I am using DEICODE on my 16S samples and I believe something weird is happening, as you can see in this plot - aitch-biplot-rarefied.qzv (1.7 MB). It seems that the vectors are somehow influencing the first axis of the PCOA and the variation I used to see is shifted to the second and third axes.
I re-did the PCOA biplot following the instructions in this other qiime2 post, and this was my resulting biplot- emperor-vis-biplot-pcoa-aitch.qzv (1.7 MB). For this last plot, I used aitchison as the metric for the qiime diversity beta step (to produce the distance matrix).
That being said, I have three questions:
- Why are the vectors of the DEICODE biplot interfering with the results of the ordination?
- What exactly is the aitchison metric doing when I select it through the qiime diversity beta method? I don’t really know what where to look for that info- as well as for the rest of the metrics here.
- Are the plots generated from the two approaches supposed to be similar? Or should I expect some differences on the resulting ordinations?