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When publishing in the physical sciences the main paper is usually something 2D, you can read it online or print it. Many journals support supplementary data in the form of pdf files and videos.

It is possible to plan a rotation/zoom scenario for a 3D scatter plot, make that into a video and attach it, but in my case I think many readers/viewer may find it helpful to do so interactively.

I use python exclusively. Starting from that, are there any ways that a 3D interactive scatterplot can be officially incorporated into a journal publication via supplementary information?

I understand that one can simply include a link to something external to the journal and find another site to support it or for the reader to download something, but here I'm asking for examples, instances or possibilities of having this as an official part of the publication the same way that supplementary videos are now supported.

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    I don't think I've ever seen a 3D scatter plot where a different type of plot wouldn't have been superior.
    – user9482
    May 2, 2022 at 14:02
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    By "3D scatter plot", do you mean a cloud of points in space? If for illustration or educational purposes, fine. If the cloud of points has a very clear or definite shape (line, arc, spiral, sphere, ...), go ahead. Otherwise, I think it'll be very hard to understand/interpret.
    – Pablo H
    May 2, 2022 at 14:09
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    @Roland do you mean that for every 3D scatter plot you've ever seen, you've actually seen the superior alternative next to it and everyone agrees it is superior, or is more like an urban legend? There are some mathematical structures that really exist in dimensions higher than 3 and even a 3D representation only suggests what's going on.
    – uhoh
    May 2, 2022 at 14:10
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    @Roland it's not surprising that there are examples where it wasn't necessary, but that doesn't automatically mean they're never helpful.
    – uhoh
    May 2, 2022 at 14:21

3 Answers 3

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Since you're using python, the easiest solution is probably to create a Jupyter notebook (formerly known as IPython) with the controllable scatterplot and see if you can upload that as supplementary information. Some journals are sticklers for what file formats they support, and might not allow such notebooks, but certainly some do, as in this example.

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    That's great! I've never used anything beyond a simple IDE and a command window, but I assume it will be straightforward to learn to use the notebooks since it's Python after all. This simultaneously allows for the publication of the scripted algorithm that generates the data so it seems to be an excellent option! Hopefully this will at least extend to the whole Physical Review constellation (e.g. PRB and PRR)
    – uhoh
    May 2, 2022 at 4:46
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    @uhoh The initial setup of Jupyter can be a bit of a hurdle, but there are good guides available online for a number of operating systems / distros. If you follow one it should be straight-forward indeed. After that step, a Jupyter notebook acts similarly to say a Mathematica notebook (which I've also seen uploaded as supplemental material) in that steps of a computation/program can be organized into cells, and you can also add explanatory text and headings, etc. with formatting. All in all, it makes for an interactive and easy-to-follow experience for your readers.
    – Anyon
    May 2, 2022 at 13:41
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    Does Jupyter notebook support exporting interactive figures to HTML? I suspect it does, but I don't use it. That might be a second format option that is more accessible for readers that don't use Jupyter notebook
    – anjama
    May 2, 2022 at 13:43
  • @anjama That is not something I've tried either, but some quick StackOverflow browsing suggests it's at least somewhat complicated. Also, the HTML probably would need something like a JavaScript component to support the interactivity. Not sure how willing publishers are to host such material.
    – Anyon
    May 2, 2022 at 14:00
  • There are a number of places which allow you to host Jupyter notebooks online, and which allow other people to run them from within their browser. (Google Colab is one, but there's others.) Even if the journal does not allow notebook files directly, it should be possible to provide the source code for the notebook as a text file (for long-term archival purposes), and then provide a link to an online-hosted version for convenience.
    – R.M.
    May 2, 2022 at 17:35
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I think Anyon's answer (Jupyter notebook) makes a lot of sense for OP's situation. But another option, for those comfortable with HTML and javascript, is to just build it as a single HTML webpage that you include in your SI. An example JS library that should make it easy (the first one I found with a quick search) is Plotly.js (3d examples).

Assuming Jupyter notebook supports exporting interactive figures to HTML (I think it does, but may be wrong), I would consider including both for OP. Anyone can open HTML files, whereas Jupyter notebook might not be as accessible for those that don't use it.

Another option is to just export your plot as a series of slides in a pdf that people can flip through to see it from different angles. This option should be universally acceptable for journals (as long as you keep the size small enough), but may be tricky depending on the complexity of the plot.

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  • Here's a StackOverflow about exporting interactive Jupyter notebooks using Plotly figures.
    – Anyon
    May 2, 2022 at 14:54
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The flow would be as follows:

  1. Export the 3D plot to a 3D model file (.step typically)

  2. Insert the STEP model into a PDF.

  3. View PDF using a 3D-enabled reader.

With models of suitable simplicity, you can insert the 3D model into the primary PDF of the article. A default 2D view will appear in 2D-only PDF readers and when printing. When opened in a 3D-enabled reader, the graph can be rotated, zoomed, etc. Works well in practice, but not too many people know to do it. I've been pleasantly surprised a few times though.

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  • Yes I see, while the PDF or on-line display of the main article may not support 3D features, the supporting information could be a PDF provided as-is, allowing those with said readers to see and use the 3D features. Interesting!
    – uhoh
    May 2, 2022 at 12:14

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