SPACEL.Scube.plot.plot_3d

SPACEL.Scube.plot.plot_3d(loc, val=None, color=None, figsize=(8, 8), return_fig=False, elev=None, azim=None, xlim=None, ylim=None, zlim=None, frameon=True, save_path=None, save_dpi=150, show=True, *args, **kwargs)

Plot all slices stacked in 3D

Plot all slices stacked with a given number of subplots rows and columns. Spots/cells colored by spatial domain.

Parameters:

  • loc – An array of the coordinates of each spots/cells in all slices, which the first three columns are X-axis, Y-axis, Z-axis coordinates.

  • val – The colors of each spots/cells given in loc use to plot.

  • color – The colors of each spots/cells given in loc use to plot.

  • figsize – Size of the figure.

  • return_fig – Whether to return the figure.

  • elev – The elevation angle in the vertical plane in degrees. If None then the initial value as specified in the Axes3D constructor is used.

  • azim – The azimuth angle in the horizontal plane in degrees. If None then the initial value as specified in the Axes3D constructor is used.

  • xlim – A tuple given the left and right xlims in X-axis.

  • ylim – A tuple given the left and right xlims in Y-axis.

  • zlim – A tuple given the left and right xlims in Z-axis.

  • frameon – Whether to hide the coordinate axes.

  • save_path – A string representing the path directory where the figure saved.

  • save_dpi – The resolution in dots per inch.

  • show – Whether to show the figure.

Returns:

A matplotlib.figure.Figure object