GO_score_evaluation error with Idents

[lindaboshans]

Hello,

Thank you for a great package. I'm trying to run the following code:

AD3 <- aut.res.clustering(obj = AD3) granule.res.4.gruffi <- AD3@misc$gruffi$'optimal.granule.res' AD3 <- reassign.small.clusters(AD3, ident = granule.res.4.gruffi) granule.res.4.gruffi <- paste0(granule.res.4.gruffi, '.reassigned')

AD3 <- GO_score_evaluation(obj = AD3, GO_term = go2, save.UMAP = TRUE, new_GO_term_computation = T, clustering = granule.res.4.gruffi), but am getting this error: Error in Idents<-: ! 'value' must be a factor or vector Run rlang::last_trace() to see where the error occurred.

ER stress GO:0034976

A <- GO_score_evaluation(obj = AD3, GO_term = go2, save.UMAP = TRUE, new_GO_term_computation = T, clustering = granule.res.4.gruffi) Error in Idents<-: ! 'value' must be a factor or vector Run rlang::last_trace() to see where the error occurred. rlang::last_trace() <error/rlang_error> Error in Idents<-: ! 'value' must be a factor or vector

Backtrace: ▆

1. └─gruffi::GO_score_evaluation(...)
2. ├─Seurat::Idents<-(*tmp*, value = obj@meta.data[clustering])

3. └─SeuratObject:::Idents<-.Seurat(*tmp*, value = obj@meta.data[clustering]) Run rlang::last_trace(drop = FALSE) to see 1 hidden frame. rlang::last_trace(drop = FALSE) <error/rlang_error> Error in Idents<-: ! 'value' must be a factor or vector

   Backtrace: ▆

4. └─gruffi::GO_score_evaluation(...)
5. ├─Seurat::Idents<-(*tmp*, value = obj@meta.data[clustering])
6. └─SeuratObject:::Idents<-.Seurat(*tmp*, value = obj@meta.data[clustering])
7. └─rlang::abort(message = "'value' must be a factor or vector")

Please advise on how to fix this.

here are my package versions: sessionInfo() R version 4.3.1 (2023-06-16) Platform: x86_64-apple-darwin20 (64-bit) Running under: macOS Ventura 13.3.1

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0

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: America/New_York tzcode source: internal

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

other attached packages: [1] ggExpress_0.7.2 ggpubr_0.6.0 ggplot2_3.4.3 gruffi_0.7.4 Seurat_4.9.9.9059 SeuratObject_4.9.9.9091 sp_2.0-0
[8] MarkdownReports_4.5.9 MarkdownHelpers_0.2.2 CodeAndRoll2_2.3.4 Stringendo_0.3.6 magrittr_2.0.3 rgl_1.1.3 AUCell_1.22.0
[15] biomaRt_2.56.1

