Visualization

class plot.Plot_Visium(segmentation, boundary_dict: Dict, type_list: List[str], colors: ndarray | None = None)[source]

Bases: object

plot(background: bool = False, cell: str = 'both', shape: str = 'cell', circle_size: int = 10, boundary: str | None = None, save: str | None = 'Visium_plot.png', background_alpha: float = 0.5, spot: bool = True, spot_width: int = 2, spot_color: Tuple[int, int, int] = (0, 0, 255), cell_boundary_color: Tuple[int, int, int] = (100, 100, 100), dpi: int = 300) → None[source]
Parameters:

  • background – If show the background.

  • cell – Which group of cell shapes to plot? [both, in, out]

  • shape – Which shape to plot? [cell, nucleus, circle]

  • circle_size – Size of the nuclei.

  • boundary – Which group of cell boundary to plot? [both, in, out]

  • save – If not none, save the figure to the path.

  • background_alpha – Opacity of the background figure.

  • spot – If plot the spot.

  • spot_width – Width of the spot.

  • spot_color – Color of the spot.

  • cell_boundary_color – Color of the cell boundaries.

  • dpi – DPI of the image plotted.

plot_legend(save: str | None = None, dpi: int = 300, background: Tuple[int, int, int] = (0, 0, 0), ncol: int = 1, word_color: Tuple[int, int, int] = (255, 255, 255), fontsize: int = 6, horizontal_distance: int = 380, show: bool = False) → None[source]
class plot.Plot_Xenium(Xenium_img: ndarray, cell_boundaries: DataFrame, nucleus_boundaries: DataFrame, type_list: List[str], cell_type: List[str], nucleus_centers: ndarray)[source]

Bases: object

plot(background: bool = False, shape: str = 'cell', save: str | None = 'Xenium_plot.png', cell_boundaries: bool = False, background_alpha: float = 0.8, circle_size: int = 10, cell_boundary_color: Tuple[int, int, int] = (100, 100, 100), cell_boundary_thickness: int = 2) → None[source]
Parameters:

  • background – If show the background.

  • shape – Which shape to plot? [cell, nucleus, circle]

  • save – If not none, save the figure to the path.

  • cell_boundaries – If plot the cell boundaries.

  • background_alpha – Opacity of the background figure.

  • circle_size – Size of the circle.

  • cell_boundary_color – Color of the cell boundaries.

  • cell_boundary_thickness – Thickness of the cell boundaries.