canns 0.14.2__py3-none-any.whl → 0.15.0__py3-none-any.whl

canns/analyzer/data/asa/cohospace.py

@@ -1,1231 +1,251 @@
 from __future__ import annotations
 
-import os
+from typing import Any
 
 import matplotlib.pyplot as plt
 import numpy as np
-from scipy.stats import circvar
+from scipy.ndimage import gaussian_filter
+from scipy.stats import binned_statistic_2d
 
 from ...visualization.core import PlotConfig, finalize_figure
+from .coho import _ensure_parent_dir, _ensure_plot_config, _extract_coords_and_times
 
 
-def _ensure_plot_config(
-    config: PlotConfig | None,
-    factory,
+def cohospace(
+    coords: np.ndarray | dict[str, Any],
+    spikes: np.ndarray,
     *,
-    kwargs: dict | None = None,
-    **defaults,
-) -> PlotConfig:
-    if config is None:
-        defaults.update({"kwargs": kwargs or {}})
-        return factory(**defaults)
-
-    if kwargs:
-        config_kwargs = config.kwargs or {}
-        config_kwargs.update(kwargs)
-        config.kwargs = config_kwargs
-    return config
-
-
-def _ensure_parent_dir(save_path: str | None) -> None:
-    if save_path:
-        parent = os.path.dirname(save_path)
-        if parent:
-            os.makedirs(parent, exist_ok=True)
-
-
-# =====================================================================
-# CohoSpace visualization and selectivity metrics (CohoScore)
-# =====================================================================
-
-
-def _coho_coords_to_degrees(coords: np.ndarray) -> np.ndarray:
-    """
-    Convert decoded coho coordinates (T x 2, radians) into degrees in [0, 360).
-    """
-    return np.degrees(coords % (2 * np.pi))
-
-
-def _align_activity_to_coords(
-    coords: np.ndarray,
-    activity: np.ndarray,
     times: np.ndarray | None = None,
-    *,
-    label: str = "activity",
-    auto_filter: bool = True,
-) -> np.ndarray:
-    """
-    Align activity to coords by optional time indices and validate lengths.
+    coords_key: str | None = None,
+    bins: int = 51,
+    coords_in_unit: bool = False,
+    smooth_sigma: float = 0.0,
+) -> dict[str, Any]:
     """
-    coords = np.asarray(coords)
-    activity = np.asarray(activity)
-
-    if times is not None:
-        times = np.asarray(times)
-        try:
-            activity = activity[times]
-        except Exception as exc:
-            raise ValueError(
-                f"Failed to index {label} with `times`. Ensure `times` indexes the original time axis."
-            ) from exc
-
-    if activity.shape[0] != coords.shape[0]:
-        # Try to reproduce decode's zero-spike filtering if lengths mismatch.
-        if auto_filter and times is None and activity.ndim == 2:
-            mask = np.sum(activity > 0, axis=1) >= 1
-            if mask.sum() == coords.shape[0]:
-                activity = activity[mask]
-            else:
-                raise ValueError(
-                    f"{label} length must match coords length. Got {activity.shape[0]} vs {coords.shape[0]}. "
-                    "If coords are computed on a subset of timepoints (e.g., decode['times']), pass "
-                    "`times=decoding['times']` or slice the activity accordingly."
-                )
-        else:
-            raise ValueError(
-                f"{label} length must match coords length. Got {activity.shape[0]} vs {coords.shape[0]}. "
-                "If coords are computed on a subset of timepoints (e.g., decode['times']), pass "
-                "`times=decoding['times']` or slice the activity accordingly."
-            )
-
-    return activity
-
+    Compute EcohoSpace rate maps and phase centers.
 
-def plot_cohospace_trajectory_2d(
-    coords: np.ndarray,
-    times: np.ndarray | None = None,
-    subsample: int = 1,
-    figsize: tuple[int, int] = (6, 6),
-    cmap: str = "viridis",
-    save_path: str | None = None,
-    show: bool = False,
-    config: PlotConfig | None = None,
-) -> plt.Axes:
-    """
-    Plot a trajectory in cohomology space.
-
-    Parameters
-    ----------
-    coords : ndarray, shape (T, 2)
-        Decoded cohomology angles (theta1, theta2). Values may be in radians or in [0, 1] "unit circle"
-        convention depending on upstream decoding; this function will convert to degrees for plotting.
-    times : ndarray, optional, shape (T,)
-        Optional time array used to color points. If None, uses arange(T).
-    subsample : int
-        Downsampling step (>1 reduces the number of plotted points).
-    figsize : tuple
-        Matplotlib figure size.
-    cmap : str
-        Matplotlib colormap name.
-    save_path : str, optional
-        If provided, saves the figure to this path.
-    show : bool
-        If True, calls plt.show(). If False, closes the figure and returns the Axes.
-
-    Returns
-    -------
-    ax : matplotlib.axes.Axes
-        The Axes containing the plot.
-
-    Examples
-    --------
-    >>> fig = plot_cohospace_trajectory_2d(coords, subsample=2, show=False)  # doctest: +SKIP
+    Mirrors GridCellTorus get_ratemaps: mean activity in coho-space bins and
+    a circular-mean center for each neuron. Optionally smooths the rate maps.
     """
+    if isinstance(coords, dict):
+        coords, times_box = _extract_coords_and_times(coords, coords_key)
+        if times is None:
+            times = times_box
 
-    try:
-        subsample_i = int(subsample)
-    except Exception:
-        subsample_i = 1
-    if subsample_i < 1:
-        subsample_i = 1
+    coords = np.asarray(coords, float)
+    if coords.ndim != 2 or coords.shape[1] < 2:
+        raise ValueError(f"coords must be (N,2+) array, got {coords.shape}")
 
-    coords = np.asarray(coords)
-    if coords.ndim != 2 or coords.shape[1] != 2:
-        raise ValueError(f"`coords` must have shape (T, 2). Got {coords.shape}.")
+    if coords_in_unit:
+        coords = coords * (2 * np.pi)
 
