for the y-axis.
+        zlabel: Label for the z-axis.
+
+    """
+    ax.set_xlabel("Add a label / unit" if xlabel is None else xlabel)
+    ax.set_ylabel("Add a label / unit" if ylabel is None else ylabel)
+    if isinstance(ax, Axes3D):
+        ax.set_zlabel("Add a label / unit" if zlabel is None else zlabel)
+
+
+def _annotate_colormap(
+    df: pd.DataFrame,
+    ax: Axes,
+    sci_annotation_bounds: tuple[float, float],
+    annotation_style: str,
+    hm: QuadMesh,
+) -> None:
+    """Annotate a heatmap with the values of the data.
+
+    Args:
+        df: Dataframe to annotate.
+        ax: Axes to annotate.
+        sci_annotation_bounds: Bounds for scientific notation.
+        annotation_style: Style for the annotations.
+        hm: QuadMesh object of the heatmap.
+
+    """
+    hm.update_scalarmappable()  # So that get_facecolor is an array
+    xpos, ypos = np.meshgrid(
+        np.arange(len(df.columns)),
+        np.arange(len(df.index)),
+    )
+    for x, y, val, color in zip(
+        xpos.flat,
+        ypos.flat,
+        hm.get_array().flat,  # type: ignore
+        hm.get_facecolor(),
+        strict=True,
+    ):
+        val_text = (
+            f"{val:.{annotation_style}}"
+            if sci_annotation_bounds[0] < abs(val) <= sci_annotation_bounds[1]
+            else f"{val:.0e}"
+        )
+        ax.text(
+            x + 0.5,
+            y + 0.5,
+            val_text,
+            ha="center",
+            va="center",
+            color="black" if _relative_luminance(color) > 0.45 else "white",  # type: ignore  # noqa: PLR2004
+        )
+
+
+def add_grid(ax: Axes) -> Axes:
+    """Add a grid to the given axis."""
+    ax.grid(visible=True)
+    ax.set_axisbelow(b=True)
+    return ax
+
+
+def rotate_xlabels(
+    ax: Axes,
+    rotation: float = 45,
+    ha: Literal["left", "center", "right"] = "right",
+) -> Axes:
+    """Rotate the x-axis labels of the given axis.
+
+    Args:
+        ax: Axis to rotate the labels of.
+        rotation: Rotation angle in degrees (default: 45).
+        ha: Horizontal alignment of the labels (default
+
+    Returns:
+        Axes object for object chaining
+
+    """
+    for label in ax.get_xticklabels():
+        label.set_rotation(rotation)
+        label.set_horizontalalignment(ha)
+    return ax
+
+
+##########################################################################
+# General plot layout
+##########################################################################
+
+
+def _default_fig_ax(
+    *,
+    ax: Axes | None,
+    grid: bool,
+    figsize: tuple[float, float] | None = None,
+) -> FigAx:
+    """Create a figure and axes if none are provided.
+
+    Args:
+        ax: Axis to use for the plot.
+        grid: Whether to add a grid to the plot.
+        figsize: Size of the figure (default: None).
+
+    Returns:
+        Figure and Axes objects for the plot.
+
+    """
+    if ax is None:
+        fig, ax = plt.subplots(nrows=1, ncols=1, figsize=figsize)
+    else:
+        fig = cast(Figure, ax.get_figure())
+
+    if grid:
+        add_grid(ax)
+    return fig, ax
+
+
+def _default_fig_axs(
+    axs: list[Axes] | None,
+    *,
+    ncols: int,
+    nrows: int,
+    figsize: tuple[float, float] | None,
+    grid: bool,
+    sharex: bool,
+    sharey: bool,
+) -> FigAxs:
+    """Create a figure and multiple axes if none are provided.
+
+    Args:
+        axs: Axes to use for the plot.
+        ncols: Number of columns for the plot.
+        nrows: Number of rows for the plot.
+        figsize: Size of the figure (default: None).
+        grid: Whether to add a grid to the plot.
+        sharex: Whether to share the x-axis between the axes.
+        sharey: Whether to share the y-axis between the axes.
+
+    Returns:
+        Figure and Axes objects for the plot.
