seurat object in ModuleEigengenes process : Error ! CheckWGCNAName(seurat_obj, wgcna_name) : invalid argument type

[drake77777]

Hello! This package is excellect. I ran it perfectly first time when i loaded a seurat v4 template object from my other project, but when I changed to Seurat v5 object, it started to show this error and even that seurat v4 object encountered this error too. i could't find where went wrong, would you please help me with this? I tried to convert a v5 assay to a v4 assay, still had the same error.

package version : hdWGCNA_0.3.00 Seurat_5.0.2 .

Here is the error message when i useing this function-ModuleEigengenes :

  mmcr <- ModuleEigengenes(seurat_obj=mmcr,group.by.vars  =  "group")
 Error in !CheckWGCNAName(seurat_obj, wgcna_name) : invalid argument type

Here are the seurat v5 and v4 objects , v5 :An object of class Seurat
23825 features across 22096 samples within 1 assay Active assay: RNA (23825 features, 4000 variable features) 3 layers present: scale.data, data, counts 4 dimensional reductions calculated: pca, integrated.Harmony, umap, tsne

v4 : An object of class Seurat
28830 features across 19468 samples within 2 assays Active assay: RNA (26830 features, 0 variable features) 2 layers present: counts, data 1 other assay present: integrated 2 dimensional reductions calculated: pca, umap

This is my code :

  mmcr<-readRDS('mmcr,rds') 
  #####convert a v5 assay to a v3/v4 assay
  mmcr[["RNA"]] = as(object = mmcr[["RNA"]], Class = "Assay")
  mmcr <- SetupForWGCNA(mmcr,wgcna_name = "Retina",gene_select = "fraction",fraction = 0.05)
  mmcr <- MetacellsByGroups(seurat_obj =  mmcr,group.by = c("celltype","group"),min_cells = 10, k = 10,max_shared=20,reduction 
  = 'umap', ident.group = 'celltype')
  mmcr <- NormalizeMetacells(mmcr)
  mmcr <- SetDatExpr(mmcr,assay = 'RNA',slot =  "data")
  mmcr <- TestSoftPowers(mmcr, networkType = 'signed')
  plot <- PlotSoftPowers(mmcr)
  wrap_plots(plot, ncol=2)
  mmcr <- ConstructNetwork(mmcr,soft_power =6,tom_name = "Retinaest",setDatExpr=F)

  mmcr <- ScaleData(mmcr,features=VariableFeatures(mmcr))
  mmcr <- ModuleEigengenes(seurat_obj=mmcr,group.by.vars  =  "group")

 Error in !CheckWGCNAName(seurat_obj, wgcna_name) : invalid argument type

R session info

sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22621)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8 LC_MONETARY=Chinese (Simplified)_China.utf8 [4] LC_NUMERIC=C LC_TIME=Chinese (Simplified)_China.utf8

time zone: Etc/GMT-8 tzcode source: internal

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

other attached packages: [1] patchwork_1.2.0 cowplot_1.1.3 lubridate_1.9.3 forcats_1.0.0 stringr_1.5.1
[6] dplyr_1.1.4 purrr_1.0.2 readr_2.1.5 tidyr_1.3.0 tibble_3.2.1
[11] tidyverse_2.0.0 hdWGCNA_0.3.00 igraph_1.6.0 WGCNA_1.72-5 fastcluster_1.2.6
[16] dynamicTreeCut_1.63-1 ggrepel_0.9.5 ggplot2_3.5.0 Seurat_5.0.2 SeuratObject_5.0.1
[21] sp_2.1-2 harmony_1.2.0 Rcpp_1.0.11

