cdiener
commented
6 years ago Hmm. Yeah good question. It will be hard to represent all of the information from the heatmaps in another plot. You could plot only a few species/genera in a single lineplot. The PCoA plots are the most common solution to do that since they show you differences in overall composition.
Is it possible to make a plot to show, in general, how the communities are shifting in tanks 1-3 across time (T0 - T2) versus how it shifts in tanks 4-6 across time? Is there an accepted way to average the replicates if they're very similar to each other? I'm thinking something that's very easy to visualize and see that there are clear shifts in species composition across the three time points and that they're clearly different between treatments.
I'm not sure we'll be able to exactly draw a clear explanation as to why the plants grew differently, but it would be nice if we could show that the communities were different, that they changed over time, and maybe we could highlight the species/genus that were significantly correlated with plant growth phenotypes?
Would it be biologically correct to remove some species except the ones which are very highly enriched? Or could someone argue that just because a species isn't highly enriched doesn't mean they aren't crucial to the processes occurring? Thinking of ways to simply the heat maps without taking away important information...
Thank you!!