Beta Diversity volatility plots v2

[bmurph79]

Hi all, Asking this as a previous post (Beta diversity volatility plots) did not seem to come to a conclusion.

Has anyone been able to plot beta diversity metrics using the volatility plot tool? According to the docs it should be possible to produce a first distances / first differences file and plug that into the volatility analysis. The generation of both seems to have run fine and I can see the resulting qza artifacts however they are not available for use when attempting to produce a volatility plot. All being done using Qiime2 Studio.

Thanks for the help.

BMurph

[Nicholas_Bokulich]

@bmurph79

I can see the resulting qza artifacts however they are not available for use when attempting to produce a volatility plot.

Could you please clarify? Maybe with a screenshot if appropriate? I can confirm that this works (at least with the command-line interface), since the first differences output is transformable to metadata, and hence can be used by this method. Thanks!

[bmurph79]

HI @Nicholas_Bokulich. I think that you may have actually answered my question. Do I understand correctly that instead of using the qza file directly as an input to the volatility that it is necessary to (and bear in mind I am using Q2studio) convert the qza file to a format where the firstdistances can be added to a metadata file as is the case when viewing alpha diversity results? As the tutorial is written I assumed that the qza file could be used directly.

As a non command line user perhaps the command “m-metadata-file” suggest that it has to be in the form of metadata?

[Nicholas_Bokulich]

@bmurph79

Do I understand correctly that instead of using the qza file directly as an input to the volatility that it is necessary to (and bear in mind I am using Q2studio) convert the qza file to a format where the firstdistances can be added to a metadata file as is the case when viewing alpha diversity results? As the tutorial is written I assumed that the qza file could be used directly.

No, you should be able to use the first distances artifact directly as input to that visualizer, though I am not sure how the q2studio interface impacts this.

Are you able to use the command line to run this visualizer? That could be the best approach if q2studio is a barrier here.

[bmurph79]

@Nicholas_Bokulich Thanks. I will have to investigate more. For some reason when attempting to generate a volatility plot the drop down menu in Q2S (Longitudinal - Visualizers - Generate interactive volatility plot) does not contain the firstdifferences artifact that has previously been generated.

I note that the description in Q2S suggests “Any numeric metadata column (and metadata-transformable artifacts, e.g., alpha diversity results) can be plotted on the y-axis, and are selectable using the “metric_column” selector”.

I will investigate and report back.