Seurat 5.1.0 DimPlot error in FetchData(): ! Cannot find any of the requested dimensions

[xyang2uchicago]

Hi,
I have a Seurat object called 'heart' for which I can run DimPlot() for 'pca; and 'harmony' but not 'umap.' Following is my code and error message that I am looking for a solution:

names(heart@reductions)
[1] "pca" "umap.bk" "harmony" "umap"
p = DimPlot(heart, reduction = "umap")
Error in FetchData():
! Cannot find any of the requested dimensions
Run rlang::last_trace() to see where the error occurred.

rlang::last_trace()
<error/rlang_error>
Error in FetchData():
! Cannot find any of the requested dimensions

---

Backtrace:
▆

1. └─Seurat::DimPlot(heart, reduction = "umap")
2. ├─SeuratObject::FetchData(...)
3. └─SeuratObject:::FetchData.Seurat(...)

4. └─base::lapply(...)
   

5.   └─SeuratObject (local) FUN(X[[i]], ...)
   

6.     ├─base::tryCatch(...)
   

7.     │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
   

8.     │   └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
   

9.     │     └─base (local) doTryCatch(return(expr), name, parentenv, handler)
   

10.     ├─SeuratObject::FetchData(...)
    

11.     └─SeuratObject:::FetchData.DimReduc(...)
    

Run rlang::last_trace(drop = FALSE) to see 1 hidden frame.

Key(object = heart)
meta.data RNA SCT pca umap.bk harmony umap
"md_" "rna_" "sct_" "PC_" "UMAPbk_" "harmony_" "UMAP_"
p = DimPlot(heart, reduction = "pca") # works !!
p = DimPlot(heart, reduction = "harmony") # works !!

sessionInfo()
Warning: ‘timedatectl’ indicates the non-existent timezone name ‘n/a’
unable to deduce timezone name from ‘America/Chicago’
R version 4.3.2 (2023-10-31)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: CentOS Linux 8

Matrix products: default
BLAS/LAPACK: /project/xyang2/software-packages/env/velocity_2022.05_xy/lib/libopenblasp-r0.3.21.so; LAPACK version 3.9.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: NA
tzcode source: system (glibc)

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

other attached packages:
[1] readxl_1.4.3 RColorBrewer_1.1-3 reshape2_1.4.4
[4] rliger_2.0.1 harmony_1.2.0 Rcpp_1.0.12
[7] patchwork_1.2.0 SeuratWrappers_0.3.5 Seurat_5.1.0
[10] SeuratObject_5.0.2 sp_2.1-4 ggrepel_0.9.5
[13] ggplot2_3.5.1 data.table_1.15.4 dplyr_1.1.4

loaded via a namespace (and not attached):
[1] jsonlite_1.8.8 magrittr_2.0.3 spatstat.utils_3.0-5
[4] ragg_1.3.2 vctrs_0.6.5 ROCR_1.0-11
[7] spatstat.explore_3.2-7 htmltools_0.5.8.1 cellranger_1.1.0
[10] sctransform_0.4.1 parallelly_1.37.1 KernSmooth_2.23-24
[13] htmlwidgets_1.6.4 ica_1.0-3 plyr_1.8.9
[16] plotly_4.10.4 zoo_1.8-12 igraph_2.0.3
[19] mime_0.12 lifecycle_1.0.4 pkgconfig_2.0.3
[22] rsvd_1.0.5 Matrix_1.6-5 R6_2.5.1
[25] fastmap_1.2.0 fitdistrplus_1.1-11 future_1.33.2
[28] shiny_1.8.1.1 digest_0.6.35 colorspace_2.1-0
[31] S4Vectors_0.40.2 tensor_1.5 RSpectra_0.16-1
[34] irlba_2.3.5.1 textshaping_0.4.0 progressr_0.14.0
[37] fansi_1.0.6 spatstat.sparse_3.1-0 httr_1.4.7
[40] polyclip_1.10-6 abind_1.4-5 compiler_4.3.2
[43] remotes_2.5.0 withr_3.0.0 fastDummies_1.7.3
[46] R.utils_2.12.3 MASS_7.3-60.0.1 tools_4.3.2
[49] lmtest_0.9-40 httpuv_1.6.15 future.apply_1.11.2
[52] goftest_1.2-3 R.oo_1.26.0 glue_1.7.0
[55] nlme_3.1-165 promises_1.3.0 grid_4.3.2
[58] Rtsne_0.17 cluster_2.1.6 generics_0.1.3
[61] gtable_0.3.5 spatstat.data_3.1-2 R.methodsS3_1.8.2
[64] tidyr_1.3.1 utf8_1.2.4 BiocGenerics_0.48.1
[67] spatstat.geom_3.2-9 RcppAnnoy_0.0.22 RANN_2.6.1
[70] pillar_1.9.0 stringr_1.5.1 spam_2.10-0
[73] RcppHNSW_0.6.0 later_1.3.2 splines_4.3.2
[76] lattice_0.22-6 survival_3.7-0 deldir_2.0-4
[79] tidyselect_1.2.1 miniUI_0.1.1.1 pbapply_1.7-2
[82] gridExtra_2.3 scattermore_1.2 stats4_4.3.2
[85] matrixStats_1.3.0 stringi_1.8.4 lazyeval_0.2.2
[88] codetools_0.2-20 tibble_3.2.1 BiocManager_1.30.23
[91] cli_3.6.2 uwot_0.2.2 xtable_1.8-4
[94] reticulate_1.38.0 systemfonts_1.1.0 munsell_0.5.1
[97] globals_0.16.3 spatstat.random_3.2-3 png_0.1-8
[100] parallel_4.3.2 dotCall64_1.1-1 listenv_0.9.1
[103] viridisLite_0.4.2 scales_1.3.0 ggridges_0.5.6
[106] leiden_0.4.3.1 purrr_1.0.2 rlang_1.1.4
[109] cowplot_1.1.3

Thank you,
Holly

[xyang2uchicago]

I figured it out, in previous version,

seu@reductions$umap@key

[1] "UMAP_"

I have to change the key to 'umap_', then the DimPlot() works.

I hope the team can allow the Seurat 5 recognizing a key 'UMAP_' as well.

Thanks,
Holly