loaded via a namespace (and not attached): [1] fs_1.6.3 matrixStats_1.0.0 spatstat.sparse_3.0-2 bitops_1.0-7 devtools_2.4.5 httr_1.4.7
[7] RColorBrewer_1.1-3 doParallel_1.0.17 backports_1.4.1 profvis_0.3.8 tools_4.3.1 sctransform_0.3.5
[13] utf8_1.2.3 R6_2.5.1 sm_2.2-5.7.1 lazyeval_0.2.2 uwot_0.1.16 GetoptLong_1.0.5
[19] withr_2.5.0 urlchecker_1.0.1 tictoc_1.2 prettyunits_1.1.1 gridExtra_2.3 progressr_0.14.0
[25] cli_3.6.1 Biobase_2.60.0 spatstat.explore_3.2-1 fastDummies_1.7.3 spatstat.data_3.0-1 readr_2.1.4
[31] ggridges_0.5.4 pbapply_1.7-2 slingshot_2.8.0 R.utils_2.12.2 vioplot_0.4.0 parallelly_1.36.0
[37] sessioninfo_1.2.2 rstudioapi_0.15.0 RSQLite_2.3.1 generics_0.1.3 shape_1.4.6 vroom_1.6.3
[43] gtools_3.9.4 ica_1.0-3 spatstat.random_3.1-5 car_3.1-2 zip_2.3.0 dplyr_1.1.3
[49] Matrix_1.6-1 fansi_1.0.4 S4Vectors_0.38.1 SCENIC_1.3.1 clipr_0.8.0 abind_1.4-5
[55] terra_1.7-39 R.methodsS3_1.8.2 lifecycle_1.0.3 SoupX_1.6.2 carData_3.0-5 SummarizedExperiment_1.30.2 [61] BiocFileCache_2.8.0 Rtsne_0.16 grid_4.3.1 blob_1.2.4 gdata_2.19.0 promises_1.2.1
[67] crayon_1.5.2 miniUI_0.1.1.1 lattice_0.21-8 cowplot_1.1.1 annotate_1.78.0 KEGGREST_1.40.0
[73] knitr_1.43 pillar_1.9.0 ComplexHeatmap_2.16.0 GenomicRanges_1.52.0 rjson_0.2.21 future.apply_1.11.0
[79] codetools_0.2-19 leiden_0.4.3 glue_1.6.2 data.table_1.14.8 remotes_2.4.2.1 vctrs_0.6.3
[85] png_0.1-8 spam_2.9-1 gtable_0.3.4 cachem_1.0.8 xfun_0.40 openxlsx_4.2.5.2
[91] princurve_2.1.6 S4Arrays_1.0.6 mime_0.12 ReadWriter_0.3.0 tidyverse_2.0.0 survival_3.5-7
[97] pheatmap_1.0.12 SingleCellExperiment_1.22.0 iterators_1.0.14 ellipsis_0.3.2 fitdistrplus_1.1-11 ROCR_1.0-11
[103] nlme_3.1-163 Seurat.utils_1.9.5 usethis_2.2.2 bit64_4.0.5 progress_1.2.2 filelock_1.0.2
[109] RcppAnnoy_0.0.21 GenomeInfoDb_1.36.2 irlba_2.3.5.1 KernSmooth_2.23-22 colorspace_2.1-0 BiocGenerics_0.46.0
[115] DBI_1.1.3 raster_3.6-23 tidyselect_1.2.0 processx_3.8.2 bit_4.0.5 compiler_4.3.1
[121] curl_5.0.2 graph_1.78.0 hdf5r_1.3.8 xml2_1.3.5 DelayedArray_0.26.7 plotly_4.10.2
[127] scales_1.2.1 lmtest_0.9-40 callr_3.7.3 rappdirs_0.3.3 stringr_1.5.0 digest_0.6.33
[133] goftest_1.2-3 spatstat.utils_3.0-3 XVector_0.40.0 base64enc_0.1-3 htmltools_0.5.6 pkgconfig_2.0.3
[139] sparseMatrixStats_1.12.2 MatrixGenerics_1.12.3 dbplyr_2.3.3 fastmap_1.1.1 rlang_1.1.1 GlobalOptions_0.1.2
[145] htmlwidgets_1.6.2 shiny_1.7.5 DelayedMatrixStats_1.22.6 zoo_1.8-12 jsonlite_1.8.7 BiocParallel_1.34.2
[151] R.oo_1.25.0 RCurl_1.98-1.12 GenomeInfoDbData_1.2.10 dotCall64_1.0-2 patchwork_1.1.3 munsell_0.5.0
[157] Rcpp_1.0.11 viridis_0.6.4 reticulate_1.31 TrajectoryUtils_1.8.0 stringi_1.7.12 zlibbioc_1.46.0
[163] MASS_7.3-60 org.Hs.eg.db_3.17.0 plyr_1.8.8 pkgbuild_1.4.2 parallel_4.3.1 listenv_0.9.0
[169] ggrepel_0.9.3 deldir_1.0-9 Biostrings_2.68.1 splines_4.3.1 tensor_1.5 hms_1.1.3
[175] circlize_0.4.15 ps_1.7.5 igraph_1.5.1 spatstat.geom_3.2-4 ggsignif_0.6.4 RcppHNSW_0.4.1
[181] reshape2_1.4.4 stats4_4.3.1 pkgload_1.3.2.1 XML_3.99-0.14 BiocManager_1.30.22 tzdb_0.4.0
[187] foreach_1.5.2 httpuv_1.6.11 RANN_2.6.1 tidyr_1.3.0 purrr_1.0.2 polyclip_1.10-4
[193] future_1.33.0 clue_0.3-64 scattermore_1.2 broom_1.0.5 xtable_1.8-4 RSpectra_0.16-1
[199] rstatix_0.7.2 ggcorrplot_0.1.4 later_1.3.1 viridisLite_0.4.2 tibble_3.2.1 memoise_2.0.1
[205] AnnotationDbi_1.62.2 IRanges_2.34.1 cluster_2.1.4 HGNChelper_0.8.1 globals_0.16.2 GSEABase_1.62.0

[jn-goe]

same as issue #10