visualizing a list of trees

[Weijian Guo]

Hi!

I'm using ggtree to visualise a phylogeny in R, and I've followed the guide for visualizing a list of trees.
However, when I add a layer of the best tree on the top of the density tree, the tiplabel was wrong. I want to know why and how to fix it. 

Here are my trees.

And here are my code.

library(ggtree)

btrees <- read.tree('samll.tre')

best_tree <- read.tree('best.tre')

df <- fortify(best_tree, branch.length='none')

ggtree(btrees, layout="slanted", color="lightblue", alpha=.3) +

  geom_tree(data=df, layout="slanted", size=3, color='firebrick')+

  geom_tiplab(size=10, color="purple")+ggtitle("trees")

ggtree(best_tree,layout="slanted")+geom_tiplab(size=5, color="purple")+ggtitle("best_tree")

Thank you.

Best wishes,

Weijian Guo

[Yu, Guangchuang]

what you need is a ggdensitree function, see https://github.com/GuangchuangYu/ggtree/issues/221.

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1. G Yu*, TTY Lam, H Zhu, Y Guan*. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution, 2018, 35(2):3041-3043. doi: 10.1093/molbev/msy194
2. 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. doi:10.1111/2041-210X.12628
3. Book: https://yulab-smu.github.io/treedata-book/
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Guangchuang Yu PhD

Professor
School of Basic Medical Sciences

Southern Medical University

Guangzhou, China

www: https://guangchuangyu.github.io

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