spcoral.plot.show_cross_align

spcoral.plot.show_cross_align(adata_omics1, adata_omics2, omics1_use_obsm, omics2_use_obsm, omics1_name='omics1', omics2_name='omics2', size_omics1=None, size_omics2=None, alpha_omics1=None, alpha_omics2=None, palette=None, figsize=None, dpi=None, title=None, ax=None, show=True, save=None, **kwargs)

Plot spatial alignment of two omics datasets.

Return type:

Optional[Axes]

Parameters:

• adata_omics1 (AnnData) –

• adata_omics2 (AnnData) –

• omics1_use_obsm (str) –

• omics2_use_obsm (str) –

• omics1_name (str) –

• omics2_name (str) –

• size_omics1 (float | None) –

• size_omics2 (float | None) –

• alpha_omics1 (float | None) –

• alpha_omics2 (float | None) –

• palette (str | List[str] | None) –

• figsize (Tuple[float, float] | None) –

• dpi (float | None) –

• title (str | None) –

• ax (Axes | None) –

• show (bool) –

• save (str | PathLike | None) –

• kwargs (Dict[str, Any]) –

Parameters:

adata_omics1anndata.AnnData

AnnData object for the first omics dataset.

adata_omics2anndata.AnnData

AnnData object for the second omics dataset.

omics1_use_obsmstr

Key in adata_omics1.obsm containing the spatial coordinates.

omics2_use_obsmstr

Key in adata_omics2.obsm containing the spatial coordinates.

omics1_namestr, default ‘omics1’

Name for the first omics dataset.

omics2_namestr, default ‘omics2’

Name for the second omics dataset.

sizeOptional[float], default None

Size of the points in the scatter plot.

paletteOptional[Union[str, List[str]]], default None

Color palette for categorical variables (Matplotlib/Seaborn palette name or list of colors).

figsizeOptional[Tuple[float, float]], default None

Figure size as (width, height).

dpiOptional[float], default None

Figure resolution in dots per inch.

titleOptional[str], default None

Title of the plot. Defaults to ‘spatial alignment’ if None.

axOptional[matplotlib.axes.Axes], default None

Matplotlib Axes object to plot on.

showbool, default True

Whether to display the plot.

saveOptional[Union[str, os.PathLike]], default None

Path to save the plot.

**kwargsDict[str, Any]

Additional arguments passed to scanpy.pl.embedding.

Returns:

: Optional[matplotlib.axes.Axes]

The Matplotlib Axes object if show=False, else None.