Newbie question, Is it possible to generate plot/figure via CLI instead open the qsv file via Qiime view?

Dear All, I just switch from Qiime 1 and really like Q2 so far. I am wondering if it possible to generate the plot/figure/chares or PDF file by CLI or other tools can work with .qsv file instead of open them from Qiime view?

Thanks.
Archie

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Hi @archie,

Yes, you can use:

qiime tools view your_visualization.qzv

to quickly open a visualization. This will still launch in a browser window because most of our visualizations are interactive.

Hope that helps!

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Thanks for reply. This doesn’t work for me. I remote control our central server. Ideally, I would like to generate the plot automatically by command line.
Thanks, Again.

Hi @archie,

Could you expand on this a little?

Just as an example, you can think of a .qzv in much the same way as a .png. You can’t actually look at the picture on the remote server (well actually you can with X-forwarding), so you would download the picture and look at it on a computer with a screen to display it. QIIME 2 visualizations work about the same way, but they are packaged-up interactive HTML plots instead of a PNG file.

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Hello Archie,

When working with Qiime on a remote server / super computer, I’ve found Cyberduck really useful. It’s an elegnat program that let’s you view, edit, and open remote files as if they were on your local machine. :duck:

Mac: https://en.softonic.com/download/cyberduck/mac/post-download?sl=1
Win: https://update.cyberduck.io/windows/Cyberduck-Installer-4.5.1.exe

Keep in mind that you can’t view a .pdf or a .qzv from the command line, but a good program will make it easy to download and view locally.

Colin

P.S. @ebolyen What a great description of .qzv files!

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great description,

What I am trying to do is automation this process, and insert the picture in to a report automatically by scripts.

I see! In that case, what kind of report are you interested in creating? All QIIME 2 visualizations are mini-websites which means you could compose them together with an index.html page, but this is all probably easier done with the QIIME 2 SDK in Python.

We used to generate the LaTeX and convert to PDF. HTML may be a better choice now for an interactive report.

Is there a tutorial about how to do this in QIIME 2 SDK?

Thanks

Hi @archie! Sorry for the delay in responding.

No, there is not a tutorial but you can check out the reference API.

I hope that helps!

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