-    theta_deg = _coho_coords_to_degrees(coords)
-    if subsample_i > 1:
-        theta_deg = theta_deg[::subsample_i]
-
-    if times is None:
-        times_vis = np.arange(theta_deg.shape[0])
-    else:
-        times_vis = np.asarray(times)
-        if times_vis.shape[0] != coords.shape[0]:
-            raise ValueError(
-                f"`times` length must match coords length. Got times={times_vis.shape[0]}, coords={coords.shape[0]}."
-            )
-        if subsample_i > 1:
-            times_vis = times_vis[::subsample_i]
-
-    config = _ensure_plot_config(
-        config,
-        PlotConfig.for_static_plot,
-        title="CohoSpace trajectory",
-        xlabel="theta1 (deg)",
-        ylabel="theta2 (deg)",
-        figsize=figsize,
-        save_path=save_path,
-        show=show,
-    )
-
-    fig, ax = plt.subplots(figsize=config.figsize)
-    sc = ax.scatter(
-        theta_deg[:, 0],
-        theta_deg[:, 1],
-        c=times_vis,
-        cmap=cmap,
-        s=3,
-        alpha=0.8,
-    )
-    cbar = plt.colorbar(sc, ax=ax)
-    cbar.set_label("Time")
-
-    ax.set_xlim(0, 360)
-    ax.set_ylim(0, 360)
-    ax.set_xlabel(config.xlabel)
-    ax.set_ylabel(config.ylabel)
-    ax.set_title(config.title)
-    ax.set_aspect("equal", adjustable="box")
-    ax.grid(True, alpha=0.2)
-
-    _ensure_parent_dir(config.save_path)
-    finalize_figure(fig, config)
-    return ax
-
-
-def plot_cohospace_trajectory_1d(
-    coords: np.ndarray,
-    times: np.ndarray | None = None,
-    subsample: int = 1,
-    figsize: tuple[int, int] = (6, 6),
-    cmap: str = "viridis",
-    save_path: str | None = None,
-    show: bool = False,
-    config: PlotConfig | None = None,
-) -> plt.Axes:
-    """
-    Plot a 1D cohomology trajectory on the unit circle.
-
-    Parameters
-    ----------
-    coords : ndarray, shape (T,) or (T, 1)
-        Decoded cohomology angles (theta). Values may be in radians or in [0, 1] "unit circle"
-        convention depending on upstream decoding; this function will plot on the unit circle.
-    times : ndarray, optional, shape (T,)
-        Optional time array used to color points. If None, uses arange(T).
-    subsample : int
-        Downsampling step (>1 reduces the number of plotted points).
-    figsize : tuple
-        Matplotlib figure size.
-    cmap : str
-        Matplotlib colormap name.
-    save_path : str, optional
-        If provided, saves the figure to this path.
-    show : bool
-        If True, calls plt.show(). If False, closes the figure and returns the Axes.
-    """
-    try:
-        subsample_i = int(subsample)
-    except Exception:
-        subsample_i = 1
-    if subsample_i < 1:
-        subsample_i = 1
-
-    coords = np.asarray(coords)
-    if coords.ndim == 2 and coords.shape[1] == 1:
-        coords = coords[:, 0]
-    if coords.ndim != 1:
-        raise ValueError(f"`coords` must have shape (T,) or (T, 1). Got {coords.shape}.")
-
-    if times is None:
-        times_vis = np.arange(coords.shape[0])
-    else:
-        times_vis = np.asarray(times)
-        if times_vis.shape[0] != coords.shape[0]:
-            raise ValueError(
-                f"`times` length must match coords length. Got times={times_vis.shape[0]}, coords={coords.shape[0]}."
-            )
-
-    if subsample_i > 1:
-        coords = coords[::subsample_i]
-        times_vis = times_vis[::subsample_i]
-
-    theta = coords % (2 * np.pi)
-    x = np.cos(theta)
-    y = np.sin(theta)
+    spikes = np.asarray(spikes)
+    if times is not None:
+        spikes = spikes[np.asarray(times).astype(int)]
 
-    config = _ensure_plot_config(
-        config,
-        PlotConfig.for_static_plot,
-        title="CohoSpace trajectory (1D)",
-        xlabel="cos(theta)",
-        ylabel="sin(theta)",
-        figsize=figsize,
-        save_path=save_path,
-        show=show,
-    )
+    if spikes.ndim == 1:
+        spikes = spikes[:, np.newaxis]
 
-    fig, ax = plt.subplots(figsize=config.figsize)
-    circle = np.linspace(0, 2 * np.pi, 200)
-    ax.plot(np.cos(circle), np.sin(circle), color="0.85", lw=1.0, zorder=0)
-    sc = ax.scatter(
-        x,
-        y,
-        c=times_vis,
-        cmap=cmap,
-        s=5,
-        alpha=0.8,
-    )
-    cbar = plt.colorbar(sc, ax=ax)
-    cbar.set_label("Time")
+    if spikes.shape[0] != coords.shape[0]:
+        raise ValueError(
+            f"spikes length must match coords length. Got {spikes.shape[0]} vs {coords.shape[0]}"
+        )
 
-    ax.set_xlim(-1.2, 1.2)
-    ax.set_ylim(-1.2, 1.2)
-    ax.set_xlabel(config.xlabel)
-    ax.set_ylabel(config.ylabel)
-    ax.set_title(config.title)
-    ax.set_aspect("equal", adjustable="box")
-    ax.grid(True, alpha=0.2)
+    edges = np.linspace(0, 2 * np.pi, bins)
+    bin_centers = edges[:-1] + (edges[1:] - edges[:-1]) / 2.0
+    xv, yv = np.meshgrid(bin_centers, bin_centers)
+    pos = np.stack([xv.ravel(), yv.ravel()], axis=1)
+    ccos = np.cos(pos)
+    csin = np.sin(pos)
+
+    num_neurons = spikes.shape[1]
+    maps = np.zeros((num_neurons, bins - 1, bins - 1))
+    centers = np.zeros((num_neurons, 2))
+
+    for n in range(num_neurons):
+        mtot_tmp, x_edge, y_edge, _ = binned_statistic_2d(
+            coords[:, 0],
+            coords[:, 1],
+            spikes[:, n],
+            statistic="mean",
+            bins=edges,
+            range=None,
+            expand_binnumbers=True,
+        )
+        mtot_tmp = np.rot90(mtot_tmp, 1).T
+        if smooth_sigma and smooth_sigma > 0:
+            nan_mask = np.isnan(mtot_tmp)
+            mtot_tmp = np.nan_to_num(mtot_tmp, nan=0.0)
+            mtot_tmp = gaussian_filter(mtot_tmp, smooth_sigma)
+            mtot_tmp[nan_mask] = np.nan
+        maps[n, :, :] = mtot_tmp.copy()
+
+        flat = mtot_tmp.flatten()
+        nans = ~np.isnan(flat)
+        if np.any(nans):
+            centcos = np.sum(ccos[nans, :] * flat[nans, np.newaxis], axis=0)
+            centsin = np.sum(csin[nans, :] * flat[nans, np.newaxis], axis=0)
+            centers[n, :] = np.arctan2(centsin, centcos) % (2 * np.pi)
+        else:
+            centers[n, :] = np.nan
 
