Merge Shannon Diversity Files

[jecohen]

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!

[Keegan-Evans]

@jecohen,

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!