stlearn.pl.trajectory.pseudotime_plot

stlearn.pl.trajectory.pseudotime_plot(adata: AnnData, library_id: str | None = None, use_label: str = 'leiden', pseudotime_key: str = 'dpt_pseudotime', list_clusters: str | list[str] | None = None, cell_alpha: float = 1.0, image_alpha: float = 1.0, edge_alpha: float = 0.8, node_alpha: float = 1.0, spot_size: float | int = 6.5, node_size: float = 5, show_color_bar: bool = True, show_axis: bool = False, show_graph: bool = True, show_trajectories: 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 = None, name: str | None = None, ax=None) → AnnData | None[source]

Global trajectory inference plot (Only DPT).

Parameters:

  • adata – Annotated data matrix.

  • library_id – Library id stored in AnnData.

  • use_label – Use label result of cluster method.

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

  • cell_alpha – Opacity of the spot.

  • image_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 – The output folder of the plot.

  • name – The filename of the plot.

Return type:

Nothing