Checking the content of qzv files

Developer Discussion
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1

Hi!

I'm working on visualization for the covariance matrix in my plugin. I've seen a couple of implemented heatmap visualizations in existing qiime2 plugins, but I use my own semantic type ("PairwiseFeatureData") specific to the problem I solve and that made me re-create the wheel.

I was following this thread by @Nicholas_Bokulich, and I found this example very helpful, thanks! So, I made this action working:

!qiime gglasso heatmap \
    --i-covariance-matrix example/data/88soils_covariance.qza \
    --p-normalize True \
    --o-visualization example/data/88soils_heatmap.qzv

and producing me .qzv file but I experience the problem with rendering HTML, anything I write down in index.html appears except the figure.

I guess there is no figure stored in the produced .qzv file, how one can check if that is true?
Now, I simply uploading it to https://view.qiime2.org/

Or maybe I save the figure in the wrong directory?
Since I work in Docker container and should I refer to the figure differently in index.html? Now, I follow the example above.
Thank you!

2

Hello!
There are several options you can to try to check the content of existing qzv file.

  1. Using export plugin in Qiime2:
qiime tools export \
    --input-path some.qzv\
    --output-path some_dir/

  1. Unzip it as a zip file via terminal

  2. In ubuntu, one can just double click on the file to open is as an archive.

Best,
Timur

3

thank you, Timur!
good news, I've exported the files and the plots are there
then the environment does not play a role since I'm rendering HTML on https://view.qiime2.org/, any ideas what's the problem?

4

Hi @Oleg ,
As a quick sanity check, you could try a different browser.

We have seen some browser-specific issues when viewing very large images. You could also attempt to create a small covariance matrix just to text if loading large images is the problem.

1 Like
5

thank you!
found the bug and fixed it, now it works :ok_hand:

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