omicverse.pl.add_pie2spatial

omicverse.pl.add_pie2spatial(adata, cell_type_columns, ax, pie_radius=15, img_key='hires', spatial_coords=None, pie_radius_px=None, min_proportion=0.01, colors=None, alpha=0.9, remainder='gap', remainder_color='lightgray', remainder_alpha=0.5, renormalize_if_sum_gt1=True, zorder=80, legend_loc=(1.05, 1.0), ncols=3)[source]

Overlay per-spot pie charts of cell-type composition on a spatial map.

Parameters:

  • adata (AnnData) – Spatial AnnData object. Requires adata.obsm['spatial'].

  • cell_type_columns (list of str) – Columns in adata.obs (or genes in adata.var_names) used as pie components.

  • ax (matplotlib.axes.Axes) – Target axes.

  • pie_radius (float, optional) – Pie radius in data coordinates when pie_radius_px is not provided.

  • img_key (str, optional) – Spatial image key used to rescale coordinates (for example 'hires').

  • spatial_coords (array-like, optional) – External coordinates overriding adata.obsm['spatial'].

  • pie_radius_px (float or None, optional) – Pie radius in pixels; converted to data units automatically.

  • min_proportion (float, optional) – Minimum slice proportion to draw.

  • colors (dict or sequence, optional) – Color mapping for cell types.

  • alpha (float, optional) – Pie transparency.

  • remainder ({'gap', 'gray', 'outline'}, optional) – How to render unassigned mass when proportions do not sum to 1.

  • remainder_color (str, optional) – Color for remainder slice when remainder='gray'.

  • remainder_alpha (float, optional) – Alpha for remainder slice.

  • renormalize_if_sum_gt1 (bool, optional) – If True, renormalize rows whose sum exceeds 1.

  • zorder (int, optional) – Drawing order for pie artists.

  • legend_loc (tuple, optional) – Legend anchor location.

  • ncols (int, optional) – Number of legend columns.

Returns:

Axes with pie overlays.

Return type:

matplotlib.axes.Axes

Examples

>>> ax = ov.pl.plot_spatial(adata)
>>> ov.pl.add_pie2spatial(adata, cell_type_columns=['T', 'B', 'Myeloid'], ax=ax)