omicverse.pl.embedding_atlas

omicverse.pl.embedding_atlas(adata, basis, color=None, *, gene_symbols=None, use_raw=None, layer=None, groups=None, title=None, figsize=(4, 4), ax=None, cmap='RdBu_r', palette=None, na_color='lightgray', na_in_legend=True, legend_loc='right margin', legend_fontsize=None, legend_fontweight='bold', legend_fontoutline=None, frameon='small', colorbar_loc='right', vmax=None, vmin=None, vcenter=None, norm=None, plot_width=800, plot_height=800, spread_px=0, how='eq_hist', show=None, save=None, return_fig=None, ncols=4, wspace=None, hspace=0.25, **kwargs)[source]

Render large-scale embeddings with Datashader.

Parameters:

  • adata (AnnData) – Annotated data object containing embedding coordinates in obsm.

  • basis (str) – Embedding key in adata.obsm (for example 'X_umap').

  • color (str or Sequence[str] or None, default=None) – Feature(s) used for coloring. Accepts obs columns or gene names.

  • gene_symbols (str or None, default=None) – Column in adata.var used for resolving gene symbols.

  • use_raw (bool or None, default=None) – Whether to draw expression values from adata.raw.

  • layer (str or None, default=None) – Layer name for expression-based coloring.

  • groups (str or None, default=None) – Optional subset of categorical groups to display.

  • title (str or Sequence[str] or None, default=None) – Plot title(s).

  • figsize (tuple[float, float], default=(4, 4)) – Single-panel figure size.

  • ax (matplotlib.axes.Axes or None, default=None) – Existing axis for single-panel plotting.

  • cmap (str or Colormap, default='RdBu_r') – Colormap for continuous variables.

  • palette (str or sequence or Cycler or None, default=None) – Palette for categorical variables.

  • na_color (ColorLike, default='lightgray') – Color for missing values.

  • na_in_legend (bool, default=True) – Whether to include missing values in categorical legends.

  • legend_loc (str, default='right margin') – Legend location mode.

  • legend_fontsize (int or float or None, default=None) – Legend font size.

  • legend_fontweight (int or str, default='bold') – Legend font weight.

  • legend_fontoutline (int or None, default=None) – Outline width for legend text.

  • frameon (bool or str or None, default='small') – Frame style.

  • colorbar_loc (str or None, default='right') – Colorbar placement.

  • vmax (Union[Any, Sequence[Any], None] (default: None)) – Color normalization controls for continuous features.

  • vmin (Union[Any, Sequence[Any], None] (default: None)) – Color normalization controls for continuous features.

  • vcenter (Union[Any, Sequence[Any], None] (default: None)) – Color normalization controls for continuous features.

  • norm (Union[Normalize, Sequence[Normalize], None] (default: None)) – Color normalization controls for continuous features.

  • plot_width (int, default=800) – Datashader canvas width in pixels.

  • plot_height (int, default=800) – Datashader canvas height in pixels.

  • spread_px (int, default=0) – Pixel spreading radius to improve sparse visibility.

  • how (str, default='eq_hist') – Datashader shading strategy.

  • show (bool or None, default=None) – Whether to display the figure immediately.

  • save (bool or str or None, default=None) – Save option forwarded to Scanpy-style behavior.

  • return_fig (bool or None, default=None) – Whether to return the figure object for multi-panel output.

  • ncols (int, default=4) – Number of columns in multi-panel mode.

  • wspace (float or None, default=None) – Horizontal spacing between panels.

  • hspace (float, default=0.25) – Vertical spacing between panels.

  • **kwargs – Additional arguments passed to lower-level plotting helpers.

Returns:

Plot object when show=False or return_fig=True; otherwise None.

Return type:

Figure or Axes or None