geoms with their own data don't work with ggtree

[markscherz]

Had everything working beautifully a few days ago, now I go to try to run the script and something is not working.

>tree<-pbtree(n=16,tip.label=LETTERS[1:16],scale=20)
>p <- ggtree(tree, size = 0.3) + 
  coord_cartesian(xlim = c(15,-30), ylim = c(-40,Ntip(tree)), expand = FALSE) +
  scale_x_continuous(breaks=seq(-30,0,10), labels=abs(seq(-30,0,10))) +
  geom_tiplab(cex = 0.7) +
  theme_tree2()
>p <- revts(p)
>p <- gggeo_scale(p, height = .03, abbrv = FALSE, neg = TRUE)
Ignoring unknown aesthetics: fill_geo_scale
>p
Error in FUN(X[[i]], ...) : object 'y' not found

Traceback yields

10. FUN(X[[i]], ...) 
9. lapply(aesthetics, rlang::eval_tidy, data = data) 
8. f(..., self = self) 
7. l$compute_aesthetics(d, plot) 
6. f(l = layers[[i]], d = data[[i]]) 
5. by_layer(function(l, d) l$compute_aesthetics(d, plot)) 
4. ggplot_build.ggplot(x) 
3. ggplot_build(x) 
2. print.ggplot(x) 
1. function (x, ...) UseMethod("print")(x)

So my guess is that it is failing because it is not able to find fill_geo_scale.
Curiously, in a second script, the error is "object 'x' not found", but I presume it is caused by the same problem.

[willgearty]

Hmm...when I run your code line for line, I get Error in FUN(X[[i]], ...) : object 'x' not found, as you do for your other script.
I've tried the code without the new "fill_geo_scale", and I'm still getting the same error:

> tree<-pbtree(n=16,tip.label=LETTERS[1:16],scale=20)
> p <- ggtree(tree, size = 0.3) + 
  coord_cartesian(xlim = c(15,-30), ylim = c(-40,Ntip(tree)), expand = FALSE) +
  scale_x_continuous(breaks=seq(-30,0,10), labels=abs(seq(-30,0,10))) +
  geom_tiplab(cex = 0.7) +
  theme_tree2()
> p <- revts(p)
> p + geom_rect(data = periods, aes(xmin = min_age, xmax = max_age), ymin = 0, ymax = 5, show.legend = FALSE)
Error in FUN(X[[i]], ...) : object 'x' not found

I'm gonna loop @GuangchuangYu in here, since this only appears to be a problem when adding the scale to ggtree objects.
Before the most recent update, the rectangles and labels were added as annotations, but now they are added as geoms, so that is the only change that could have caused the new issue. My best guess is that there's a conflict between the data used by ggtree and the data supplied by my package? Especially since the following works:

> p + geom_rect(xmin = -5, xmax = 0, ymin = -5, ymax = 0, show.legend = FALSE)

[markscherz]

That sounds possible. ggtree was having some really bad problems interacting with phytools over the last few days as well. I have repeatedly had to clear my environment and clean-sheet to get my other scripts working.

[willgearty]

@markscherz, until this is resolved you should be able to use the old version of deeptime (before the most recent changes) using the following:
install_github("willgearty/deeptime", ref = "37a00cd")
(I just checked and this works for your example)

[markscherz]

@willgearty excellent, thanks!