Manually modifying or providing dates on axis (themetree2)

[BaylorSci]

Is there a way to manually provide the dates to be used in theme_tree2? Specifically, i am interested in writing the dates between 1-11th in increments of two days.

I have two samples, taken at two different times. Despite using mrsd and setting the final sampled date (April 11th), the tree does not line up with the date line , nor does the dates presented encompass the sampled timeframe. With these files, i am able to successfully visualize this on nextstrain, but i want higher quality figures. I have tried modifying scale_x_ggtree, and various other options, but only got errors (presuming similar commands to ggplot options)

ggtree(tree, mrsd=sampling_dates[2]) + geom_tippoint(color="darkorchid",size=4, shape=18)+ geom_tiplab(size=6, as_ylab=FALSE, linesize=3,fontface=2, hjust=-0.01)+ geom_nodelab(size = 1.5, na.rm = TRUE, nudge_x = 0.045) + geom_nodepoint(color="goldenrod", size=4, alpha=1/2) + theme_tree2(bgcolor = "white")+ coord_cartesian(clip = 'off')+ xlab("Sampling period (April 2025)")+ myTheme

If i force dates (which the sampling dates as date format anyway) with as.Date=TRUE in ggtree(), i get image 2, which weirdly lengthens the branch length.

`
version 4.4.1 (2024-06-14 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 11 x64 (build 26100)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] cowplot_1.2.0 ggplot2_4.0.0 dplyr_1.1.4 ape_5.8-1 ggtree_3.12.0

loaded via a namespace (and not attached):
[1] jsonlite_2.0.0 gtable_0.3.6 crayon_1.5.3 compiler_4.4.1 tidyselect_1.2.1
[6] Rcpp_1.1.0 aplot_0.2.9 gridGraphics_0.5-1 parallel_4.4.1 ggplotify_0.1.2
[11] tidyr_1.3.1 ggfun_0.2.0 scales_1.4.0 lattice_0.22-6 R6_2.6.1
[16] tcltk_4.4.1 labeling_0.4.3 patchwork_1.3.2 generics_0.1.4 tidytree_0.4.6
[21] yulab.utils_0.2.1 tibble_3.2.1 pillar_1.11.1 RColorBrewer_1.1-3 treeio_1.28.0
[26] rlang_1.1.5 fs_1.6.6 S7_0.2.0 lazyeval_0.2.2 cli_3.6.4
[31] withr_3.0.2 magrittr_2.0.3 digest_0.6.37 grid_4.4.1 rstudioapi_0.17.1
[36] rappdirs_0.3.3 lifecycle_1.0.4 nlme_3.1-164 vctrs_0.6.5 glue_1.8.0
[41] farver_2.1.2 sessioninfo_1.2.3 purrr_1.1.0 tools_4.4.1 pkgconfig_2.0.3
`

[BaylorSci]

Eventually figured this out, and thought i would post for anyone else who may run into the same issue. If i take the initial script and use scale_x_ggtree, this is possible, although i am still trying to figure out how to allign the dated nodes with the defined scales

figure_mod <- f1 + scale_x_ggtree(breaks = c(0,0.01,0.03,0.04), labels = c("Apr 1","Apr 04","Apr 7", "Apr 12"))