I love the opportunity to do a biplot with Aichison distances in emperor! But for some reason I cannot change the sample points’ size as I used to in a normal PCoA. The dots are now too small to distinguish the colors in a publication figure (and even for a presentation, but we are currently finalising a manuscript ) I attached one of my figures as an example.
How can I fix this?
In addition, if you can tell me how I can replace the Seq_* with the actual taxonomy (I know which they are, e.g. 00001 is F. prausnitzii) I would be very happy
Thanks so much for your help!
To get taxonomy in the biplot you can use
- a collapsed table as input table
- edit html file inside of the qzv and replace manually or with a script all hashes on assigned taxonomy.
Its strange that you can’t change size - in my biplots I can easily resize, recolor or reshape all samples according to the metadata file provided.
Keep in mind that if you are using a collapsed table the showed in the biplot bacteria can be different from represented hashes (since several hashes can be assigned to the same taxonomy).
Would you mind sharing the emperor plot that produced that figure? I would like to have a look and see if I can debug this. You should see a
Scale tab on the right sidebar. However, if this isn’t showing, there might be something else going on.
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