Visualization

class plot.Plot_Visium(segmentation, boundary_dict, type_list, colors=None)

Bases: object

plot(background=False, cell='both', shape='cell', circle_size=10, boundary=None, save='Visium_plot.png', background_alpha=0.5, spot=True, spot_width=2, spot_color=(0, 0, 255), cell_boundary_color=(100, 100, 100), dpi=300)

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=None, dpi=300, background=(0, 0, 0), ncol=1, word_color=(255, 255, 255), fontsize=6, horizontal_distance=380)

class plot.Plot_Xenium(Xenium_img, cell_boundaries, nucleus_boundaries, type_list, cell_type, nucleus_centers)

Bases: object

plot(background=False, shape='cell', save='Xenium_plot.png', cell_boundaries=False, background_alpha=0.8, circle_size=10, cell_boundary_color=(100, 100, 100), cell_boundary_thickness=2)

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.