agglomerateByRank issue

[tfccheng]

agglomerateByRank(tse, rank = "Phylum", #any rank failed agglomerateTree=TRUE)

Error: rownames of 'x' mismatch with node labels of the tree Try 'changeTree' with 'rowNodeLab' provided. In addition: Warning message: In toTree(td) : The root is added with label 'ALL'

If I add na.rm = TRUE, no error, but I don't want to use this call.

I checked getTaxonomyLabels(tse) and rownames(tse), they are identical ASVs. I use makeTreeSummarizedExperimentFromPhyloseq to get tse object.

[TuomasBorman]

Hello!

Thanks for creating this issue! I will look at it as soon as time allows

-Tuomas

[TuomasBorman]

Hi!

Please, can you provide sessionInfo()?

Also, it would help me to find the error if you could provide reproducible example

-Tuomas

[antagomir]

@tfccheng any updates / info?

[tfccheng]

If agglomerateTree = TRUE, it failed. So I only can turn it off.

Error: rownames of 'x' mismatch with node labels of the tree Try 'changeTree' with 'rowNodeLab' provided. In addition: Warning message: In toTree(td) : The root is added with label 'ALL'

[tfccheng]

sessionInfo() R version 4.2.2 (2022-10-31 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8 [4] LC_NUMERIC=C LC_TIME=English_United States.utf8

attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] ggplot2_3.4.0 edgeR_3.40.0 limma_3.54.0 DESeq2_1.38.1
[5] DT_0.26 tidyr_1.2.1 ANCOMBC_2.0.1 SIAMCAT_2.2.0
[9] mlr3_0.14.1 phyloseq_1.42.0 mia_1.6.0 MultiAssayExperiment_1.24.0
[13] TreeSummarizedExperiment_2.6.0 Biostrings_2.64.1 XVector_0.36.0 SingleCellExperiment_1.20.0
[17] SummarizedExperiment_1.28.0 Biobase_2.56.0 GenomicRanges_1.48.0 GenomeInfoDb_1.34.3
[21] IRanges_2.30.1 S4Vectors_0.34.0 BiocGenerics_0.44.0 MatrixGenerics_1.10.0
[25] matrixStats_0.62.0 dplyr_1.0.10 Maaslin2_1.12.0 dada2_1.26.0
[29] Rcpp_1.0.9

