treedata object: cannot join on data column other than "node"

[nick-youngblut]

Works:

library(ape)
data(woodmouse)
d <- dist.dna(woodmouse)
tr <- nj(d)
bp <- boot.phylo(tr, woodmouse, function(x) nj(dist.dna(x)))
bp2 <- tibble(X=1:Nnode(tr) + Ntip(tr), bootstrap = bp)
full_join(tr, bp2, by=c('node'='X'))

Does not work:

library(ape)
data(woodmouse)
d <- dist.dna(woodmouse)
tr <- nj(d)
bp <- boot.phylo(tr, woodmouse, function(x) nj(dist.dna(x)))
bp2 <- tibble(X=1:Nnode(tr) + Ntip(tr), bootstrap = bp)
full_join(as.treedata(tr), bp2, by=c('node'='X'))

Error:

Error in match.arg(by, c("node", "label")) : 
  'arg' should be one of “node”, “label”

It appears that full_join() on a treedata object does not work with the standard dplyr UI of by=c('columnX'='columnY'), but instead, one MUST use by=c('node').

sessionInfo

R version 4.2.1 (2022-06-23)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

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

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

other attached packages:
 [1] heatmaply_1.4.0       viridis_0.6.2         viridisLite_0.4.1     tidygraph_1.2.2       ggrepel_0.9.2        
 [6] ggtree_3.6.2          tidytree_0.4.1        treeio_1.22.0         ape_5.6-2             data.tree_1.0.0      
[11] lubridate_1.9.0       timechange_0.1.1      memoise_2.0.1         tidytable_0.9.1       data.table_1.14.6    
[16] plotly_4.10.1         ggplot2_3.4.0         visNetwork_2.1.2      reactable_0.3.0       collapsibleTree_0.1.7
[21] shinyTree_0.2.7       shinyWidgets_0.7.5    shinycssloaders_1.0.0 shinyBS_0.61.1        jsonlite_1.8.3       
[26] paws_0.1.12           styler_1.8.1          lintr_3.0.2           languageserver_0.3.14 dbplyr_2.2.1         
[31] dplyr_1.0.10          RPostgres_1.4.4       DBI_1.1.3             shiny_1.7.3           aws.signature_0.6.0  
[36] aws.s3_0.3.21         httr_1.4.4           

loaded via a namespace (and not attached):
 [1] colorspace_2.0-3              ellipsis_0.3.2                rsconnect_0.8.28             
 [4] rprojroot_2.0.3               base64enc_0.1-3               aplot_0.1.8                  
 [7] paws.security.identity_0.1.12 rstudioapi_0.14               farver_2.1.1                 
[10] remotes_2.4.2                 bit64_4.0.5                   fansi_1.0.3                  
[13] xml2_1.3.3                    codetools_0.2-18              R.methodsS3_1.8.2            
[16] cachem_1.0.6                  R.oo_1.25.0                   BiocManager_1.30.19          
[19] compiler_4.2.1                assertthat_0.2.1              fastmap_1.1.0                
[22] lazyeval_0.2.2                cli_3.4.1                     later_1.3.0                  
[25] htmltools_0.5.3               tools_4.2.1                   igraph_1.3.5                 
[28] gtable_0.3.1                  glue_1.6.2                    reshape2_1.4.4               
[31] Rcpp_1.0.9                    jquerylib_0.1.4               vctrs_0.5.1                  
[34] nlme_3.1-157                  iterators_1.0.14              crosstalk_1.2.0              
[37] paws.common_0.5.1             stringr_1.4.1                 ps_1.7.2                     
[40] mime_0.12                     lifecycle_1.0.3               renv_0.15.5                  
[43] dendextend_1.16.0             ca_0.71.1                     scales_1.2.1                 
[46] TSP_1.2-1                     hms_1.1.2                     promises_1.2.0.1             
[49] rex_1.2.1                     parallel_4.2.1                RColorBrewer_1.1-3           
[52] yaml_2.3.6                    curl_4.3.3                    gridExtra_2.3                
[55] ggfun_0.0.9                   yulab.utils_0.0.5             sass_0.4.2                   
[58] stringi_1.7.8                 desc_1.4.2                    foreach_1.5.2                
[61] seriation_1.4.0               cyclocomp_1.1.0               rlang_1.0.6                  
[64] pkgconfig_2.0.3               lattice_0.20-45               fontawesome_0.4.0            
[67] purrr_0.3.5                   patchwork_1.1.2               htmlwidgets_1.5.4            
[70] labeling_0.4.2                bit_4.0.5                     processx_3.8.0               
[73] tidyselect_1.2.0              plyr_1.8.8                    magrittr_2.0.3               
[76] R6_2.5.1                      generics_0.1.3                pillar_1.8.1                 
[79] withr_2.5.0                   tibble_3.1.8                  crayon_1.5.2                 
[82] utf8_1.2.2                    grid_4.2.1                    reactR_0.4.4                 
[85] blob_1.2.3                    callr_3.7.3                   webshot_0.5.4                
[88] digest_0.6.30                 xtable_1.8-4                  R.cache_0.16.0               
[91] tidyr_1.2.1                   httpuv_1.6.6                  gridGraphics_0.5-1           
[94] R.utils_2.12.2                munsell_0.5.0                 registry_0.5-1               
[97] ggplotify_0.1.0               bslib_0.4.1 

[nick-youngblut]

Also, the docs at https://yulab-smu.top/treedata-book/chapter2.html#link-external-data do not explicitly state whether other joins (e.g., left_join()) can be used instead of full_join()

[nick-youngblut]

It would also be helpful to include explicit docs/examples of joining on "label" instead of "node" at https://yulab-smu.top/treedata-book/chapter2.html#link-external-data, especially given that most users probably will be joining on tip labels versus the node numbers.