FR: add qzv taxonomy bar-plot results without "Unassigned"

[splaisan]

Dear,

I found it quite difficult to generate this myself because the inputs are located outside of the "results" folder in different places and difficult to locate for a non Qiime2 expert.

This also mean they are not transferred to the final user if, like we do, only the "result" folder is provided.
I realise that the info is present in the BIOM objects and could be worked with in phyloseq but it is easier for me to directly use original Qiime commands and objects to operate extra filtering).

Would it be possible to add (can be optional!) the generation of the extra taxonomy-filtered .qzv barplot results to the final result folder without "Unassigned"? These tend to be numerous in certain samples and affect the visual by compressing the assigned taxa bars.

Thanks

in the meanwhile, can you please confirm that what I did below is correct.

cd pb-16s-nf
cd results

metadata=../run_53_metadata.tsv

# vsearch version
taxonomy="taxonomy.vsearch.qza"
taxpfx="vsearch"

# alt: naive bayes version
# taxonomy="best_tax.qza"
# taxpfx="nb"

# filter the final DADA2 table
qiime taxa filter-table \
  --i-table ../dada2/dada2-ccs_table_filtered.qza \
  --i-taxonomy ${taxonomy} \
  --p-exclude Unassigned \
  --o-filtered-table ../dada2/dada2-ccs_table_filtered_assigned.qza

# create new barplot
qiime taxa barplot \
  --i-table ../dada2/dada2-ccs_table_filtered_assigned.qza \
  --i-taxonomy ${taxonomy} \
  --m-metadata-file ${metadata} \
  --o-visualization taxonomy_barplot_${taxpfx}_assigned.qzv