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 <[email protected]> on behalf of Carleson, Nick <[email protected]> Sent: 24 August 2018 17:04 To: [email protected] 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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