I’ve been enjoying using QIIME2 for processing my amplicon data. One of the main features of QIIME2 is to generate visualization files (qzv) for users to explore the results interactively. I wonder if it’s possible to combine html files from different QZVs into one, which can then be used as a report for a study or project. Say, I’d like to combine the sequence quality overview, donoising stats, taxanomic bar plots and diversity analysis into one html file and use that as my report. Any suggestions are greatly appreciated!
Hey there @yanxianl, this is a great question! We don’t currently have any kind of automated way to do this, but, I have some thoughts to get you started. You can export your QZVs, then you could create and edit a new HTML file that either combined the assets from the individual visualizations, or, did something like an iframe to merge everything wholesale.
This is a really interesting point though, it might be neat to come up with a mechanism to merge visualizations (or, “bundle” them).
Would you consider developing a new function like qiime tool merge-qzv or qiime tool generate report? I believe this will be a really useful feature to make better use of visualization files and to generate automatic reports.
I found an excellent tool called MultiQC in a shotgun metagenomic workshop, which does exactly what I was looking for. MultiQC “recursively searches through any provided file paths and finds files that it recognises. It parses relevant information from these and generates a single stand-alone HTML report file”. Unfortunately, it doesn’t support outputs from QIIME2.