plot_tree() queries

[marwa38]

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:

method
(Optional). Character string. Default "sampledodge". The name of the annotation method to use. This will be expanded in future versions. Currently only "sampledodge" and "treeonly" are supported. The "sampledodge" option results in points drawn next to leaves if individuals from that taxa were observed, and a separate point is drawn for each sample.

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. base.spacing = 0.01 and base.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 figure

4- the abundances are the abundances of phyla asvs?

5- the branch length doesn't represent the higher abundance?

Thank you
M

[marwa38]

any advice or comments please @joey711

[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!

[marwa38]

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.