How to make a 3D scatter plot in Python?

Question

I am currently have a nx3 matrix array. I want plot the three columns as three axis's. How can I do that?

I have googled and people suggested using Matlab, but I am really having a hard time with understanding it. I also need it be a scatter plot.

Can someone teach me?

Answer 1

You can use matplotlib for this. matplotlib has a mplot3d module that will do exactly what you want.

from matplotlib import pyplot
from mpl_toolkits.mplot3d import Axes3D
import random


fig = pyplot.figure()
ax = Axes3D(fig)

sequence_containing_x_vals = list(range(0, 100))
sequence_containing_y_vals = list(range(0, 100))
sequence_containing_z_vals = list(range(0, 100))

random.shuffle(sequence_containing_x_vals)
random.shuffle(sequence_containing_y_vals)
random.shuffle(sequence_containing_z_vals)

ax.scatter(sequence_containing_x_vals, sequence_containing_y_vals, sequence_containing_z_vals)
pyplot.show()

The code above generates a figure like:

Answer 2

Use the following code it worked for me:

# Create the figure
   fig = plt.figure()
   ax = fig.add_subplot(111, projection='3d')

   # Generate the values
   x_vals = X_iso[:, 0:1]
   y_vals = X_iso[:, 1:2]
   z_vals = X_iso[:, 2:3]

   # Plot the values
   ax.scatter(x_vals, y_vals, z_vals, c = 'b', marker='o')
   ax.set_xlabel('X-axis')
   ax.set_ylabel('Y-axis')
   ax.set_zlabel('Z-axis')

   plt.show()

while X_iso is my 3-D array and for X_vals, Y_vals, Z_vals I copied/used 1 column/axis from that array and assigned to those variables/arrays respectively.

Answer 3

Use asymptote instead!

This is what it can look like:

http://asymptote.sourceforge.net/gallery/3D%20graphs/helix.pdf

This is the code: http://asymptote.sourceforge.net/gallery/3D%20graphs/helix.asy

Asymptote can also read in data files.

And the full gallery: http://asymptote.sourceforge.net/gallery/

To use asymptote from within Python:

http://www.tex.ac.uk/tex-archive/graphics/asymptote/base/asymptote.py