SPADEResult

densitree.result.SPADEResult(labels_, tree_, X_down, down_idx, n_features, feature_names=None, _cluster_stats=None) dataclass

Rich output object from a SPADE run.

Attributes:

Name	Type	Description
labels_	(ndarray[int], shape(n_cells))	Cluster assignment for every original cell.
tree_	Graph	MST connecting cluster centroids. Each node has size (int) and median (ndarray) attributes.
X_down	(ndarray, shape(n_down, n_features))	Downsampled cells used for clustering.
down_idx	(ndarray[int], shape(n_down))	Indices into the original array for the downsampled cells.
cluster_stats_	DataFrame	One row per cluster with size and median_<feature> columns. Built lazily on first access.

plot_tree(color_by=None, size_by='count', backend='matplotlib')

Visualize the SPADE tree.

Parameters:

Name	Type	Description	Default
color_by	int | str | None	Feature index (int) or name (str) to color nodes by median expression. None colors all nodes the same.	None
size_by	str	'count' scales node size by cell count. Any other value uses uniform size.	'count'
backend	str	'matplotlib' for static plots, 'plotly' for interactive.	'matplotlib'

Source code in densitree/result.py

def plot_tree(
    self,
    color_by: int | str | None = None,
    size_by: str = "count",
    backend: str = "matplotlib",
):
    """Visualize the SPADE tree.

    Parameters
    ----------
    color_by:
        Feature index (int) or name (str) to color nodes by median expression.
        ``None`` colors all nodes the same.
    size_by:
        ``'count'`` scales node size by cell count. Any other value uses uniform size.
    backend:
        ``'matplotlib'`` for static plots, ``'plotly'`` for interactive.
    """
    if backend == "matplotlib":
        from densitree.plot.matplotlib import plot_tree as _plot
    elif backend == "plotly":
        try:
            from densitree.plot.plotly import plot_tree as _plot
        except ImportError as e:
            raise ImportError(
                "plotly is required for backend='plotly'. "
                "Install it with: pip install plotly"
            ) from e
    else:
        raise ValueError(f"Unknown backend '{backend}'. Use 'matplotlib' or 'plotly'.")

    return _plot(self, color_by=color_by, size_by=size_by)