display only certain labels with geom_tiplab() or geom_tiplab2()

[Mordecai Guzmann]

Hello!

I am trying to make a circular tree with some reference sequences and I only want to add labels of the reference sequences.
How would you solve it?

Thank you, M

[bena...@gmail.com]

Hi Mordecai,

There are a few options, the easiest one depends on your labels. You can subset explicitly inside geom_tiplab2, or use a matching expression if all the reference sequences have a common labeling scheme.

Can you post an example dataset?

[Mordecai Guzmann]

Hello and thanks for the quick and nice reply!

I cannot show the data, but I can show how I get my tree. Firstly:

>tree <- read.tree("filename.tre")        

>tree_p <- ggtree(tree, layout="fan", branch.length="none", open.angle=10)

>tree$Nnode

[1] 1031

> tree$tip.label
[1] "S5-MP..."                     
[2] "S5-MP..."

[...]                     
[971] "REF..."     #This i want to label, but not the first lines!

So I get my round tree. Which I want to use with gheatmap() later on, to display information about the found species. However some of the tips I would like to label before plotting the heatmap:

 >tree_p + geom_tiplab()

*shows the tree with all labels attached*

Now I don`t know how to tell geom_tiplab2() to only put labels on certain tips. (like tip number 971) 

So, it is not such a complicated problem, but I haven`t found any good documentations on geom_tiplab2().

All the labels I want start with "REF" and all the ones I don`t need start with "S", so this is an easy way to discriminate.

Thank you for your help and have a nice day!
Mordecai

[bena...@gmail.com]

Hello,

To produce a reproducible example, I use the ape package and the rcoal() function to make sample trees. The following example shows how you can use the aes() and the subset=() fucntions to plot tips based on node number, or instead based on a match in the name.  Hope this helps.

library(ape)
library(ggtree)

tree <- rcoal(5)
tree$tip.label <- c("REF-1","REF-2","S1","S2","S3")
full_tree    <- ggtree(tree) + xlim(0,2) + geom_tiplab()
full_tree
#Since we know the first two are reference, use the order
limited_tree1 <- ggtree(tree) + xlim(0,2) + geom_tiplab(aes(subset=(node %in% c(1,2))))
limited_tree1
#But we also know the names are different, so we can use that as well
#grepl() searches for 'RE' in the label, and returns true if found
#we use aes(subset=()) to only print those with the subset condition == TRUE
limited_tree2 <- ggtree(tree) + xlim(0,2) + geom_tiplab(aes(
      subset=(grepl('RE',label,fixed=TRUE)==TRUE)))
limited_tree2

[Mordecai Guzmann]

Hello Bena!

I played around with subset and grepl but I could not figure out how to solve it or use them together. Thank you for our advice! This helps me so much!

Thanks a lot!
M

[Yu, Guangchuang]

The discussion in <https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/aIK0h7XDUYg/MxmsOJL8EQAJ> may also helpful.

--
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, 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

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

[Mordecai Guzmann]

Thank you!

This also helps, as further examples help me understand the syntax better!
I am glad  there are so many helpful poeple :D

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