+
+    """
+    if axs is None or len(axs) == 0:
+        fig, axs_array = plt.subplots(
+            nrows=nrows,
+            ncols=ncols,
+            sharex=sharex,
+            sharey=sharey,
+            figsize=figsize,
+            squeeze=False,
+            layout="constrained",
+        )
+        axs = list(axs_array.flatten())
+    else:
+        fig = cast(Figure, axs[0].get_figure())
+
+    if grid:
+        for ax in axs:
+            add_grid(ax)
+    return fig, axs
+
+
+def two_axes(
+    *,
+    figsize: tuple[float, float] | None = None,
+    sharex: bool = True,
+    sharey: bool = False,
+    grid: bool = False,
+) -> FigAxs:
+    """Create a figure with two axes."""
+    return _default_fig_axs(
+        None,
+        ncols=2,
+        nrows=1,
+        figsize=figsize,
+        sharex=sharex,
+        sharey=sharey,
+        grid=grid,
+    )
+
+
+def grid_layout(
+    n_groups: int,
+    *,
+    n_cols: int = 2,
+    col_width: float = 3,
+    row_height: float = 4,
+    sharex: bool = True,
+    sharey: bool = False,
+    grid: bool = True,
+) -> tuple[Figure, list[Axes]]:
+    """Create a grid layout for the given number of groups."""
+    n_cols = min(n_groups, n_cols)
+    n_rows = math.ceil(n_groups / n_cols)
+    figsize = (n_cols * col_width, n_rows * row_height)
+
+    return _default_fig_axs(
+        None,
+        ncols=n_cols,
+        nrows=n_rows,
+        figsize=figsize,
+        sharex=sharex,
+        sharey=sharey,
+        grid=grid,
+    )
+
+
+##########################################################################
+# Plots
+##########################################################################
+
+
+def bars(
+    x: pd.DataFrame,
+    *,
+    ax: Axes | None = None,
+    grid: bool = True,
+) -> FigAx:
+    """Plot multiple lines on the same axis."""
+    fig, ax = _default_fig_ax(ax=ax, grid=grid)
+    sns.barplot(data=x, ax=ax)
+    _default_labels(ax, xlabel=x.index.name, ylabel=None)
+    ax.legend(x.columns)
+    return fig, ax
+
+
+def lines(
+    x: pd.DataFrame | pd.Series,
+    *,
+    ax: Axes | None = None,
+    grid: bool = True,
+) -> FigAx:
+    """Plot multiple lines on the same axis."""
+    fig, ax = _default_fig_ax(ax=ax, grid=grid)
+    ax.plot(x.index, x)
+    _default_labels(ax, xlabel=x.index.name, ylabel=None)
+    ax.legend(x.columns)
+    return fig, ax
+
+
+def lines_grouped(
+    groups: list[pd.DataFrame] | list[pd.Series],
+    *,
+    n_cols: int = 2,
+    col_width: float = 3,
+    row_height: float = 4,
+    sharex: bool = True,
+    sharey: bool = False,
+    grid: bool = True,
+) -> FigAxs:
+    """Plot multiple groups of lines on separate axes."""
+    fig, axs = grid_layout(
+        len(groups),
+        n_cols=n_cols,
+        col_width=col_width,
+        row_height=row_height,
+        sharex=sharex,
+        sharey=sharey,
+        grid=grid,
+    )
+
+    for group, ax in zip(groups, axs, strict=False):
+        lines(group, ax=ax, grid=grid)
+
+    for i in range(len(groups), len(axs)):
+        axs[i].set_visible(False)
+
+    return fig, axs
+
+
+def line_autogrouped(
+    s: pd.Series | pd.DataFrame,
+    *,
+    n_cols: int = 2,
+    col_width: float = 4,
+    row_height: float = 3,
+    max_group_size: int = 6,
+    grid: bool = True,
+) -> FigAxs:
+    """Plot a series or dataframe with lines grouped by order of magnitude."""