-    _ensure_parent_dir(config.save_path)
-    finalize_figure(fig, config)
-    return ax
+    return {
+        "rate_maps": maps,
+        "centers": centers,
+        "x_edge": x_edge,
+        "y_edge": y_edge,
+        "bins": bins,
+        "smooth_sigma": smooth_sigma,
+    }
 
 
-def plot_cohospace_neuron_2d(
-    coords: np.ndarray,
-    activity: np.ndarray,
-    neuron_id: int,
-    mode: str = "fr",  # "fr" or "spike"
-    top_percent: float = 5.0,  # Used in FR mode
-    times: np.ndarray | None = None,
-    auto_filter: bool = True,
-    figsize: tuple = (6, 6),
-    cmap: str = "hot",
-    save_path: str | None = None,
-    show: bool = True,
+def plot_cohospace(
+    cohospace_result: dict[str, Any],
+    *,
+    neuron_id: int = 0,
     config: PlotConfig | None = None,
-) -> plt.Figure:
-    """
-    Overlay a single neuron's activity on the cohomology-space trajectory.
-
-    This is a visualization helper:
-    - mode="fr": marks the top `top_percent`%% time points by firing rate for the given neuron.
-    - mode="spike": marks all time points where spike > 0 for the given neuron.
-
-    Parameters
-    ----------
-    coords : ndarray, shape (T, 2)
-        Decoded cohomology angles (theta1, theta2), in radians.
-    activity : ndarray, shape (T, N)
-        Activity matrix (continuous firing rate or binned spikes).
-    times : ndarray, optional, shape (T_coords,)
-        Optional indices to align activity to coords when coords are computed on a subset of timepoints.
-    auto_filter : bool
-        If True and lengths mismatch, auto-filter activity with activity>0 to mimic decode filtering.
-    neuron_id : int
-        Neuron index to visualize.
-    mode : {"fr", "spike"}
-    top_percent : float
-        Used only when mode="fr". For example, 5.0 means "top 5%%" time points.
-    figsize, cmap, save_path, show : see `plot_cohospace_trajectory_2d`.
-
-    Returns
-    -------
-    ax : matplotlib.axes.Axes
-
-    Examples
-    --------
-    >>> plot_cohospace_neuron_2d(coords, spikes, neuron_id=0, show=False)  # doctest: +SKIP
-    """
-    coords = np.asarray(coords)
-    activity = _align_activity_to_coords(
-        coords, activity, times, label="activity", auto_filter=auto_filter
-    )
-    theta_deg = _coho_coords_to_degrees(coords)
-
-    signal = activity[:, neuron_id]
-
-    if mode == "fr":
-        # Select the neuron's top `top_percent`% time points
-        threshold = np.percentile(signal, 100 - top_percent)
-        idx = signal >= threshold
-        color = signal[idx]
-        title = f"Neuron {neuron_id} FR top {top_percent:.1f}% on coho-space"
-        use_cmap = cmap
-    elif mode == "spike":
-        idx = signal > 0
-        color = None
-        title = f"Neuron {neuron_id} spikes on coho-space"
-        use_cmap = None
-    else:
-        raise ValueError("mode must be 'fr' or 'spike'")
-
-    config = _ensure_plot_config(
-        config,
-        PlotConfig.for_static_plot,
-        title=title,
-        xlabel="Theta 1 (°)",
-        ylabel="Theta 2 (°)",
-        figsize=figsize,
-        save_path=save_path,
-        show=show,
-    )
-
-    fig, ax = plt.subplots(figsize=config.figsize)
-    sc = ax.scatter(
-        theta_deg[idx, 0],
-        theta_deg[idx, 1],
-        c=color if mode == "fr" else "red",
-        cmap=use_cmap,
-        s=5,
-        alpha=0.9,
-    )
-
-    if mode == "fr":
-        cbar = plt.colorbar(sc, ax=ax)
-        cbar.set_label("Firing rate")
-
-    ax.set_xlim(0, 360)
-    ax.set_ylim(0, 360)
-    ax.set_xlabel(config.xlabel)
-    ax.set_ylabel(config.ylabel)
-    ax.set_title(config.title)
-
-    _ensure_parent_dir(config.save_path)
-    finalize_figure(fig, config)
-
-    return fig
-
-
-def plot_cohospace_neuron_1d(
-    coords: np.ndarray,
-    activity: np.ndarray,
-    neuron_id: int,
-    mode: str = "fr",
-    top_percent: float = 5.0,
-    times: np.ndarray | None = None,
-    auto_filter: bool = True,
-    figsize: tuple = (6, 6),
-    cmap: str = "hot",
     save_path: str | None = None,
-    show: bool = True,
-    config: PlotConfig | None = None,
+    show: bool = False,
+    figsize: tuple[int, int] = (5, 5),
+    cmap: str = "viridis",
 ) -> plt.Figure:
     """
-    Overlay a single neuron's activity on the 1D cohomology trajectory (unit circle).
+    Plot a single-neuron EcohoSpace rate map.
     """
-    coords = np.asarray(coords)
-    if coords.ndim == 2 and coords.shape[1] == 1:
-        coords = coords[:, 0]
-    if coords.ndim != 1:
-        raise ValueError(f"coords must have shape (T,) or (T, 1), got {coords.shape}")
-
-    activity = _align_activity_to_coords(
-        coords[:, None], activity, times, label="activity", auto_filter=auto_filter
-    )
-
-    signal = activity[:, neuron_id]
-
-    if mode == "fr":
-        threshold = np.percentile(signal, 100 - top_percent)
-        idx = signal >= threshold
-        color = signal[idx]
-        title = f"Neuron {neuron_id} FR top {top_percent:.1f}% on coho-space (1D)"
-        use_cmap = cmap
-    elif mode == "spike":
-        idx = signal > 0
-        color = None
-        title = f"Neuron {neuron_id} spikes on coho-space (1D)"
-        use_cmap = None
-    else:
-        raise ValueError("mode must be 'fr' or 'spike'")
-
-    theta = coords % (2 * np.pi)
-    x = np.cos(theta)
-    y = np.sin(theta)
-
     config = _ensure_plot_config(
         config,
         PlotConfig.for_static_plot,
-        title=title,
-        xlabel="cos(theta)",
-        ylabel="sin(theta)",
+        title="EcohoSpace",
+        xlabel="",
+        ylabel="",
         figsize=figsize,
         save_path=save_path,
         show=show,
     )
 
