Merge Shannon Diversity Files

Hi! I'm attempting to make some plots of Shannon Diversity in R, and I was hoping to merge both of my shannon_vector.qza files from two different plates in order to visualize all my data together. Is there a way to merge SampleData[AlphaDiversity] files in qiime2? I tried

qiime feature-table merge --i-tables /center1/AMPLICON/jecohen/QiimePlate001_16S/filtered/core-metrics-results/shannon_P1-16S.qza --i-tables /center1/AMPLICON/jecohen/QiimePlate002_16S/filtered/core-metrics-results/shannon_P2-16S.qza --o-merged-table /center1/AMPLICON/jecohen/merged/shannon_16S.qza

To no avail, but that was to be expected as I'm not dealing with tables here. Let me know if this can be performed in Qiime2! Thanks!


Unfortunately you cannot merge after performing the alpha-diversity analysis. There is no merge method available for Artifacts of the type SampleData[AlphaDiversity], this method is not really possible as you need to normalize all of the data before performing an alpha-diversity analysis. See this tutorial and these videos from one of our online workshops: Even Sampling Depth, Rarefaction, and Alpha Diversity Metrics for more information on this.

What you can do is merge your data before running the alpha-diversity analysis. To do this import and de-noise your data, then use feature-table merge (DOCS) to combine your data, and then run your alpha-diversity analysis.

Hope this helps!

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