I am just dipping my toe in microbiota analysis and have gotten some count output from the QIIME2 online platform which drills down to the species level. These data were downloaded from the taxa-bar-plot.qzv page/file which allows for count output at each taxonomic level. In the output, at the species and genus level there are taxanomic descriptions that are incomplete, going only to family and sometimes higher. The counts for each taxonomic description appear to be the sum of the counts for each feature that corresponds to each taxa found in the feature table.
If I sum the number of counts from the feature table, the array will not include incomplete taxa descriptions as have been included in the taxa-bar-plot.qzv output.
My question is: Can I use the taxa-bar-plots output to calculate % abundance and if so, do I include those rows that contain incomplete taxonomic names in that calculation?
