Combining scatter plot with surface plot

Question

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?

Answer 1

To combine various types of plots in the same graph you should use the function

plt.hold(True).

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

from mpl_toolkits.mplot3d import *
import matplotlib.pyplot as plt
import numpy as np
from random import random, seed
from matplotlib import cm


fig = plt.figure()
ax = fig.gca(projection='3d')               # to work in 3d
plt.hold(True)

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);    # 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()

result:

http://s9.postimage.org/ge0wb8kof/3d_scatter_surface_plt.gif

you can see some other examples with 3d plots here:
http://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html

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

EDIT: To fix that issue, it should be used transparency in the colormap of the surface plot; adding the code in: Transparent colormap and changing the line:

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

to

ax.plot_surface(x_surf, y_surf, z_surf, cmap=theCM);

we get:

http://s16.postimage.org/5qiqn0p5h/3d_scatter_surface_plt_transparent.gif

Answer 2

Using siluaty's example; instead of using transparency through the cmap=theCM command, you can adjust the alpha value. This may get you what you want?

ax.plot_surface(x_surf, y_surf, z_surf, cmap=cm.hot, alpha=0.2)