+    group_names = _split_large_groups(
+        _partition_by_order_of_magnitude(s)
+        if isinstance(s, pd.Series)
+        else _partition_by_order_of_magnitude(s.max()),
+        max_size=max_group_size,
+    )
+
+    groups: list[pd.Series] | list[pd.DataFrame] = (
+        [s.loc[group] for group in group_names]
+        if isinstance(s, pd.Series)
+        else [s.loc[:, group] for group in group_names]
+    )
+
+    return lines_grouped(
+        groups,
+        n_cols=n_cols,
+        col_width=col_width,
+        row_height=row_height,
+        grid=grid,
+    )
+
+
+def line_mean_std(
+    df: pd.DataFrame,
+    *,
+    label: str | None = None,
+    ax: Axes | None = None,
+    color: str | None = None,
+    alpha: float = 0.2,
+    grid: bool = True,
+) -> FigAx:
+    """Plot the mean and standard deviation using a line and fill."""
+    fig, ax = _default_fig_ax(ax=ax, grid=grid)
+    color = _default_color(ax=ax, color=color)
+
+    mean = df.mean(axis=1)
+    std = df.std(axis=1)
+    ax.plot(
+        mean.index,
+        mean,
+        color=color,
+        label=label,
+    )
+    ax.fill_between(
+        df.index,
+        mean - std,
+        mean + std,
+        color=color,
+        alpha=alpha,
+    )
+    _default_labels(ax, xlabel=df.index.name, ylabel=None)
+    return fig, ax
+
+
+def lines_mean_std_from_2d_idx(
+    df: pd.DataFrame,
+    *,
+    names: list[str] | None = None,
+    ax: Axes | None = None,
+    alpha: float = 0.2,
+    grid: bool = True,
+) -> FigAx:
+    """Plot the mean and standard deviation of a 2D indexed dataframe."""
+    if len(cast(pd.MultiIndex, df.index).levels) != 2:  # noqa: PLR2004
+        msg = "MultiIndex must have exactly two levels"
+        raise ValueError(msg)
+
+    fig, ax = _default_fig_ax(ax=ax, grid=grid)
+
+    for name in df.columns if names is None else names:
+        line_mean_std(
+            df[name].unstack().T,
+            label=name,
+            alpha=alpha,
+            ax=ax,
+        )
+    ax.legend()
+    return fig, ax
+
+
+def heatmap(
+    df: pd.DataFrame,
+    *,
+    annotate: bool = False,
+    colorbar: bool = True,
+    invert_yaxis: bool = True,
+    cmap: str = "RdBu_r",
+    norm: Normalize | None = None,
+    ax: Axes | None = None,
+    cax: Axes | None = None,
+    sci_annotation_bounds: tuple[float, float] = (0.01, 100),
+    annotation_style: str = "2g",
+) -> tuple[Figure, Axes, QuadMesh]:
+    """Plot a heatmap of the given data."""
+    fig, ax = _default_fig_ax(
+        ax=ax,
+        figsize=(
+            max(4, 0.5 * len(df.columns)),
+            max(4, 0.5 * len(df.index)),
+        ),
+        grid=False,
+    )
+    if norm is None:
+        norm = _norm_with_zero_center(df)
+
+    hm = ax.pcolormesh(df, norm=norm, cmap=cmap)
+    ax.set_xticks(
+        np.arange(0, len(df.columns), 1) + 0.5,
+        labels=df.columns,
+    )
+    ax.set_yticks(
+        np.arange(0, len(df.index), 1) + 0.5,
+        labels=df.index,
+    )
+
+    if annotate:
+        _annotate_colormap(df, ax, sci_annotation_bounds, annotation_style, hm)
+
+    if colorbar:
+        # Add a colorbar
+        cb = fig.colorbar(hm, cax, ax)
+        cb.outline.set_linewidth(0)  # type: ignore
+
+    if invert_yaxis:
+        ax.invert_yaxis()
+    rotate_xlabels(ax, rotation=45, ha="right")
+    return fig, ax, hm
+
+
+def heatmap_from_2d_idx(
+    df: pd.DataFrame,
+    variable: str,
+    ax: Axes | None = None,
+) -> FigAx:
+    """Plot a heatmap of a 2D indexed dataframe."""
