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I'm doing some 3d scatter plots with jupyter notebooks in VSCode, and they aren't showing properly.

3d scatter plot from docs

I went to the documentation in matlab and downloaded the jupyter notebook for the 3d scatter plot and tried running that in vscode, getting the same results, the z label gets cut off.

I've seen a lot of questions about making the plot interactive with matplotlib magic, and some of those solutions (%matplotlib qt) do work (the image isn't cropped anymore, but gets created in a separate window. I want the plot to be inline, because I'm doing a lot of them and having one 40 windows created every time is a mess.

I've tried the magic %matplotlib widget and %matplotlib notebook, as suggested here, and the %matplotlib ipympl as suggested here but when I use those the plot stops showing, appearing only after I change to %matplotlib inline and showing any plot I've done before at that point (all cropped).

I've also checked the code in jupyter lab and it does not have this problem, the image shows completely fine, so it seems to be a problem with Jupyter notebooks in VsCode.

I'm not trying to change the position of the z axis, It's fine where it is, I just want to make the image bigger so the z label is shown properly.

Just in case, I've tried the comment of Trenton McKinney of doing ax.zaxis._axinfo['juggled'] = (1, 2, 2) to change the z-label to the other side, and it still gets cut, just in the other side of the image.

3d scatter plot from docs with the z axes on the other side

So it's not an issue of where the z axes and label are.

PS: As requested, I put the from the example here for ease of use.

import matplotlib.pyplot as plt
import numpy as np

# Fixing random state for reproducibility
np.random.seed(19680801)


def randrange(n, vmin, vmax):
    """
    Helper function to make an array of random numbers having shape (n, )
    with each number distributed Uniform(vmin, vmax).
    """
    return (vmax - vmin)*np.random.rand(n) + vmin

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

n = 100

# For each set of style and range settings, plot n random points in the box
# defined by x in [23, 32], y in [0, 100], z in [zlow, zhigh].
for m, zlow, zhigh in [('o', -50, -25), ('^', -30, -5)]:
    xs = randrange(n, 23, 32)
    ys = randrange(n, 0, 100)
    zs = randrange(n, zlow, zhigh)
    ax.scatter(xs, ys, zs, marker=m)

ax.set_xlabel('X Label')
ax.set_ylabel('Y Label')
ax.set_zlabel('Z Label')

plt.show()

Update: I've posted an issue in the github VSCode repo, link here

Update on the update: The issue has been found to be a matplotlib/jupyter problem, so I've opened a new issue in the matplotlib repo, link here

David Siret Marqués
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    The issue has to do with being an inline plot, not necessarily the coding environment. The label can be move to the other arm with `ax.zaxis._axinfo['juggled'] = (1, 2, 2)` – Trenton McKinney May 29 '23 at 19:32
  • The thing is that I've done it before, and I tried in other IDE and it works without a problem – David Siret Marqués May 30 '23 at 11:25
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    This probably has to do with version changes in matplotlib. This occurs in in 3.7 for me. – Trenton McKinney May 30 '23 at 12:00
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    Ok, As I've said, its a problem with VSCode, not the code itself, as doing the code in jupyterlab showed the image fine, so I'm not sure if copying the code will have any effect... – David Siret Marqués May 31 '23 at 14:17
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    Same issue for me, only with VSCode. @DavidSiretMarqués Have you tried to raise an issue on VSCode github? Otherwise I'll do it. – fma Jun 06 '23 at 10:30
  • Nope, my issue is with VSCode. I tried with jupyterLab to check if it was a problem within VSCode or within the general notebook, and checked it's in VSCode. Raise the issue on github, I don't really know how to do it... (but I'll check and report if I do) – David Siret Marqués Jun 06 '23 at 10:48
  • please, report if you raise the issue with a link to support it, @fma – David Siret Marqués Jun 06 '23 at 11:00
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    Issue posted in the VSCode extensions repo in github, here's the [link](https://github.com/microsoft/vscode-jupyter/issues/13661) – David Siret Marqués Jun 06 '23 at 13:36

1 Answers1

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So, after a pair of issues in github, I've finally found an answer. I'll leave here the answer in github for reference

It appears the problem is caused by the default inline backend saving the figure with bbox_inches= 'tight' which causes the code to crop the image. this can be solved using the inline magic

%config InlineBackend.print_figure_kwargs = {'bbox_inches':None}

which overthrows the default and gives you a nice, big image with plenty of room for labels and everything else. In case this doesn't work (the image created is rather big) I leave here the link to the docs.

Another option is to add padding, which can be done with the magic

%config InlineBackend.print_figure_kwargs = {'pad_inches': .3}

This option might need some trial and error to get the size right. In my case 0.3 worked as a charm.

David Siret Marqués
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