ehrapy.plot.paga_compare(adata, basis=None, edges=False, color=None, alpha=None, groups=None, components=None, projection='2d', legend_loc='on data', legend_fontsize=None, legend_fontweight='bold', legend_fontoutline=None, color_map=None, palette=None, frameon=False, size=None, title=None, right_margin=None, left_margin=0.05, show=None, save=None, title_graph=None, groups_graph=None, *, pos=None, **paga_graph_params)[source]#

Scatter and PAGA graph side-by-side.

Consists in a scatter plot and the abstracted graph. See paga() for all related parameters.

  • adata (AnnData) – AnnData object object containing all observations.

  • basis – String that denotes a plotting tool that computed coordinates.

  • edges – Whether to display edges.

  • color – Keys for annotations of observations/patients or features, or a hex color specification, e.g., ‘ann1’, ‘#fe57a1’, or [‘ann1’, ‘ann2’].

  • alpha – Alpha value for the image

  • groups – Key of the grouping used to run PAGA. If None, defaults to adata.uns[‘paga’][‘groups’].

  • components – For example, '1,2,3' means [1, 2, 3], first, second, third principal component.

  • projection (Literal['2d', '3d']) – One of ‘2d’ or ‘3d’

  • legend_loc – Location of the legend.

  • legend_fontsize (Union[int, float, Literal['xx-small', 'x-small', 'small', 'medium', 'large', 'x-large', 'xx-large'], None]) – Font size of the legend.

  • legend_fontweight (Union[int, Literal['light', 'normal', 'medium', 'semibold', 'bold', 'heavy', 'black']]) – Font weight of the legend.

  • legend_fontoutline – Font outline of the legend.

  • color_map – Matplotlib color map.

  • palette – Matplotlib color palette.

  • frameon – Whether to display the labels frameon.

  • size – Size of the plot.

  • title – Title of the plot.

  • right_margin – Margin to the right of the plot.

  • left_margin – Margin to the left of the plot.

  • show – Whether to show the plot.

  • save – Whether or where to save the plot.

  • title_graph – The title of the graph.

  • groups_graph – Graph labels.

  • pos – Position of the plot.

  • **paga_graph_params – Keywords for paga() and keywords for scatter().

Return type:

Axes | None


Matplotlib axes.