I have some code to plot 3D surfaces in Python using matplotlib:

import math import numpy as np
import matplotlib.pyplot as plt
from pylab import meshgrid,cm,imshow,contour,clabel,colorbar,axis
from mpl_toolkits.mplot3d import Axes3D
from matplotlib.ticker import LinearLocator, FormatStrFormatter
import seaborn as sns
sns.set(style="white")def surface_map(func, xmin=0, xmax=1, ymin=0, ymax=1, step_size=0.05, maxz=25000):X, Y = meshgrid(np.arange(xmin, xmax, step_size),np.arange(ymin, ymax, step_size))Z = np.zeros(X.shape)for i in range(X.shape[0]):for j in range(X.shape[1]):Z[i, j] = min(func(X[i, j], Y[i, j]), maxz)return X, Y, Zdef plot_surface(X, Y, Z, xlabel, ylabel, zlabel, title, point=None, size=25):fig = plt.figure()ax = fig.gca(projection='3d')surf = ax.plot_surface(X, Y, Z, rstride=1, cstride=1, vmin=0, vmax=20*1000,cmap=cm.RdBu, linewidth=0, antialiased=True)ax.zaxis.set_major_locator(LinearLocator(10))ax.zaxis.set_major_formatter(FormatStrFormatter('%.02f'))ax.set_xlabel(xlabel)ax.set_ylabel(ylabel)ax.set_zlabel(zlabel)ax.set_title(title)fig.colorbar(surf, shrink=0.5, aspect=5)if point:ax.hold(True)func, fpr, recall = pointax.scatter([fpr], [recall], [func(fpr, recall)], s=size, c='b', marker='.', zorder=10)plt.show()

And then I call it like so:

# create mesh 
R, FPR, FuncValue = surface_map(my_function, xmin=0, xmax=1, ymin=0, ymax=1, step_size=0.05, maxz=20*1000)# plot it
plot_surface(R, FPR, FuncValue, xlabel="Recall", ylabel="FPR", zlabel="Function Value", title="Recall Settings Payout Function",point=(my_function, 0.5, 0.5))

I'm setting ax.scatter to use large marker sizes and a high zorder, but no point gets drawn on the surface when the plot gets rendered.

What am I missing?

The point you are looking for is there, but hidden "inside" the surface. This is a common problem in matplotlib.

I see two options here:

1. Make the surface plot semitransparent, i.e. use alpha=.8 or similar.
2. Use plot instead of scatter.