Is there a way of choosing how to scale the axis in Emperor? In Qiime 1 we have the option of scaling coordinates by percent explained.
The reason I am asking this is because I have a plot in which PC2 explains 19% and PC1 explains 43% but regardless of which axis I plot PC2, it is always twice as large as PC1.
AFAIK that feature is still in the works in the developer’s version of Emperor so at this point the easiest will be to use the old version. Just note that the PCoA files from QIIME2 are not compatible with QIIME1. Thus, the shortest path is to take your distance file and run principal_coordinates.py in QIIME1.
Thanks, to the best of my knowledge it should be fine that one axis is longer than the other, so I wouldn’t worry about that too much. We plan to add the functionality to scale axes soon, but don’t really have a specific ETA.