How can I control the color and opacity of each point in a python scatter plot?

Question

I'm looking to graph a 4D data set (X, Y, Z, intensity) using opacity to represent intensity. I also want the color to be dependent on the Z variable as well to better show depth.

Here is the relevant code so far, I am a novice when it comes to Python:

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x_list #list of x values as floats
y_list #list of y values as floats
z_list #list of z values as floats
i_list #list of intensity values as floats

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import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')

Axes3D.scatter(ax, x_list, y_list, z_list)
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So how can I do this?

I'm thinking the color could be a linear relationship between z_list and a color map (hsv for example), and opacity could be linear as well, i_list/max(i_list) or something along those lines.

Answer 1

I would do something like the following:

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

# choose your colormap
cmap = plt.cm.jet

# get a Nx4 array of RGBA corresponding to zs
# cmap expects values between 0 and 1
z_list = np.array(z_list) # if z_list is type `list`
colors = cmap(z_list / z_list.max())

# set the alpha values according to i_list
# must satisfy 0 <= i <= 1
i_list = np.array(i_list)
colors[:,-1] = i_list / i_list.max()

# then plot
fig = plt.figure()
ax = fig.add_subplot(111, projection='3d')
ax.scatter(x_list, y_list, z_list, c=colors)
plt.show()

Here's an example with x_list = y_list = z_list = i_list . You can choose any of the colormaps here or make your own :