I recently started using Qiime2 and I love it!
However I was not able to figure out how to get the cool emperor visualization for my data that can be seen
In the Provenance tab of this example, it says you only need one step from the deduplication output (table & sequences) to the 3D pcoa.
However it seems much more complicated to me. When I checked the necessary input for:
qiime emperor plot --i-pcoa [file].qza […other input and otutput options]
it says it needs an already calculated “PCoAResults”-artifact.
So I looked up how to make that and I found:
qiime diversity pcoa --i-distance-matrix [some_file].qza --o-pcoa [out_file].qza
So to get the pcoa file I need a distance matrix. I looked up how to get that and found:
qiime metadata distance-matrix --m-metadata-column [another_file].qza [other options…]
So, now I am stuck here.
On the one hand this long trail of commands seems wrong, because in the example it was just one step from the table & sequence files. On the other hand it might be the only way to generate the pcoa data. In this case I do not understand what the –m-metadata-column file should be. Do I have to generate the numbers for my samples outside of qiime2?
I could not find other entries dealing with this and because emperor seems to be added quite recently I decided to post in this group! Thank you for your help and creating qiime2!