-    fig, ax = plt.subplots(figsize=config.figsize)
-    circle = np.linspace(0, 2 * np.pi, 200)
-    ax.plot(np.cos(circle), np.sin(circle), color="0.85", lw=1.0, zorder=0)
-    sc = ax.scatter(
-        x[idx],
-        y[idx],
-        c=color if mode == "fr" else "red",
-        cmap=use_cmap,
-        s=8,
-        alpha=0.9,
-    )
-
-    if mode == "fr":
-        cbar = plt.colorbar(sc, ax=ax)
-        cbar.set_label("Firing rate")
-
-    ax.set_xlim(-1.2, 1.2)
-    ax.set_ylim(-1.2, 1.2)
-    ax.set_xlabel(config.xlabel)
-    ax.set_ylabel(config.ylabel)
-    ax.set_title(config.title)
-    ax.set_aspect("equal", adjustable="box")
-
-    _ensure_parent_dir(config.save_path)
-    finalize_figure(fig, config)
-
-    return fig
-
-
-def plot_cohospace_population_2d(
-    coords: np.ndarray,
-    activity: np.ndarray,
-    neuron_ids: list[int] | np.ndarray,
-    mode: str = "fr",  # "fr" or "spike"
-    top_percent: float = 5.0,  # Used in FR mode
-    times: np.ndarray | None = None,
-    auto_filter: bool = True,
-    figsize: tuple = (6, 6),
-    cmap: str = "hot",
-    save_path: str | None = None,
-    show: bool = True,
-    config: PlotConfig | None = None,
-) -> plt.Figure:
-    """
-    Plot aggregated activity from multiple neurons in cohomology space.
-
-    For mode="fr":
-    - For each neuron, select its top `top_percent`%% time points by firing rate.
-    - Aggregate (sum) firing rates over the selected points and plot as colors.
-
-    For mode="spike":
-    - For each neuron, count spikes at each time point (spike > 0).
-    - Aggregate counts over neurons and plot as colors.
-
-    Parameters
-    ----------
-    coords : ndarray, shape (T, 2)
-    activity : ndarray, shape (T, N)
-    times : ndarray, optional, shape (T_coords,)
-        Optional indices to align activity to coords when coords are computed on a subset of timepoints.
-    auto_filter : bool
-        If True and lengths mismatch, auto-filter activity with activity>0 to mimic decode filtering.
-    neuron_ids : iterable[int]
-        Neuron indices to include (use range(N) to include all).
-    mode : {"fr", "spike"}
-    top_percent : float
-        Used only when mode="fr".
-    figsize, cmap, save_path, show : see `plot_cohospace_trajectory_2d`.
-
-    Returns
-    -------
-    ax : matplotlib.axes.Axes
-
-    Examples
-    --------
-    >>> plot_cohospace_population_2d(coords, spikes, neuron_ids=[0, 1, 2], show=False)  # doctest: +SKIP
-    """
-    coords = np.asarray(coords)
-    activity = _align_activity_to_coords(
-        coords, activity, times, label="activity", auto_filter=auto_filter
-    )
-    neuron_ids = np.asarray(neuron_ids, dtype=int)
-
-    theta_deg = _coho_coords_to_degrees(coords)
-
-    T = activity.shape[0]
-    mask = np.zeros(T, dtype=bool)
-    agg_color = np.zeros(T, dtype=float)
+    maps = cohospace_result["rate_maps"]
+    x_edge = cohospace_result["x_edge"]
+    y_edge = cohospace_result["y_edge"]
 
-    for n in neuron_ids:
-        signal = activity[:, n]
-
-        if mode == "fr":
-            threshold = np.percentile(signal, 100 - top_percent)
-            idx = signal >= threshold
-            agg_color[idx] += signal[idx]
-            mask |= idx
-        elif mode == "spike":
-            idx = signal > 0
-            agg_color[idx] += 1.0
-            mask |= idx
-        else:
-            raise ValueError("mode must be 'fr' or 'spike'")
-
-    config = _ensure_plot_config(
-        config,
-        PlotConfig.for_static_plot,
-        title=f"{len(neuron_ids)} neurons on coho-space",
-        xlabel="Theta 1 (°)",
-        ylabel="Theta 2 (°)",
-        figsize=figsize,
-        save_path=save_path,
-        show=show,
-    )
+    if neuron_id < 0 or neuron_id >= maps.shape[0]:
+        raise ValueError(f"neuron_id out of range: {neuron_id}")
 
-    fig, ax = plt.subplots(figsize=config.figsize)
-    sc = ax.scatter(
-        theta_deg[mask, 0],
-        theta_deg[mask, 1],
-        c=agg_color[mask],
+    fig, ax = plt.subplots(1, 1, figsize=config.figsize)
+    im = ax.imshow(
+        maps[neuron_id],
+        origin="lower",
+        extent=[x_edge[0], x_edge[-1], y_edge[0], y_edge[-1]],
         cmap=cmap,
-        s=5,
-        alpha=0.9,
     )
-    cbar = plt.colorbar(sc, ax=ax)
-    label = "Aggregate FR" if mode == "fr" else "Spike count"
-    cbar.set_label(label)
-
-    ax.set_xlim(0, 360)
-    ax.set_ylim(0, 360)
-    ax.set_xlabel(config.xlabel)
-    ax.set_ylabel(config.ylabel)
-    ax.set_title(config.title)
+    ax.set_aspect("equal", "box")
+    ax.set_xticks([])
+    ax.set_yticks([])
+    ax.set_title(f"EcohoSpace Rate Map (neuron {neuron_id})", fontsize=10)
+    plt.colorbar(im, ax=ax, fraction=0.046, pad=0.04, label="Mean activity")
 
+    fig.tight_layout()
     _ensure_parent_dir(config.save_path)
     finalize_figure(fig, config)
-
     return fig
 
