How to convert relative abundance data (from other tools) to QIIME2 taxa bar plots?


I have some abundance data generated from other tools in the form of .csv data.
They contain the taxa ids and their levels of abundance.
Is there a way to visualize these data as QIIME2 taxa bar plots, so I can combine these with my other data that were analyzed with QIIME2?

Many thanks!

1 Convert a .csv file to .tsv and then to a biom file. This one you can import to Qiime as a feature table.

biom convert -i feature-table.tsv -o feature-table.biom --table-type="OTU table" --to-hdf5

qiime tools import \
  --input-path feature-table.biom \
  --type 'FeatureTable[Frequency]' \
  --input-format BIOMV210Format \
  --output-path feature-table.qza

2 You need a taxonomy file. If you have it outside of Qiime, make sure that it looks like a .tsv file used in Qiime2 taxonomy artifact. To check, how it should be formated, you can open as an archive a taxonomy.qza file, produced earlier in Qiime2 and navigate to data/ directory inside. When the file properly formatted, import it to Qiime.

qiime tools import \
  --type 'FeatureData[Taxonomy]' \
  --input-path taxonomy.tsv \
  --output-path taxonomy.qza

3 You also need a metadata file for this data.

If you have all three files, you are good to go and create a barplot.


Hi @timanix,

Thank you so much for your super helpful reply!

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