scirpy.pl.embedding

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scirpy.pl.embedding#

scirpy.pl.embedding(adata, basis, *, color=None, panel_size=(4, 4), palette=None, legend_loc='right margin', ax=None, ncols=3, show=False, hspace=0.25, wspace=None, **kwargs)#

A customized wrapper to the scanpy.pl.embedding() function.

The differences to the scanpy embedding function are:

  • allows to specify a panel_size

  • Allows to specify a different basis, legend_loc and palette for each panel. The number of panels is defined by the color parameter.

  • Use a patched version for adding “on data” labels. The original raises a flood of warnings when coords are nan.

  • For columns with many categories, cycles through colors instead of reverting to grey

  • allows to specify axes, even if multiple colors are set.

Parameters:

  • adata (AnnData) – annotated data matrix

  • basis (str) – embedding to plot. Get the coordinates from the “X_{basis}” key in adata.obsm. This can be a list of the same length as color to specify different bases for each panel.

  • color (Union[Sequence[str], str, None] (default: None)) – Keys for annotations of observations/cells or variables/genes, e.g., 'ann1' or ['ann1', 'ann2'].

  • panel_size (tuple[float, float] (default: (4, 4))) – Size tuple (width, height) of a single panel in inches

  • palette (Union[str, Cycler, Sequence[str], Sequence[Cycler], None] (default: None)) – Colors to use for plotting categorical annotation groups. The palette can be a valid ListedColormap name ('Set2', 'tab20', …) or a Cycler object. It is possible to specify a list of the same size as color to choose a different color map for each panel.

  • legend_loc (str (default: 'right margin')) – Location of legend, either 'on data', 'right margin' or a valid keyword for the loc parameter of Legend.

  • ax (Union[Axes, Sequence[Axes], None] (default: None)) – A matplotlib axes object or a list with the same length as color thereof.

  • ncols (int (default: 3)) – Number of columns for multi-panel plots

  • show (bool | None (default: False)) – If True, show the firgure. If false, return a list of Axes objects

  • wspace (Optional[float] (default: None)) – Adjust the width of the space between multiple panels.

  • hspace (float (default: 0.25)) – Adjust the height of the space between multiple panels.

  • **kwargs – Arguments to pass to scanpy.pl.embedding().

Return type:

None | Sequence[Axes]

Returns:

axes A list of axes objects, containing one element for each color, or None if show == True.

See also

scanpy.pl.embedding()

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