SOAPy_st.pl.show_celltype_niche_heatmap
- SOAPy_st.pl.show_celltype_niche_heatmap(adata: AnnData, norm_method: Literal['normalization', 'z_score', 'proportion'] = 'normalization', niche_bar: bool = True, niche_bar_kwargs: Mapping[str, Any] = mappingproxy({}), title: str | None = None, figsize: Tuple[float, float] | None = None, dpi: int = 100, cmap: LinearSegmentedColormap | None = None, show: bool = True, save: str | PathLike | None = None, **kwargs) Tuple[Figure, list[Axes]] | None
The heatmap shows the cell composition of each niche, and the bar plot graph shows the number of each niche in all samples.
Parameters
- adataanndata.AnnData
An AnnData object containing spatial omics data and spatial information.
- niche_barbool
Whether to show a bar plot of the cell number of each niche.
- niche_bar_kwargsAny
Other parameters in sns.countplot() of cell type’s bar plot.
- norm_methodLiteral[‘normalization’, ‘z_score’, ‘proportion’]
Methods of standardization ‘normalization’: x^ = (x - min(x)) / (max(x) - min(x)) ‘z_score’: x^ = (x - mean(x)) / std(x) ‘proportion’: x^ = x / sum(x)
- figsizeTuple[float, float], optional
(Width, height) of the figure.
- dpifloat, optional
The resolution of the figure.
- titlestr, optional
The title of shown figure.
- showbool
Show the plot, do not return axis.
- saveUnion[str, PathLike], optional
The path where the image is stored.
- cmap
Color map to use for continous variables.
- kwargsAny
Other params of sns.heatmap()
Returns
If show==False, return Tuple[Figure, list[Axes]]