+    if len(cast(pd.MultiIndex, df.index).levels) != 2:  # noqa: PLR2004
+        msg = "MultiIndex must have exactly two levels"
+        raise ValueError(msg)
+
+    fig, ax = _default_fig_ax(ax=ax, grid=False)
+    df2d = df[variable].unstack()
+
+    ax.set_title(variable)
+    # Note: pcolormesh swaps index/columns
+    hm = ax.pcolormesh(df2d.T)
+    ax.set_xlabel(df2d.index.name)
+    ax.set_ylabel(df2d.columns.name)
+    ax.set_xticks(
+        np.arange(0, len(df2d.index), 1) + 0.5,
+        labels=[f"{i:.2f}" for i in df2d.index],
+    )
+    ax.set_yticks(
+        np.arange(0, len(df2d.columns), 1) + 0.5,
+        labels=[f"{i:.2f}" for i in df2d.columns],
+    )
+
+    rotate_xlabels(ax, rotation=45, ha="right")
+
+    # Add colorbar
+    fig.colorbar(hm, ax=ax)
+    return fig, ax
+
+
+def heatmaps_from_2d_idx(
+    df: pd.DataFrame,
+    *,
+    n_cols: int = 3,
+    col_width_factor: float = 1,
+    row_height_factor: float = 0.6,
+    sharex: bool = True,
+    sharey: bool = False,
+) -> FigAxs:
+    """Plot multiple heatmaps of a 2D indexed dataframe."""
+    idx = cast(pd.MultiIndex, df.index)
+
+    fig, axs = grid_layout(
+        n_groups=len(df.columns),
+        n_cols=min(n_cols, len(df)),
+        col_width=len(idx.levels[0]) * col_width_factor,
+        row_height=len(idx.levels[1]) * row_height_factor,
+        sharex=sharex,
+        sharey=sharey,
+        grid=False,
+    )
+    for ax, var in zip(axs, df.columns, strict=False):
+        heatmap_from_2d_idx(df, var, ax=ax)
+    return fig, axs
+
+
+def violins(
+    df: pd.DataFrame,
+    *,
+    ax: Axes | None = None,
+    grid: bool = True,
+) -> FigAx:
+    """Plot multiple violins on the same axis."""
+    fig, ax = _default_fig_ax(ax=ax, grid=grid)
+    sns.violinplot(df, ax=ax)
+    _default_labels(ax=ax, xlabel="", ylabel=None)
+    return fig, ax
+
+
+def violins_from_2d_idx(
+    df: pd.DataFrame,
+    *,
+    n_cols: int = 4,
+    row_height: int = 2,
+    sharex: bool = True,
+    sharey: bool = False,
+    grid: bool = True,
+) -> FigAxs:
+    """Plot multiple violins of a 2D indexed dataframe."""
+    if len(cast(pd.MultiIndex, df.index).levels) != 2:  # noqa: PLR2004
+        msg = "MultiIndex must have exactly two levels"
+        raise ValueError(msg)
+
+    fig, axs = grid_layout(
+        len(df.columns),
+        n_cols=n_cols,
+        row_height=row_height,
+        sharex=sharex,
+        sharey=sharey,
+        grid=grid,
+    )
+
+    for ax, col in zip(axs[: len(df.columns)], df.columns, strict=True):
+        ax.set_title(col)
+        violins(df[col].unstack(), ax=ax)
+
+    for ax in axs[len(df.columns) :]:
+        for axis in ["top", "bottom", "left", "right"]:
+            ax.spines[axis].set_linewidth(0)
+        ax.yaxis.set_ticks([])
+
+    for ax in axs:
+        rotate_xlabels(ax)
+    return fig, axs
+
+
+def shade_protocol(
+    protocol: pd.Series,
+    *,
+    ax: Axes,
+    cmap_name: str = "Greys_r",
+    vmin: float | None = None,
+    vmax: float | None = None,
+    alpha: float = 0.5,
+    add_legend: bool = True,
+) -> None:
+    """Shade the given protocol on the given axis."""
