enrichplot Error in offspring.tbl_tree_item(.data = .data, .node = .node, tiponly = tiponly, : could not find function "offspring.tbl_tree

LEfse %>%

ggdiffclade(obj=.,
```
          alpha=0.3, linewd=0.2, 
```
```
          skpointsize=0.6,
```
```
          taxlevel=3,
```
```
          settheme=FALSE, 
```
```
          setColors=FALSE,
```

          cladetext=1.5, removeUnknown = F) +

guides(color = guide_legend(keywidth = 0.1,

                          keyheight = 0.6,

```
                          order = 3, 
```
```
                          ncol=1)) + 
```
scale_fill_manual(values=c("#008B45FF","#EE0000FF","purple")) +
guides(fill=guide_legend(order = 1,reverse = T,keyheight = 0.1,keywidth = 0.6))+
theme(panel.background=element_rect(fill=NA),
```
    legend.position="right",
```
```
    plot.margin=margin(0,0,0,0),
```

    legend.spacing.x = unit(0.02, "cm"),

```
    legend.title=element_text(size=7),
```
```
    legend.text=element_text(size=6),
```

    legend.box.spacing=unit(0.02,"cm"))

! # Invaild edge matrix for . A <tbl_df> is returned. ! # Invaild edge matrix for . A <tbl_df> is returned. ! # Invaild edge matrix for . A <tbl_df> is returned. ! # Invaild edge matrix for . A <tbl_df> is returned. Error in offspring.tbl_tree_item(.data = .data, .node = .node, tiponly = tiponly, : could not find function "offspring.tbl_tree_item"

Jul 23 '23 06:07 Leekate11

I have a similar error when running "treeplot". The error seems to happen in other packages as well. https://support.bioconductor.org/p/9153366/

! # Invaild edge matrix for . A <tbl_df> is returned. Error in offspring.tbl_tree_item(.data = .data, .node = .node, tiponly = tiponly, : could not find function "offspring.tbl_tree_item"

Aug 11 '23 04:08 AhmedMohamed1993

I know this is an old thread, but this is what worked for me:

just load these functions from the tidytree package:

nodeid.tbl_tree <- utils::getFromNamespace("nodeid.tbl_tree", "tidytree") rootnode.tbl_tree <- utils::getFromNamespace("rootnode.tbl_tree", "tidytree") offspring.tbl_tree <- utils::getFromNamespace("offspring.tbl_tree", "tidytree") offspring.tbl_tree_item <- utils::getFromNamespace(".offspring.tbl_tree_item", "tidytree") child.tbl_tree <- utils::getFromNamespace("child.tbl_tree", "tidytree") parent.tbl_tree <- utils::getFromNamespace("parent.tbl_tree", "tidytree")

Oct 31 '23 15:10 jdilme

Hello, It seems that this isssue is still present with the current version. Although the work-around provided above works, it would benefit all users if the functions were properly imported to the package itself. Thank you!

> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Rocky Linux 8.9 (Green Obsidian)

Matrix products: default
BLAS/LAPACK: /cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/flexiblas/3.0.4/lib64/libflexiblas.so.3.0

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

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

other attached packages:
 [1] cowplot_1.1.1         enrichplot_1.16.2     strex_2.0.0
 [4] ReactomePA_1.40.0     clusterProfiler_4.4.4 DOSE_3.22.1
 [7] lubridate_1.9.3       forcats_1.0.0         stringr_1.5.0
[10] dplyr_1.1.3           purrr_1.0.2           readr_2.1.4
[13] tidyr_1.3.0           tibble_3.2.1          ggplot2_3.4.4
[16] tidyverse_2.0.0

loaded via a namespace (and not attached):
  [1] ggnewscale_0.4.10      fgsea_1.22.0           colorspace_2.1-0
  [4] ggtree_3.4.4           qvalue_2.28.0          XVector_0.36.0
  [7] fs_1.6.3               aplot_0.2.2            farver_2.1.1
 [10] graphlayouts_1.0.1     ggrepel_0.9.4          bit64_4.0.5
 [13] AnnotationDbi_1.58.0   fansi_1.0.5            scatterpie_0.2.1
 [16] codetools_0.2-18       splines_4.2.1          cachem_1.0.8
 [19] GOSemSim_2.22.0        polyclip_1.10-6        jsonlite_1.8.7
 [22] GO.db_3.15.0           png_0.1-8              graph_1.74.0
 [25] ggforce_0.4.1          graphite_1.42.0        compiler_4.2.1
 [28] httr_1.4.7             Matrix_1.6-1.1         fastmap_1.1.1
 [31] lazyeval_0.2.2         cli_3.6.1              org.Mm.eg.db_3.15.0
 [34] tweenr_2.0.2           tools_4.2.1            igraph_1.5.1
 [37] gtable_0.3.4           glue_1.6.2             GenomeInfoDbData_1.2.8
 [40] reshape2_1.4.4         DO.db_2.9              rappdirs_0.3.3
 [43] fastmatch_1.1-4        Rcpp_1.0.11            Biobase_2.56.0
 [46] vctrs_0.6.4            Biostrings_2.64.1      ape_5.7-1
 [49] nlme_3.1-157           ggraph_2.1.0           timechange_0.2.0
 [52] lifecycle_1.0.3        zlibbioc_1.42.0        MASS_7.3-57
 [55] scales_1.2.1           tidygraph_1.2.3        reactome.db_1.81.0
 [58] ragg_1.2.6             hms_1.1.3              parallel_4.2.1
 [61] RColorBrewer_1.1-3     memoise_2.0.1          gridExtra_2.3
 [64] downloader_0.4         ggfun_0.1.3            yulab.utils_0.1.0
 [67] stringi_1.8.3          RSQLite_2.3.1          S4Vectors_0.34.0
 [70] tidytree_0.4.5         BiocGenerics_0.42.0    BiocParallel_1.30.4
 [73] GenomeInfoDb_1.32.4    systemfonts_1.0.5      rlang_1.1.3
 [76] pkgconfig_2.0.3        bitops_1.0-7           lattice_0.20-45
 [79] labeling_0.4.3         treeio_1.20.2          patchwork_1.1.2
 [82] shadowtext_0.1.2       bit_4.0.5              tidyselect_1.2.0
 [85] plyr_1.8.9             magrittr_2.0.3         R6_2.5.1
 [88] IRanges_2.30.1         generics_0.1.3         DBI_1.1.3
 [91] pillar_1.9.0           withr_2.5.1            KEGGREST_1.36.3
 [94] RCurl_1.98-1.12        crayon_1.5.2           utf8_1.2.4
 [97] tzdb_0.4.0             viridis_0.6.4          grid_4.2.1
[100] data.table_1.14.8      blob_1.2.4             digest_0.6.33
[103] textshaping_0.3.7      gridGraphics_0.5-1     stats4_4.2.1
[106] munsell_0.5.0          viridisLite_0.4.2      ggplotify_0.1.2

May 15 '24 22:05 DelongZHOU