Plot augur refine tree with ggtree

[diegogotex]

Hi all,

I’ve been trying to plot the calibrated tree from Augur Refine using GGTree in R, but the scale on the x-axis doesn’t match that on the Auspice visualisation.

I ran augur-refine with the following command:

augur refine \
        --tree $RESULTS/aligment.fasta.treefile \
        --alignment $RESULTS/aligment.fasta \
        --metadata $RESULTS/filtered_metadata.tsv \
        --output-tree $RESULTS/time_solved.tree \
        --output-node-data $RESULTS/time_solved_node_data.json \
        --timetree \
        --coalescent 'opt' \
        --date-confidence \
        --date-inference 'joint' \
        --root 'best' \
        --seed 1234567

and this is the tree when exported into auspice:

So, in R, I’ve ran:

tree <- read.newick("~/Desktop/Phylo/ML/results/time_solved.tree")


tree_plot <- ggtree(tree, 
                    mrsd="2025-10-08",
                    color="gray30")+
          theme_tree2()

tree_plot+
  expand_limits(y=-250)

The topology and branch length seem to be the same. However, the temporal scale on the x axis is different.

Therefore, I had to adjust the length of the tree to fit the temporal scale, reproducing an approximate scale of the Auspice visualisation by multiplying the length of the edges by 3270. I tried multiple values before settling on this one, which seems to be the closest to the Auspice scaling.

tree <- read.newick("~/Desktop/Phylo/ML/results/time_solved.tree")
tree$edge.length <- tree$edge.length * 3270

tree_plot <- ggtree(rsva_tree, 
                    mrsd="2025-10-08",
                    color="gray30")+
          theme_tree2()+
          expand_limits(y=-150)+
          scale_x_continuous(limits = c(1920,2026),
                     breaks = seq(1920,2025,by=5)
                     )

tree_plot

Does anyone know if there is a solution for importing and visualising exact values in ggtree?

Best regards,
Diego

[jonr]

Maybe this thread will help? How to get the correct time axis when using augur refine and timetree? - Nextstrain Discussion

I extracted “node_dates” from each node in branch_lengths.json and then used the minimum and maximum node dates for calibrating the x-axis. I also calculated a “scale_factor” which was the x-range (max node date - min node date) divided by the maximum tree height (max(node.depth.edgelength(tree))). I used plot.phylo from phytools though… Let me know if you need the exact code.