+    from matplotlib import colormaps
+    from matplotlib.colors import Normalize
+    from matplotlib.legend import Legend
+    from matplotlib.patches import Patch
+
+    cmap = colormaps[cmap_name]
+    norm = Normalize(
+        vmin=protocol.min() if vmin is None else vmin,
+        vmax=protocol.max() if vmax is None else vmax,
+    )
+
+    t0 = pd.Timedelta(seconds=0)
+    for t_end, val in protocol.items():
+        t_end = cast(pd.Timedelta, t_end)
+        ax.axvspan(
+            t0.total_seconds(),
+            t_end.total_seconds(),
+            facecolor=cmap(norm(val)),
+            edgecolor=None,
+            alpha=alpha,
+        )
+        t0 = t_end  # type: ignore
+
+    if add_legend:
+        ax.add_artist(
+            Legend(
+                ax,
+                handles=[
+                    Patch(
+                        facecolor=cmap(norm(val)),
+                        alpha=alpha,
+                        label=val,
+                    )  # type: ignore
+                    for val in protocol
+                ],
+                labels=protocol,
+                loc="lower right",
+                bbox_to_anchor=(1.0, 0.0),
+                title="protocol" if protocol.name is None else cast(str, protocol.name),
+            )
+        )
+
+
+##########################################################################
+# Plots that actually require a model :/
+##########################################################################
+
+
+def trajectories_2d(
+    model: Model,
+    x1: tuple[str, ArrayLike],
+    x2: tuple[str, ArrayLike],
+    y0: dict[str, float] | None = None,
+    ax: Axes | None = None,
+) -> FigAx:
+    """Plot trajectories of two variables in a 2D phase space.
+
+    Examples:
+        >>> trajectories_2d(
+        ...     model,
+        ...     ("S", np.linspace(0, 1, 10)),
+        ...     ("P", np.linspace(0, 1, 10)),
+        ... )
+
+    Args:
+        model: Model to use for the plot.
+        x1: Tuple of the first variable name and its values.
+        x2: Tuple of the second variable name and its values.
+        y0: Initial conditions for the model.
+        ax: Axes to use for the plot.
+
+    """
+    name1, values1 = x1
+    name2, values2 = x2
+    n1 = len(values1)
+    n2 = len(values2)
+    u = np.zeros((n1, n2))
+    v = np.zeros((n1, n2))
+    y0 = model.get_initial_conditions() if y0 is None else y0
+    for i, ii in enumerate(values1):
+        for j, jj in enumerate(values2):
+            rhs = model.get_right_hand_side(y0 | {name1: ii, name2: jj})
+            u[i, j] = rhs[name1]
+            v[i, j] = rhs[name2]
+
+    fig, ax = _default_fig_ax(ax=ax, grid=False)
+    ax.quiver(values1, values2, u.T, v.T)
+    return fig, ax
+
+
+##########################################################################
+# Label Plots
+##########################################################################
+
+
+def relative_label_distribution(
+    mapper: LabelMapper | LinearLabelMapper,
+    concs: pd.DataFrame,
+    *,
+    subset: list[str] | None = None,
+    n_cols: int = 2,
+    col_width: float = 3,
+    row_height: float = 3,
+    sharey: bool = False,
+    grid: bool = True,
+) -> FigAxs:
+    """Plot the relative distribution of labels in the given data."""
+    variables = list(mapper.label_variables) if subset is None else subset
+    fig, axs = grid_layout(
+        n_groups=len(variables),
+        n_cols=n_cols,
+        col_width=col_width,
+        row_height=row_height,
+        sharey=sharey,
+        grid=grid,
+    )
+    if isinstance(mapper, LabelMapper):
+        for ax, name in zip(axs, variables, strict=False):
+            for i in range(mapper.label_variables[name]):
+                isos = mapper.get_isotopomers_of_at_position(name, i)
+                labels = cast(pd.DataFrame, concs.loc[:, isos])
+                total = concs.loc[:, f"{name}__total"]
+                ax.plot(labels.index, (labels.sum(axis=1) / total), label=f"C{i+1}")
+            ax.set_title(name)
+            ax.legend()
+    else:
+        for ax, (name, isos) in zip(
+            axs, mapper.get_isotopomers(variables).items(), strict=False
+        ):
+            ax.plot(concs.index, concs.loc[:, isos])
+            ax.set_title(name)
+            ax.legend([f"C{i+1}" for i in range(len(isos))])
+
+    return fig, axs