Issue with dotplot due to "duplicate row.names" in seurat object even though they are unique

[HOEFSLE]

Hi,
I'm running into an issue displaying a dotplot with my data. According to the error message there are duplicate rownames in my data. However, when check for it my rownames (barcodes as well as features) appear to be unique. Weirdly I can run VlnPlot on the same object and vlnplot behaves as expected.

Thanks and best regards

any(duplicated(rownames(seu_obj.integrated)))
[1] FALSE
> any(duplicated(stringr::str_split_fixed(Cells(seu_obj.integrated),'_',1)))
[1] FALSE
> DotPlot(seu_obj.integrated,features= df$ensembl_gene_id, group.by = "cell_ontology",split.by = "cohort")
Error in `.rowNamesDF<-`(x, value = value) : 
  duplicate 'row.names' are not allowed
In addition: Warning message:
non-unique values when setting 'row.names':

 VlnPlot(seu_obj.integrated,features=df$ensembl_gene_id,group.by ="cell_ontology",split.plot = TRUE,split.by = "cohort")

sessionInfo()
R version 4.3.1 (2023-06-16 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale:
[1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8
[3] LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C
[5] LC_TIME=German_Germany.utf8

time zone: Europe/Berlin
tzcode source: internal

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

other attached packages:
[1] ggthemes_5.0.0 ggplot2_3.4.4 dplyr_1.1.3 Seurat_5.0.1
[5] SeuratObject_5.0.1 sp_2.1-0

loaded via a namespace (and not attached):
[1] RColorBrewer_1.1-3 jsonlite_1.8.7 magrittr_2.0.3
[4] ggbeeswarm_0.7.2 spatstat.utils_3.0-3 farver_2.1.1
[7] zlibbioc_1.46.0 vctrs_0.6.3 ROCR_1.0-11
[10] memoise_2.0.1 spatstat.explore_3.2-3 RCurl_1.98-1.12
[13] progress_1.2.2 htmltools_0.5.7 curl_5.1.0
[16] sctransform_0.4.1 parallelly_1.36.0 KernSmooth_2.23-21
[19] htmlwidgets_1.6.3 ica_1.0-3 plyr_1.8.9
[22] plotly_4.10.3 zoo_1.8-12 cachem_1.0.8
[25] igraph_1.5.1 mime_0.12 lifecycle_1.0.4
[28] pkgconfig_2.0.3 Matrix_1.6-4 R6_2.5.1
[31] fastmap_1.1.1 GenomeInfoDbData_1.2.10 fitdistrplus_1.1-11
[34] future_1.33.0 shiny_1.8.0 digest_0.6.33
[37] colorspace_2.1-0 patchwork_1.1.3 AnnotationDbi_1.62.2
[40] S4Vectors_0.38.1 tensor_1.5 RSpectra_0.16-1
[43] irlba_2.3.5.1 RSQLite_2.3.3 labeling_0.4.3
[46] filelock_1.0.2 progressr_0.14.0 fansi_1.0.5
[49] spatstat.sparse_3.0-2 httr_1.4.7 polyclip_1.10-6
[52] abind_1.4-5 compiler_4.3.1 withr_2.5.2
[55] bit64_4.0.5 DBI_1.1.3 fastDummies_1.7.3
[58] biomaRt_2.56.1 MASS_7.3-60 rappdirs_0.3.3
[61] tools_4.3.1 vipor_0.4.5 lmtest_0.9-40
[64] beeswarm_0.4.0 httpuv_1.6.11 future.apply_1.11.0
[67] goftest_1.2-3 glue_1.6.2 nlme_3.1-162
[70] promises_1.2.1 grid_4.3.1 Rtsne_0.16
[73] cluster_2.1.4 reshape2_1.4.4 generics_0.1.3
[76] gtable_0.3.4 spatstat.data_3.0-3 tidyr_1.3.0
[79] hms_1.1.3 data.table_1.14.8 xml2_1.3.5
[82] XVector_0.40.0 utf8_1.2.4 BiocGenerics_0.46.0
[85] spatstat.geom_3.2-5 RcppAnnoy_0.0.21 ggrepel_0.9.4
[88] RANN_2.6.1 pillar_1.9.0 stringr_1.5.1
[91] spam_2.10-0 RcppHNSW_0.5.0 later_1.3.1
[94] splines_4.3.1 BiocFileCache_2.8.0 lattice_0.21-8
[97] survival_3.5-5 bit_4.0.5 deldir_1.0-9
[100] httpgd_1.3.1 tidyselect_1.2.0 Biostrings_2.68.1
[103] miniUI_0.1.1.1 pbapply_1.7-2 gridExtra_2.3
[106] IRanges_2.34.1 scattermore_1.2 stats4_4.3.1
[109] Biobase_2.60.0 matrixStats_1.0.0 stringi_1.7.12
[112] lazyeval_0.2.2 codetools_0.2-19 tibble_3.2.1
[115] cli_3.6.1 uwot_0.1.16 systemfonts_1.0.5
[118] xtable_1.8-4 reticulate_1.34.0 munsell_0.5.0
[121] GenomeInfoDb_1.36.4 Rcpp_1.0.11 globals_0.16.2
[124] spatstat.random_3.1-6 dbplyr_2.3.0 png_0.1-8
[127] ggrastr_1.0.2 XML_3.99-0.16 parallel_4.3.1
[130] ellipsis_0.3.2 assertthat_0.2.1 blob_1.2.4
[133] prettyunits_1.2.0 dotCall64_1.1-1 bitops_1.0-7
[136] listenv_0.9.0 viridisLite_0.4.2 scales_1.3.0
[139] ggridges_0.5.4 crayon_1.5.2 leiden_0.4.3.1
[142] purrr_1.0.2 rlang_1.1.1 cowplot_1.1.1
[145] KEGGREST_1.40.1

[igrabski]

Hi, can you double-check if colnames(seu_obj.integrated) has any duplicates, as well as whether there are duplicates in df$ensembl_gene_id?