Tool:ggtree: phylogenetic tree visualization and annotation

Question

[Guangchuang Yu]

ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

The ggtree package extending the ggplot2 package. It based on grammar of graphics and takes all the good parts of ggplot2. ggtree is designed for not only viewing phylogenetic tree but also displaying annotation data in the tree.

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.

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Homepage: https://guangchuangyu.github.io/ggtree/

Documentation: https://guangchuangyu.github.io/ggtree/documentation/

Featured Articles: https://guangchuangyu.github.io/ggtree/featuredArticles/

Report issues: https://guangchuangyu.github.io/ggtree/#feedback

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Examples

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[Naresh]

Can we see species in this tree. (The tree of life)

[Farbod]

Dear Guangchuang Yu, Hi

Sorry for my simple question but would you please help me for importing a Newick file (e.g test.nwk) in ggtree for drawing phylogenic tree?

I am using Rstudio.

~ Best

[Farbod]

I have solve it as below, would you check it please :

biocLite("ggtree", type = "source") #for solving the Error: StatTreeHorizontal was built with an incompatible version of ggproto.

library(ape)
library("ggplot2")
library(ggtree)
tree <- read.tree(file = "test.nwk")
ggtree(tree)

[Guangchuang Yu]

that is correct. Actually, you don't need to load ape and ggplot2. Only library(ggtree) would be fine.

[Farbod]

Dear Guangchuang, Hi

I sometimes received the following error from the nwk files I have exported from MEGA6.

Have you any idea about it ?

Error in read.tree(file = "2.nwk") : The tree has apparently singleton node(s): cannot read tree file. Reading Newick file aborted at tree no. 1

[Guangchuang Yu]

pls google search it before posting question. see http://stackoverflow.com/a/35633663/3844636.

[Farbod]

Hi, I have searched but I did not find any related topic. Thank you for your help.

[abdul.suboor123]

I want to know that How to execute my sequences file which I have already loaded in Rstudio? I don't know how to use my file in command for constructing circular Tree. Every time I got an "unexpected error".

[Joe]

Please ask a separate question with all the necessary details. Tool posts are typically just for advertising that the tool exists, and not for extended discussion of issues or errors.

[1769mkc]

i have a tree I wanted to label the tree with external annotation. How to do that I been looking at the manual but not clear. I have made an annotation file which has the tip label and its associated data which i want to overlay on my final plot..Any example you can cite in your manual?