Open marwa38 opened 1 year ago
any advice or comments please @joey711
You might find ggtree package more useful for customization. If you search around, you should find some examples of phyloseq + ggtree. Basically, handing off data from phyloseq object to ggtree. Hope that helps!
Thanks @joey711 should the tree be binary for visualisation in plot_tree()? I tried ggtree beforehand but I found it much easier to use plot_tree(). I will use ape package to draw a scale bar on the tree. Please comment on my queries, thanks for your inputs.
Hi guys Thank you so much for plot_tree() it is making things easier. Could you please help me with my queries; 1- According to the info you provided about the function that the points represented, how many times was observed. as in the excerpt:
Does this mean the number of families and beyond or the number of phyla or taxa only (count abundances or relative abundances)?
2- how to avoid the overlap? I tried different spacing, but it didn't work.
4- the abundances are the abundances of phyla asvs?
![image](https://user-images.githubusercontent.com/68851733/202032141-eb2cdbb4-2f33-4979-b030-4bcb3e5223db.png)
base.spacing = 0.01
andbase.spacing = 0.03
, also changed the ggsave options:ggsave("trees/ps.prev.tree_phylum.tiff", height = 7, width = 15, scale = 1.2)
3- can't I add a ruler of the length as the above figure5- the branch length doesn't represent the higher abundance?
Thank you M