Good morning,
I'm analyzing a dataset of fungal sequences and so far it's going quite well. However, I'm not sure if I am understanding well some outputs of the core metrics. I am mostly interested in alpha diversity and therefore I am looking at "shannon", "evenness" and "observed features".
My question is: what does "observed features" means or being more specifically, what is the meaning of the numbers in the y axis ?
I am confused because I thought I would have to see in the y axis the number of ASVs. In my feature table, the final number of ASVs is 122. In the graph, the maximum value in the y axis is 38. Therefore I thought it could mean OTU ?!
The number of observed features - ASVs or OTUs depending on your workflow.
I guess 122 is number of observed features in your entire dataset in general. On the boxplots, samples are distributed by groups. In each group, you have from 5 to 10 samples. Some samples are sharing the same ASVs, some are not. But you can not find all 122 ASVs in one sample, since it is a summary of all ASVs across all samples. It is why maximum value at Y axis is much lower than 122
