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 : Sequence[str] | str | NoneUnion[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 : str | Cycler | Sequence[str] | Sequence[Cycler] | NoneUnion[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 : Axes | Sequence[Axes] | NoneUnion[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 | NoneOptional[bool] (default: False): If True, show the firgure. If false, return a list of Axes objects
wspace : float | NoneOptional[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]Optional[Sequence[Axes]]

Returns

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