Targeted Gene Metagenomic Data Analysis    ◾    293

qiime metadata tabulate \

--m-input-file dada2/vsearch_tax_yoga_dada2.qza \

--o-visualization dada2/vsearch_tax_yoga_dada2.qzv

qiime tools view dada2/vsearch_tax_yoga_dada2.qzv

Visualizing the pre-fitted naïve bayes classifier taxonomy assignment:

qiime metadata tabulate \

--m-input-file dada2/nb_tax_yoga_dada2.qza \

--o-visualization dada2/nb_tax_yoga_dada2.qzv

qiime tools view dada2/nb_tax_yoga_dada2.qzv

Visualizing the trained naïve bayes classifier taxonomy assignment:

qiime metadata tabulate \

--m-input-file dada2/nb2_tax_yoga_dada2.qza \

--o-visualization dada2/nb2_tax_yoga_dada2.qzv

qiime tools view dada2/nb2_tax_yoga_dada2.qzv

You can compare between the taxonomy classification of the different classifiers. The fea-

ture table displayed on the Internet browser has three columns: Feature ID, Taxon, and

consensus (for alignment-based classifier) or confidence (for machine learning classifier).

The taxon column indicates the taxonomy assignment for each feature (k__ for kingdom,

p__ for phylum, c__ for class, o__ for order, f__ for family, g__ for genus, and s__ for spe-

cies). For example, in Figure 7.15, the naïve bayes classifier predicted the taxa of the first

feature up to the family level “f__Coriobacteriaceae;” with a confidence of 0.994, but it did

not assign a genus or a species to that feature. However, for the second feature, the classifier

predicted taxa up to the species level with confidence of 0.76. The confidence reflects the

probability that the taxonomy is correct.

Instead of confidence, alignment-based classifiers provide consensus that is based on

the agreement of the alignment hits. For example, a consensus of 1 means that all hits

aligned to the feature agreed on the taxa.

A taxonomy bar plot visualization can also be created with “taxa barplot” using the

taxonomy predicted by the classifiers and the filtered feature table artifact generated in the

clustering or denoising step as input.

FIGURE 7.15  Taxa assigned to features using naïve bayes classifier.