Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

geom_taxalink error "as_string() Can't convert NULL to a string." #615

Open
4 tasks done
ammaraziz opened this issue May 24, 2024 · 3 comments
Open
4 tasks done

geom_taxalink error "as_string() Can't convert NULL to a string." #615

ammaraziz opened this issue May 24, 2024 · 3 comments

Comments

@ammaraziz
Copy link

Prerequisites

  • Have you read Feedback and follow the guide?
    • make sure your are using the latest release version
    • read the documents
    • google your question/issue

Describe you issue

From the ggtree book example here:

library(ggtree)
library(treeio)

treetext = "(((ADH2:0.1[&&NHX:S=human], ADH1:0.11[&&NHX:S=human]):
0.05 [&&NHX:S=primates:D=Y:B=100],ADHY:
0.1[&&NHX:S=nematode],ADHX:0.12 [&&NHX:S=insect]):
0.1[&&NHX:S=metazoa:D=N],(ADH4:0.09[&&NHX:S=yeast],
ADH3:0.13[&&NHX:S=yeast], ADH2:0.12[&&NHX:S=yeast],
ADH1:0.11[&&NHX:S=yeast]):0.1[&&NHX:S=Fungi])[&&NHX:D=N];"

tree <- read.nhx(textConnection(treetext))
ggtree(tree) + geom_tiplab() + geom_taxalink(taxa1='A', taxa2='E')

Produces this error:

Error in `as_string()`:
! Can't convert `NULL` to a string.
Run `rlang::last_trace()` to see where the error occurred.
> rlang::last_trace()
<error/rlang_error>
Error in `as_string()`:
! Can't convert `NULL` to a string.
---
Backtrace:
    ▆
 1. └─ggplot2:::`+.gg`(...)
 2.   └─ggplot2:::add_ggplot(e1, e2, e2name)
 3.     ├─ggplot2::ggplot_add(object, p, objectname)
 4.     └─ggtree:::ggplot_add.taxalink(object, p, objectname)
 5.       ├─base::as.vector(object$data[[as_name(object$mapping$taxa1)]])
 6.       └─rlang::as_name(object$mapping$taxa1)
 7.         └─rlang::as_string(x)
Run rlang::last_trace(drop = FALSE) to see 2 hidden frames.

I have also tried using mapping:

dat <- data.frame(from=c("A", "F", "L"), 
                  to=c("E", "K", "M"), 
                  h=c(1, 1, 0.1), 
                  type=c("t1", "t2", "t3"), 
                  s=c(2, 1, 2))
p4 <- ggtree(tree, layout="inward_circular", xlim=c(150, 0)) +
    geom_taxalink(data=dat, 
                  mapping=aes(taxa1=from, 
                              taxa2=to, 
                              color=type, 
                              size=s), 
                  ncp=10,
                  offset=0.15) + 
    geom_tiplab(hjust=1) +
    scale_size_continuous(range=c(1,3))

Error:

Error in `ggplot_add()`:
! The taxa: A, F, L, E, K, M can not be found.

Newly installed R4.4 and latest ggtree.

Software Versions

> sessionInfo()
R version 4.4.0 (2024-04-24)
Platform: aarch64-apple-darwin20
Running under: macOS Ventura 13.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.0

