omicverse.utils.plot_paga

omicverse.utils.plot_paga(adata, basis=None, vkey='velocity', color=None, layer=None, title=None, threshold=None, layout=None, layout_kwds=None, init_pos=None, root=0, labels=None, single_component=False, dashed_edges='connectivities', solid_edges='transitions_confidence', transitions='transitions_confidence', node_size_scale=1, node_size_power=0.5, edge_width_scale=0.4, min_edge_width=None, max_edge_width=2, arrowsize=15, random_state=0, pos=None, node_colors=None, normalize_to_color=False, cmap=None, cax=None, cb_kwds=None, add_pos=True, export_to_gexf=False, plot=True, use_raw=None, size=None, groups=None, components=None, figsize=None, dpi=None, show=None, save=None, ax=None, ncols=None, scatter_flag=None, **kwargs)[source]

Plot PAGA graph and optional embedding-level annotations.

Parameters:

  • adata (AnnData) – AnnData with PAGA graph stored in adata.uns['paga'].

  • basis (str or None, optional) – Embedding basis used for overlay (for example 'umap'). Set None to draw graph layout only.

  • vkey (str, optional) – Velocity key used by scVelo when velocity-aware plotting is enabled.

  • color (str or sequence of str, optional) – Cell-level annotation(s) used for coloring.

  • layer (str or None, optional) – Layer used for expression coloring.

  • title (str or None, optional) – Plot title.

  • threshold (float or None, optional) – Minimum edge threshold.

  • layout (str or None, optional) – Graph layout algorithm name.

  • layout_kwds (dict or None, optional) – Additional layout options.

  • init_pos (str or None, optional) – Initialization for graph layout.

  • root (int or None, optional) – Root index used by tree-like layouts.

  • labels (str or None, optional) – Node labels to display.

  • single_component (bool, optional) – Keep only the largest connected component.

  • dashed_edges (str or None, optional) – Key for dashed edges.

  • solid_edges (str or None, optional) – Key for solid edges.

  • transitions (str or None, optional) – Transition-confidence edge key.

  • node_size_scale (float, optional) – Scale factor for node sizes.

  • node_size_power (float, optional) – Exponent for node-size scaling.

  • edge_width_scale (float, optional) – Scale factor for edge widths.

  • min_edge_width (float or None, optional) – Lower bound for edge widths.

  • max_edge_width (float, optional) – Upper bound for edge widths.

  • arrowsize (float, optional) – Arrow size for directed edges.

  • random_state (int, optional) – Random seed used by layout routines.

  • pos (dict or None, optional) – Precomputed node positions.

  • node_colors (dict or sequence, optional) – Custom node colors.

  • normalize_to_color (bool, optional) – Whether to normalize values before color mapping.

  • cmap (str or matplotlib colormap, optional) – Colormap.

  • cax (matplotlib.axes.Axes or None, optional) – Colorbar axis.

  • cb_kwds (dict or None, optional) – Colorbar keyword arguments.

  • add_pos (bool, optional) – Whether to save computed positions back to adata.uns.

  • export_to_gexf (bool, optional) – Whether to export graph to GEXF.

  • plot (bool, optional) – If False, only compute/return graph data.

  • use_raw (bool or None, optional) – Whether to use adata.raw.

  • size (float or None, optional) – Point size for scatter overlay.

  • groups (str or sequence or None, optional) – Category subset.

  • components (str or sequence or None, optional) – Embedding components to plot.

  • figsize (tuple or None, optional) – Figure size.

  • dpi (int or None, optional) – Figure dpi.

  • show (bool or None, optional) – Whether to immediately show the figure.

  • save (str or bool or None, optional) – Save path or Scanpy-style save flag.

  • ax (matplotlib.axes.Axes or None, optional) – Existing axis.

  • ncols (int or None, optional) – Number of columns when plotting multiple panels.

  • scatter_flag (bool or None, optional) – Whether to add embedding scatter underlay.

  • **kwargs – Additional arguments forwarded to scvelo.pl.paga.

Returns:

Return value from scvelo.pl.paga.

Return type:

Any

Examples

>>> ov.utils.plot_paga(adata, basis='umap', color='celltype', threshold=0.05)