KasperSkytte
Ordination plots do not use equally scaled axes/coordinate system
Ordination plots (biplots/joint plots) should use a coordinate system where 1 unit change in the x direction is equal to 1 unit change in the y direction. This allows a true visual interpretation of distances on the plot being a 2-d approximation of the distances in the original data.
All of the ordination methods in ampvis should be visualised within a coordinate system with a fixed aspect ratio of 1.
The solution to this issue is to add + coord_fixed(ratio = 1) to the base plot object after it is created and before other layers are added (for simplicity's sake).
While I agree, some people would be interested in looking at invididual axes only. But could make it optional with a default.
If you are only looking at a single axis, then there is no other axis to visualize and coord_fixed(1) would do nothing (there is not other axis to be fixed against), so there is no harm (unless you are plotting something derived on the y axis (like a density or histogram), in which case sure, you don't need equal scaling.