I essentially just want to describe how richness changes between my three O2 regimes.
Here are my basic questions:
Do I interpret these as standard box and whiskers plots? Specifically, does each box denote interquartile ranges, with the horizontal line showing the median value, and the whiskers showing the maximum and minimum values?
If #1 is correct, then is there a way for me to obtain the actual median values? Like, as calculated by QIIME, and not just me drawing a line to the y-axis?
Using QIIME, is there a way to perform a Kruskal-Wallis test with a Benjamini-Hochberg correction on these Chao1 estimates the same way you can with other diversity metics (evenness, phylogenetic diversity, etc.)?
Overall, I know richness is lowest in the orange bin (labeled 3_below 1), but I would like to say quantitatively (or statistically) how much lower it is compared to the other bins. Does that make sense?
Yes, it does, but it is highlighting alpha diversity at different sampling depths. It is not really comparing between groups.
This isn't not really available. The boxplots are bigger in alpha-group-significance so it is easier to roughly see the mean. Also from alpha group significance you can download the raw tsv of the data and calculate the median value for each group through that.
Yes! So what you are going to is generate the chao1 diversity vector through qiime diversity alpha and then run alpha-group-significance.
Overall, I think that this visualization isn't exactly what you need to answer your questions. I think the directions above should fix this!
I have remaining question, though: I've run the core-metrics-phylogenetic method already, but it didn't seem to produce a chao1.qza file. Is there a way to do this? So far, I've only produced a chao1.qzv file (the one I attached above) using the qiime diversity alpha-rarefaction visualizer, but I can't input this file for the alpha-group-significance method.