SOAPy_st.pl.show_ccc_dotplot

SOAPy_st.pl.show_ccc_dotplot(adata: AnnData, sample: str | list | None = None, lr_type: Literal['contact', 'secretory'] = 'contact', affinity_cutoff: float = 0.05, strength_cutoff: float = 2.0, lrs_name: list | None = None, cts_name: list | None = None, n_top_lrs: int | None = 10, n_top_cts: int | None = 15, figsize: Tuple[Any, Any] = (7, 5), cmap: Colormap | str = 'Spectral_r', strength_min: float | None = None, strength_max: float | None = None, size: int = 10, sig_color: str = '#000000', ax: Axes | None = None, show: bool = False, save: str | None = None, **kwargs) → Axes | None

Dotplot for cell communication analysis are presented, either specifying the cell type pairs and ligand-receptor pairs to be presented or showing the most significant cell type pairs and ligand-receptor pairs after ranking by significance level.

Parameters

adataanndata.Anndata

An AnnData object containing spatial omics data and spatial information.

sampleUnion[str, list]

Name of sample.

lr_typeLiteral[‘contact’, ‘secretory’]

Types of ligand-receptor pairs.

affinity_cutofffloat

The threshold at which affinity was significant, and affinity below this threshold were considered significant.

strength_cutofffloat

The threshold at which strength was significant, and strength above this threshold were considered significant.

lrs_nameOptional[list]

Ligand-receptor pairs that need to be show. e.g. [‘Endothelial cell,Macrophage’, ‘Macrophage,Endothelial cell’]

cts_nameOptional[list]

cell type pairs that need to be show. e.g. [‘FGF2:FGFR1’, ‘WNT3A:FZD7&LRP5’]

n_top_lrsint

Maximum number of ligand-receptor pairs presented, ordered according to the number of cell type pairs for which a ligand-receptor pair was significant.

n_top_ctsint

The maximum number of cell type pairs shown, ordered according to the number of significant ligand-receptor pairs for a cell type pair.

figsizeTuple[Any, Any]

The size of format figure.(width, height)

cmapUnion[Colormap, str]

Color map of dotplot.

strength_min, strength_maxOptional[float]

The extreme value of the strength that is displayed, the value that is not in the range will be displayed in the

same color as the corresponding extreme value.

sizeint

Size of the points in figure.

sig_colorstr

Points that were considered significant were highlighted by the color.

axmatplotlib.figure.Axes

A matplotlib.axes object.

showstr

Show this plot.

saveOptional[str]

The path where the image is stored.

kwargs: Any, optional

Other params of ax.scatter()

Returns

If show==False, return Axes