I understand that view.qiime2.org does all the processing locally, on the client side. And once I load the page in the browser, I can turn off my internet and work offline. But, is there a way to save the page locally, so I can open it whenever I am offline and view a QIIME 2 artifact? Or another way to view artifacts offline?
I tried saving the page in Chrome and in Safari (with “Save Page As…”) in the different possible formats, but I got errors when trying to use any of them - perhaps I am not saving it the right way? Or there is another solution?
It’s kind of a hacky solution, but I often use a Jupyter Notebook interface to view my visualizations. I open a jupyter notebook (
jupyter notebook) with a python kernel and then use the code to import the visualization object.
from qiime2 import Visualization
Then, can just view the visualization in the notebook. For instance, if I have a emperor plot called
emperor.qza, I would run
emp_viz = Visualization.load(emperor.qza)
And the plot will display below that cell, not internet connection needed. It is worth noting that you may need to install an extensions the first time you go to use QIIME 2; it will prompt you with the appropriate command. Just show down your notebook, restart, and run your code.
It’s also worth noting that the visualizations reset whenever you restart your kernel, so if you want to show the results again, you have to run the visualization.
Hey there @psps!
This is a great question! @jwdebelius brought up a great solution, so please check that out when you get a chance. Another option is to use q2cli (which is included with QIIME 2 when installing using our official installation instructions):
# Opens an offline browser page with the visualization
# specified in the command. Provenance is not available, though.
qiime tools view my-visualization.qzv
Please note, this only works for Visualizations (QZV files), not Artifacts (QZA files).
Let us know how it goes!
Thanks @jwdebelius and @thermokarst.
Both of these methods work well for viewing the visualization - and that jupyter notebook functionality is awesome! I didn’t know you could do that.
I work with collaborators who are located in areas without good access to the internet. I like sharing the QIIME 2 .qzv and .qza formats with view.qiime2.org because it contains all the bioinformatics results along with the “Provenance” - what tools and parameters were used - very convenient. Is there a way to view the “Provenance” tab? I noticed it doesn’t show up with either method. I found this post viewing provenance from command line to show details available from view.qiime2.org but I wasn’t sure how to parse the extracted output, and I was hoping I could view it as it appears on view.qiime2.org.
If not, I kindly request this as a feature .
Hi @psps, I am glad that was helpful!
No, unfortunately not, please see my note above:
It is on our todo list!
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