add a scale to unrooted tree

[Miguel Morard Pedrouzo]

I am trying to add a scale to an unrooted tree with geom_treescale, but when I use it, the tree completely collapses and I am not able to set anything that fix it. Anybody has any idea on how to do it ?

[Yu, Guangchuang]

you can set x and y positions manually in geom_treescale. Besides, using +theme_grey() is useful if you have no idea of the coordination.

set.seed(20180224)
x = rtree(30)
ggtree(x, layout='unrooted') -> p
p + ggplot2::theme_grey() + geom_treescale(x=7, y=-5.5, offset=.1)

​

On Wed, Feb 21, 2018 at 5:41 PM, Miguel Morard Pedrouzo <miguel...@gmail.com> wrote:

I am trying to add a scale to an unrooted tree with geom_treescale, but when I use it, the tree completely collapses and I am not able to set anything that fix it. Anybody has any idea on how to do it ?

--
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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--

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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

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[ksw]

Dear all,

Thank you for the above messages on this and for a fantastic resource. I am also having trouble adding a tree_scale to an unrooted tree even when I follow the steps above because the coordinates shown with the theme_grey() seem to be inconsistent with those for geom_treescale(). 

I am trying the following, with the attached tree file: 

tre = read.tree('results/tree/vitoria.treefile')

# Add tree_scale
p <- ggtree(tre, layout="unrooted") + ggplot2::theme_grey()
p + geom_treescale(x = .003, y = -.001)

Any suggestions would be fantastic. Thank you very much!

On Saturday, February 24, 2018 at 3:30:08 AM UTC-7 gc...@connect.hku.hk wrote:

you can set x and y positions manually in geom_treescale. Besides, using +theme_grey() is useful if you have no idea of the coordination.

set.seed(20180224)
x = rtree(30)
ggtree(x, layout='unrooted') -> p
p + ggplot2::theme_grey() + geom_treescale(x=7, y=-5.5, offset=.1)

​

On Wed, Feb 21, 2018 at 5:41 PM, Miguel Morard Pedrouzo <miguel...@gmail.com> wrote:

I am trying to add a scale to an unrooted tree with geom_treescale, but when I use it, the tree completely collapses and I am not able to set anything that fix it. Anybody has any idea on how to do it ?

--
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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