pythonmatplotlibscatter-plotsurfacematplotlib-3d

Combining scatter plot with surface plot


How can I combine a 3D scatter plot with a 3D surface plot while keeping the surface plot transparent so that I can still see all the points?


Solution

  • The following code plots a 3D scatter plot with a 3D surface plot:

    import matplotlib.pyplot as plt
    import numpy as np
    from random import random, seed
    from matplotlib import cm
    import matplotlib as mpl
    
    fig = plt.figure(figsize=(10, 10))
    ax = fig.add_subplot(projection='3d')              # to work in 3d
    
    x_surf=np.arange(0, 1, 0.01)                # generate a mesh
    y_surf=np.arange(0, 1, 0.01)
    x_surf, y_surf = np.meshgrid(x_surf, y_surf)
    z_surf = np.sqrt(x_surf+y_surf)             # ex. function, which depends on x and y
    ax.plot_surface(x_surf, y_surf, z_surf, cmap=cm.hot, ec='k')  # plot a 3d surface plot
    
    n = 100
    seed(0)                                     # seed let us to have a reproducible set of random numbers
    x=[random() for i in range(n)]              # generate n random points
    y=[random() for i in range(n)]
    z=[random() for i in range(n)]
    ax.scatter(x, y, z);                        # plot a 3d scatter plot
    
    ax.set_xlabel('x label')
    ax.set_ylabel('y label')
    ax.set_zlabel('z label')
    
    plt.show()
    

    enter image description here

    You can see some other examples with 3d plots here.

    I've changed the colors of the surface plot from the default to a colormap hot, in order to distinguish the colors of the two plots - now, it's seen that the surface plot overrides the scatter plot, independently of the order.

    To fix that issue, it should be used transparency in the colormap of the surface plot; adding the code from Transparent colormap

    and changing the line:

    ax.plot_surface(x_surf, y_surf, z_surf, cmap=cm.hot)  # plot a 3d surface plot
    

    to

    theCM = mpl.colormaps.get_cmap('bwr')
    theCM._init()
    alphas = np.abs(np.linspace(-1.0, 1.0, theCM.N))
    theCM._lut[:-3,-1] = alphas
    
    # other code
    
    ax.plot_surface(x_surf, y_surf, z_surf, cmap=theCM)
    

    enter image description here