Visualization¶

coral.utils.visualization.plot_spatial(adata, res: float = 0.1, size: float = 15, use_rep_for_cluster: str | None = None, to_plot_var: str | None = None, need_lognormed: bool | None = None, color_list: list[str] | None = None, figsize: tuple[float, float] = (4, 4), legd: bool = False, invert_yaxis: bool = True, axis_: bool = False, file_name: str | None = None, bbox_to_anchor: tuple[float, float] = (1.01, 0.8), legend_fontsize: int = 10, legend_markerscale: float = 5, return_cluster: bool = False, n_neighbors: int = 100, dpi: int = 150)¶

Plot spatial clusters from a spatial transcriptomics AnnData object.

Parameters:

adata (AnnData) – The annotated data matrix with .obsm[‘spatial’] coordinates.
res (float, optional) – Resolution parameter for Leiden clustering (default: 0.1).
size (float, optional) – Marker size in the scatter plot (default: 15).
use_rep_for_cluster (str or None, optional) – Key in adata.obsm to use for neighbor graph computation (e.g. ‘X_pca’). If None, PCA will be computed automatically.
need_lognormed (bool or None, optional) – If True, applies Scanpy’s total count normalization and log1p. If None, assumes pre-normalized input.
color_list (list of str, optional) – List of colors for clusters. If None, a default color palette will be used.
figsize (tuple, optional) – Figure size in inches (default: (4, 4)).
legd (bool, optional) – Whether to display the legend (default: False).
return (bool, optional) – If True, returns (fig, ax, adata_) instead of displaying only.
invert_yaxis (bool, optional) – Whether to invert y-axis (default: True, consistent with spatial plots).
axis (bool, optional) – Whether to display axis ticks and frames (default: False).
file_name (str or None, optional) – Optional path to save the figure (e.g. “spatial_cluster.pdf”).
bbox_to_anchor (tuple, optional) – Anchor position of the legend (default: (1.01, 0.8)).
legend_fontsize (int, optional) – Font size of legend labels (default: 10).
legend_markerscale (float, optional) – Scale factor of legend markers (default: 5).

Returns:

fig, ax, adata_ – Returned only if return_ is True.

Return type:

tuple

coral.utils.visualization.plot_umap(adata, res: float = 0.1, size: float = 15, use_rep_for_cluster: str | None = None, to_plot_var: str | None = None, need_lognormed: bool | None = None, color_list: list[str] | None = None, figsize: tuple[float, float] = (4, 4), legd: bool = False, return_: bool = False, invert_yaxis: bool = True, axis_: bool = False, file_name: str | None = None, bbox_to_anchor: tuple[float, float] = (1.01, 0.8), legend_fontsize: int = 10, legend_markerscale: float = 5, dpi: int = 150)¶