Hello,
I am hoping to get some clarification on how to view results from the alpha/beta diversity calculations. I chose and ran each of the following -
Brillouin's Index, Chao1 Index, Pielou's Index, Simpson's evenness; Sokal-Michener Coefficient, and Yule index.
The alpha diversity files came out as a * SampleData[AlphaDiversity]" tyope in the format: "AlphaDiversityDirectoryFormat", as a qza file as I expected.
The beta diversity files saved as distance matrices in "DistanceMatrixDirectoryFormat".
I've been looking through this forum trying out a few different suggestions but nothing is helping. I tried using the diversitypcoa/emperorplot commands but the metadata file will not work (even though Kleemi validates it). The Moving Pictures tutorial is unclear in this (that tutorial is often linked to with tis problem). How can I create visualizatins for these 6 diversity statistics?
Thank you
As you have discovered, there's a lot of ways to work with beta diversity measurements, and a lot of indexes, files types, and visualization involved. As you have also discovered, metadata is central to this question and has to be just right.
Would you be willing to post the errors you are getting, along with the commands and metadata file? Let's see if we can get the commands working, and look for bugs and better examples along the way.
I'm not sure if I was running the correct commands to get my visualizations, but I tried basing it off of this post [Cant see results of non-phylogenetic beta-diverisity metrics] to view results from Sokal-Michener and Yule. This is what my metadata looks like, I used a .tsv of this data -
The error I got from running the code in the post I mentioned above said the filepath was incorrect or the file was not a correct/expected metadata file. I made sure the file path was correct and the used Keemei to validate the metadata. Is there data missing here? I previously included barcode sequences as well but thought this was not necessary to have in the file anymore.
Thank you !
Hi @Hayley_Guay, we really can't help you without seeing the actual error message, as well as the commands you ran - this is all important context that helps us diagnose and understand the situation. Please share your commands and error messages (when run with --verbose, or attach the error log created) - thanks!
Not sure if shutting down restarting helped me or Qiime more, but the same commands worked when I ran it again today. Thank you for being ready to help and sorry for the false alarm!
just right 
