Challenges on documenting reproducible results in QIIME2

Dear all,

QIIME2 provides interactive visualization for users to explore output files. Often, we may want to change the configurations on the webpage and download the files for presentation or publication, such as barplot and PCoA plot. However, it’s difficult to make proper documentation so that readers can reproduce exactly what we show to them. To do that, I guess we need to extract/export qza files and make tables/figures using other tools such as R so that they can be reproduced again? In future releases, is it possible to make use of provenance information contained in qza files to do automatic and reproducible analyses within QIIME2?


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Hey there @yanxianl!

This is a great question, and it is something that has been on our minds for a long time, but unfortunately we don’t have a great generalized way to do this yet. Some visualizations (like those in q2-emperor) support exporting a config file, while is used to config the rendered plot after-the-fact. This is certainly on our radar, but I don’t have an ETA for when this might land. Do you have any particular ideas about how to tackle this? We are always open to feature contributions! :t_rex:

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