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I'm having trouble with labeling single tips in my tree with ggtree. I'm trying to highlight and label nodes from a tree with geom_hilight and geom_cladelabel. This seems to work fine with nodes that have more than 1 tree tip, but when I try to label a single tip, I receive a warning message and the tip doesn't get labeled.

Example:

library(dplyr)
library(ggtree)

library(dplyr)
library(ggtree)

#Create tree
set.seed(123)
tree <- rtree(30)
ggtree(tree)

#Highlight and label clade
ggtree(tree) + geom_text(aes(label=node)) + geom_tiplab(size=3, offset=0.1) +
  geom_hilight(node=3, fill="steelblue", alpha=0.5) +
  geom_hilight(node=38, fill="pink", alpha=0.5) +
    geom_cladelabel(node=38, label="clade 2", align=T, 
                  color='black', fontsize=4)

enter image description here

As you can see, I'm able to highlight both node 38 and 3 with geom_hilight. I also labeled node 38 with the text "Clade 2" with geom_cladelabel.

However, when I try to label node 3 with geom_cladelabel, I receive a warning message:

#Highlight and label single tip
ggtree(tree) + geom_text(aes(label=node)) + geom_tiplab(size=3, offset=0.1) +
  geom_hilight(node=3, fill="steelblue", alpha=0.5) +
  geom_hilight(node=38, fill="pink", alpha=0.5) +
    geom_cladelabel(node=3, label="clade 1", align=T, 
                  color='black', fontsize=4) +
    geom_cladelabel(node=38, label="clade 2", align=T, 
                  color='black', fontsize=4)

Warning messages:
1: In max(sp.df$x, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
2: In min(y) : no non-missing arguments to min; returning Inf
3: In max(y) : no non-missing arguments to max; returning -Inf
4: In max(sp.df$x, na.rm = TRUE) :
  no non-missing arguments to max; returning -Inf
5: In min(y) : no non-missing arguments to min; returning Inf
6: In max(y) : no non-missing arguments to max; returning -Inf

The line from the clade label ends up covering the entire tree for some reason: enter image description here

Is there a way that I can label a single tip in the same fashion as clade_geomlabel does for regular nodes?

Any help is appreciated.

Kak Schoen
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  • Hi.. there's actually not such error when i try it. Also, you should set a seed so that the data and error can be reproduced. I tried it on single nodes and it works, I am on ggtree_1.16.6 dplyr_0.8.3 in R 3.6.1 – StupidWolf Mar 23 '20 at 00:33
  • Hi SW, I updated my question. I'm also running the same versions as you. I set a seed now so you can try to replicate my problem. – Kak Schoen Mar 23 '20 at 11:43
  • Thanks for the update. I still don't get the error. I have placed my session Info below and check some of the packages loaded via namespace. Those might be giving you the problem – StupidWolf Mar 23 '20 at 12:21

1 Answers1

1

This is not really an answer, but hoping to help you to troubleshoot since I don't have get the error. See below for the code,plot and session info. Seems like error came from clade_functions.R. First thing I would try is to check tidyr and tidytree packages, this part seems to rely heavily on that.

library(dplyr)
library(ggtree)

#Create tree
set.seed(123)
tree <- rtree(30)
ggtree(tree)

ggtree(tree) + geom_text(aes(label=node)) + 
geom_tiplab(size=3, offset=0.1) +
geom_hilight(node=3, fill="steelblue", alpha=0.5) +
geom_hilight(node=38, fill="pink", alpha=0.5) +
geom_cladelabel(node=3, label="clade 1", align=T, 
                  color='black', fontsize=2) +
geom_cladelabel(node=38, label="clade 2", align=T, 
                  color='black', fontsize=2)

enter image description here

R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: OS X El Capitan 10.11.6

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

locale:
[2] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[2] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[2] ggtree_1.16.6 dplyr_0.8.3  

loaded via a namespace (and not attached):
 [2] Rcpp_1.0.2          magrittr_1.5        tidyselect_0.2.5   
 [4] munsell_0.5.0       colorspace_1.4-1    ape_5.3            
 [7] lattice_0.20-38     R6_2.4.0            rlang_0.4.1        
[10] parallel_3.6.1      grid_3.6.1          nlme_3.1-140       
[13] gtable_0.3.0        lazyeval_0.2.2      assertthat_0.2.1   
[16] lifecycle_0.1.0     tibble_2.1.3        crayon_1.3.4       
[19] treeio_1.8.2        BiocManager_1.30.10 purrr_0.3.3        
[22] ggplot2_3.2.1       tidyr_1.0.0         vctrs_0.2.0        
[25] zeallot_0.1.0       tidytree_0.3.2      glue_1.3.1         
[28] labeling_0.3        compiler_3.6.1      pillar_1.4.2       
[31] backports_1.1.5     rvcheck_0.1.5       scales_1.0.0       
[34] jsonlite_1.6        pkgconfig_2.0.3
StupidWolf
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