geom_nodelab reports an error, when using the offset argument.

[FelixErnst]

trafficstars

Hi,

geom_nodelab reports an error, when using the offset argument.

> nwk <- system.file("extdata", "sample.nwk", package="treeio")
> tree <- read.tree(nwk)
> td <- as_tibble(tree)
> td$label <- LETTERS[seq.int(1L, nrow(td))]
> # works
> ggplot(tidytree::as.treedata(td), aes(x, y)) + geom_tree() + theme_tree()
> # works
> ggplot(tidytree::as.treedata(td), aes(x, y)) + geom_tree() + theme_tree() + geom_tiplab(offset = .1)
> # doesn't work
> ggplot(tidytree::as.treedata(td), aes(x, y)) + geom_tree() + theme_tree() + geom_tiplab(offset = .1) + geom_nodelab(offset = .1)
Error in geom_tiplab(mapping, offset = nudge_x, nudge_y = nudge_y, geom = geom,  : 
  formal argument "offset" matched by multiple actual arguments

I am not sure, whether the offset option should be supported by geom_nodelab, but I guess so. In any event the error or error message are wrong and point to an underlying mix up of arguments.

Is something, you would regard as worth fixing and fixable? Thanks for any help and/or advice.

Felix

edit:

sessionInfo

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)
Matrix products: default
locale:
[1] LC_COLLATE=English_Germany.1252  LC_CTYPE=English_Germany.1252    LC_MONETARY=English_Germany.1252 LC_NUMERIC=C                     LC_TIME=English_Germany.1252
attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base
other attached packages:
[1] ggtree_2.4.0                     tibble_3.0.4                     miaViz_0.0.0.9000                ggplot2_3.3.2                    mia_0.0.0.9002

[6] MicrobiomeExperiment_0.99.0.9014 Biostrings_2.58.0                XVector_0.30.0                   TreeSummarizedExperiment_1.6.0   SingleCellExperiment_1.12.0

[11] SummarizedExperiment_1.20.0      Biobase_2.50.0                   GenomicRanges_1.42.0             GenomeInfoDb_1.26.0              IRanges_2.24.0

[16] S4Vectors_0.28.0                 BiocGenerics_0.36.0              MatrixGenerics_1.2.0             matrixStats_0.57.0
loaded via a namespace (and not attached):
[1] viridis_0.5.1             BiocSingular_1.6.0        tidyr_1.1.2               jsonlite_1.7.1            viridisLite_0.3.0         DelayedMatrixStats_1.12.0 scuttle_1.0.0

[8] assertthat_0.2.1          BiocManager_1.30.10       rvcheck_0.1.8             GenomeInfoDbData_1.2.4    vipor_0.4.5               pillar_1.4.6              lattice_0.20-41

[15] glue_1.4.2                beachmat_2.6.0            digest_0.6.27             colorspace_1.4-1          Matrix_1.2-18             pkgconfig_2.0.3           zlibbioc_1.36.0

[22] purrr_0.3.4               patchwork_1.0.1           tidytree_0.3.3            scales_1.1.1              BiocParallel_1.24.0       generics_0.1.0            farver_2.0.3

[29] ellipsis_0.3.1            withr_2.3.0               lazyeval_0.2.2            cli_2.1.0                 magrittr_1.5              crayon_1.3.4              fansi_0.4.1

[36] nlme_3.1-150              beeswarm_0.2.3            tools_4.0.3               scater_1.18.0             lifecycle_0.2.0           stringr_1.4.0             aplot_0.0.6

[43] munsell_0.5.0             DelayedArray_0.16.0       irlba_2.3.3               compiler_4.0.3            rsvd_1.0.3                rlang_0.4.8               grid_4.0.3

[50] RCurl_1.98-1.2            BiocNeighbors_1.8.0       rstudioapi_0.11           bitops_1.0-6              labeling_0.4.2            gtable_0.3.0              R6_2.5.0

[57] gridExtra_2.3             dplyr_1.0.2               treeio_1.14.0             ape_5.4-1                 stringi_1.5.3             ggbeeswarm_0.6.0          Rcpp_1.0.5

[64] vctrs_0.3.4               tidyselect_1.1.0          sparseMatrixStats_1.2.0

[xiangpin]

please use nudge_x in geom_nodelab instead of offset.

[FelixErnst]

How does this translate, when I plot a circular tree plot? From what I understood there used to be a geom_nodelab2 function, but that seams to be deprecated.

Should I also use nudge_x for geom_tiplab?

Also it seams that geom_nodelab does not have an effect for circular plots. Can you comment on that? Is this to be expected?

[xiangpin]

In geom_tiplab, you should use offset to control the distance. It seems that the position of node labels might need to be adjusted horizontally (nudge_x) and vertically (nudge_y), and nudge_x and nudge_y inherits geom_text of ggplot2.

geom_nodelab has supported both rectangular and circluar layout. So geom_nodelab2 was deprecated.

[FelixErnst]

This doesn't work.

Starting from the example given above:

ggplot(tidytree::as.treedata(td), aes(x, y)) + geom_tree(layout="circular") + theme_tree()

does not produce a circular plot as suggested by ?geom_tree. (The layout argument is shown there). However,

ggtree(tidytree::as.treedata(td), layout="circular") + theme_tree() + geom_nodelab()

produces a circular plot, but no node labels are shown.

I would say something is going on in the state of denmark.

[GuangchuangYu]

the circular layout is produced by :

ggplot(tree) + geom_tree() + layout_circular()

[FelixErnst]

the circular layout is produced by :

ggplot(tree) + geom_tree() + layout_circular()

So the layout argument for geom_tree is not used in any event? This seams to be man page issue then.

[GuangchuangYu]

@xiayh17 pls update the geom_tree() man file accordingly.