SOAPy_st.pl.show_ccc_chordplot
- SOAPy_st.pl.show_ccc_chordplot(adata: AnnData, sample: str | list | None = None, lr_type: Literal['contact', 'secretory'] = 'contact', min_ints: int = 2, n_top_ccis: int = 10, cmap: str | None = None, label_size: int = 10, label_rotation: float = 0, ax: Axes | None = None, figsize: tuple = (8, 8), dpi: int = 100, show: bool = True, save: str | None = None) Axes | None
Visualize ligand-receptor interactions between two cell types in spatial omics data using chord plot.
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.
- sampleUnion[str, list]
Name of sample.
- lr_typeLiteral[‘contact’, ‘secretory’]
Types of ligand-receptor pairs.
- min_intsint
Minimum number of interactions for a connection to be considered.
- n_top_ccisint
Maximum number of top ligand-receptor pairs to display.
- cmapstr
Colormap for visualizing cell types.
- label_sizeint
Font size for node labels.
- label_rotationfloat
Rotation angle for node labels.
Returns
- axmatplotlib.axes.Axes
The axes object containing the chord plot.
References
- Pham, D. et al. Robust mapping of spatiotemporal trajectories and cell–cell interactions in healthy and diseased
tissues. Nat Commun 14, 7739 (2023).