Unable to add annotation information
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Hello
I'm trying to use the microbiomeViZ package. I obtained error with my data and so tried with microbiomeViZ example.
I'm obtaining the following error :
Warning messages:
1: Computation failed in stat_clad_bar()
.
Caused by error in UseMethod()
:
! no applicable method for 'offspring' applied to an object of class "data.frame"
2: Computation failed in stat_clade_text()
.
here are my code and session info. I updated all my packages. thanks in advance
Regards
`> library(ggtree)
library(tidytree)
library(ggplot2)
library(microbiomeViz)tr <- parseMetaphlanTSV(SRS014459_Stool_profile)
p <- tree.backbone(tr)
anno.data <- data.frame(node = c("c__Clostridia", "g__Roseburia", "s__Bacteroides_ovatus"),
-
color = 'red', stringsAsFactors = FALSE)
library(dplyr)
p <- clade.anno(p1, anno.data)
! # 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.
! # 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.
! # 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.
! # Invaild edge matrix for . A <tbl_df> is returned.
! # Invaild edge matrix for . A <tbl_df> is returned.
p
Warning messages:
1: Computation failed instat_clad_bar()
.
Caused by error inUseMethod()
:
! no applicable method for 'offspring' applied to an object of class "data.frame"
2: Computation failed instat_clade_text()
.
Caused by error inUseMethod()
:
! no applicable method for 'offspring' applied to an object of class "data.frame"
3: Computation failed instat_clad_bar()
.
Caused by error inUseMethod()
:
! no applicable method for 'offspring' applied to an object of class "data.frame"
4: Computation failed instat_clade_text()
.
Caused by error inUseMethod()
:
! no applicable method for 'offspring' applied to an object of class "data.frame"
5: Computation failed instat_clad_bar()
.
Caused by error inUseMethod()
:
! no applicable method for 'offspring' applied to an object of class "data.frame"
6: Computation failed instat_clade_text()
.
Caused by error inUseMethod()
:
! no applicable method for 'offspring' applied to an object of class "data.frame"sessionInfo()
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8
[3] LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.1.4 microbiomeViz_0.1.0 ggplot2_3.5.0 tidytree_0.4.6
[5] ggtree_3.6.2 phyloseq_1.42.0
loaded via a namespace (and not attached):
[1] nlme_3.1-160 bitops_1.0-7 fs_1.6.3 usethis_2.2.3
[5] devtools_2.4.5 GenomeInfoDb_1.34.9 profvis_0.3.8 tools_4.2.2
[9] utf8_1.2.4 R6_2.5.1 vegan_2.6-4 DBI_1.2.2
[13] lazyeval_0.2.2 BiocGenerics_0.44.0 mgcv_1.8-41 colorspace_2.0-3
[17] permute_0.9-7 rhdf5filters_1.10.1 ade4_1.7-22 withr_3.0.0
[21] urlchecker_1.0.1 tidyselect_1.2.1 compiler_4.2.2 cli_3.6.2
[25] Biobase_2.58.0 shadowtext_0.1.3 labeling_0.4.3 scales_1.3.0
[29] readr_2.1.5 stringr_1.5.1 digest_0.6.33 yulab.utils_0.1.4
[33] XVector_0.38.0 pkgconfig_2.0.3 htmltools_0.5.7 sessioninfo_1.2.2
[37] fastmap_1.1.1 htmlwidgets_1.6.4 rlang_1.1.3 rstudioapi_0.15.0
[41] shiny_1.8.0 farver_2.1.1 gridGraphics_0.5-1 generics_0.1.3
[45] jsonlite_1.8.8 RCurl_1.98-1.13 magrittr_2.0.3 ggplotify_0.1.2
[49] GenomeInfoDbData_1.2.9 biomformat_1.26.0 patchwork_1.2.0 Matrix_1.6-4
[53] Rcpp_1.0.11 munsell_0.5.0 S4Vectors_0.36.2 Rhdf5lib_1.20.0
[57] fansi_1.0.6 ape_5.7-1 lifecycle_1.0.4 stringi_1.8.3
[61] MASS_7.3-58.1 zlibbioc_1.44.0 rhdf5_2.42.1 pkgbuild_1.4.3
[65] plyr_1.8.9 grid_4.2.2 parallel_4.2.2 promises_1.2.1
[69] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.20-45 Biostrings_2.66.0
[73] splines_4.2.2 multtest_2.54.0 hms_1.1.3 pillar_1.9.0
[77] igraph_1.6.0 reshape2_1.4.4 codetools_0.2-19 stats4_4.2.2
[81] pkgload_1.3.4 glue_1.7.0 ggfun_0.1.4 remotes_2.4.2.1
[85] data.table_1.14.10 vctrs_0.6.5 treeio_1.22.0 tzdb_0.4.0
[89] httpuv_1.6.13 foreach_1.5.2 gtable_0.3.4 purrr_1.0.1
[93] tidyr_1.3.0 cachem_1.0.8 mime_0.12 xtable_1.8-4
[97] later_1.3.2 survival_3.4-0 tibble_3.2.1 iterators_1.0.14
[101] aplot_0.2.2 memoise_2.0.1 IRanges_2.32.0 cluster_2.1.4
[105] ellipsis_0.3.2`