I am new at this, so my apologies if I have overlooked what should be a simple answer and is already in the Forum… I have looked but cannot find whether there’s code to run just a simple Jaccard similarity coefficient between two populations:
S = a / (a + b + c)
where S = Jaccard similarity coefficient,
a = number of species in Sample A and Sample B (joint occurrences)
b = number of species in Sample B but not in Sample A
c = number of species in Sample A but not in Sample B
I understand and know of the Jaccard’s plot possible in Emperor plots, but I want something far more basic when I’m comparing only two populations (or species, or samples, or whatever).
Also, just a simple calculation of Shannon’s H for each sample/population? Is that possible?
where bacteria-table.qza is my filtered table (removed eukaryotes, archaeans, and bacteria identified only to the Domain level), this should be analogous to the table.qza from the Moving Pictures tutorial.
I did generate shannon_table.qza, but I am unsure of the commands necessary to visualize the results! I know this should be easy, but I just cannot seem to get the correct syntax…
Also, is there a way to integrate my metadata file so that I can see the two groups?
Any help with the visualization is appreciated! Thank you!
Okay, one last question (I think)-- is there a way to integrate sampling depth into these analyses? As I currently have the arguments structured, they are using a table.qza (specifically bacteria-table.qza, as specified in my earlier post) that hasn't accounted for sampling depth. Thus, it appears that all of my samples are included in the analyses.
Wait, when I ran the qiime diversity core-metrics-phylogenetics and created the output directory I just noticed that there’s a shannon_vector.qza and a jaccard_distance_matrix.qza within that directory. Are these based off of the sampling depth I set in that same command??? If so, then I have answered my own question???
Pretty sure my face should be pretty red with embarrassment at the moment…