 
-def plot_cohospace_population_1d(
-    coords: np.ndarray,
-    activity: np.ndarray,
-    neuron_ids: list[int] | np.ndarray,
-    mode: str = "fr",
-    top_percent: float = 5.0,
-    times: np.ndarray | None = None,
-    auto_filter: bool = True,
-    figsize: tuple = (6, 6),
-    cmap: str = "hot",
-    save_path: str | None = None,
-    show: bool = True,
+def plot_cohospace_skewed(
+    cohospace_result: dict[str, Any],
+    *,
+    neuron_id: int = 0,
     config: PlotConfig | None = None,
+    save_path: str | None = None,
+    show: bool = False,
+    figsize: tuple[int, int] = (5, 5),
+    cmap: str = "viridis",
+    show_grid: bool = True,
 ) -> plt.Figure:
     """
-    Plot aggregated activity from multiple neurons on the 1D cohomology trajectory.
+    Plot a single-neuron EcohoSpace rate map in skewed torus coordinates.
     """
-    coords = np.asarray(coords)
-    if coords.ndim == 2 and coords.shape[1] == 1:
-        coords = coords[:, 0]
-    if coords.ndim != 1:
-        raise ValueError(f"coords must have shape (T,) or (T, 1), got {coords.shape}")
-
-    activity = _align_activity_to_coords(
-        coords[:, None], activity, times, label="activity", auto_filter=auto_filter
-    )
-    neuron_ids = np.asarray(neuron_ids, dtype=int)
-
-    T = activity.shape[0]
-    mask = np.zeros(T, dtype=bool)
-    agg_color = np.zeros(T, dtype=float)
-
-    for n in neuron_ids:
-        signal = activity[:, n]
-
-        if mode == "fr":
-            threshold = np.percentile(signal, 100 - top_percent)
-            idx = signal >= threshold
-            agg_color[idx] += signal[idx]
-            mask |= idx
-        elif mode == "spike":
-            idx = signal > 0
-            agg_color[idx] += 1.0
-            mask |= idx
-        else:
-            raise ValueError("mode must be 'fr' or 'spike'")
-
-    theta = coords % (2 * np.pi)
-    x = np.cos(theta)
-    y = np.sin(theta)
-
     config = _ensure_plot_config(
         config,
         PlotConfig.for_static_plot,
-        title=f"{len(neuron_ids)} neurons on coho-space (1D)",
-        xlabel="cos(theta)",
-        ylabel="sin(theta)",
+        title="EcohoSpace (Skewed)",
+        xlabel=r"$\theta_1 + \frac{1}{2}\theta_2$",
+        ylabel=r"$\frac{\sqrt{3}}{2}\theta_2$",
         figsize=figsize,
         save_path=save_path,
         show=show,
     )
 
-    fig, ax = plt.subplots(figsize=config.figsize)
-    circle = np.linspace(0, 2 * np.pi, 200)
-    ax.plot(np.cos(circle), np.sin(circle), color="0.85", lw=1.0, zorder=0)
-    sc = ax.scatter(
-        x[mask],
-        y[mask],
-        c=agg_color[mask],
-        cmap=cmap,
-        s=6,
-        alpha=0.9,
-    )
-    cbar = plt.colorbar(sc, ax=ax)
-    label = "Aggregate FR" if mode == "fr" else "Spike count"
-    cbar.set_label(label)
-
-    ax.set_xlim(-1.2, 1.2)
-    ax.set_ylim(-1.2, 1.2)
-    ax.set_xlabel(config.xlabel)
-    ax.set_ylabel(config.ylabel)
-    ax.set_title(config.title)
-    ax.set_aspect("equal", adjustable="box")
-
-    _ensure_parent_dir(config.save_path)
-    finalize_figure(fig, config)
-
-    return fig
-
-
-def compute_cohoscore_2d(
-    coords: np.ndarray,
-    activity: np.ndarray,
-    top_percent: float = 2.0,
-    times: np.ndarray | None = None,
-    auto_filter: bool = True,
-) -> np.ndarray:
-    """
-    Compute a simple cohomology-space selectivity score (CohoScore) for each neuron.
-
-    For each neuron:
-    - Select "active" time points:
-        - If top_percent is None: all time points with activity > 0
-        - Else: top `top_percent`%% time points by activity value
-    - Compute circular variance for theta1 and theta2 on the selected points.
-    - CohoScore = 0.5 * (var(theta1) + var(theta2))
+    maps = cohospace_result["rate_maps"]
+    x_edge = cohospace_result["x_edge"]
+    y_edge = cohospace_result["y_edge"]
 
-    Interpretation:
-    - Smaller score => points are more concentrated in coho space => higher selectivity.
+    if neuron_id < 0 or neuron_id >= maps.shape[0]:
+        raise ValueError(f"neuron_id out of range: {neuron_id}")
 
-    Parameters
-    ----------
-    coords : ndarray, shape (T, 2)
-        Decoded cohomology angles (theta1, theta2), in radians.
-    activity : ndarray, shape (T, N)
-    times : ndarray, optional, shape (T_coords,)
-        Optional indices to align activity to coords when coords are computed on a subset of timepoints.
-    auto_filter : bool
-        If True and lengths mismatch, auto-filter activity with activity>0 to mimic decode filtering.
-        Activity matrix (FR or spikes).
-    top_percent : float | None
-        Percentage for selecting active points (e.g., 2.0 means top 2%%). If None, use activity>0.
-
-    Returns
-    -------
-    scores : ndarray, shape (N,)
-        CohoScore per neuron (NaN for neurons with too few points).
-
-    Examples
-    --------
-    >>> scores = compute_cohoscore_2d(coords, spikes)  # doctest: +SKIP
-    >>> scores.shape[0]  # doctest: +SKIP
-    """
-    coords = np.asarray(coords)
-    activity = _align_activity_to_coords(
-        coords, activity, times, label="activity", auto_filter=auto_filter
-    )
-    T, N = activity.shape
+    th1, th2 = np.meshgrid(x_edge, y_edge, indexing="xy")
+    X = th1 + 0.5 * th2
+    Y = (np.sqrt(3) / 2.0) * th2
 
-    theta = coords % (2 * np.pi)  # Ensure values are in [0, 2π)
-    scores = np.zeros(N, dtype=float)
+    fig, ax = plt.subplots(1, 1, figsize=config.figsize)
+    im = ax.pcolormesh(X, Y, maps[neuron_id], shading="auto", cmap=cmap)
 
