Tree tips not colored according to specified colors about ggtree

[brj1]

I cannot reproduce the error message. I don't know what your tree (which package is ncbi_tree from?) or CSV file look like.

Though this will probably won't fix your issue, assigning colour to plot elements does not work in ggplot by passing the colours directly through an aesthetic. You want to put the parameter to be coloured (in your case Trait) in the aes call and then modify the colouring by scaling the aesthetic (adding scale_colour_manual). See below:

p = ggtree(fungi_tree)
p= p %<+% Taxon_List_clean +
geom_tiplab(aes(x, y, color=Trait)) +
geom_highlight(node=28, fill="purple", type="rect", to.bottom=FALSE) +
geom_highlight(node=31, fill="black", type="rect", to.bottom=FALSE) +
geom_highlight(node=44, fill="blue", type="rect", to.bottom=FALSE) +
ggtitle(label="Observed fungi species phylogenetic tree",
subtitle="biotrophic in green, necrotrophic in black, hemibiotrophic in gray"
) + 
scale_colour_manual(values = c("biotroph"="green",
"necrotroph"="black",
"hemibiotroph"="gray"
))

[floridaman-93]

Hi @JakobDrumm @brj1
I have experienced a similar issue. The correction proposed by @brj1 doesn't work.
I had a script ready autumn last year and was generating this plot without any issues. This is something new.
@brj1 The code will go through after applying your correction, but the tips remain gray. The plot legend says that under grouping variable, you have "NA".
Anyone else has an idea how to solve this?