Dear all,
I want to plot an ultrametric BEAST2 tree with circles in the nodes colored
by posterior probability: > 0.95 black, between 0.5 and 0.95 gray and 0.5
and below no circle (or white). Is that possible? I have tried several
packages and solutions and the more close solution I figured out is:
# Load the required libraries
library(treeio)
library(phytools)
# Set the working directory
setwd("~/Documents/Anolis_Ana/BEAST2/")
# Read the tree from the file
my_tree <- read.beast("anolis_ND2.tre")
posterior <- my_tree$posterior
# Define colors based on posterior probabilities
colors <- ifelse(posterior > 0.95, "black",
ifelse(posterior > 0.5, "darkgray", "white"))
# Assign colors to tree nodes
my_tree$node.color <- colors
# Plot the tree with custom node colors
plot(my_tree,direction="upwards",show.tip.label = F, node.color = colors)
The problem is it colors the branches instead of the nodes. Any ideas?
Thank you very much!
Pedro
-----
Dr. Pedro P. G. Taucce
Postdoctoral Researcher (CNPq - PDJ)
National Institute of Amazonian Research (INPA)
Av. André Araújo 2936, Petrópolis
CEP 69.067-375 Manaus, AM
www.pedrotaucce.org
Lattes <http://lattes.cnpq.br/6010051338306653> | LinkedIn
<http://linkedin.com/in/pedrotaucce> | ResearchGate
<https://www.researchgate.net/profile/Pedro-Taucce>
Associate Editor, *The Herpetological Journal
<https://www.thebhs.org/publications/the-herpetological-journal>*
Subject Editor, *Zoosystematics and Evolution <https://zse.pensoft.net/>*
Subject Editor, *Neotropical Biology and Conservation
<https://neotropical.pensoft.net/>*
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