SOAPy_st.pl.show_ccc_embedding
- SOAPy_st.pl.show_ccc_embedding(adata: AnnData, ligand: str | list, receptor: str | list, ligand_clusters: list | str | int, receptor_clusters: list | str | int, cluster_key: str = 'cell_type', ligand_region: Tuple[Any, Any] | None = None, receptor_region: Tuple[Any, Any] | None = None, ligand_color: Colormap | str | None = None, receptor_color: Colormap | str | None = None, row_region: Tuple[Any, Any] | None = None, col_region: Tuple[Any, Any] | None = None, agg_method: Literal['mean', 'min', 'gmean'] = 'gmean', title: str | None = None, figsize: Tuple[Any, Any] | None = None, dpi: int = 100, ax: Axes | None = None, size: float | None = None, obsm_spatial_label: str = 'spatial', show: bool = True, save: str | None = None, cbar_kwargs: dict | None = {}, **kwargs) Axes | None
To map the distribution of ligands and receptors expression of different cell type in a situ map of tissue.
Parameters
- adataanndata.AnnData
An AnnData object containing spatial omics data and spatial information.
- figsizeTuple[float, float], optional
(Width, height) of the figure.
- dpifloat, optional
The resolution of the figure.
- titlestr, optional
The title of shown figure.
- axAxes
A matplotlib axes object.
- showbool
Show the plot, do not return axis.
- saveUnion[str, PathLike], optional
The path where the image is stored.
- ligandUnion[str, list]
Ligand name or a list containing ligand subunits
- receptorUnion[str, list]
Receptor name or a list containing receptor subunits
- ligand_clustersUnion[list, str, int]
The cell type clusters of the ligand shown, cannot be duplicated with the clusters of the receptor, otherwise overlap would occur.
- receptor_clustersUnion[list, str, int]
The cell type clusters of the receptor shown, cannot be duplicated with the clusters of the ligand, otherwise overlap would occur.
- cluster_keystr
The label of cluster in adata.obs.
- ligand_regionTuple[Any, Any]
The range of values of the ligand. (ligand_min, ligand_max)
- receptor_regionTuple[Any, Any]
The range of values of the receptor. (receptor_min, receptor_max)
- ligand_colorUnion[Colormap, str]
The color of the ligand.
- receptor_colorUnion[Colormap, str]
The color of the receptor.
- row_regionTuple[Any, Any]
The row coordinate threshold of the region in the situ map is displayed, and the expression of the whole situ map is displayed by default. (row_low, row_high)
- col_regionTuple[Any, Any]
The row coordinate threshold of the region in the situ map is displayed, and the expression of the whole situ map is displayed by default. (row_low, row_high)
- agg_methodstr
Integrated subunit to calculate ligand or receptor. ‘min’: ligand or receptor = min(sub1, sub2, sub3, …) ‘mean’: ligand or receptor = mean(sub1, sub2, sub3, …) ‘gmean’: geometrical mean, ligand or receptor = np.gmean(sub1, sub2, sub3, …)
- sizeOptional[float]
Size of the points in figure.
- obsm_spatial_labelstr
The key of spatial coordinates in adata.obsm.
- cbar_kwargsOptional[dict]
Other parameters in plt.colorbar().
- kwargsAny, optional
Other params of ax.scatter()
Returns
If show==False, return Axes