Questions tagged [ggtree]
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10 questions
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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 ...
1
vote
1
answer
118
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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 ...
2
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1
answer
498
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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 ...
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2
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1
answer
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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 ...
- 118
1
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0
answers
92
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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
...
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2
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1
answer
200
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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.
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3
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2
answers
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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 ...
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2
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1
answer
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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. ...
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1
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1
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515
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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 ...
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2
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1
answer
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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 :
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