plot_tree: combining "treeonly" with taxonomy table or instead have only one geom_point per leaf?

[RJ333]

Hello everyone,

I'm trying really hard to generate a tree which does not display the geom_points per sample (I have about 300 samples) but displays the taxonomic name + OTU id. I thought this would be the same question (#617) but on the suggested page there was no tree similar to what I'm looking for.

So I tried to use "treeonly" to get rid of the geom_points, but (if I haven't done anything wrong) this also removes the possibility to display anything else apart from the Otu names (or ASV or how you want to call them, the link between the different phyloseq-slots)).

# fine, but gives me a lot of sample points which I don't need
plot_tree(ps, label.tips = "Genus")
# this works also fine, but the sequence header alone does not help me
plot_tree(ps, "treeonly", label.tips = "taxa_names")
# this would be what I want:
plot_tree(ps, "treeonly", label.tips = "Genus")
# but gives
Don't know how to automatically pick scale for object of type taxonomyTable. Defaulting to continuous.
Error in as(x, "matrix")[i, j, drop = FALSE] :
  incorrect number of dimensions

Do you say a way to get there? And if not, e.g. if the geom_points are required to map the taxonomic data, could they be reduced to a single geom_point per leaf?

Thank you very much!

René

BTW: this (#1039) is a related issue, but not the same!

[nachishankar]

Hi,
I'm having exactly the same issue with my tree - but neither of these posts have got any solution to the problem. Could someone please let me know if you did find a way to get tree tip labels something other than the OUT001, 0002 etc.. to actual genus/family etc names?