I realize this might be niche–and the current stuff out there that is tree specific don’t apply in my case.
Trying to annotate the branches of a phylogenetic tree. So these are amino acid sequences. I want the branches to have what are the specific amino acid changes relative to the first sequence in the alignment (also imported). When I check the annotations, the positions are correct, the specific mutations (non-synonymous) not so much. But it is between my “step 7” and “step 8” that things go south. Here is the current script with the specific error when run:

# Load necessary packages
library(ape)
library(seqinr)
library(ggtree)
library(tidytree)
library(dplyr)

# Step 1: Read and parse the existing Newick tree
tree <- read.tree("test.newick")

# Debug: Print the tree to check structure
print(tree)

# Step 2: Read the amino acid sequences
sequences <- read.fasta(file = "test.fasta", as.string = TRUE)
seq_names <- names(sequences)

# Debug: Print sequences to check
print(seq_names)

# Step 3: Identify non-synonymous changes relative to the first sequence
ref_sequence <- sequences[[1]]
ref_aa <- strsplit(ref_sequence, "")[[1]]

non_syn_changes <- lapply(sequences[-1], function(seq) {
  compare_aa <- strsplit(seq, "")[[1]]
  changes <- which(ref_aa != compare_aa)
  changes
})

# Debug: Print non-synonymous changes
print(non_syn_changes)

# Step 4: Create a data frame for branch annotations
annotations <- data.frame(
  node = (Ntip(tree) + 1):(Ntip(tree) + Nnode(tree)),
  label = "",
  stringsAsFactors = FALSE
)

# Step 5: Populate annotations with amino acid changes
for (i in seq_along(non_syn_changes)) {
  changes <- non_syn_changes[[i]]
  if (length(changes) > 0) {
    annotations$label[i] <- paste("Amino acid changes:", paste(changes, collapse = ","))
  }
}

# Debug: Print annotations to check
print(annotations)

# Step 6: Convert tree to ggtree object
ggt <- ggtree(tree)

# Debug: Print ggtree object
print(ggt)

# Step 7: Add annotation of amino acid changes
annotations <- filter(annotations, label != "")  # Filter out empty labels

# Ensure correct node mapping for annotations
ggt <- ggt %<+% annotations + geom_text(aes(label = label), hjust = -0.3)

# Debug: Print ggtree object after annotation
print(ggt)

# Step 8: Save the plot as PDF
ggsave("annotated_phylogenetic_tree.pdf", ggt, width = 10, height = 8)

And this is the error I keep getting:

Error in `auto_copy()`:
! `x` and `y` must share the same src.
ℹ `x` is a <tbl_tree/tbl_tree/tbl_df/tbl/data.frame> object.
ℹ `y` is an integer vector.
ℹ Set `copy = TRUE` if `y` can be copied to the same source as `x` (may be slow).
Run `rlang::last_trace()` to see where the error occurred.

I have tried a number of various workarounds and even adapting pre-existing tools. But a tree should be considered a “graph”. I am trying to get Figure 5 in terms of the tree from (https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210x.12628)