Question: How can I use 'geom_taxalink()' with the circular layout in the 'ggtree' package in R?
0
26 days ago by
sd.gamboa.t50
sd.gamboa.t50 wrote:

Hello,

I want to create a figure of an annotated phylogenetic tree in circular layout with ggtree in R. Some tips 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, example code and output, desired result, and session info.

I'd appreciate any help to get my desired output.

Thanks!

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)


The result I get:

Desired result:

Session Info

info <- 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}

rstats ggtree ggplot2 R phylogeny • 208 views
ADD COMMENTlink
modified 23 days ago • written 26 days ago by sd.gamboa.t50
1

Cross-posted: https://support.bioconductor.org/p/132539/

ADD REPLYlink written 26 days ago by Kevin Blighe63k
1

I see what you mean. 'Curvature' is usually controlled by the curvature parameter that is passed to geom_taxalink(); however, it only works for the non-circular layout, as inferred from here: https://bioconnector.github.io/workshops/r-ggtree.html

Note that in your second plot, you have already added that line manually - is that not an option?

ADD REPLYlink written 25 days ago by Kevin Blighe63k
1

The images I posted were an example of what I need to achieve. Actually, I have a tree with over 8,000 tip nodes and more than 140,000 connections between tips. I can easily create the tree with ITOL (https://itol.embl.de/), but I've been having trouble exporting it. I assume it's because of the size of the tree as I have no problem with smaller ones (I'll try with a faster computer and see what happens).

ADD REPLYlink written 25 days ago by sd.gamboa.t50
1

I see. You could contact ITOL, too, or create an issue / feature request on the ggplot2 GitHub repository. There is always going to be a way to manually add lines, text, etc to any plot - difficult to cater for all end use-cases.

ADD REPLYlink written 25 days ago by Kevin Blighe63k

There now seems to be a solution: https://support.bioconductor.org/p/132539/#132589

ADD REPLYlink written 23 days ago by Kevin Blighe63k
1
23 days ago by
sd.gamboa.t50
sd.gamboa.t50 wrote:

The solution is to upgrade to the version 2.3.2 (last version as for July 15, 2020), which is hosted on github by the author of the package:

devtools::install_github("YuLab-SMU/ggtree")

ADD COMMENTlink modified 23 days ago by genomax87k • written 23 days ago by sd.gamboa.t50
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