-    for n in range(N):
-        signal = activity[:, n]
-
-        if top_percent is None:
-            idx = signal > 0  # Use all time points with spikes
-        else:
-            threshold = np.percentile(signal, 100 - top_percent)
-            idx = signal >= threshold
-
-        if np.sum(idx) < 5:
-            scores[n] = np.nan  # Too sparse; unreliable
-            continue
-
-        theta1 = theta[idx, 0]
-        theta2 = theta[idx, 1]
-
-        var1 = circvar(theta1, high=2 * np.pi, low=0)
-        var2 = circvar(theta2, high=2 * np.pi, low=0)
-
-        scores[n] = 0.5 * (var1 + var2)
-
-    return scores
-
-
-def compute_cohoscore_1d(
-    coords: np.ndarray,
-    activity: np.ndarray,
-    top_percent: float = 2.0,
-    times: np.ndarray | None = None,
-    auto_filter: bool = True,
-) -> np.ndarray:
-    """
-    Compute 1D cohomology-space selectivity score (CohoScore) for each neuron.
-
-    For each neuron:
-    - Select "active" time points:
-        - If top_percent is None: all time points with activity > 0
-        - Else: top `top_percent`%% time points by activity value
-    - Compute circular variance for theta on the selected points.
-    - CohoScore = var(theta)
-    """
-    coords = np.asarray(coords)
-    if coords.ndim == 2 and coords.shape[1] == 1:
-        coords = coords[:, 0]
-    if coords.ndim != 1:
-        raise ValueError(f"coords must have shape (T,) or (T, 1), got {coords.shape}")
-
-    activity = _align_activity_to_coords(
-        coords[:, None], activity, times, label="activity", auto_filter=auto_filter
-    )
-    _, n_neurons = activity.shape
-
-    theta = coords % (2 * np.pi)
-    scores = np.zeros(n_neurons, dtype=float)
-
-    for n in range(n_neurons):
-        signal = activity[:, n]
-
-        if top_percent is None:
-            idx = signal > 0
-        else:
-            threshold = np.percentile(signal, 100 - top_percent)
-            idx = signal >= threshold
-
-        if np.sum(idx) < 5:
-            scores[n] = np.nan
-            continue
-
-        var1 = circvar(theta[idx], high=2 * np.pi, low=0)
-        scores[n] = var1
-
-    return scores
-
-
-def skew_transform_torus(coords):
-    """
-    Convert torus angles (theta1, theta2) into coordinates in a skewed parallelogram fundamental domain.
-
-    Given theta1, theta2 in radians, map:
-        x = theta1 + 0.5 * theta2
-        y = (sqrt(3)/2) * theta2
-
-    This is a linear change of basis that turns the square [0, 2π)×[0, 2π) into a 60-degree
-    parallelogram, which is convenient for visualizing wrap-around behavior on a 2-torus.
-
-    Parameters
-    ----------
-    coords : ndarray, shape (T, 2)
-        Angles (theta1, theta2) in radians.
-
-    Returns
-    -------
-    xy : ndarray, shape (T, 2)
-        Skewed planar coordinates.
-    """
-    coords = np.asarray(coords)
-    if coords.ndim != 2 or coords.shape[1] != 2:
-        raise ValueError(f"coords must be (T,2), got {coords.shape}")
-
-    theta1 = coords[:, 0]
-    theta2 = coords[:, 1]
-
-    # Linear change of basis (NO nonlinear scaling)
-    x = theta1 + 0.5 * theta2
-    y = (np.sqrt(3) / 2.0) * theta2
-
-    return np.stack([x, y], axis=1)
-
-
-def draw_torus_parallelogram_grid(ax, n_tiles=1, color="0.7", lw=1.0, alpha=0.8):
-    """
-    Draw parallelogram grid corresponding to torus fundamental domain.
-
-    Fundamental vectors:
-        e1 = (2π, 0)
-        e2 = (π, √3 π)
-
-    Parameters
-    ----------
-    ax : matplotlib axis
-    n_tiles : int
-        How many tiles to draw in +/- directions (visual aid).
-        n_tiles=1 means draw [-1, 0, 1] shifts.
-    """
-    e1 = np.array([2 * np.pi, 0.0])
-    e2 = np.array([np.pi, np.sqrt(3) * np.pi])
-
-    shifts = range(-n_tiles, n_tiles + 1)
-
-    for i in shifts:
-        for j in shifts:
-            origin = i * e1 + j * e2
-            corners = np.array([origin, origin + e1, origin + e1 + e2, origin + e2, origin])
-            ax.plot(corners[:, 0], corners[:, 1], color=color, lw=lw, alpha=alpha)
-
-
-def tile_parallelogram_points(xy, n_tiles=1):
-    """
-    Tile points in the skewed (parallelogram) torus fundamental domain.
-
-    This is mainly for static visualizations so you can visually inspect continuity
-    across domain boundaries.
-
-    Parameters
-    ----------
-    points : ndarray, shape (T, 2)
-        Points in the skewed plane (same coordinates as returned by `skew_transform_torus`).
-    n_tiles : int
-        Number of tiles to extend around the base domain.
-        - n_tiles=1 produces a 3x3 tiling
-        - n_tiles=2 produces a 5x5 tiling
-
-    Returns
-    -------
-    tiled : ndarray
-        Tiled points.
-    """
-    xy = np.asarray(xy, dtype=float)
-
-    e1 = np.array([2 * np.pi, 0.0])
-    e2 = np.array([np.pi, np.sqrt(3) * np.pi])
-
-    out = []
-    for i in range(-n_tiles, n_tiles + 1):
-        for j in range(-n_tiles, n_tiles + 1):
-            out.append(xy + i * e1 + j * e2)
-
-    return np.vstack(out) if len(out) else xy
-
-
-def plot_cohospace_neuron_skewed(
-    coords,
-    activity,
-    neuron_id,
-    mode="spike",
-    top_percent=2.0,
-    times: np.ndarray | None = None,
-    auto_filter: bool = True,
-    save_path=None,
-    show=None,
-    ax=None,
-    show_grid=True,
-    n_tiles=1,
-    s=6,
-    alpha=0.8,
-    config: PlotConfig | None = None,
-):
-    """
-    Plot single-neuron CohoSpace on skewed torus domain.
-
-    Parameters
-    ----------
-    coords : ndarray, shape (T, 2)
-        Decoded circular coordinates (theta1, theta2), in radians.
-    activity : ndarray, shape (T, N)
-        Activity matrix aligned with coords.
-    neuron_id : int
-        Neuron index.
-    mode : {"spike", "fr"}
-        spike: use activity > 0
-        fr: use top_percent threshold
-    top_percent : float
-        Percentile for FR thresholding.
-    auto_filter : bool
-        If True and lengths mismatch, auto-filter activity with activity>0 to mimic decode filtering.
-    """
-    coords = np.asarray(coords)
-    activity = _align_activity_to_coords(
-        coords, activity, times, label="activity", auto_filter=auto_filter
-    )
-
-    # --- normalize angles to [0, 2π)
-    coords = coords % (2 * np.pi)
-
-    # --- select neuron activity
-    a = activity[:, neuron_id]
-
-    if mode == "spike":
-        mask = a > 0
-    elif mode == "fr":
-        thr = np.percentile(a, 100 - top_percent)
-        mask = a >= thr
-    else:
-        raise ValueError(f"Unknown mode: {mode}")
-
-    val = a[mask]  # Used for FR-mode coloring
-
-    if config is None:
-        config = PlotConfig.for_static_plot(
-            title=f"Neuron {neuron_id} – CohoSpace (skewed, mode={mode})",
-            xlabel=r"$\theta_1 + \frac{1}{2}\theta_2$",
-            ylabel=r"$\frac{\sqrt{3}}{2}\theta_2$",
-            figsize=(5, 5),
-            save_path=save_path,
-            show=bool(show) if show is not None else False,
-        )
-    else:
-        if save_path is not None:
-            config.save_path = save_path
-        if show is not None:
-            config.show = show
-        if not config.title:
-            config.title = f"Neuron {neuron_id} – CohoSpace (skewed, mode={mode})"
-        if not config.xlabel:
-            config.xlabel = r"$\theta_1 + \frac{1}{2}\theta_2$"
-        if not config.ylabel:
-            config.ylabel = r"$\frac{\sqrt{3}}{2}\theta_2$"
-
-    created_fig = ax is None
-    if created_fig:
-        fig, ax = plt.subplots(figsize=config.figsize)
-    else:
-        fig = ax.figure
-
-    # --- fundamental domain vectors in skew plane
-    e1 = np.array([2 * np.pi, 0.0])
-    e2 = np.array([np.pi, np.sqrt(3) * np.pi])
-
-    def _draw_single_domain(ax):
-        P00 = np.array([0.0, 0.0])
-        P10 = e1
-        P01 = e2
-        P11 = e1 + e2
-        poly = np.vstack([P00, P10, P11, P01, P00])
-        ax.plot(poly[:, 0], poly[:, 1], lw=1.2, color="0.35")
-
-    def _annotate_corners(ax):
-        P00 = np.array([0.0, 0.0])
-        P10 = e1
-        P01 = e2
-        P11 = e1 + e2
-
-        corners = np.vstack([P00, P10, P01, P11])
-        xmin, ymin = corners.min(axis=0)
-        xmax, ymax = corners.max(axis=0)
-        padx = 0.02 * (xmax - xmin)
-        pady = 0.02 * (ymax - ymin)
-
-        bbox = dict(facecolor="white", edgecolor="none", alpha=0.7, pad=1.0)
-
-        ax.text(
-            P00[0] + padx, P00[1] + pady, "(0,0)", fontsize=10, ha="left", va="bottom", bbox=bbox
-        )
-        ax.text(
-            P10[0] - padx, P10[1] + pady, "(2π,0)", fontsize=10, ha="right", va="bottom", bbox=bbox
-        )
-        ax.text(P01[0] + padx, P01[1] - pady, "(0,2π)", fontsize=10, ha="left", va="top", bbox=bbox)
-        ax.text(
-            P11[0] - padx, P11[1] - pady, "(2π,2π)", fontsize=10, ha="right", va="top", bbox=bbox
-        )
-
-    # --- skew transform
-    xy = skew_transform_torus(coords[mask])
-
-    # Tiling: if points are tiled, values must be tiled too (FR mode) to keep lengths consistent
-    if n_tiles and n_tiles > 0:
-        xy = tile_parallelogram_points(xy, n_tiles=n_tiles)
-        if mode == "fr":
-            val = np.tile(val, (2 * n_tiles + 1) ** 2)
-
-    # --- scatter
-    if mode == "fr":
-        sc = ax.scatter(xy[:, 0], xy[:, 1], c=val, s=s, alpha=alpha, cmap="viridis")
-        fig.colorbar(sc, ax=ax, shrink=0.85, pad=0.02, label="activity")
-    else:
-        ax.scatter(xy[:, 0], xy[:, 1], s=s, alpha=alpha, color="tab:blue")
-
-    # Always draw the base domain boundary
-    _draw_single_domain(ax)
-
-    # Grid is optional (debug aid); when tiles=0 only the base domain is drawn
     if show_grid:
-        draw_torus_parallelogram_grid(ax, n_tiles=n_tiles)
-
-    _annotate_corners(ax)
-
-    # Fix view limits: tiles=0 shows base domain; tiles>0 shows the tiled extent
-    base = np.vstack([[0, 0], e1, e2, e1 + e2])
-
-    if n_tiles and n_tiles > 0:
-        # Expand view by n_tiles rings around the base domain
-        # Translation vectors for tiling are i*e1 + j*e2
-        shifts = []
-        for i in range(-n_tiles, n_tiles + 1):
-            for j in range(-n_tiles, n_tiles + 1):
-                shifts.append(i * e1 + j * e2)
-        shifts = np.asarray(shifts)  # ((2n+1)^2, 2)
-
-        all_corners = (base[None, :, :] + shifts[:, None, :]).reshape(-1, 2)
-        xmin, ymin = all_corners.min(axis=0)
-        xmax, ymax = all_corners.max(axis=0)
-    else:
-        xmin, ymin = base.min(axis=0)
-        xmax, ymax = base.max(axis=0)
-
-    padx = 0.03 * (xmax - xmin)
-    pady = 0.03 * (ymax - ymin)
+        e1 = np.array([2 * np.pi, 0.0])
+        e2 = np.array([np.pi, np.sqrt(3) * np.pi])
+        poly = np.vstack([np.zeros(2), e1, e1 + e2, e2, np.zeros(2)])
+        ax.plot(poly[:, 0], poly[:, 1], lw=1.1, color="0.35")
+
+    ax.set_aspect("equal", "box")
+    ax.set_xticks([])
+    ax.set_yticks([])
+    ax.set_title(f"EcohoSpace Rate Map (skewed, neuron {neuron_id})", fontsize=10)
+    plt.colorbar(im, ax=ax, fraction=0.046, pad=0.04, label="Mean activity")
+
+    corners = np.vstack(
+        [
+            [0.0, 0.0],
+            [2 * np.pi, 0.0],
+            [np.pi, np.sqrt(3) * np.pi],
+            [3 * np.pi, np.sqrt(3) * np.pi],
+        ]
+    )
+    xmin, ymin = corners.min(axis=0)
+    xmax, ymax = corners.max(axis=0)
+    padx = 0.02 * (xmax - xmin)
+    pady = 0.02 * (ymax - ymin)
     ax.set_xlim(xmin - padx, xmax + padx)
     ax.set_ylim(ymin - pady, ymax + pady)
 
