How to make a 3D scatter plot in Python?

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:

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.

Use asymptote instead!

This is what it can look like:

https://asymptote.sourceforge.io/gallery/3Dgraphs/helix.html

This is the code: https://asymptote.sourceforge.io/gallery/3Dgraphs/helix.asy

Asymptote can also read in data files.

And the full gallery: https://asymptote.sourceforge.io/gallery/index.html

To use asymptote from within Python:

https://ctan.org/tex-archive/graphics/asymptote/base/asymptote.py