Dear qiimers,
As I’m having a hard time figuring out the available options for --p-metric in performing many longitudinal on beta diversity data. But i’m referring at the moment to “longitudinal pairwise-differences” just as an example.
when I pass beta diversity results (distance_matrix.qza), it get an error “_There was an issue with viewing the artifac_t”, so I tried with pcoa.qza but I get an error “metric must be a valid metadata or feature table column”.
I saw people have already raised similar issues and I saw some older topics like
this one Alpha and Beta Diversity Explanations and Commands
however, even when I tried options like braycurtis, beta, pcoa, axis1 or many other variations it wouldn’t accept it. While I know that this is not a bug, rather lack of information, I feel that this part is not clear in the official documentation of qiime2.
In any case, I will be happy if you guys can tell me where can i find more details about these options and which files to use.
In most cases, the metric name comes from your sample metadata file, which is a file you must create yourself (this file contains information about your study, there is no way QIIME 2 or any other software could really know the specifics about that).
As always, thanks for your reply @thermokarst
I’m aware of that the metric name comes from my sample metadata file. but I was asking about the “metadata-transformable artifacts” (including alpha diversity vectors, PCoA results, and many other QIIME 2 artifacts). I was able to use alpha diversity vectors (e.g. shannon or pielou_e) by visualizing the file with “metadata tabulate” and using the numerical column name. But, i couldn’t figure out, as indicated in the previous message, how to use the PCoA. So my question is: what is the metric that I could write when I’m using a PCoA result? and what are the “many other QIIME2 artifacts”?
This is a trickier problem - we haven't quite implemented a good way to figure out what kinds of artifacts are viewable as Metadata (or how to learn about the naming of the MetadataColumns inside the artifact).
The easiest suggestion I have right now is to use the metadata tabulate command on the artifact you are interested in using. If it is viewable as Metadata, the command will generate an interactive table viz. In there, you can learn about the specific MetadataColumns within.
:qiime2: