Support for arbitrary taxonomic ranks

MicrobiomeAnalyst
1

Dear developers,
Thank you very much for developing MicrobiomeAnalyst. I just started to use it, but it appears to be very helpful for my future analyses.
I don’t know, if I am doing something wrong, but I am running the Marker Data Profiling module and it ignores my custom rank names which I included in my taxonomy file. In the attached file, I simply used ranks called “A”, “B”, and “C” as a minimal example. I would expect that, for example, the drop-down menu where I can select the taxonomic rank in the “Visual Exploration” analysis would contain my custom labels (“A”, “B”, and “C”). Instead, it shows “Phylum”, “Class”, and “Order”. Is there any way that I can modify my taxonomy file to overwrite the standard rank names? Currently, I am working with the RDP taxonomy that contains the ranks: domain, phylum, class, subclass, order, suborder, family, genus, species, strain. Some viral taxonomies have yet different ranks, so I think this function would be also helpful for other users besides me.
Have a nice day,
Felix

foobar_tax.txt (72 Bytes)
foobar_otu.txt (98 Bytes)
foobar_metadata.txt (106 Bytes)

2

Hello,

Thanks for bring up this issue. I get your concern. Currently, most our analysis deal with the taxonomy based the rank system from phylum to species. You don’t necessarily need to provide all the ranks but should use the same name systems for the ranking, then our tool can automatically recognize the input taxonomy level. The domain/kingdom are automatically removed currently as usually there’s only one kingdom in the taxonomy table.

If your case is a common issue, we can maybe add another selection to support user’s taxonomy. But it might take some time.

For now, you can either ignore the taxonomy name on the website, or use our R package to customize the rank name within the result table and figures.

Hope this helps!

1 Like
3

Dear Yao,
Thank you for your swift reply. I think it would definitely be useful to support custom rank names and custom numbers of ranks in MicrobiomeAnalyst. Nevertheless, this feature also appears to be missing in other web services like Namco.
For the time being, I will try your workarounds. Thank you!
Have a nice day,
Felix