Questions tagged [ggtree]

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Error importing Maximum Credibility Tree from BEAST into R using treeio's read.beast()

I've encountered an issue that I'm hoping someone can help with. I constructed a phylogenetic tree using BEAST1 and then extracted the Maximum Credibility Tree using treeannotator. I'm trying to ...
Gerald Vasquez Aleman's user avatar
0 votes
1 answer
47 views

Scale on the y-axis in a tree rotated with 'layout_dendrogram()' using ggtree

I'm editing a time-scaled tree using ggtree. The dates are correctly adjusted when I apply the 'mrsd' command and 'theme_tree2()', but when I try to rotate the tree with 'layout_dendrogram()', the ...
Gerald Vasquez Aleman's user avatar
2 votes
1 answer
339 views

Using R `ggtree`, attach extra data next to the nodes on an illustrated tree/newick file

This is really a programming question but ggtree might be too obscure for this question to be posted on StackOverFlow as a general R related question. I am having ...
Sudoh's user avatar
  • 217
2 votes
1 answer
70 views

Converting Pairwise single- linkage clustering distance data to "newick" format

I have pairwise distance data for single linkage cluster and I would like to convert it to newick format. I was unable to find a conversion algorithm. I require newick format for visualization and ...
SuleymanSelim's user avatar
1 vote
0 answers
71 views

difficult in runing the R code for ggtree

I tried to run the below code but ended having issue. I have checked thoroughly and I didn't find any mismatch in fasta sequence ...
Manasa K.G.'s user avatar
2 votes
1 answer
156 views

drawing multiple sequence alignment as tree in R

I am very new here. Please help me with my codes as am trying to draw multiple sequence alignment as tree suing ggtree package in R and i have following error. ...
Manasa K.G.'s user avatar
3 votes
2 answers
2k views

R ggtree apply colors to branches with multiple colors

This question was also asked on StackOverflow I have a phylogenetic tree made with a Newick format ((a:1,b:1):2, (c:1, d:1):3):1; The output will be I have drawn ...
SG Kwon's user avatar
  • 45
2 votes
1 answer
69 views

ggtree:How to keep leading zero ‘0’ in the tiplabel?

I am using ggtree to draw a phylogenetic tree. Some taxa IDs have a 0 at the beginning. However, when I plot the tiplabel the leading zero is automatically dropped. ...
YP CHEN's user avatar
  • 81
1 vote
1 answer
414 views

How to import a phylogenetic tree (in nexus format) with node support values in R

I have a phylogenetic tree in nexus format that was generated with RAxML. In the tree file, there are node support values. I want to plot this tree in R with the support values showing. However, when ...
user12167116's user avatar
2 votes
1 answer
380 views

Plot information stored in dataframe within a tree (ggtree)

Hello to the entire Stackoverflow community! I'm writing to you because I'm currently building a phylogeny with ggtree and I have in parallel a table like this one: df : ...
chippycentra's user avatar