You can create a plot that uses spheres instead of circle markers by drawing one at each location as described here. Here's an example:
import numpy as np
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
def drawSphere(xCenter, yCenter, zCenter, r):
#draw sphere
u, v = np.mgrid[0:2*np.pi:20j, 0:np.pi:10j]
x=np.cos(u)*np.sin(v)
y=np.sin(u)*np.sin(v)
z=np.cos(v)
# shift and scale sphere
x = r*x + xCenter
y = r*y + yCenter
z = r*z + zCenter
return (x,y,z)
x = 10*np.random.rand(20)
y = 10*np.random.rand(20)
z = 10*np.random.rand(20)
r = np.random.rand(20)
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
# draw a sphere for each data point
for (xi,yi,zi,ri) in zip(x,y,z,r):
(xs,ys,zs) = drawSphere(xi,yi,zi,ri)
ax.plot_wireframe(xs, ys, zs, color="r")
plt.show()
To fix the label positioning problem try adding a second line as described here.
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