I am having trouble wrapping my head around and describing the meaning of the changes in my emperor plot after adding the custom axis option. I am comparing microbial communities from samples collected from the same individuals pre and post treatment. I have colored the points on my plot based on the categorical variable of "Pre" or "Post", in order to make a custom axis using a continuous variable, I changed the pre and post to numbers representing the day since the start of the experiment. I have attached screenshots of the original emperor plot, the same plot utilizing a custom axis, and the results of a PERMANOVA test for significance on the pre vs. post metadata column.
I would greatly appreciate if someone could explain to me how the changes in the clustering of the plots are generated and what this means in a broader view of the biological trends present.