How to make scatterplot with nested array of arrays

Question

I am trying to make a scatter plot with the list of coordinates I have. I'm just confused how to separate these coordinates into x and y so that I can plug it into the plt.scatter() function, especially considering it is a nested array of arrays.

   array([array([1., 0.]), array([ 0., -1.]), array([-1.,  0.]),
   array([-1., -1.]), array([ 1., -1.]), array([ 0., -2.]),
   array([-2.,  0.]), array([2., 0.]), array([-2., -1.]),
   array([ 2., -1.]), array([-1., -2.]), array([ 1., -2.]),
   array([-2., -2.]), array([ 2., -2.]), array([ 0., -3.]),
   array([3., 0.]), array([-3.,  0.]), array([ 1., -3.]),
   array([-1., -3.]), array([ 3., -1.]), array([-3., -1.]),
   array([-2., -3.]), array([ 3., -2.]), array([-3., -2.]),
   array([ 2., -3.]), array([-4.,  0.]), array([4., 0.]),
   array([-4., -1.]), array([ 4., -1.]), array([-3., -3.]),
   array([ 3., -3.]), array([ 4., -2.]), array([-4., -2.]),
   array([ 4., -3.]), array([-4., -3.]), array([-1., -5.]),
   array([ 1., -5.]), array([-5., -1.]), array([-5., -2.]),
   array([-5., -3.]), array([ 3., -5.]), array([-3., -5.]),
   array([-6.,  0.]), array([-6., -1.]), array([-6., -2.]),
   array([-6., -3.]), array([-5., -5.]), array([-7., -1.]),
   array([ 1., -7.]), array([-1., -7.]), array([-7., -2.]),
   array([-3., -7.]), array([-7., -3.]), array([ 3., -7.]),
   array([-7., -5.]), array([-5., -7.]), array([-1., -9.]),
   array([ 1., -9.]), array([ 3., -9.]), array([-3., -9.]),
   array([-7., -7.]), array([-5., -9.]), array([  1., -11.]),
   array([ -1., -11.]), array([ -3., -11.]), array([  3., -11.]),
   array([-7., -9.]), array([ -5., -11.]), array([ -7., -11.])],
  dtype=object)

Maybe np.array(my_data, dtype=float).T to get rid of that pesky dtype=object? — JohanC
– JohanC, Commented Apr 22, 2022 at 21:42
When I try transposing, it says 'ValueError: too many values to unpack (expected 2)' — youtube
– youtube, Commented Apr 22, 2022 at 21:52
Pay close attention to what you have. What's the shape? The dtype is object. To make a scatter plot you need a (n,2) array, with float dtype. If the shape is 1d (e.g. (69,)), then np.stack(arr) should work. Transposing a 1d object array does nothing. — hpaulj
– hpaulj, Commented Apr 22, 2022 at 22:12

Michael Hodel · Accepted Answer · 2022-04-22 22:32:52Z

1

import numpy as np
import matplotlib.pyplot as plt

arr = np.array([
    0,
    np.array([0.,  3.]),
    np.array([2., 4.]),
    np.array([-3., -1.]),
    np.array([-4.,  2.]),
    np.array([2., 0.]),
    np.array([-2., -2.])
], dtype=object)[1:]
print(repr(arr))

prints:

array([array([0., 3.]), array([2., 4.]), array([-3., -1.]),
       array([-4.,  2.]), array([2., 0.]), array([-2., -2.])],
      dtype=object)

then you can use np.stack (as others have already suggested in the comments) to convert arr to a 2d-array:

arr = np.stack(arr)
print(repr(arr))

which prints:

array([[ 0.,  3.],
       [ 2.,  4.],
       [-3., -1.],
       [-4.,  2.],
       [ 2.,  0.],
       [-2., -2.]])

and is much easier to plot:

plt.scatter(arr[:, 0], arr[:, 1])

edited Apr 22, 2022 at 22:32

answered Apr 22, 2022 at 21:47

Michael Hodel

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3 Comments

youtube Over a year ago

This didn't work for me, it says: 'IndexError: too many indices for array: array is 1-dimensional, but 2 were indexed'

hpaulj Over a year ago

MIchael, when you print your arr, does it show nesting arrays as the OP's does? If it is a 2d float array, then you did not replicate his case,

Michael Hodel Over a year ago

hpaulj thanks for pointing this out. It indeed did not replicate OP's case, but now I think it does.

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