loaded via a namespace (and not attached): [1] rsvd_1.0.5 Hmisc_4.7-2 corpcor_1.6.10 ps_1.7.2 class_7.3-20
[6] Rsamtools_2.14.0 foreach_1.5.2 glmnet_4.1-4 crayon_1.5.2 rbibutils_2.2.10
[11] MASS_7.3-58.1 rhdf5filters_1.10.0 nlme_3.1-160 backports_1.4.1 rlang_1.0.6
[16] ROCR_1.0-11 readxl_1.4.1 microbiome_1.20.0 irlba_2.3.5.1 callr_3.7.3
[21] nloptr_2.0.3 optparse_1.7.3 scater_1.26.1 BiocParallel_1.30.4 bit64_4.0.5
[26] glue_1.6.2 pheatmap_1.0.12 rngtools_1.5.2 processx_3.8.0 parallel_4.2.2
[31] vipor_0.4.5 AnnotationDbi_1.60.0 tidyselect_1.2.0 usethis_2.1.6 XML_3.99-0.12
[36] palmerpenguins_0.1.1 ggpubr_0.5.0 GenomicAlignments_1.34.0 xtable_1.8-4 magrittr_2.0.3
[41] mlr3learners_0.5.5 evaluate_0.18 Rdpack_2.4 scuttle_1.8.0 cli_3.4.1
[46] zlibbioc_1.42.0 hwriter_1.3.2.1 rstudioapi_0.14 doRNG_1.8.2 miniUI_0.1.1.1
[51] rpart_4.1.19 BiocStyle_2.26.0 treeio_1.22.0 shiny_1.7.3 BiocSingular_1.14.0
[56] xfun_0.35 pkgbuild_1.3.1 multtest_2.54.0 cluster_2.1.4 biomformat_1.26.0
[61] KEGGREST_1.38.0 tibble_3.1.8 expm_0.999-6 PathoStat_1.24.0 ggrepel_0.9.2
[66] logging_0.10-108 mlr3misc_0.11.0 ape_5.6-2 listenv_0.8.0 png_0.1-7
[71] permute_0.9-7 future_1.29.0 withr_2.5.0 bitops_1.0-7 plyr_1.8.8
[76] cellranger_1.1.0 pcaPP_2.0-3 e1071_1.7-12 pROC_1.18.0 coda_0.19-4
[81] pillar_1.8.1 RcppParallel_5.1.5 cachem_1.0.6 Rmpfr_0.8-9 fs_1.5.2
[86] gmodels_2.18.1.1 hash_2.2.6.2 DelayedMatrixStats_1.20.0 vctrs_0.5.1 ellipsis_0.3.2
[91] generics_0.1.3 devtools_2.4.5 tools_4.2.2 foreign_0.8-83 beeswarm_0.4.0
[96] munsell_0.5.0 LiblineaR_2.10-22 emmeans_1.8.2 proxy_0.4-27 DelayedArray_0.24.0
[101] pkgload_1.3.2 fastmap_1.1.0 compiler_4.2.2 abind_1.4-5 httpuv_1.6.6
[106] sessioninfo_1.2.2 beanplot_1.3.1 plotly_4.10.1 DescTools_0.99.47 mlr3tuning_0.17.0
[111] decontam_1.18.0 GenomeInfoDbData_1.2.9 gridExtra_2.3 lattice_0.20-45 deldir_1.0-6
[116] utf8_1.2.2 later_1.3.0 jsonlite_1.8.3 scales_1.2.1 gld_2.6.6
[121] ScaledMatrix_1.6.0 tidytree_0.4.1 pbapply_1.6-0 carData_3.0-5 sparseMatrixStats_1.10.0
[126] estimability_1.4.1 lazyeval_0.2.2 promises_1.2.0.1 car_3.1-1 doParallel_1.0.17
[131] latticeExtra_0.6-30 checkmate_2.1.0 rmarkdown_2.18 webshot_0.5.4 Rtsne_0.16
[136] igraph_1.3.5 survival_3.4-0 numDeriv_2016.8-1.1 yaml_2.3.6 htmltools_0.5.3
[141] memoise_2.0.1 profvis_0.3.7 lgr_0.4.4 locfit_1.5-9.6 paradox_0.11.0
[146] viridisLite_0.4.1 gmp_0.6-8 digest_0.6.30 assertthat_0.2.1 mime_0.12
[151] RSQLite_2.2.18 yulab.utils_0.0.5 Exact_3.2 remotes_2.4.2 data.table_1.14.6
[156] urlchecker_1.0.1 blob_1.2.3 vegan_2.6-4 lpsymphony_1.26.0 bbotk_0.7.1
[161] splines_4.2.2 Formula_1.2-4 labeling_0.4.2 DECIPHER_2.26.0 Rhdf5lib_1.20.0
[166] RCurl_1.98-1.9 broom_1.0.1 hms_1.1.2 rhdf5_2.42.0 colorspace_2.0-3
[171] base64enc_0.1-3 BiocManager_1.30.19 ggbeeswarm_0.6.0 shape_1.4.6 nnet_7.3-18
[176] mvtnorm_1.1-3 fansi_1.0.3 parallelly_1.32.1 R6_2.5.1 grid_4.2.2
[181] lifecycle_1.0.3 ShortRead_1.56.0 rootSolve_1.8.2.3 ggsignif_0.6.4 gdata_2.18.0.1
[186] minqa_1.2.5 getopt_1.20.3 robustbase_0.95-0 Matrix_1.5-3 RColorBrewer_1.1-3
[191] iterators_1.0.14 stringr_1.4.1 htmlwidgets_1.5.4 beachmat_2.14.0 purrr_0.3.5
[196] mgcv_1.8-41 CVXR_1.0-11 globals_0.16.2 lmom_2.9 htmlTable_2.4.1
[201] codetools_0.2-18 gtools_3.9.3 prettyunits_1.1.1 gridBase_0.4-7 gtable_0.3.1
[206] DBI_1.1.3 httr_1.4.4 stringi_1.7.8 progress_1.2.2 reshape2_1.4.4
[211] farver_2.1.1 uuid_1.1-0 annotate_1.76.0 viridis_0.6.2 rentrez_1.2.3
[216] infotheo_1.2.0.1 PRROC_1.3.1 boot_1.3-28 shinyjs_2.1.0 BiocNeighbors_1.16.0
[221] lme4_1.1-31 interp_1.1-3 ade4_1.7-20 geneplotter_1.76.0 energy_1.7-10
[226] DEoptimR_1.0-11 bit_4.0.5 jpeg_0.1-9 pkgconfig_2.0.3 lmerTest_3.1-3
[231] gsl_2.1-7.1 DirichletMultinomial_1.40.0 biglm_0.9-2.1 rstatix_0.7.1 corrplot_0.92

[antagomir]

Hmm I wonder about the status of this one?

[Daenarys8]

This issue is probably stale.