-    ax.set_aspect("equal")
-    ax.set_xlabel(config.xlabel)
-    ax.set_ylabel(config.ylabel)
-    ax.set_title(config.title)
-
-    if created_fig:
-        _ensure_parent_dir(config.save_path)
-        finalize_figure(fig, config)
-    else:
-        if config.save_path is not None:
-            _ensure_parent_dir(config.save_path)
-            fig.savefig(config.save_path, **config.to_savefig_kwargs())
-        if config.show:
-            plt.show()
-
-    return ax
-
-
-def plot_cohospace_population_skewed(
-    coords,
-    activity,
-    neuron_ids,
-    mode="spike",
-    top_percent=2.0,
-    times: np.ndarray | None = None,
-    auto_filter: bool = True,
-    save_path=None,
-    show=False,
-    ax=None,
-    show_grid=True,
-    n_tiles=1,
-    s=4,
-    alpha=0.5,
-    config: PlotConfig | None = None,
-):
-    """
-    Plot population CohoSpace on skewed torus domain.
-
-    neuron_ids : list or ndarray
-        Neurons to include (e.g. top-K by CohoScore).
-    auto_filter : bool
-        If True and lengths mismatch, auto-filter activity with activity>0 to mimic decode filtering.
-    """
-    coords = np.asarray(coords)
-    activity = _align_activity_to_coords(
-        coords, activity, times, label="activity", auto_filter=auto_filter
-    )
-    coords = coords % (2 * np.pi)
-
-    if config is None:
-        config = PlotConfig.for_static_plot(
-            title=f"Population CohoSpace (skewed, n={len(neuron_ids)}, mode={mode})",
-            xlabel=r"$\theta_1 + \frac{1}{2}\theta_2$",
-            ylabel=r"$\frac{\sqrt{3}}{2}\theta_2$",
-            figsize=(5, 5),
-            save_path=save_path,
-            show=show,
-        )
-    else:
-        if save_path is not None:
-            config.save_path = save_path
-        if show is not None:
-            config.show = show
-        if not config.title:
-            config.title = f"Population CohoSpace (skewed, n={len(neuron_ids)}, mode={mode})"
-        if not config.xlabel:
-            config.xlabel = r"$\theta_1 + \frac{1}{2}\theta_2$"
-        if not config.ylabel:
-            config.ylabel = r"$\frac{\sqrt{3}}{2}\theta_2$"
-
-    created_fig = ax is None
-    if created_fig:
-        fig, ax = plt.subplots(figsize=config.figsize)
-    else:
-        fig = ax.figure
-
-    # --- fundamental domain vectors in skew plane
-    e1 = np.array([2 * np.pi, 0.0])
-    e2 = np.array([np.pi, np.sqrt(3) * np.pi])
-
-    def _draw_single_domain(ax):
-        P00 = np.array([0.0, 0.0])
-        P10 = e1
-        P01 = e2
-        P11 = e1 + e2
-        poly = np.vstack([P00, P10, P11, P01, P00])
-        ax.plot(poly[:, 0], poly[:, 1], lw=1.2, color="0.35")
-
-    # --- scatter each neuron
-    for nid in neuron_ids:
-        a = activity[:, nid]
-        if mode == "spike":
-            mask = a > 0
-        else:
-            thr = np.percentile(a, 100 - top_percent)
-            mask = a >= thr
+    fig.tight_layout()
+    _ensure_parent_dir(config.save_path)
+    finalize_figure(fig, config)
+    return fig
 
