stlearn.pl.trajectory.pseudotime_plot

stlearn.pl.trajectory.pseudotime_plot(adata: anndata._core.anndata.AnnData, library_id: str = None, use_label: str = 'louvain', use_pseudotime: str = 'dpt_pseudotime', list_cluster: Union[str, list] = None, data_alpha: float = 1.0, tissue_alpha: float = 1.0, edge_alpha: float = 0.8, node_alpha: float = 1.0, spot_size: Union[float, int] = 6.5, node_size: float = 5, show_color_bar: bool = True, show_axis: bool = False, show_graph: bool = True, show_trajectory: bool = False, reverse: bool = False, show_node: bool = True, show_plot: bool = True, cropped: bool = True, margin: int = 100, dpi: int = 150, output: str = None, name: str = None, copy: bool = False) → Optional[anndata._core.anndata.AnnData]

Global trajectory inference plot (Only DPT).

Parameters

• adata – Annotated data matrix.

• library_id – Library id stored in AnnData.

• use_label – Use label result of clustering method.

• list_cluster – Choose set of clusters that will display in the plot.

• data_alpha – Opacity of the spot.

• tissue_alpha – Opacity of the tissue.

• edge_alpha – Opacity of edge in PAGA graph in the tissue.

• node_alpha – Opacity of node in PAGA graph in the tissue.

• cmap – Color map to use.

• spot_size – Size of the spot.

• node_size – Size of node in PAGA graph in the tissue.

• show_color_bar – Show color bar or not.

• show_axis – Show axis or not.

• show_graph – Show PAGA graph or not.

• show_legend – Show legend or not.

• show_plot – Show plot or not

• dpi – DPI of the output figure.

• output – Save the figure as file or not.

• copy – Return a copy instead of writing to adata.

Returns

Return type

Nothing