Hi Nick,

There is a fantastic package for visualizing trees, the "ggtree" package:


https://github.com/GuangchuangYu/ggtree


Here is a vignette with several examples on how to display trees, including 
your circular phylogram visualization:


https://bioconductor.org/packages/devel/bioc/vignettes/ggtree/inst/doc/treeVisualization.html#phylogram-and-cladogram


You can read the documentation to figure out how to plot tip labels, I'm sure 
it's possible. The ggtree package is very powerful but also different in 
comparison with ape, as it is built on top of the "grammar of graphics" ggplot 
package.


Best,

Bjørn Tore Kopperud


G Yu, DK Smith, H Zhu, Y Guan, TTY Lam*. ggtree: an R package for visualization 
and annotation of phylogenetic trees with their covariates and other associated 
data. Methods in Ecology and Evolution. 2017, 8(1):28-36.?



________________________________
From: R-sig-phylo <r-sig-phylo-boun...@r-project.org> on behalf of Carleson, 
Nick <carle...@oregonstate.edu>
Sent: 24 August 2018 17:04
To: r-sig-phylo@r-project.org
Subject: [R-sig-phylo] Aligning tree tip labels together in ape

Hello all,

I'm using the R package 'ape' to make non-ultrametric phylogenetic trees . I 
want to align tip labels together when drawing a tree with plot.phylo(), and 
also add on more labels using the tiplabels() function. But, I can't get 
additional tip labels from tiplabels aligned properly with those from 
plot.phylo. When I call tiplabels, the labels are being drawn at the true edge 
length instead of neatly around the plot with the tip labels drawn by 
plot.phylo. So, in the plot below, I want the tip labels (circles) to be 
aligned adjacent to the tip labels (names) drawn by plot.phylo.

Good: tips like t30, t31, and t2
Bad: tips like t1, t20, and t21

[cid:ii_jl74vfw93_16568e27b224020e]


Can anyone help me out?

Below is the code to produce the tree above. I'm using ape version 5.1 and R 
version 3.4.3.

library(ape)
set.seed(31)
sim_tree <- rlineage(0.1, 0.05)
plot.phylo(sim_tree, type = "fan", align.tip.label = TRUE)
tiplabels(pch = 19, col = rainbow(3), offset = 6)

Thanks all!


Nick Carleson

PhD Student | Oregon State University
Graduate Research Assistant | Botany and Plant Pathology
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