ehrapy.plot.paga_compare

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ehrapy.plot.paga_compare#

ehrapy.plot.paga_compare(edata, 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.

Parameters:

  • edata (EHRData) – Central data object.

  • basis (default: None) – String that denotes a plotting tool that computed coordinates.

  • edges (default: False) – Whether to display edges.

  • color (default: None) – Keys for annotations of observations/patients or features, or a hex color specification, e.g., ‘ann1’, ‘#fe57a1’, or [‘ann1’, ‘ann2’].

  • alpha (default: None) – Alpha value for the image

  • groups (default: None) – Key of the grouping used to run PAGA. If None, defaults to edata.uns[‘paga’][‘groups’].

  • components (default: None) – For example, '1,2,3' means [1, 2, 3], first, second, third principal component.

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

  • legend_loc (default: 'on data') – Location of the legend.

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

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

  • legend_fontoutline (default: None) – Font outline of the legend.

  • color_map (default: None) – Matplotlib color map.

  • palette (default: None) – Matplotlib color palette.

  • frameon (default: False) – Whether to display the labels frameon.

  • size (default: None) – Size of the plot.

  • title (default: None) – Title of the plot.

  • right_margin (default: None) – Margin to the right of the plot.

  • left_margin (default: 0.05) – Margin to the left of the plot.

  • show (default: None) – Whether to show the plot.

  • save (default: None) – Whether or where to save the plot.

  • title_graph (default: None) – The title of the graph.

  • groups_graph (default: None) – Graph labels.

  • pos (default: None) – Position of the plot.

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

Return type:

Sequence[Axes] | list[Axes] | None

Returns:

Matplotlib axes.

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