stereo.plots.PlotVec3D.plot_vec_3d#

PlotVec3D.plot_vec_3d(x_raw, y_raw, z_raw, ptime, num_cell=20, fil_type='gauss', sigma_val=1, radius_val=3)[source]#

Plot vector field of cell trajectories embodied in 3D space.

Parameters:

  • x_raw – Array of x coordinates, taken from the first column in adata spatial axis array

  • y_raw – Array of y coordinates, taken from the second column in adata spatial axis array

  • z_raw – Array of z coordinates, taken from the third column in adata spatial axis array, or other equivalent methods

  • ptime – Array of pseudo-time, suggested being calculated by StereoPy dpt process

  • num_cell – Number of cells along the shortest coordinates among x, y and z. Number of cells among other coordinates will be calculated proportionally to their respective axis length

  • fil_type – Filter type when smoothing the ptime voxelized result. Allowed values are: ‘gaussian’: using Gaussian filter ‘mean’: using Mean filter

  • sigma_val –

    Sigma of filter when smoothing the voxelized ptime result using Gaussian filter, by passing ‘gaussian’ to fil_type. Use this website to help understand kernel results when assigning different

    sigma values: http://demofox.org/gauss.html. Value neglected when passing ‘mean’ to fil_type

  • radius_val – Size of ‘extended radius’ of kernel, when smoothing the voxelized ptime result using Mean filter, by passing ‘mean’ to fil_type. The diameter of kernel d equals to (2 * radius_val + 1) Value neglected when passing ‘gaussian’ to fil_type

Returns: