Unknown error using confirmed working script and sample data

[Alana Babcock]

Hi, 

I am trying to run a script from our group that has been used before to make a figure with the sample data I am using. I keep getting this error:

Error in `stat_tree()`:
! Problem while converting geom to grob.
ℹ Error occurred in the 1st layer.
Caused by error:
! Unknown colour name:

---
Backtrace:
     ▆
  1. ├─ggplot2::ggsave(...)
  2. │ ├─grid::grid.draw(plot)
  3. │ └─ggplot2:::grid.draw.ggplot(plot)
  4. │   ├─base::print(x)
  5. │   └─ggplot2:::print.ggplot(x)
  6. │     ├─ggplot2::ggplot_gtable(data)
  7. │     └─ggplot2:::ggplot_gtable.ggplot_built(data)
  8. │       └─ggplot2:::by_layer(...)
  9. │         ├─rlang::try_fetch(...)
 10. │         │ ├─base::tryCatch(...)
 11. │         │ │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
 12. │         │ │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
 13. │         │ │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
 14. │         │ └─base::withCallingHandlers(...)
 15. │         └─ggplot2 (local) f(l = layers[[i]], d = data[[i]])
 16. │           └─l$draw_geom(d, layout)
 17. │             └─ggplot2 (local) draw_geom(..., self = self)
 18. │               └─self$geom$draw_layer(...)
 19. │                 └─ggplot2 (local) draw_layer(..., self = self)
 20. │                   └─base::lapply(...)
 21. │                     └─ggplot2 (local) FUN(X[[i]], ...)
 22. │                       ├─rlang::inject(self$draw_panel(data, panel_params, coord, !!!params))
 23. │                       └─self$draw_panel(...)
 24. │                         └─ggplot2 (local) draw_panel(..., self = self)
 25. │                           └─GeomPath$draw_panel(...)
 26. │                             └─ggplot2 (local) draw_panel(..., self = self)
 27. │                               ├─grid::polylineGrob(...)
 28. │                               │ └─grid::grob(...)
 29. │                               ├─grid::gpar(...)
 30. │                               │ └─grid:::validGP(list(...))
 31. │                               │   └─grid (local) numnotnull("fontsize")
 32. │                               └─scales::alpha(munched$colour, munched$alpha)
 33. │                                 └─farver::decode_colour(colour, alpha = TRUE)
 34. │                                   └─farver:::decode_c(...)
 35. └─base::.handleSimpleError(`<fn>`, "Unknown colour name: ", base::quote(NULL))
 36.   └─rlang (local) h(simpleError(msg, call))
 37.     └─handlers[[1L]](cnd)
 38.       └─cli::cli_abort(...)

 39.         └─rlang::abort(...)

No matter how I try to adapt my script the error persists. I feel like it might be a compatibilty issue between the version of R I have and the packages. I am running on version 4.3.2 but the error also occurs on version 4.3.3. I have the version of ggplot2 (3.5.0), ggtreeExtra (1.12.0), ggnewscale (0.4.10), ggtree (3.10.1).  

Here is my script:

library(msaR)
library(msa)
library(rio)
library(seqinr)
library(ape)
library(ggtree)
library(ggplot2)
library(treeio)
library(ggnewscale)
library(ggstar)
library(ggtreeExtra)
library(scales)
library(Biostrings)
library(tidytree)

#Add dataframes
mySequences <- readAAStringSet('/Users/grahamscott/Documents/Phylogenetic-Tree-Sample/active_rAMPage.fasta')
sample_data <- import("/Users/grahamscott/Documents/Phylogenetic-Tree-Sample/pep_char.csv")

#Create MSA
activerAMPageMSA <- msa(mySequences)

#Convert MSA to distance alignment
rAMPage_converted <- msaConvert(activerAMPageMSA, type = 'seqinr::alignment')
d <- dist.alignment(rAMPage_converted, "identity")

#Create tree
d_matrix <- as.matrix(d)
tree <- nj(d_matrix)

#Convert tree to ggtree format
#tree is written and then read in order to convert from format used by ape into format used by ggtree
written_tree <- ape::write.tree(tree, 'active_rAMPage_tree')
converted_tree <- treeio::read.tree('active_rAMPage_tree')
converted_tree

#Tree with AMP names coloured by family membership and ring with colours depicting dataset origin
family_dataset_tree <- ggtree(converted_tree, layout='circular', size=0.2, options(ignore.negative.edge=TRUE))  %<+% sample_data +
  aes(color = I(family))+
  scale_color_manual(name = 'Family',
    breaks = c("Nigrocin","Brevinin-1","Brevinin-2","Apidaecin","NA"),
    labels = c("Nigrocin","Brevinin-1","Brevinin-2","Apidaecin","NA"),
    values = c("#0992ad","#a30584","blue","#60a106","black"),
    na.value = "black")+
  new_scale_fill()+
  geom_fruit(geom=geom_tile,
             mapping=aes(fill=dataset),
             width=0.02,
             offset=0.25)+
  scale_fill_manual(name = "Dataset",
                    breaks = c("Insect","Amphibian"),
                    labels = c("Insect","Amphibian"),
                    values = c("brown","#339900"))+
  geom_tiplab(offset = 0.01, size=3.5)


#Above tree with BLASTp percent identity results added (percent identity to top hit)
blastp_tree <- family_dataset_tree +
  new_scale_fill()+
  geom_fruit(geom=geom_tile,
             mapping=aes(fill=percent_identical),
             width=0.02,
             offset=0.05)+
  scale_fill_gradient2(
    name = "Percent Identity",
    low = "#3ee6ca",
    mid = "white",
    high = "#031b54",
    midpoint = 50
  )

#Above tree with black/red dots at tip points depicting which are known AMPs
novel_tree <- blastp_tree +
  new_scale_color() +
  geom_tippoint(
    mapping = aes(color= top_hit_known_amp),
    size = 1.5
  ) +
  scale_color_manual(
    name = "Top Hit Antimicrobial",
    breaks = c("yes","no"),
    labels = c("yes","no"),
    values = c("black","red")
  )

#Above tree with distance scale
novel_tree + geom_treescale()
ggsave("Tree.pdf", height = 8.25, width = 8.25, units = "in", dpi=800)