prepare barplots from collapse taxa

Hi, I am working with QIIME2. I want to prepare barplots for top 10 features at class level. For that, I am using filtered-table.qza where features present in less than 2 samples were removed. This filtered-table.qza was used as input for qiime taxa collapse. when I am using the output from taxa collapse in preparing barplots, I am getting the following error:

Plugin error from taxa:

Feature IDs found in the table are missing from the taxonomy: {'k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria', 'k__Bacteria;p__Actinobacteria;c__Coriobacteriia', 'k__Bacteria;p__Firmicutes;c__Negativicutes', 'k__Bacteria;p__Tenericutes;c__Mollicutes', 'k__Bacteria;p__Firmicutes;c__Bacilli', 'k__Bacteria;p__Proteobacteria;c__Deltaproteobacteria', 'k__Bacteria;p__Proteobacteria;', 'k__Bacteria;p__Firmicutes;c__Tissierellia', 'k__Bacteria;p__Verrucomicrobia;c__Verrucomicrobiae', 'k__Bacteria;;', 'k__Bacteria;p__Fusobacteria;c__Fusobacteriia', 'k__Archaea;p__Euryarchaeota;c__Methanobacteria', 'k__Bacteria;p__Actinobacteria;c__Actinomycetia', 'k__Bacteria;p__Bacteroidetes;c__Bacteroidia', 'k__Bacteria;p__Firmicutes;', 'k__Bacteria;p__Firmicutes;c__Erysipelotrichia', 'k__Bacteria;p__Proteobacteria;c__Betaproteobacteria', 'k__Bacteria;p__Firmicutes;c__Clostridia', 'k__Bacteria;p__Bacteroidetes;__'}

Please suggest.


You don't need to collapse your feature table for barplot visualization. So you can just provide your filtered table that you used for creating collapsed table.

Without collapsing, I created the barplots. But, for visualization of top 10 features at any taxa level, I have to collapse the feature table. I may be wrong. Please suggest.

You can filter out all undesired features from the feature table before barplot creation. In that case your top 10 features will be rescalled as 100% of the community. Another way will be just choosing top 10 features in taxabarplot visualization withh all features (click on the colored square of top 10 features in the legend of visualization). That will show only top 10 taxa at desired level (you can change taxa level in the same visualization) on the scale of the total community.

Thank you very much for your suggestion. I selected top 10 features in taxa barplot visualization. But this is creating empty spaces in the plot for features which are not included in top 10. Is there a way to remove these empty spaces.

In that case you need to filter out all other taxa except top 10. But I would prefer to leave empty spaces since otherwise information about which part of the community represent top 10 taxa will be lost.

Thank you, Timur. I'm learning a lot through your instant suggestions. I'll keep troubling you for sometime ( as I'm midway my analysis).

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