Hello,

I want to create a figure of an annotated phylogenetic tree in circular layout with ggtree in R. Some tip nodes must be linked by a curve line. I can achieve this with the geom_taxalink() function in the rectangular layout, but it doesn't work in the circular layout. This seems to be because the geom_taxalink() uses geom_curve(), which doesn't support non-linear coordinates. I get the following message:

"Warning message: geom_curve is not implemented for non-linear coordinates"

Below: reproducible code, the output I get, the output I want, and session info.

I'd appreciate any help to get the result I need.

Thanks!

Samuel

Example code:

library(treeio)
library(ggtree)
library(ggplot2)

raxml_file <- system.file("extdata/RAxML", 
                          "RAxML_bipartitionsBranchLabels.H3",
                          package="treeio")

raxml <- read.raxml(raxml_file)
raxml <- as_tibble(raxml)
raxml$label <- gsub("_.*$", "", raxml$label)
raxml <- as.treedata(raxml)

my_tree <- ggtree(raxml, layout = "circular", branch.length = "none") +
  geom_tiplab2(size = 3, hjust = 1) +
  geom_taxalink("EU857082", 
                "YGSIV1534",
                color = "red") +
  scale_x_reverse(limits = c(100, 0))

ggsave("my_tree.png", my_tree,
       width = 10, height = 10, units = "in",
       dpi = 300)

Link to the result I get: https://raw.githubusercontent.com/sdgamboa/ggtree_example/master/my_tree.png

Link to the result I need: https://raw.githubusercontent.com/sdgamboa/ggtree_example/master/my_tree2.png

tinfo <- sessionInfo()
toLatex(info, locale = FALSE)
# \begin{itemize}\raggedright
# \item R version 4.0.2 (2020-06-22), \verb|x86_64-pc-linux-gnu|
#   \item Running under: \verb|Ubuntu 18.04.4 LTS|
#   \item Matrix products: default
# \item BLAS:   \verb|/usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1|
#   \item LAPACK: \verb|/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1|
#   \item Base packages: base, datasets, graphics, grDevices, methods,
# stats, utils
# \item Other packages: ggplot2~3.3.2, ggtree~2.2.1, treeio~1.12.0
# \item Loaded via a namespace (and not attached): ape~5.4,
# aplot~0.0.4, assertthat~0.2.1, BiocManager~1.30.10, cli~2.0.2,
# colorspace~1.4-1, compiler~4.0.2, crayon~1.3.4, dplyr~1.0.0,
# ellipsis~0.3.1, fansi~0.4.1, farver~2.0.3, generics~0.0.2,
# glue~1.4.1, grid~4.0.2, gtable~0.3.0, jsonlite~1.7.0, labeling~0.3,
# lattice~0.20-41, lazyeval~0.2.2, lifecycle~0.2.0, magrittr~1.5,
# munsell~0.5.0, nlme~3.1-148, parallel~4.0.2, patchwork~1.0.1,
# pillar~1.4.6, pkgconfig~2.0.3, purrr~0.3.4, R6~2.4.1, Rcpp~1.0.5,
# rlang~0.4.7, rstudioapi~0.11, rvcheck~0.1.8, scales~1.1.1,
# tibble~3.0.3, tidyr~1.1.0, tidyselect~1.1.0, tidytree~0.3.3,
# tools~4.0.2, vctrs~0.3.1, withr~2.2.0
# \end{itemize}

We've updated ggtree (v=2.3.2, currently in github) to extend geom_taxalink to support circular layout.

Currently your code will produce:

[image: image.png]