-        xy = skew_transform_torus(coords[mask])
 
-        if n_tiles and n_tiles > 0:
-            xy = tile_parallelogram_points(xy, n_tiles=n_tiles)
+def cohospace_upgrade(*args, **kwargs) -> dict[str, Any]:
+    """Legacy alias for EcohoSpace (formerly cohospace_upgrade)."""
+    return cohospace(*args, **kwargs)
 
-        ax.scatter(xy[:, 0], xy[:, 1], s=s, alpha=alpha)
 
-    # Always draw the base domain boundary
-    _draw_single_domain(ax)
+def ecohospace(*args, **kwargs) -> dict[str, Any]:
+    """Alias for EcohoSpace (GridCellTorus-style)."""
+    return cohospace(*args, **kwargs)
 
-    if show_grid:
-        draw_torus_parallelogram_grid(ax, n_tiles=n_tiles)
 
-    # Fix view limits: tiles=0 shows base domain; tiles>0 shows the tiled extent
-    base = np.vstack([[0, 0], e1, e2, e1 + e2])
+def plot_cohospace_upgrade(*args, **kwargs) -> plt.Figure:
+    """Legacy alias for EcohoSpace plotting (formerly plot_cohospace_upgrade)."""
+    return plot_cohospace(*args, **kwargs)
 
-    if n_tiles and n_tiles > 0:
-        # Expand view by n_tiles rings around the base domain
-        # Translation vectors for tiling are i*e1 + j*e2
-        shifts = []
-        for i in range(-n_tiles, n_tiles + 1):
-            for j in range(-n_tiles, n_tiles + 1):
-                shifts.append(i * e1 + j * e2)
-        shifts = np.asarray(shifts)  # ((2n+1)^2, 2)
 
-        all_corners = (base[None, :, :] + shifts[:, None, :]).reshape(-1, 2)
-        xmin, ymin = all_corners.min(axis=0)
-        xmax, ymax = all_corners.max(axis=0)
-    else:
-        xmin, ymin = base.min(axis=0)
-        xmax, ymax = base.max(axis=0)
+def plot_cohospace_upgrade_skewed(*args, **kwargs) -> plt.Figure:
+    """Legacy alias for EcohoSpace skewed plotting."""
+    return plot_cohospace_skewed(*args, **kwargs)
 
-    padx = 0.03 * (xmax - xmin)
-    pady = 0.03 * (ymax - ymin)
-    ax.set_xlim(xmin - padx, xmax + padx)
-    ax.set_ylim(ymin - pady, ymax + pady)
 
-    ax.set_aspect("equal")
-    ax.set_xlabel(config.xlabel)
-    ax.set_ylabel(config.ylabel)
-    ax.set_title(config.title)
+def plot_ecohospace(*args, **kwargs) -> plt.Figure:
+    """Alias for EcohoSpace plotting."""
+    return plot_cohospace(*args, **kwargs)
 
-    if created_fig:
-        _ensure_parent_dir(config.save_path)
-        finalize_figure(fig, config)
-    else:
-        if config.save_path is not None:
-            _ensure_parent_dir(config.save_path)
-            fig.savefig(config.save_path, **config.to_savefig_kwargs())
-        if config.show:
-            plt.show()
 
-    return ax
+def plot_ecohospace_skewed(*args, **kwargs) -> plt.Figure:
+    """Alias for EcohoSpace skewed plotting."""
+    return plot_cohospace_skewed(*args, **kwargs)