How to make a 3D scatter plot

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.

Maddalena

Are you looking for an application to do the plot, or do you want to write code (in whatever language) that draws the plot? – Pyelography

Use asymptote - it is free, powerful, and the quality is awesome! – Kajdan

If you have an array, I'd assume you have a program and this array is part of it. Please give us a chance to help you by indicating what kind of program (language) it is! – Cindelyn

I would still use asymptote (as a lib), or just generate the input file for it. Check out it's amazing output quality! – Kajdan

If it's an n by 3 array, you will get a plot of a curve in 3 dimensions. For a "3-d plot", you would need an n x m x l array. Do you want a curve, with any one tuple (x,y,z) representing a point on the curve? – Maltz

Answer 1

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

import matplotlib.pyplot as plt
import random

fig = plt.figure(figsize=(12, 12))
ax = fig.add_subplot(projection='3d')

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)
plt.show()

The code above generates a figure like:

Angadresma

Nice solution. Note that plt.zlabel('zlabel') wont work. To label the z axis you need to use: ax.set_zlabel('Z'). – Histone

instead of from matplotlib.pyplot it should be import matplotlib.pyplot – Arrival

@Arrival Good spot. The previous editor made that mistake in formatting the post which I've now corrected. – Flosi

This was exactly what I was looking for, thanks! Just to add onto this, I also wanted my 3D scatterplot to rotate (I needed a gif of this), and found this blog post that described how to do it with the solution you listed – Joyance

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.

Stain

Answer 3

from mpl_toolkits import mplot3d
import numpy as np
import matplotlib.pyplot as plt
fig = plt.figure()
ax = plt.axes(projection='3d')

scatter plot

zdata = 15 * np.random.random(100)
xdata = np.sin(zdata) + 0.1 * np.random.randn(100)
ydata = np.cos(zdata) + 0.1 * np.random.randn(100)
ax.scatter3D(xdata, ydata, zdata);

Colab notebook

Accompanyist

Answer 4

Using plotly - Easiest and most functional and nice plots

import plotly.express as px
df = px.data.iris()
fig = px.scatter_3d(df, x='sepal_length', y='sepal_width', z='petal_width',
              color='species')
fig.show()

https://plotly.com/python/3d-scatter-plots/

Urbai

Agreed, if all you want is a 3D plot, plotly is the simplest and cleanest solution. – Joyance