I am a new qiime2 user and I need help with qiime view.
My volatility plot file is not showing, page is white.
My command was:
qiime longitudinal volatility --i-table genus-rf-table_3xTg.qza --p-state-column time.on.diet --m-metadata-file sample-metadata_3xTg.txt diversity-core-metrics-phylogenetic_3xTg/jaccard_pcoa_results.qza --p-individual-id-column fastqfile --p-default-group-column diet --o-visualization volatility-plot-1_3xTg_genus_jaccard.qzv
here the screeshot:
I tried either on Firefox and Chrome. I have an Ubuntu 20.
Thank you very much
Hello @mavino, have you tried running the command to generate the .qzv again? I'm not sure what's happening here, but something may have just ended up corrupted somehow. Thank you.
Thank you for your reply...I do not understand what you mean...if you are asking me if I have re-tried the same command I posted above, yes, many times and with different input files...unfortunately I cannot see them...
So you've run
qiime longitudinal volatility with many different inputs and the resulting .qzv is never visible?
I ran it on another experiment but still the qzv is not visible:
qiime longitudinal volatility --i-table genus-rf-table_Het.qza --p-state-column time.on.diet --m-metadata-file sample-metadata_Het.txt diversity-core-metrics-phylogenetic_Het/jaccard_pcoa_results.qza --p-individual-id-column fastqfile --p-default-group-column diet --o-visualization volatility-plot-1_Het_genus_jaccard.qzv
same thing when I run qiime longitudinal feature-volatility:
qiime longitudinal feature-volatility --i-table filtered-genus-table_3xTg.qza --m-metadata-file sample-metadata_3xTg.txt diversity-core-metrics-phylogenetic_3xTg/weighted_unifrac_pcoa_results.qza --p-individual-id-column fastqfile --p-state-column time.on.diet --output-dir volatility-plot_3xTg_genus_unifrac
my volatility_plot.qzv file will not be visible, but the accuracy_results.qzv file will be...
Can you DM me your input data so I can try to reproduce this? I'm currently not sure how this is happening.
@mavino, I was able to reproduce the issue, but I was unable to figure out what caused it, so I did some digging and found this post that features the same issue. It looks like you might need to filter out some of your features.
This is very strange, I had already filtered out low abundance features, now I collapsed to order level, I have just 10 features left and still I cannot see it...
qiime longitudinal volatility --i-table order-rf-table_3xTg.qza --p-state-column time.on.diet --m-metadata-file sample-metadata_3xTg.txt diversity-core-metrics-phylogenetic_3xTg/jaccard_pcoa_results.qza --p-individual-id-column fastqfile --p-default-group-column diet --o-visualization volatility-plot_3xTg_order_jaccard.qzv
order-rf-table_3xTg.qza (51.6 KB)
volatility-plot_3xTg_order_jaccard.qzv (590.4 KB)
One of our mods was able to figure out where the issue is coming from (thanks @fedarko!) - long story short, it appears that the periods in the
time.on.diet metadata column (which you've selected as your state column) is the source of the error. Replacing
. with dashes (as an example) in your metadata before re-generating this plot will fix the issue, and allow for your data to be rendered successfully.
With that being said, this was something that was reported a few years ago that should have since been fixed by Vega (the visualization tool that we are using to render this plot). I'm going to do some testing on my end to see what we can do to resolve this as a general issue, because including
. should be permitted within metadata columns.
Yes it works now, thank you very much
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