Filter_taxa issue (No "taxon_id" column in the data set "3", so there are no taxon IDs)

[SimonMorvan]

Hello,

Thank you for building this package!

I'm running into a problem with the filter_taxa function. I want to plot my metadiversity tree up to order level, but i keep getting an error: There is no "taxon_id" column in the data set "3", so there are no taxon IDs.

When I print the metacoder object (see below), I do have a "taxon_id" column in the otu table and the tax data but not in the sample_data (but it wouldn't make any sense to have that column in the sample_data). I generated the metacoder object using the parse_phyloseq() function.

I got filter_taxa to work by removing the sample_data() part of the metacoder_object but I need this information for plotting purposes.

Do you know a workaround this problem?

Thank you!

Simon

[zachary-foster]

Sorry, I did not see this before. Are you still having this issue? That warning is to be expected since the sample data table does indeed not have any taxa assigned to the rows. This should not cause any problems with filtering the other tables (other than throwing a warning). If it does cause errors then that's an bug. The sample data is put there in the case of parse_phyloseq to consolidate all the information from the phyloseq object into a single taxmap object output. It is probably better as a separate table. It will still be usable for plotting in a separate table same as it would be as a table in the taxmap object since it does not have taxon IDs anyway so does not gain any functionality from being in the taxmap object.

Let me know if you have more questions and I will try to respond this time.