plotting 3d scatter in matplotlib

Question

I have a collection of Nx3 matrices in scipy/numpy and I\'d like to make a 3 dimensional scatter of it, where the X and Y axes are determined by the values of first and second c

Answer 1

Try replacing 'ax.scatter' with ax.plot', possibly with the 'o' parameter to get similar circles. This fixes the transparency and the legend.

import matplotlib as mpl
from mpl_toolkits.mplot3d import Axes3D
import numpy as np
import matplotlib.pyplot as plt
from numpy.random import random

mpl.rcParams['legend.fontsize'] = 10

fig = plt.figure(1)
fig.clf()
ax = Axes3D(fig)
datasets = random((8,100,3))*512
my_labels = ['a', 'b', 'c', 'd', 'e', 'f', 'g', 'h']

colors = ['k', "#B3C95A", 'b', '#63B8FF', 'g', "#FF3300",
          'r', 'k']
index = 0
for data, curr_color in zip(datasets, colors):
    ax.plot(np.log2(data[:, 0]), np.log2(data[:, 1]), 
                   np.log2(data[:, 2]), 'o', c=curr_color, label=my_labels[index])
    index += 1

ax.set_zlim3d([-1, 9])
ax.set_ylim3d([-1, 9])
ax.set_xlim3d([-1, 9])

ax.set_xticks(range(0,11))
ax.set_yticks([1,2,8])
ax.set_zticks(np.arange(0,9,.5))

ax.legend(loc = 'upper left')
    
plt.draw()

plt.show()

I added a few lines and tweaks to get some sample data and get the rest of your demo working. I assume you'll be able to get it to work.

Setting the ticks requires the August 2010 update to mplot3d as described here. I got the latest mplot3d from Sourceforge. I'm not quite sure if Matplotlib 1.0.1 contains this latest update as I'm still running Python 2.6 with Matplotlib 1.0.0.

Edit

A quick and dirty dummy plot for the legends while keeping the 3d transparency effect you get from scatter:

index = 0
for data, curr_color in zip(datasets, colors):
    ax.scatter(np.log2(data[:, 0]), np.log2(data[:, 1]), 
                   np.log2(data[:, 2]), 'o', c=curr_color, label=my_labels[index])
    ax.plot([], [], 'o', c = curr_color, label=my_labels[index])                    
    index += 1