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
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
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!
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.
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.
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!
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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