loaded via a namespace (and not attached): [1] IRanges_2.34.1 R.methodsS3_1.8.2 urlchecker_1.0.1 nnet_7.3-19 ggfittext_0.10.2
[6] goftest_1.2-3 phytools_2.1-1 Biostrings_2.68.1 vctrs_0.6.4 spatstat.random_3.2-2
[11] digest_0.6.33 png_0.1-8 shape_1.4.6.1 proxy_0.4-27 deldir_2.0-2
[16] parallelly_1.37.0 combinat_0.0-8 MASS_7.3-60 reshape2_1.4.4 httpuv_1.6.11
[21] foreach_1.5.2 BiocGenerics_0.46.0 qvalue_2.32.0 withr_3.0.0 ggrastr_1.0.2
[26] xfun_0.42 ggfun_0.1.4 ellipsis_0.3.2 survival_3.5-8 memoise_2.0.1
[31] ggbeeswarm_0.7.2 clusterProfiler_4.8.3 gson_0.1.0 profvis_0.3.8 tidytree_0.4.6
[36] zoo_1.8-12 GlobalOptions_0.1.2 pbapply_1.7-2 R.oo_1.26.0 Formula_1.2-5
[41] rematch2_2.1.2 KEGGREST_1.40.1 promises_1.2.1 scatterplot3d_0.3-44 httr_1.4.7
[46] downloader_0.4 globals_0.16.2 fitdistrplus_1.1-11 rstudioapi_0.15.0 miniUI_0.1.1.1
[51] generics_0.1.3 DOSE_3.26.2 base64enc_0.1-3 curl_5.2.0 S4Vectors_0.38.2
[56] zlibbioc_1.46.0 ggraph_2.1.0 polyclip_1.10-6 GenomeInfoDbData_1.2.11 quadprog_1.5-8
[61] xtable_1.8-4 doParallel_1.0.17 evaluate_0.23 preprocessCore_1.64.0 hms_1.1.3
[66] irlba_2.3.5.1 colorspace_2.1-0 ROCR_1.0-11 reticulate_1.34.0 spatstat.data_3.0-4
[71] magrittr_2.0.3 lmtest_0.9-40 later_1.3.1 viridis_0.6.5 ggtree_3.8.2
[76] lattice_0.21-8 spatstat.geom_3.2-7 future.apply_1.11.1 scattermore_1.2 shadowtext_0.1.3
[81] matrixStats_1.2.0 RcppAnnoy_0.0.21 Hmisc_5.1-1 pillar_1.9.0 nlme_3.1-162
[86] iterators_1.0.14 compiler_4.3.1 RSpectra_0.16-1 stringi_1.7.12 tensor_1.5
[91] devtools_2.4.5 plyr_1.8.9 crayon_1.5.2 abind_1.4-5 gridGraphics_0.5-1
[96] graphlayouts_1.0.2 bit_4.0.5 fastmatch_1.1-4 codetools_0.2-19 paletteer_1.6.0
[101] GetoptLong_1.0.5 plotly_4.10.4 mime_0.12 splines_4.3.1 circlize_0.4.16
[106] fastDummies_1.7.3 HDO.db_0.99.1 knitr_1.45 blob_1.2.4 utf8_1.2.3
[111] clue_0.3-65 fs_1.6.3 listenv_0.9.1 checkmate_2.3.1 pkgbuild_1.4.3
[116] expm_0.999-9 ggplotify_0.1.2 Matrix_1.6-4 tzdb_0.4.0 tweenr_2.0.2
[121] pkgconfig_2.0.3 pheatmap_1.0.12 tools_4.3.1 cachem_1.0.8 RSQLite_2.3.5
[126] viridisLite_0.4.2 DBI_1.2.2 numDeriv_2016.8-1.1 impute_1.76.0 fastmap_1.1.1
[131] rmarkdown_2.25 scales_1.3.0 grid_4.3.1 usethis_2.2.3 ica_1.0-3
[136] FNN_1.1.4 coda_0.19-4.1 BiocManager_1.30.22 dotCall64_1.1-1 RANN_2.6.1
[141] rpart_4.1.19 farver_2.1.1 tidygraph_1.3.0 scatterpie_0.2.1 deeptime_1.0.1
[146] foreign_0.8-84 cli_3.6.1 stats4_4.3.1 tester_0.1.7 leiden_0.4.3.1
[151] lifecycle_1.0.4 uwot_0.1.16 Biobase_2.60.0 sessioninfo_1.2.2 backports_1.4.1
[156] BiocParallel_1.34.2 timechange_0.3.0 gtable_0.3.4 rjson_0.2.21 ggridges_0.5.6
[161] progressr_0.14.0 parallel_4.3.1 ape_5.7-1 jsonlite_1.8.8 RcppHNSW_0.5.0
[166] bitops_1.0-7 bit64_4.0.5 Rtsne_0.17 yulab.utils_0.1.4 spatstat.utils_3.0-4
[171] GOSemSim_2.26.1 R.utils_2.12.3 lazyeval_0.2.2 shiny_1.8.0 htmltools_0.5.7
[176] enrichplot_1.20.3 GO.db_3.17.0 sctransform_0.4.1 glue_1.6.2 spam_2.10-0
[181] XVector_0.40.0 RCurl_1.98-1.13 treeio_1.24.3 mnormt_2.1.1 gridExtra_2.3
[186] R6_2.5.1 labeling_0.4.3 cluster_2.1.4 pkgload_1.3.4 aplot_0.2.2
[191] GenomeInfoDb_1.36.3 tidyselect_1.2.0 vipor_0.4.7 htmlTable_2.4.2 maps_3.4.2
[196] ggforce_0.4.1 AnnotationDbi_1.62.2 future_1.33.1 munsell_0.5.0 KernSmooth_2.23-22
[201] optimParallel_1.0-2 data.table_1.14.10 htmlwidgets_1.6.4 fgsea_1.26.0 ComplexHeatmap_2.16.0
[206] RColorBrewer_1.1-3 rlang_1.1.1 clusterGeneration_1.3.8 spatstat.sparse_3.0-3 spatstat.explore_3.2-5 [211] remotes_2.4.2.1 ggnewscale_0.4.10 phangorn_2.11.1 fansi_1.0.5 beeswarm_0.4.0
 

Screenshots

More than one problem? If you have more than one problem with hdWGCNA, create separate issues for your individual problems.

[smorabit]

Can you please re-install the package and try again?

[drake77777]

Thank you for your kindly help, but that dindn't work, tried reinstall hdWGCNA and Seurat package, also didn't work, now trying reinstall dependent packages.

[drake77777]

Thanks a lot! After i reinstall hdWGCNA three times, it worked!