Entering edit mode
I am fairly new to ggtree and it had been working until today.
Today, several functions stopped working:
-- MRCA(), geom_hilight(), and geom_cladelab()
I have searched the web for answers.
Example:
> sessionInfo( )
R version 4.3.1 (2023-06-16)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ape_5.7-1 tidytree_0.4.4 ggtree_3.8.0
loaded via a namespace (and not attached):
[1] gtable_0.3.3 jsonlite_1.8.7 BiocManager_1.30.21 dplyr_1.1.2
[5] compiler_4.3.1 tidyselect_1.2.0 aplot_0.1.10 Rcpp_1.0.11
[9] gridGraphics_0.5-1 parallel_4.3.1 ggplotify_0.1.1 tidyr_1.3.0
[13] ggfun_0.1.1 scales_1.2.1 lattice_0.21-8 ggplot2_3.4.2
[17] R6_2.5.1 labeling_0.4.2 generics_0.1.3 patchwork_1.1.2
[21] yulab.utils_0.0.6 tibble_3.2.1 munsell_0.5.0 pillar_1.9.0
[25] rlang_1.1.1 treeio_1.24.2 utf8_1.2.3 lazyeval_0.2.2
[29] cli_3.6.1 withr_2.5.0 magrittr_2.0.3 digest_0.6.33
[33] grid_4.3.1 rstudioapi_0.15.0 lifecycle_1.0.3 nlme_3.1-162
[37] vctrs_0.6.3 glue_1.6.2 farver_2.1.1 fansi_1.0.4
[41] colorspace_2.1-0 purrr_1.0.1 tools_4.3.1 pkgconfig_2.0.3
> nwk <- system.file("extdata", "sample.nwk", package="treeio")
> tree <- read.tree(nwk)
> p <- ggtree(tree) + geom_text2(aes(subset=!isTip, label=node), hjust=-.3) +
+ geom_tiplab()
> p
> MRCA(tree, tip=c('A', 'E'))
Error in MRCA.phylo(tree, tip = c("A", "E")) :
argument ".node1" is missing, with no default
> MRCA(p, tip=c('A', 'E'))
Error in MRCA.ggtree(p, tip = c("A", "E")) :
argument ".node1" is missing, with no default
> p$data[17,]
! # Invaild edge matrix for <phylo>. A <tbl_df> is returned.
# A tibble: 1 × 9
parent node branch.length label isTip x y branch angle
<int> <int> <dbl> <chr> <lgl> <dbl> <dbl> <dbl> <dbl>
1 16 17 10 NA FALSE 27 9.94 22 275.
> p + geom_hilight(node=18, fill="blue")
> p + geom_cladelab(node=18, label="Node 18")
Error in offspring.tbl_tree_item(.data = .data, .node = .node, tiponly = tiponly, :
could not find function "offspring.tbl_tree_item"
geom_hilight() highlights only a very thin bad just at the internal node 17, and does not highlight the entire clade.
p + geom_cladelab(node=18, label="Node 18") does not draw a cladogram.
I wonder if there is a conflict with some of my packages, but would like to avoid unloading and reloading hundreds of packages in my R framework.
I'm at a loss, and open to any suggestions. Thank you all for your time and attention!
I started having this exact same problem with
geom_hilightandgeom_cladelabseveral days ago as well. I don't know why this is the case, but I was able to trace it to an update in thetidytreepackage. When I reverted back to a previous version oftidytree(see below), both functions started working again.Thanks! I just tried it and it is "working" again, and now I get this warning:
Warning messages: 1: The following aesthetics were dropped during statistical transformation: node, parent This can happen when ggplot fails to infer the correct grouping structure in the data. Did you forget to specify agroupaesthetic or to convert a numerical variable into a factor?Hmm, I've not seen that warning before.