R plots in Jupyter notebook no longer visible in preview

Post author
Micah Rickles-Young

I've noticed that at some point there was a change in how Jupyter notebook outputs are displayed in preview mode on Terra. I can still see the warning messages and print command outputs, but I can't see any of the ggplot outputs without running the notebook. I had been using the notebook to display figures for collaborators who don't know how to actually run notebooks on Terra, so I'd really like to be able to display the plots without having to run the notebook. Is there still some setting I can edit or command I can include to make these plots visible again?

Thanks,

-Micah

 

Comments

4 comments

  • Comment author
    Josh Evans

    Hi Micah,

    Thanks for writing in! I'd like to take a look at the notebook file if I could. Can you share the workspace where you are seeing this issue with Terra Support by clicking the Share button in your workspace? The Share option is in the three-dots menu at the top-right.

    1. Toggle the "Share with support" button to "Yes"
    2. Click Save

    Please provide us with a link to your workspace and the name of the notebook file. We’ll be happy to take a closer look as soon as we can!

    Kind regards,

    Josh

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  • Comment author
    Micah Rickles-Young

    Sorry for the delay on this, Josh! I've shared with support and here is the link to the notebook: https://app.terra.bio/#workspaces/broadtagteam/MMRF_DuplexTumorOnly_RUO/analysis/launch/mmrf-duplex-data-qc.ipynb

     

    If you launch the notebook in playground mode, you'll see a bunch of ggplot plots that should ideally be visible in the preview but aren't anymore for some reason.

    Thanks!

    -Micah 

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  • Comment author
    Josh Evans

    Hi Micah,

    Thanks for providing access.  I took a look at the workspace and did some research.  As it turns out, the issue you're having is a known issue where the application has difficulty rendering the markdown of file.  This can include image files.  

    We're aware of the issue, and I've already added your name to our bug report to let the engineers know of this request.  We'll contact you if a bug is deployed to resolve this issue.

    Please let me know if you have any questions.

    Best,

    Josh

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  • Comment author
    Micah Rickles-Young

    Josh Evans Have there been any updates on this? We still can't see plots in jupyter notebooks without running them.

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