How to flip over the positions between a tip node and a inner node(with the same parent)

[lingling zheng]

Hi all:

      I want to modify the structure of a tree in figure1, and move node1 on the top of the tree. The only way I thought of is to flip over many times, may be it's not a good idea. However, when I flip over between node 14 (with two child nodes 7 and 8) and node 1, the node 8 and node 2 overlapped together (figure 2). I have tried to collapse node 14 first, but it comes with another error in flipping over between a tip node and a collapsed node.

     Please find the attachment of figer1 and figure2, thanks for your help!

Best wishes!

Lily

[Yu, Guangchuang]

can you provide a reproducible example?

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

--~--~---------~--~----~------------~-------~--~----~

Guangchuang Yu PhD

Postdoc researcher
State Key Laboratory of Emerging Infectious Diseases
School of Public Health
The University of Hong Kong

Hong Kong SAR, China

www: https://guangchuangyu.github.io

-~----------~----~----~----~------~----~------~--~---

[lingling zheng]

OK, please find the attachment of the tree file which is saved by NCBI common tree, and my code is:

test.Matazoa<-read.tree(file="/path/to/phyliptree_test.phy")

test<-ggtree(test.Matazoa) 

test + geom_text2(aes(label=node), hjust=-.3)  + xlim(0,8)

test<-flip(test,15,1)

##collapse node 15
cp <- ggtree(test.Matazoa) %>% ggtree::collapse(15)

cp  + geom_text2(aes(label=node), hjust=-.3)  + xlim(0,8)

flip(cp,15,1)

在 2018年1月22日星期一 UTC+8下午2:02:09，Yu, Guangchuang写道：

can you provide a reproducible example?

On Mon, Jan 22, 2018 at 1:53 PM, lingling zheng <zhlin...@gmail.com> wrote:

Hi all:

      I want to modify the structure of a tree in figure1, and move node1 on the top of the tree. The only way I thought of is to flip over many times, may be it's not a good idea. However, when I flip over between node 14 (with two child nodes 7 and 8) and node 1, the node 8 and node 2 overlapped together (figure 2). I have tried to collapse node 14 first, but it comes with another error in flipping over between a tip node and a collapsed node.

     Please find the attachment of figer1 and figure2, thanks for your help!

Best wishes!

Lily

--
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
 
Homepage: https://guangchuangyu.github.io/ggtree
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[Yu, Guangchuang]

all these two issues had been fixed in release v = 1.10.3 and devel v = 1.11.5.

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[lingling zheng]

Thanks for your help, but how can i get the version of ggtree (1.10.3)? I have updated the version of bioconductor to 3.6 and R version to 3.4.3, here's my code:

> source("https://bioconductor.org/biocLite.R")

Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help

> biocLite("ggtree")

BioC_mirror: https://bioconductor.org

Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30).

Installing package(s) ‘ggtree’

trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/ggtree_1.10.2.zip'

Content type 'application/zip' length 8564807 bytes (8.2 MB)

downloaded 8.2 MB

在 2018年1月22日星期一 UTC+8下午2:07:03，lingling zheng写道：

[Yu, Guangchuang]

You need to wait 2-3 days for Bioconductor to update tarballs.

Otherwise, you can use devel branch.

biocLite(c("tidytree", "guangchuangyu/treeio", "guangchuangyu/ggtree"))

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