phyloXML and missing branch lengths

[jvolkening]

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Session Info

> sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS/LAPACK: /home/jeremy/miniconda3/envs/vIL4/lib/libopenblasp-r0.3.26.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] ggtree_3.2.0      treeio_1.27.0.002 lubridate_1.9.2   forcats_1.0.0    
 [5] stringr_1.5.1     dplyr_1.1.4       purrr_1.0.2       readr_2.1.4      
 [9] tidyr_1.3.1       tibble_3.2.1      ggplot2_3.4.2     tidyverse_2.0.0  

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.12        pillar_1.9.0       compiler_4.1.3     yulab.utils_0.1.4 
 [5] tools_4.1.3        aplot_0.1.10       digest_0.6.34      jsonlite_1.8.8    
 [9] memoise_2.0.1      tidytree_0.4.6     lifecycle_1.0.4    gtable_0.3.3      
[13] nlme_3.1-162       timechange_0.2.0   lattice_0.21-8     pkgconfig_2.0.3   
[17] rlang_1.1.3        ggplotify_0.1.0    cli_3.6.2          patchwork_1.1.2   
[21] parallel_4.1.3     fastmap_1.1.1      withr_3.0.0        gridGraphics_0.5-1
[25] fs_1.6.3           generics_0.1.3     vctrs_0.6.5        hms_1.1.3         
[29] grid_4.1.3         tidyselect_1.2.0   glue_1.7.0         R6_2.5.1          
[33] fansi_1.0.6        farver_2.1.1       tzdb_0.4.0         magrittr_2.0.3    
[37] scales_1.2.1       colorspace_2.1-0   ape_5.7-1          labeling_0.4.2    
[41] utf8_1.2.4         stringi_1.8.3      lazyeval_0.2.2     munsell_0.5.0     
[45] cachem_1.0.8       ggfun_0.0.9       

Recent versions of treeio don't appear to parse the branch lengths of phyloXML files. With version 1.18.0, running:

library(treeio)
library(ggtree)
xmlfile1 <- system.file("extdata/phyloxml", "test_x2.xml", package="treeio")
px1 <- read.phyloxml(xmlfile1)
px1
ggplot(px1) + geom_tree()

prints to the console (truncated):

Phylogenetic tree with 10 tips and 9 internal nodes.

Tip labels:
  t7, t2, t3, t8, t1, t5, ...

Rooted; includes branch lengths.

and plots:

In later versions (tested v1.22 through latest 1.27.0.002 from devtools::install_github("YuLab-SMU/treeio")), running the same code I see:

Phylogenetic tree with 10 tips and 9 internal nodes.

Tip labels:
  t7, t2, t3, t8, t1, t5, ...

Rooted; no branch lengths.

and plots:

Expected: phyloXML file containing branch lengths is recognized as such in read.phyloxml

Observed: Resulting tree object does not contain branch lengths

Possibly related to changes in PR #88 ?

[IdoBar]

@GuangchuangYu
Is there any solution to this? I'm having similar issues with reading a tree from a Newick file, modifying the labels, saving to tree data to a csv file and then trying to convert the data bac into a tree (with either as.phylo() or as.treedata().