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: X
tzcode source: internal

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

other attached packages:
[1] treeio_1.28.0 ggtree_3.12.0

loaded via a namespace (and not attached):
 [1] jsonlite_1.8.8     gtable_0.3.5       crayon_1.5.2       dplyr_1.1.4       
 [5] compiler_4.4.0     tidyselect_1.2.1   Rcpp_1.0.12        aplot_0.2.2       
 [9] gridGraphics_0.5-1 parallel_4.4.0     ggplotify_0.1.2    tidyr_1.3.1       
[13] ggfun_0.1.4        scales_1.3.0       fastmap_1.2.0      lattice_0.22-6    
[17] ggplot2_3.5.1      R6_2.5.1           patchwork_1.2.0    generics_0.1.3    
[21] tidytree_0.4.6     yulab.utils_0.1.4  tibble_3.2.1       munsell_0.5.1     
[25] pillar_1.9.0       rlang_1.1.3        utf8_1.2.4         cachem_1.1.0      
[29] fs_1.6.4           lazyeval_0.2.2     memoise_2.0.1      cli_3.6.2         
[33] magrittr_2.0.3     digest_0.6.35      grid_4.4.0         lifecycle_1.0.4   
[37] nlme_3.1-164       vctrs_0.6.5        glue_1.7.0         ape_5.8           
[41] fansi_1.0.6        colorspace_2.1-0   purrr_1.0.2        tools_4.4.0       
[45] pkgconfig_2.0.3   
@ammaraziz
Copy link
Author

I am happy to roll back to an R/ggtree version that works, if you could provide guidance which to test?

@xiangpin
Copy link
Member

The taxa1 and taxa2 should be the tip.label or node number of tree.

> tree
'treedata' S4 object'.

...@ phylo:

Phylogenetic tree with 8 tips and 4 internal nodes.

Tip labels:
  ADH2, ADH1, ADHY, ADHX, ADH4, ADH3, ...

Rooted; includes branch lengths.

with the following features available:
  'V1', 'B', 'D', 'S'.

# The associated data tibble abstraction: 12 × 7
# The 'node', 'label' and 'isTip' are from the phylo tree.
    node label isTip    V1     B D     S
   <int> <chr> <lgl> <dbl> <dbl> <chr> <chr>
 1     1 ADH2  TRUE     NA    NA NA    human
 2     2 ADH1  TRUE     NA    NA NA    human
 3     3 ADHY  TRUE     NA    NA NA    nematode
 4     4 ADHX  TRUE     NA    NA NA    insect
 5     5 ADH4  TRUE     NA    NA NA    yeast
 6     6 ADH3  TRUE     NA    NA NA    yeast
 7     7 ADH2  TRUE     NA    NA NA    yeast
 8     8 ADH1  TRUE     NA    NA NA    yeast
 9     9 NA    FALSE    NA    NA N     NA
10    10 NA    FALSE    NA    NA N     metazoa
# ℹ 2 more rows
# ℹ Use `print(n = ...)` to see more rows
ggtree(tree, layout='circluar') + geom_tiplab() + geom_taxalink(taxa1=2, taxa2=4, hratio=3)

ggtree(tree) + geom_tiplab() + geom_taxalink(taxa1='ADHY', taxa2='ADH3')

Please refer to the help information of geom_taxalink using ?geom_taxalink

@aforestsomewhere
Copy link

aforestsomewhere commented Oct 23, 2024

I also encountered this error today, with R 4.2.2 and ggtree 3.9.1. This is using the character tip.labels as taxa1 and taxa2.

`

library(ggtree)
library(treeio)

treetext = "(((ADH2:0.1[&&NHX:S=human], ADH1:0.11[&&NHX:S=human]):
0.05 [&&NHX:S=primates:D=Y:B=100],ADHY:
0.1[&&NHX:S=nematode],ADHX:0.12 [&&NHX:S=insect]):
0.1[&&NHX:S=metazoa:D=N],(ADH4:0.09[&&NHX:S=yeast],
ADH3:0.13[&&NHX:S=yeast], ADH2:0.12[&&NHX:S=yeast],
ADH1:0.11[&&NHX:S=yeast]):0.1[&&NHX:S=Fungi])[&&NHX:D=N];"

tree <- read.nhx(textConnection(treetext))
ggtree(tree) + geom_tiplab() + geom_taxalink(taxa1='A', taxa2='E')

Error in as_string():
! Can't convert NULL to a string.
Run rlang::last_trace() to see where the error occurred.
`

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

3 participants