grepl does not work inside geom_tiplab2 while working inside geom_tiplab?

[Ales Bucek]

Hi!
I wan to draw a circular tree with only those tip labels shown which match a "Mqua" pattern. I want to use geom_tiplab2 to nicely orient the tip labels, but grepl apparently does not work and all tip labels are shown instead:

ggtree(tree1_midpointrooted, branch.length="none", layout="circular", aes(angle=angle)) +
+     geom_tiplab2(aes(label=label, subset=(grepl("Mqua",label)==TRUE)), color="green")

On the other side, when I use geom_tiplab, only the labels containing "Mqua" are shown according to my expectation:

ggtree(tree1_midpointrooted, branch.length="none", layout="circular", aes(angle=angle)) +
+     geom_tiplab(aes(label=label, subset=(grepl("Mqua",label)==TRUE)), color="green")

Do you have any hints how to get the nice orientation of labels as in geom_tiplab2() while also using subset and grepl to select particular labels?

Thanks in advance!
Ales

[Yu, Guangchuang]

In github version of ggtree, geom_tiplab2 can work with user define subsetting.

library(ggtree)
set.seed(20180224)
x = rtree(30)
ggtree(x, layout='circular') + 
    geom_tiplab2(aes(subset = node < 15))

​

--
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

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

[gc...@connect.hku.hk]

In github version of ggtree, geom_tiplab2 can work with user define subsetting.

library(ggtree)
set.seed(20180224)
x = rtree(30)
ggtree(x, layout='circular') + 
    geom_tiplab2(aes(subset = node < 15))

[Ales Bucek]

Dear Guangchuang,
thanks for your response!
Would you give me an example how to subset tips based on a presence of a substring in their name? (i.e. as in my original example, select tips with names which include "Mqua" string). I apparently did not figure out the syntax. Thanks for any advice!
Ales

On Saturday, February 24, 2018 at 8:39:05 PM UTC+9, Yu, Guangchuang wrote:

In github version of ggtree, geom_tiplab2 can work with user define subsetting.

library(ggtree)
set.seed(20180224)
x = rtree(30)
ggtree(x, layout='circular') + 
    geom_tiplab2(aes(subset = node < 15))

​

On Thu, Feb 22, 2018 at 3:59 PM, Ales Bucek <bucek...@gmail.com> wrote:

Hi!
I wan to draw a circular tree with only those tip labels shown which match a "Mqua" pattern. I want to use geom_tiplab2 to nicely orient the tip labels, but grepl apparently does not work and all tip labels are shown instead:

ggtree(tree1_midpointrooted, branch.length="none", layout="circular", aes(angle=angle)) +
+     geom_tiplab2(aes(label=label, subset=(grepl("Mqua",label)==TRUE)), color="green")

On the other side, when I use geom_tiplab, only the labels containing "Mqua" are shown according to my expectation:

ggtree(tree1_midpointrooted, branch.length="none", layout="circular", aes(angle=angle)) +
+     geom_tiplab(aes(label=label, subset=(grepl("Mqua",label)==TRUE)), color="green")

Do you have any hints how to get the nice orientation of labels as in geom_tiplab2() while also using subset and grepl to select particular labels?

Thanks in advance!
Ales

--
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]

aes(subset=(grepl("Mqua",label)))

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[Ales Bucek]

Ah, I see. geom_tiplab2 is apparently not working with subset because I do not have the "github" version of ggtree as you suggested above. I tried to install it via

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

but I get an error while loading the package:

>library(ggtree)
Error: package or namespace load failed for ‘ggtree’:
 object ‘groupClade’ is not exported by 'namespace:treeio'

Do you have a suggestion how to solve this?
Thanks!

aes(subset=(grepl("Mqua",label)))

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